accession string | title string | description string | name string | publications list | locus_tags list | release_date timestamp[us] | data_types list | external_links list |
|---|---|---|---|---|---|---|---|---|
PRJNA1295998 | Food and Environmental Pathogens | Food and Environmental Pathogens | null | [] | [
{
"biosample_id": "SAMN50195128",
"assembly_id": null,
"value": "ACU60C"
},
{
"biosample_id": "SAMN50195132",
"assembly_id": null,
"value": "ACUN3F"
},
{
"biosample_id": "SAMN50195133",
"assembly_id": null,
"value": "ACUN3I"
},
{
"biosample_id": "SAMN50195129",
... | null | [
"Genome sequencing"
] | [] |
PRJNA340993 | Campylobacter lanienae strain:P0084 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0084 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687013",
"assembly_id": "GCA_002138435",
"value": "CBY17"
},
{
"biosample_id": "SAMN05687013",
"assembly_id": null,
"value": "CLANP84"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341000 | Campylobacter lanienae strain:P0121 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0121 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687020",
"assembly_id": "GCA_002139375",
"value": "CBY28"
},
{
"biosample_id": "SAMN05687020",
"assembly_id": null,
"value": "CLANP121"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341003 | Campylobacter lanienae strain:P154 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P154 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687023",
"assembly_id": "GCA_002138515",
"value": "CBY06"
},
{
"biosample_id": "SAMN05687023",
"assembly_id": null,
"value": "CLANP154"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341009 | Campylobacter lanienae strain:RM6987 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM6987 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687029",
"assembly_id": "GCA_002138605",
"value": "CBY15"
},
{
"biosample_id": "SAMN05687029",
"assembly_id": null,
"value": "CLAN6987"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1458769 | Analytical Performance Verification of the Deeplex Myc-TB Assay Using Well-Characterized Mycobacterium tuberculosis Proficiency Testing Isolates | This project contains both whole-genome sequencing (WGS) and targeted next-generation sequencing (tNGS) data generated from Mycobacterium tuberculosis isolates using the deeplex assay</p><p>Both datasets are paired-end Illumina reads prepared using the Illumina DNA prep Library protocol | null | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1187189 | Brachyteles arachnoides (southern muriqui), isolate monalisa, primary haplotype | The southern muriqui is a critically endangered primate species native to the Atlantic forest of Brazil. This study aimed to sequence the genome of a zoo-housed female southern muriqui as a reference genome for the species (primary haplotype). | Brachyteles arachnoides | [] | [
{
"biosample_id": "SAMN44786511",
"assembly_id": null,
"value": "ACJEN7"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA1027365 | GenomeTrakr Project: West Virginia Department of Agriculture | Whole genome sequencing of cultured Listeria spp. as part of the US Food and Drug Administration's WGS surveillance effort for the rapid traceback of foodborne pathogens. | Listeria spp. | [] | [
{
"biosample_id": "SAMN42232350",
"assembly_id": null,
"value": "ABXZ34"
},
{
"biosample_id": "SAMN42232347",
"assembly_id": null,
"value": "ABXZ35"
},
{
"biosample_id": "SAMN42232345",
"assembly_id": null,
"value": "ABXZ37"
},
{
"biosample_id": "SAMN42232349",
... | null | [
"Genome sequencing and assembly"
] | [] |
PRJNA340989 | Campylobacter lanienae strain:P0007 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0007 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687009",
"assembly_id": "GCA_002138445",
"value": "CBY05"
},
{
"biosample_id": "SAMN05687009",
"assembly_id": null,
"value": "CLANP7"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340997 | Campylobacter lanienae strain:P0101 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0101 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687017",
"assembly_id": "GCA_002138565",
"value": "CBY10"
},
{
"biosample_id": "SAMN05687017",
"assembly_id": null,
"value": "CLANP101"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341005 | Campylobacter lanienae strain:P163 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P163 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687025",
"assembly_id": "GCA_002138525",
"value": "CBY02"
},
{
"biosample_id": "SAMN05687025",
"assembly_id": null,
"value": "CLANP163"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341012 | Campylobacter lanienae strain:RM8001 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM8001 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687032",
"assembly_id": "GCA_002139415",
"value": "CCB79"
},
{
"biosample_id": "SAMN05687032",
"assembly_id": null,
"value": "CLAN8001"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340990 | Campylobacter lanienae strain:P0018 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0018 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687010",
"assembly_id": "GCA_002138485",
"value": "CBY03"
},
{
"biosample_id": "SAMN05687010",
"assembly_id": null,
"value": "CLANP18"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1106506 | Genome evolution and reproductive barriers in Xiphophorus | Sequence read data for Xiphophorus cortezi, Xiphophorus birchmanni, and their natural and artificial hybrids, and a reference genome assembly for Xiphophorus cortezi. | Xiphophorus | [
{
"pubdate": "2024-08-26T00:00:00",
"id": "10.1371/journal.pbio.3002742",
"db": "DOI"
},
{
"pubdate": "2025-03-26T00:00:00",
"id": "10.1038/s41559-025-02669-9",
"db": "DOI"
}
] | [] | null | [
"Genome sequencing"
] | [
{
"category": null,
"label": "associated GitHub repository",
"url": "https://github.com/stepfanie-aguillon/swordtail-reproductive-barriers"
}
] |
PRJNA1514246 | Whole-Genome Sequencing of Escherichia coli from Humans and Livestock at Slaughterhouses in Banten, Indonesia | This project investigates the genomic characteristics of Escherichia coli isolated from humans and livestock at slaughterhouses in Banten Province, Indonesia. Whole-genome sequencing was performed to characterize antimicrobial resistance genes, virulence-associated genes, phylogroups, serotypes, and genomic relatedness... | null | [
{
"pubdate": "2026-07-31T00:00:00",
"id": "10.14202/IJOH.2026.192-204",
"db": "DOI"
}
] | [] | null | [
"genome sequencing"
] | [] |
PRJNA340988 | Campylobacter lanienae strain:P0006 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0006 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687008",
"assembly_id": "GCA_002139215",
"value": "CBY25"
},
{
"biosample_id": "SAMN05687008",
"assembly_id": null,
"value": "CLANP6"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341006 | Campylobacter lanienae strain:RM10079 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM10079 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687026",
