cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002276
title: Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [RNA-Seq]

description: Nrf2(A502Y) mutant failed to recognize cis-element required for induction of Nrf2 target genes.To examine whether Nrf2(A502Y) supports expression of a distinct gene set from that supported by Nrf2, RNA-Seq analysis was performed. We compared gene expression profiles in peritoneal macrophages from Nrf2+/+ and Nrf2AY/AY mice between basal and DEM (which is an electorophilic stress agent promoting Nrf2 induction)-treated conditions. Overall design: mRNA profiles of wild type (WT) and Nrf2AY/AY (AY) mutant macrophages under basal and DEM-treated condition were generated by deep sequencing, in triplicate.
DOI: 10.26036/cnphis0002277
title: Lateolabrax maculatus Transcriptome or Gene expression

description: The goal of this project is to identified Lateolabrax maculatus transcripts using de novo assembly of NextGen sequences
DOI: 10.26036/cnphis0002278
title: Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America

description: Microbiome and resistome of human fecal and environmental microbiota from rural El Salvador and peri-urban Lima, Peru
DOI: 10.26036/cnphis0002279
title: Genomic sequences of several pinned museum beetles

description: Natural history collections are invaluable resources that not only serve as repositories for material from previous studies but also as sources of data for novel biological discoveries. While traditionally viewed as a resource for taxonomic and systematic research, they are now being utilized across diverse biological disciplines. Increasingly, museum specimens, especially those in herbaria and vertebrate collections, are also being used in molecular studies. In this study, 13 dry mounted beetles from natural history collections, ranging in age from 84 years to 4 years old, were genomically sequenced in order to assess the effectiveness of high-throughput sequencing for ancient specimens and determine the beetle's phylogenetic placement.
DOI: 10.26036/cnphis0001597
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001598
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001599
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001600
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001601
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001602
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001603
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001604
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002280
title: The SPOP-containing Complex Functions as an E3 Ligase for SETD2 to Regulate Gene-Specific H3K36me3