"assembly_id": "GCA_002139425",
"value": "CB880"
},
{
"biosample_id": "SAMN05687026",
"assembly_id": null,
"value": "CLAN10079"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341008 | Campylobacter lanienae strain:RM6140 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM6140 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687028",
"assembly_id": "GCA_002138595",
"value": "CBY13"
},
{
"biosample_id": "SAMN05687028",
"assembly_id": null,
"value": "CLAN6140"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341011 | Campylobacter lanienae strain:RM6997 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM6997 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687031",
"assembly_id": "GCA_002138635",
"value": "CBY08"
},
{
"biosample_id": "SAMN05687031",
"assembly_id": null,
"value": "CLAN6997"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340995 | Campylobacter lanienae strain:P0099 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0099 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687015",
"assembly_id": "GCA_002139265",
"value": "CBY20"
},
{
"biosample_id": "SAMN05687015",
"assembly_id": null,
"value": "CLANP99"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341002 | Campylobacter lanienae strain:P147 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P147 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687022",
"assembly_id": "GCA_002138535",
"value": "CBY11"
},
{
"biosample_id": "SAMN05687022",
"assembly_id": null,
"value": "CLANP147"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA239089 | Pelagomonas calceolata strain:CCMP1756 Genome sequencing | Pelagomonas calceolata genome sequencing | Pelagomonas calceolata strain:CCMP1756 | [] | [
{
"biosample_id": "SAMN01985059",
"assembly_id": null,
"value": "BV24"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA340996 | Campylobacter lanienae strain:P0100 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0100 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687016",
"assembly_id": "GCA_002139275",
"value": "CBY22"
},
{
"biosample_id": "SAMN05687016",
"assembly_id": null,
"value": "CLANP100"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341007 | Campylobacter lanienae strain:RM10695 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM10695 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687027",
"assembly_id": "GCA_002138675",
"value": "CBY12"
},
{
"biosample_id": "SAMN05687027",
"assembly_id": null,
"value": "CLAN10695"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1163283 | Report of a food-human genetic cluster of extended-spectrum beta-lactamase--producing Klebsiella pneumoniae ST14 identified in Basel, Switzerland, between May 2018 and January 2019 | We describe a cluster of genetically related ESBL-K. pneumoniae sequence type ST14 recovered from clinical samples and an alfalfa-cress sample collected by systematic food sampling within nine months in Basel, Switzerland. This suggests that foodstuffs mayrepresent an important reservoir contributing to the continuous ... | Klebsiella pneumoniae | [
{
"pubdate": "2018-02-01T00:00:00",
"id": "10.1136/bmjopen-2018-021823",
"db": "DOI"
},
{
"pubdate": null,
"id": "38075908",
"db": "Pubmed"
},
{
"pubdate": "2021-07-15T00:00:00",
"id": "10.1093/cid/ciaa1164",
"db": "DOI"
},
{
"pubdate": null,
"id": "41017082",... | [
{
"biosample_id": "SAMN50677882",
"assembly_id": null,
"value": "AC66X9"
},
{
"biosample_id": "SAMN50677881",
"assembly_id": null,
"value": "AC66Y0"
},
{
"biosample_id": "SAMN43844647",
"assembly_id": "GCA_060240615",
"value": "AC7E73"
},
{
"biosample_id": "SAMN43... | null | [
"Genome sequencing"
] | [] |
PRJNA1479465 | The interactive effects of early-life antibiotic exposure, FMT and subsequent HFD on gut microbiota in C57BL/6 mice | This project examines the interplay between early-life antibiotic exposure (vancomycin and gentamicin, 2 weeks), fecal microbiota transplantation (FMT) restoration, and subsequent short-term high-fat diet (HFD) challenge on gut microbiota in C57BL/6 mice. Fecal samples were collected across multiple time points and ana... | null | [
{
"pubdate": "2026-12-31T00:00:00",
"id": "10.1080/19490976.2026.2718681",
"db": "DOI"
}
] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1472647 | GEO accession GSE333836 is currently private and is scheduled to be released on Aug 20, 2029. | If GEO accession GSE333836 has been cited in a publication, please notify us at geo@ncbi.nlm.nih.gov to initiate the public release of associated data. | GEO accession GSE333836 is currently private and is scheduled to be released on Aug 20, 2029. | [
{
"pubdate": "2026-06-04T00:00:00",
"id": "42239312",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1472650 | GEO accession GSE333838 is currently private and is scheduled to be released on Aug 20, 2029. | If GEO accession GSE333838 has been cited in a publication, please notify us at geo@ncbi.nlm.nih.gov to initiate the public release of associated data. | GEO accession GSE333838 is currently private and is scheduled to be released on Aug 20, 2029. | [
{
"pubdate": "2026-06-04T00:00:00",
"id": "42239312",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1118572 | Carbapenem resistant Pseudomonas aeruginosa from Vietnam (Hanoi) | Genome sequence from P. aeruginosa isolates from Vietnam (Hanoi) | Pseudomonas aeruginosa strain:LH-PA-05 | isolate:LH-PA-05 | [] | [
{
"biosample_id": "SAMN41611569",
"assembly_id": null,
"value": "ABL333"
},
{
"biosample_id": "SAMN46289152",
"assembly_id": null,
"value": "AC7GR3"
},
{
"biosample_id": "SAMN46289149",
"assembly_id": null,
"value": "AC7GRU"
},
{
"biosample_id": "SAMN46289146",
... | null | [
"Genome sequencing"
] | [] |
PRJNA1187201 | Brachyteles arachnoides (southern muriqui), isolate serena, primary haplotype | The southern muriqui is a critically endangered primate species native to the Atlantic forest of Brazil. This study aimed to sequence the genome of a zoo-housed female southern muriqui (primary haplotype) . | Brachyteles arachnoides | [
{
"pubdate": "2025-04-17T00:00:00",
"id": "10.1093/g3journal/jkaf034",
"db": "DOI"
}
] | [
{
"biosample_id": "SAMN44786512",
"assembly_id": null,
"value": "ACJEN5"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA1187204 | Brachyteles arachnoides (southern muriqui), isolate serena, alternate haplotype | The southern muriqui is a critically endangered primate species native to the Atlantic forest of Brazil. This study aimed to sequence the genome of a zoo-housed female southern muriqui (alternate haplotype). | Brachyteles arachnoides | [
{
"pubdate": "2025-04-17T00:00:00",
"id": "10.1093/g3journal/jkaf034",
"db": "DOI"
}
] | [
{
"biosample_id": "SAMN44786512",
"assembly_id": null,
"value": "ACJEN6"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA1443055 | Streptomyces murinus strain:LB53 Genome sequencing | This project presents the whole genome sequence of Streptomyces sp. LB53, a strain isolated from the rhizosphere soil of healthy Amomum villosum. The genome was sequenced using PacBio platform, generating approximately 873 Mb of raw data with an estimated coverage of 102.7. The final assembled genome size is approximat... | Streptomyces murinus strain:LB53 | [] | [
{
"biosample_id": "SAMN56715064",
"assembly_id": null,
"value": "AC07MM"
},
{
"biosample_id": "SAMN56715064",
"assembly_id": null,
"value": "AC1C36"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA341004 | Campylobacter lanienae strain:P158 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P158 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687024",
"assembly_id": "GCA_002139385",
"value": "CBY27"
},
{
"biosample_id": "SAMN05687024",
"assembly_id": null,
"value": "CLANP158"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341010 | Campylobacter lanienae strain:RM6995 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:RM6995 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687030",
"assembly_id": "GCA_002138615",
"value": "CBY19"
},
{
"biosample_id": "SAMN05687030",
"assembly_id": null,
"value": "CLAN6995"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340994 | Campylobacter lanienae strain:P0086 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0086 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687014",
"assembly_id": "GCA_002139255",
"value": "CBY23"
},
{
"biosample_id": "SAMN05687014",
"assembly_id": null,
"value": "CLANP86"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340998 | Campylobacter lanienae strain:P0102 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0102 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687018",
"assembly_id": "GCA_002139315",
"value": "CBY21"
},
{
"biosample_id": "SAMN05687018",
"assembly_id": null,
"value": "CLANP102"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1431560 | Host phenology drives directional assembly of the fruit endophytic mycobiome and precedes disease-associated community dominance in cranberry | This project contains raw ITS2 amplicon sequencing data generated from cranberry (Vaccinium macrocarpon) fruit tissues collected across multiple phenological stages. The objective of this study is to characterize the fungal communities associated with cranberry fruit rot and evaluate temporal shifts in pathogen composi... | Vaccinium macrocarpon | [
{
"pubdate": "2026-08-08T00:00:00",
"id": "10.1186/s40793-026-00942-3",
"db": "DOI"
}
] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1515323 | 16S rRNA gene amplicon sequencing (V3-V4 region) of fecal samples from temporal lobe epilepsy model mice. Samples contain mixed bacterial communities from the mouse gut microbiota. Targeted loci | This study investigates the effects of Dingxian Pill (DXP), a traditional Chinese medicine formula, on gut microbiota composition in a mouse model of temporal lobe epilepsy (TLE). Fecal samples were collected from two groups of mice: a control group receiving vehicle treatment and a treatment group receiving DXP at 1.2... | Mus musculus gut metagenome | [] | [] | null | [
"targeted loci"
] | [] |
PRJNA1502796 | GEO accession GSE341465 is currently private and is scheduled to be released on Aug 04, 2027. | If GEO accession GSE341465 has been cited in a publication, please notify us at geo@ncbi.nlm.nih.gov to initiate the public release of associated data. | GEO accession GSE341465 is currently private and is scheduled to be released on Aug 04, 2027. | [] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA340991 | Campylobacter lanienae strain:P0027 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0027 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687011",
"assembly_id": "GCA_002138455",
"value": "CBY04"
},
{
"biosample_id": "SAMN05687011",
"assembly_id": null,
"value": "CLANP27"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA341001 | Campylobacter lanienae strain:P0129 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0129 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687021",
"assembly_id": "GCA_002139335",
"value": "CCB78"
},
{
"biosample_id": "SAMN05687021",
"assembly_id": null,
"value": "CLANP129"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1357913 | Genome sequencing of Acer miaotaiense | Raw genome sequencing reads of Acer miaotaiense. | null | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA340992 | Campylobacter lanienae strain:P0034 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0034 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687012",
"assembly_id": "GCA_002139235",
"value": "CBY24"
},
{
"biosample_id": "SAMN05687012",
"assembly_id": null,
"value": "CLANP34"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA340999 | Campylobacter lanienae strain:P0104 Genome sequencing and assembly | Genomic and taxonomic analysis of Campylobacter lanienae and C. lanienae related organisms | Campylobacter lanienae strain:P0104 | [
{
"pubdate": "2017-07-01T00:00:00",
"id": "28854596",
"db": "Pubmed"
}
] | [
{
"biosample_id": "SAMN05687019",
"assembly_id": "GCA_002139345",
"value": "CBY26"
},
{
"biosample_id": "SAMN05687019",
"assembly_id": null,
"value": "CLANP104"
}
] | 2017-05-15T00:00:00 | [
"Genome sequencing and assembly"
] | [] |
PRJNA1187200 | Brachyteles arachnoides (southern muriqui), isolate monalisa, alternate haplotype | The southern muriqui is a critically endangered primate species native to the Atlantic forest of Brazil. This study aimed to sequence the genome of a zoo-housed female southern muriqui as a reference genome for the species (alternate haplotype). | Brachyteles arachnoides | [
{
"pubdate": null,
"id": "10.1093/g3journal/jkaf03",
"db": "DOI"
}
] | [
{
"biosample_id": "SAMN44786511",
"assembly_id": null,
"value": "ACJEN8"
}
] | null | [
"Genome sequencing"
] | [] |
PRJNA1266409 | Genomic analysis of multidrug resistant Salmonella enterica serotype Typhi Isolates from Algeria | Following a genomic survey of 39 Salmonella enterica serotype Typhi isolates from Algeria (2010-2022), we performed a long-read sequencing of two representative multidrug resistance isolates | null | [] | [
{
"biosample_id": "SAMN48678141",
"assembly_id": null,
"value": "ACQ803"
},
{
"biosample_id": "SAMN48678142",
"assembly_id": null,
"value": "ACQ81D"
},
{
"biosample_id": "SAMN48678141",
"assembly_id": null,
"value": "ACQ8W2"
},
{
"biosample_id": "SAMN48678142",
... | null | [
"genome sequencing"
] | [] |
PRJNA1193010 | Base editing of trinucleotide repeats that cause Huntingtons disease and Friedreichs ataxia reduces somatic repeat expansions in patient cells and in mice | Trinucleotide repeat (TNR) diseases are neurological disorders that affect ~ 1 in 3,000 individuals worldwide and are caused by genomic expanded trinucleotide repeats that become unstable in somatic cells in a length-dependent manner. The most common pathogenic triplet base pair sequence, CAG/CTG, occurs in roughly one... | null | [
{
"pubdate": null,
"id": "40419681",
"db": "Pubmed"
}
] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA813969 | Consortium able to degrade Carbon tetrachloride | Consortium enriched from groundwater in Tohoku region in Japan, able to degrade carbon tetrachloride | null | [] | [
{
"biosample_id": "SAMN29232539",
"assembly_id": null,
"value": "NH234"
},
{
"biosample_id": "SAMN29232539",
"assembly_id": null,
"value": "NHU88"
}
] | null | [
"raw sequence reads"
] | [] |
PRJNA1514296 | Culture driven microbiome dynamics governs the hierarchical assembly of microbial cellulose, influence its structure, mechanics, and biological function | Dr. Gowri M. Balachander, Assistant Professor, School of Biomedical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi;</p><p>Dr. Balamurugan Ramadass, Additional Professor, Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar.</p><p>The aim of the study is to e... | SCOBY microbial community | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJEB112871 | Impact of Coxiella burnetii associated abortions in Finnish forest reindeer within a zoo on public health appeared negligible succeeding mitigation strategies | Coxiella burnetii is a Gram-negative ubiquitous bacterium that may infect many animal species,
as well as humans. In this study, transmission of Coxiella burnetii during an outbreak of abortions
in a herd of Finnish forest reindeer (Rangifer tarandus fennicus) in a Dutch zoo was investigated.
Diagnostic sampling showed... | Coxiella burnetii from Finnish forest reindeer | [] | [
{
"biosample_id": "SAMEA123136950",
"assembly_id": "GCA_987209625",
"value": "AC7H8U"
}
] | null | [
"Other"
] | [] |
PRJNA1415719 | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [ChIP-Seq] | Accumulating evidence underscores the role of p53 mutations in inducing genomic instability, yet the underlying mechanisms remain largely elusive. Our study reveals that the p53-R273H mutation leads to the accumulation of R-loops. Specifically, p53-R273H forms abnormal condensates with BRCA2, impairing the chromatin bi... | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [ChIP-Seq] | [
{
"pubdate": "2026-06-12T00:00:00",
"id": "42277940",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1415153 | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag] | Accumulating evidence underscores the role of p53 mutations in inducing genomic instability, yet the underlying mechanisms remain largely elusive. Our study reveals that the p53-R273H mutation leads to the accumulation of R-loops. Specifically, p53-R273H forms abnormal condensates with BRCA2, impairing the chromatin bi... | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag] | [
{
"pubdate": "2026-06-12T00:00:00",
"id": "42277940",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1167343 | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag ] | Accumulating evidence underscores the role of p53 mutations in inducing genomic instability, yet the underlying mechanisms remain largely elusive. Our study reveals that the p53-R273H mutation leads to the accumulation of R-loops. Specifically, p53-R273H forms abnormal condensates with BRCA2, impairing the chromatin bi... | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag ] | [
{
"pubdate": "2026-06-12T00:00:00",
"id": "42277940",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1415740 | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag] | Accumulating evidence underscores the role of p53 mutations in inducing genomic instability, yet the underlying mechanisms remain largely elusive. Our study reveals that the p53-R273H mutation leads to the accumulation of R-loops. Specifically, p53-R273H forms abnormal condensates with BRCA2, impairing the chromatin bi... | DNA-contact mutant p53 displaces BRCA2 from chromatin and drives R-loop associated genome instability [CUT&Tag] | [
{
"pubdate": "2026-06-12T00:00:00",
"id": "42277940",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1372805 | NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq | This SuperSeries is composed of the SubSeries listed below. | NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1327363 | A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease | The maintenance of a healthy epithelial-endothelial juxtaposition requires cross-talk within glomerular cellular niches. We sought to understand the spatially-anchored regulation and transition of endothelial and mesangial cells from health to injury in DKD. From 74 human kidney samples, an integrated multi-omics appro... | A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease | [
{
"pubdate": "2026-04-30T00:00:00",
"id": "42055320",
"db": "Pubmed"
}
] | [] | null | [
"Other"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1331843 | In vivo screen for osteoclast derived osteogenic factors using non-resorptive osteoclasts in zebrafish bone | Bone homeostasis requires the balanced action of bone forming osteoblasts and bone resorbing osteoclasts and is maintained through local as well as systemic factors. Loss of osteoclast resorptive activity leads to development of osteopetrosis with increased bone volume but reduced skeletal integrity. Work on osteopetro... | In vivo screen for osteoclast derived osteogenic factors using non-resorptive osteoclasts in zebrafish bone | [
{
"pubdate": "2026-08-20T00:00:00",
"id": "42622061",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1379431 | Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties | Microglia arise from yolk sac (YS) progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain u... | Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties | [
{
"pubdate": "2026-03-13T00:00:00",
"id": "41819099",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1330804 | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [ChIP-seq] | Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. To addre... | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [ChIP-seq] | [
{
"pubdate": "2026-06-30T00:00:00",
"id": "42373303",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1265499 | Hyaluronan induces ERK activation with minimal transcriptomic changes in pancreatic ฮฑ-cells | Type 1 diabetes (T1D) is driven by the immune-mediated destruction of pancreatic b cells. Hyaluronan (HA), an extracellular matrix glycosaminoglycan, accumulates in pancreatic islets in patients with T1D and animal models, and has been implicated in promoting chronic inflammation. Inhibition of HA synthesis in T1D mode... | Hyaluronan induces ERK activation with minimal transcriptomic changes in pancreatic ฮฑ-cells | [
{
"pubdate": "2026-03-12T00:00:00",
"id": "41816223",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1279070 | ATG-9-Mediated Synaptic Autophagy Promotes Aversive Learning under Stress in C. elegans | Autophagy is a degradative process that maintains cellular homeostasis and functions. Autophagy biogenesis at neuronal synapses requires synaptic proteins, but its impact on synaptic functions is incompletely understood. Here we show that, in Caenorhabditis elegans, synaptic ATG-9, the only transmembrane protein in the... | ATG-9-Mediated Synaptic Autophagy Promotes Aversive Learning under Stress in C. elegans | [
{
"pubdate": "2026-06-11T00:00:00",
"id": "42268891",
"db": "Pubmed"
}
] | [] | null | [
"Other"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA675769 | Differential migration mechanics and immune responses of glioma subtypes | An RNA-seq study of altered gene expression in mouse glioblastomas comparing tumor samples to normal mouse brain tissue. | Differential migration mechanics and immune responses of glioma subtypes | [
{
"pubdate": "2026-07-14T00:00:00",
"id": "42447444",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1446745 | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin | Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. To addre... | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin | [
{
"pubdate": "2026-06-30T00:00:00",
"id": "42373303",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1330805 | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [RNA-seq] | Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. To addre... | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [RNA-seq] | [
{
"pubdate": "2026-06-30T00:00:00",
"id": "42373303",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1331847 | Arabidopsis YEATS domain proteins facilitate DNA double strand break repair via homologous recombination pathways | DNA double-strand break (DSB) repair is required to maintain genome integrity and organismal fitness. This process occurs within chromatin and although accurate repair requires extensive changes in chromatin structure and composition, chromatin effectors facilitating DSB repair remain largely unknown in plants. Using r... | Arabidopsis YEATS domain proteins facilitate DNA double strand break repair via homologous recombination pathways | [
{
"pubdate": "2026-06-08T00:00:00",
"id": "42258726",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1329196 | TIF1ฮณ regulates stability of T regulatory cells during inflammation [ATAC-seq] | Regulatory T cells are a suppressor population critical to control inflammation and maintain tissue homeostasis. The TGF-ฮฒ pathway is a fundamental signal for regulatory T cell differentiation, yet the molecular determinants of how TGF-ฮฒ signals regulate all these processes are not completely understood. TIF1ฮณ promotes... | TIF1ฮณ regulates stability of T regulatory cells during inflammation [ATAC-seq] | [
{
"pubdate": "2026-08-12T00:00:00",
"id": "42581187",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1439414 | Antigen-Specific mRNAโLNP Vaccination with mTOR Inhibition Promotes Treg Cells and Limits Allergy | Immune tolerance to T helper 2 (Th2)-mediated allergic reactions relies largely on antigen-specific T helper 1 (Th1) and regulatory T cells, which modulate downstream immune responses upon antigen exposure and mitigate allergic diseases. While allergen-encoded mRNA-lipid nanoparticle (mRNA-LNP) vaccine elicits Th1 and ... | Antigen-Specific mRNAโLNP Vaccination with mTOR Inhibition Promotes Treg Cells and Limits Allergy | [
{
"pubdate": "2026-06-10T00:00:00",
"id": "42263787",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1167341 | p53 mutation hijacks BRCA2 to induce genomic instability [ChIP-Seq] | Accumulating evidence underscores the role of p53 mutations in inducing genomic instability, yet the underlying mechanisms remain largely elusive. Our study reveals that the p53-R273H mutation leads to the accumulation of R-loops. Specifically, p53-R273H forms abnormal condensates with BRCA2, impairing the chromatin bi... | p53 mutation hijacks BRCA2 to induce genomic instability [ChIP-Seq] | [
{
"pubdate": "2026-06-12T00:00:00",
"id": "42277940",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1312112 | Sorbs2 Deficiency Causes Diastolic Dysfunction Through Dysregulation of Cytoskeletal Networks and Calcium Handling | Sorbin and SH3 domainโcontaining protein 2 (Sorbs2) is a cytoskeletal adaptor protein implicated in cardiomyocyte adhesion, cytoskeletal remodeling, and calcium handling. We investigated its role in diastolic dysfunction using Sorbs2 knockout (KO) mice. Sorbs2 KO mice developed progressive diastolic dysfunction with pr... | Sorbs2 Deficiency Causes Diastolic Dysfunction Through Dysregulation of Cytoskeletal Networks and Calcium Handling | [
{
"pubdate": "2026-06-18T00:00:00",
"id": "42310189",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1476575 | Tracing the origins of de novo coronary collateral formation in cardiac repair [CUT&RUN] | Coronary collateral arteries have been proposed to form de novo through artery reassembly, a process in which arterial endothelial cells (ECs) migrate away from pre-existing arteries and reassemble into new arteries. Using genetic tools that trace arterial ECs, we found that their contribution to collateral is minor. D... | Tracing the origins of de novo coronary collateral formation in cardiac repair [CUT&RUN] | [
{
"pubdate": "2026-08-20T00:00:00",
"id": "42623479",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1431535 | Postnatal dynamics and maturation of the epidermal immune compartment is coordinated by niche intrinsic signals, but not microbial colonization | The murine epidermis harbors two key resident immune populationsโLangerhans cells (LCs) and dendritic epidermal T cells (DETCs)โwhich play critical roles in maintaining tissue homeostasis, immune surveillance, and barrier integrity. Although their origin from fetal progenitors have been defined, the cellular and molecu... | Postnatal dynamics and maturation of the epidermal immune compartment is coordinated by niche intrinsic signals, but not microbial colonization | [
{
"pubdate": "2026-08-14T00:00:00",
"id": "42600005",
"db": "Pubmed"
}
] | [] | null | [
"Other"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1271499 | Canonical microRNA loss drives tumor development implicating therapeutic efficacy of enoxacin in angiosarcoma | Angiosarcoma (AS) is a rare and aggressive tumor originating from vascular endothelial cells, characterized by a high metastatic rate and poor prognosis. Our prior work established that endothelial loss of Dicer1, a key enzyme in microRNA (miRNA) processing, drives AS formation in mice, suggesting a tumor suppressive r... | Canonical microRNA loss drives tumor development implicating therapeutic efficacy of enoxacin in angiosarcoma | [
{
"pubdate": "2026-02-27T00:00:00",
"id": "41748289",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1452994 | PBRM1 RNA-seq [4T1] | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | PBRM1 RNA-seq [4T1] | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1365246 | NMuMG PBRM1 ChIP-seq | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | NMuMG PBRM1 ChIP-seq | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1456115 | 4T1 ATAC-seq | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | 4T1 ATAC-seq | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1456116 | 4T1 Cut&Run | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | 4T1 Cut&Run | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1242000 | DNBSeq of Microsporidia MB from Busia Kenya: Individually extracted whole Anopheles gambiae s.s. and Anopheles arabiensis mosquitoes positive with Microsporidia MB | The goal is to assess genetic diversity of Microsporidia sp. MB in Anopheles gambiae s.s. and Anopheles</p><p>arabiensis mosquito samples from Busia and compare to the original reference strain isolated from Ahero,</p><p>Kenya. | null | [
{
"pubdate": "2025-10-02T00:00:00",
"id": "10.1186/s12866-025-04324-6",
"db": "DOI"
}
] | [] | null | [
"Genome sequencing"
] | [] |
PRJNA1232633 | Gene networks are conserved across reproductive development between the fern Ceratopteris richardii and the flowering plant Arabidopsis thaliana | How plants first invented seeds is a longstanding unresolved evolutionary question. Seed-bearing plants arose from within seedless vascular plants, with ferns as their closest relatives, but how seed development originated from ancestral reproductive development has remained unresolved by comparative morphology or the ... | Gene networks are conserved across reproductive development between the fern Ceratopteris richardii and the flowering plant Arabidopsis thaliana | [
{
"pubdate": "2026-06-20T00:00:00",
"id": "42321160",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA243546 | Phosphate Starvation in Chlamydomonas reinhardtii | Phosphorus (P) is an essential nutrient that is limiting in many environments. When P is scarce organisms employ strategies for conservation of internal stores, and to efficiently scavenge P from their external surroundings. In this study we investigated the acclimation response of Chlamydomonas reinhardtii to P defici... | Chlamydomonas reinhardtii | [
{
"pubdate": "2014-04-22T00:00:00",
"id": "24748044",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1335139 | RNA sequencing of bethanechol- or vehicle-treated mouse colon cancer organoids | To profile transcriptomic alterations induced by muscarinic receptor stimulation, we treated Apcฮ/ฮ, KrasG12D/ฮ, Trp53ฮ/ฮ mouse colon cancer organoids with bethanechol or vehicle and then performed RNA sequencing. | RNA sequencing of bethanechol- or vehicle-treated mouse colon cancer organoids | [
{
"pubdate": "2026-07-25T00:00:00",
"id": "42497870",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1432056 | Targeting the CHD3 chromatin remodeler exploits a synthetic lethal vulnerability in dual SMARCA4/SMARCA2-deficient cancers via derepression of PARD3B | SWI/SNF-deficient cancers characterized by dual SMARCA4/SMARCA2 loss, including subsets of lung adenocarcinoma and small cell carcinoma of the ovary, hypercalcemic type, represent a major therapeutic challenge. While SMARCA2 paralog-targeting strategies exist for single-subunit loss of SMARCA4, dual SMARCA4/SMARCA2-def... | Targeting the CHD3 chromatin remodeler exploits a synthetic lethal vulnerability in dual SMARCA4/SMARCA2-deficient cancers via derepression of PARD3B | [
{
"pubdate": "2026-05-23T00:00:00",
"id": "42174139",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1469164 | Case of Complete Response to Immunotherapy in MMR-Deficient Prostate Cancer Associated with NK-like and CD4+CD8+ T-cells | Mismatch repair deficiency (dMMR) and microsatellite instability (MSI-H) are rare in prostate cancer, occurring in 2-4% of cases. These defects result in increased genomic instability and elevated tumor mutational burden (TMB), which can support responses to immune checkpoint inhibitors (ICIs). Here, we report a patien... | Case of Complete Response to Immunotherapy in MMR-Deficient Prostate Cancer Associated with NK-like and CD4+CD8+ T-cells | [
{
"pubdate": "2026-06-27T00:00:00",
"id": "42361800",
"db": "Pubmed"
}
] | [] | null | [
"Other"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1271058 | NMuMG PBRM1 ATAC-seq | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | NMuMG PBRM1 ATAC-seq | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Epigenomics"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1121912 | PBRM1 RNA-seq | Mammalian SWI/SNF or BAF are multi-subunit complexes that regulate cell-type specific gene expression by modulating chromatin accessibility, in coordination with transcription factors and other chromatin regulators. PBRM1 is the complex defining subunit of PBAF class of SWI/SNF complexes. It is mutated in ~40% of clear... | PBRM1 RNA-seq | [
{
"pubdate": "2025-11-24T00:00:00",
"id": "41280014",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1406198 | Nanoparticulate Immunoactive Complex (IMAX) for local chemoimmunotherapy: From murine models to pilot canine study. | A nanoparticulate IMmunoActive compleX (IMAX) was developed for local treatment of locatable and accessible tumors. This was used to treat naturally-occuring cancers in dogs. Several naturally-occuring canine cancers resemble the same disease in humans. | Nanoparticulate Immunoactive Complex (IMAX) for local chemoimmunotherapy: From murine models to pilot canine study. | [
{
"pubdate": "2026-05-29T00:00:00",
"id": "42210794",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1299485 | S100A4 is a high glucose-induced fibrotic factor in Dupuytrenโs contracture | Dupuytrenโs contracture is a superficial fibrotic disease of the hand, which causes flexion contracture of the affected finger. Among several risk factors for Dupuytrenโs contracture, diabetes mellitus (DM) is a well-known risk factor for this disease. While epidemiological studies demonstrated a high prevalence of DM ... | S100A4 is a high glucose-induced fibrotic factor in Dupuytrenโs contracture | [
{
"pubdate": "2026-05-23T00:00:00",
"id": "42173860",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1426449 | Highlights of Tuft Cells in Mouse and Human Salivary Glands | Tuft cells (TCs) are rare chemosensory epithelial cells that regulate mucosal homeostasis in several organs, but their role in salivary glands (SGs) remains unclear. This study investigated TC features in both mouse and human SGs. In mouse samples, transmission electron microscopy (TEM), histological analysis, bulk RNA... | Highlights of Tuft Cells in Mouse and Human Salivary Glands | [
{
"pubdate": "2026-04-13T00:00:00",
"id": "41972672",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1468517 | Conserved structural features of the lncRNA HOTAIR in breast cancer cells | Long noncoding RNAs (lncRNAs) regulate diverse cellular processes and are frequently implicated in disease, but their functional mechanisms often remain elusive. One such lncRNA, HOTAIR (Hox transcript antisense intergenic RNA), is a ~2.1 kb mammalian transcript whose overexpression promotes invasion and metastasis in ... | Conserved structural features of the lncRNA HOTAIR in breast cancer cells | [
{
"pubdate": "2026-06-04T00:00:00",
"id": "42239237",
"db": "Pubmed"
}
] | [] | null | [
"Other"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1469556 | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [scRNA-Seq] | Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. To addre... | Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [scRNA-Seq] | [
{
"pubdate": "2026-06-30T00:00:00",
"id": "42373303",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1329192 | TIF1ฮณ regulates stability of T regulatory cells during inflammation [RNA-seq] | Regulatory T cells are a suppressor population critical to control inflammation and maintain tissue homeostasis. The TGF-ฮฒ pathway is a fundamental signal for regulatory T cell differentiation, yet the molecular determinants of how TGF-ฮฒ signals regulate all these processes are not completely understood. TIF1ฮณ promotes... | TIF1ฮณ regulates stability of T regulatory cells during inflammation [RNA-seq] | [
{
"pubdate": "2026-08-12T00:00:00",
"id": "42581187",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1516136 | Transcriptome profiling of Mus musculus bone marrow-derived dendritic cells | RNA sequencing was performed to characterize the transcriptomic profiles of bone marrow-derived dendritic cells (BMDCs) from Mus musculus. This dataset was generated to investigate gene expression changes between experimental and control groups. | Mus musculus strain:C57BL/6J | [] | [
{
"biosample_id": null,
"assembly_id": null,
"value": "AC7GHL"
}
] | null | [
"genome sequencing"
] | [] |
PRJNA1516180 | Medicago sativa cultivar:Queen, Eureka+ Raw sequence reads | Fall dormancy is a key trait affecting winter survival and regional adaptation in alfalfa. We performed RNA-seq on two cultivars, Queen (fall-dormant) and Eureka+ (non-fall-dormant), at the radicle emergence stage to explore early molecular responses. This dataset offers transcriptomic resources for studying fall dorma... | Medicago sativa cultivar:Queen, Eureka+ | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1516124 | Reithrodontomys humulis (eastern harvest mouse) genome, mReiHum1, haplotype 1 | The eastern harvest mouse (Reithrodontomys humulis) is a species of rodent in the family Cricetidae. It is endemic to the Southeastern United States. Its natural habitats are subtropical or tropical seasonally wet or flooded lowland grassland, swamps, and pastureland (from Wikipedia entry). This sample of a male indivi... | Reithrodontomys humulis isolate:mReiHum1 | [
{
"pubdate": null,
"id": "33911273",
"db": "Pubmed"
}
] | [
{
"biosample_id": null,
"assembly_id": null,
"value": "AC7GHJ"
}
] | null | [
"genome sequencing and assembly"
] | [
{
"category": null,
"label": "Richard Miller",
"url": "https://www.richmillerlab.com/"
},
{
"category": null,
"label": "Wendy Hood",
"url": "https://cosam.auburn.edu/directory/profile.php?id=wrh0001"
},
{
"category": null,
"label": "Geoffrey Hill",
"url": "https://cosam.a... |
PRJNA1151621 | Redefining HexR regulatory landscape in Pseudomonas putida through integrative systems biology [RNA-Seq] | Pseudomonas putida strains are highly valued biocatalysts due to their abilities to degrade various chemicals, tolerate organic solvents, and resist environmental stressors. Fineโtuning the regulation of primary carbon metabolism is essential for their successful adaptation, with HexR emerging as a key regulator. While... | Redefining HexR regulatory landscape in Pseudomonas putida through integrative systems biology [RNA-Seq] | [
{
"pubdate": "2025-11-20T00:00:00",
"id": "41260329",
"db": "Pubmed"
}
] | [] | null | [
"Transcriptome or Gene expression"
] | [
{
"category": null,
"label": "",
"url": null
}
] |
PRJNA1516114 | Gossypium hirsutum Raw sequence reads | In this study, we used the wild-type cotton line X142 as the experimental material. Ovules collected on the day of flowering (0 days post-anthesis, 0-DPA) were cultured in vitro with exogenous jasmonic acid (JA) supplementation. After 10 days of in vitro culture, mixed tissues containing ovules and fibers were collecte... | Gossypium hirsutum | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1516177 | Bacteria protist interaction in the rhizosphere of Neltuma laevigata | Bacteria protist interaction in the rhizosphere of Neltuma laevigata across arid soils under land use change | null | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1516123 | Reithrodontomys humulis (eastern harvest mouse) genome, mReiHum1, haplotype 2 | The eastern harvest mouse (Reithrodontomys humulis) is a species of rodent in the family Cricetidae. It is endemic to the Southeastern United States. Its natural habitats are subtropical or tropical seasonally wet or flooded lowland grassland, swamps, and pastureland (from Wikipedia entry). This sample of a male indivi... | Reithrodontomys humulis isolate:mReiHum1 | [
{
"pubdate": null,
"id": "33911273",
"db": "Pubmed"
}
] | [
{
"biosample_id": null,
"assembly_id": null,
"value": "AC7GHI"
}
] | null | [
"genome sequencing and assembly"
] | [
{
"category": null,
"label": "Richard Miller",
"url": "https://www.richmillerlab.com/"
},
{
"category": null,
"label": "Wendy Hood",
"url": "https://cosam.auburn.edu/directory/profile.php?id=wrh0001"
},
{
"category": null,
"label": "Geoffrey Hill",
"url": "https://cosam.a... |
PRJNA1516129 | AID and ATID mediated precise deletion system | Next-generation amplicon sequencing of AID and ATID in wheat and triticale | null | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1516145 | 16S rRNA amplicon sequencing of poplar-associated soil microbial communities | This project investigates soil microbial communities associated with poplar using paired-end 16S rRNA amplicon sequencing. Samples were collected in China and include control and treatment groups for comparative analysis of bacterial community composition. | null | [] | [] | null | [
"raw sequence reads"
] | [] |
PRJNA1516072 | Kharituwe: A pragmatic RCT trial of TB household contact investigation at two sites in South Africa | In an effort to find evidence-based strategies to improve TB household contact investigation yield, Kharituwe (Let's go in isiVenda) aimed to evaluate two novel strategies for the timing of household contact investigation in South Africa. The study compared standard contact investigation conducted during regular busine... | null | [
{
"pubdate": "2025-10-15T00:00:00",
"id": "40576365",
"db": "Pubmed"
},
{
"pubdate": null,
"id": "41607590",
"db": "Pubmed"
},
{
"pubdate": null,
"id": "40503514",
"db": "Pubmed"
}
] | [] | null | [
"raw sequence reads"
] | [
{
"category": null,
"label": "Published analysis of WGS data",
"url": "https://doi.org/10.1093/infdis/jiaf326"
},
{
"category": null,
"label": "Published analysis of Kharituwe trial",
"url": "https://doi.org/10.1016/j.eclinm.2025.103744"
},
{
"category": null,
"label": "Clini... |
End of preview. Expand in Data Studio
OmicIDX 2026-10
OmicIDX is a regularly refreshed, analysis-ready copy of public genomics
metadata: NCBI SRA (studies, samples, experiments, runs, accessions), NCBI GEO
(series, samples, platforms), NCBI and EBI BioSample, BioProject, and PubMed.
It also ships the sradb.* and geometadb.* marts. Everything is plain
Parquet that any engine can read.
This is the monthly release 2026-10, a verbatim copy of the daily publish
v2026-10-20/. Pin it with the @2026-10 revision. For the daily-refreshed copy, use
R2 latest/ at https://data.omicidx.cancerdatasci.org/latest/. Documentation lives at https://omicidx.cancerdatasci.org.
Provenance
| Publish date | 2026-10-20 |
| Published at | 2026-10-20T11:29:35.571633+00:00 |
| Transform SHA | 90688e92966330aac9ecd5a4fb8dc1d126f7982f |
| Lake snapshot id | 4171 |
The full provenance record is manifest.json.
Tables
28 files, 73.1 GB in total.
| View | File | Rows | Size (GB) |
|---|---|---|---|
bioprojects |
bioprojects.parquet |
1,128,196 | 0.25 |
biosamples |
biosamples.parquet |
60,427,250 | 7.85 |
geo_platforms |
geo_platforms.parquet |
28,819 | 0.01 |
geo_samples |
geo_samples.parquet |
8,678,255 | 2.33 |
geo_series |
geo_series.parquet |
293,571 | 0.16 |
geo_series_with_rnaseq_counts |
geo_series_with_rnaseq_counts.parquet |
27,714 | 0.00 |
geometadb.geo_supplemental_files |
geometadb/geo_supplemental_files.parquet |
7,026,380 | 0.21 |
geometadb.gpl |
geometadb/gpl.parquet |
28,819 | 0.00 |
geometadb.gse |
geometadb/gse.parquet |
293,571 | 0.14 |
geometadb.gse_gpl |
geometadb/gse_gpl.parquet |
341,054 | 0.00 |
geometadb.gse_gsm |
geometadb/gse_gsm.parquet |
10,447,481 | 0.05 |
geometadb.gsm |
geometadb/gsm.parquet |
8,678,255 | 3.21 |
pubmed_articles |
pubmed_articles.parquet |
41,267,953 | 37.11 |
sra_accessions |
sra_accessions.parquet |
162,771,320 | 5.19 |
sra_experiments |
sra_experiments.parquet |
42,615,764 | 3.85 |
sra_runs |
sra_runs.parquet |
45,493,391 | 1.71 |
sra_samples |
sra_samples.parquet |
44,636,830 | 4.24 |
sra_studies |
sra_studies.parquet |
774,584 | 0.18 |
sradb.experiment |
sradb/experiment.parquet |
42,615,764 | 0.76 |
sradb.human_runs |
sradb/human_runs.parquet |
8,535,912 | 0.12 |
sradb.mouse_runs |
sradb/mouse_runs.parquet |
4,413,081 | 0.06 |
sradb.rnaseq_runs |
sradb/rnaseq_runs.parquet |
9,046,637 | 0.14 |
sradb.run |
sradb/run.parquet |
45,638,775 | 0.74 |
sradb.run_with_study |
sradb/run_with_study.parquet |
45,638,775 | 0.65 |
sradb.sample |
sradb/sample.parquet |
44,636,830 | 1.27 |
sradb.sra |
sradb/sra.parquet |
45,638,775 | 2.59 |
sradb.study |
sradb/study.parquet |
774,584 | 0.15 |
sradb.wgs_runs |
sradb/wgs_runs.parquet |
9,589,280 | 0.16 |
Querying
DuckDB, one file:
SELECT count(*) FROM 'hf://datasets/seandavis/omicidx@2026-10/sra_studies.parquet';
DuckDB, every table as a view (views.sql points at this release):
curl -sL https://huggingface.co/datasets/seandavis/omicidx/resolve/2026-10/views.sql | duckdb omicidx.duckdb
duckdb omicidx.duckdb -c "SELECT count(*) FROM sradb.study"
Python (polars):
import polars as pl
df = pl.scan_parquet("hf://datasets/seandavis/omicidx@2026-10/sra_studies.parquet").head(10).collect()
R (arrow):
url <- "https://huggingface.co/datasets/seandavis/omicidx/resolve/2026-10/sra_studies.parquet"
tf <- tempfile(fileext = ".parquet")
download.file(url, tf, mode = "wb")
studies <- arrow::read_parquet(tf)
License
The OmicIDX code is MIT-licensed (https://github.com/seandavi/omicidx). The data are redistributed from NCBI (SRA, GEO, BioSample, BioProject, PubMed) and EBI (BioSamples) and remain under those providers' terms of use.
Citation
@misc{omicidx_2026_10,
title = {OmicIDX, release 2026-10},
author = {Davis, Sean},
year = {2026},
url = {https://huggingface.co/datasets/seandavis/omicidx/tree/2026-10}
}
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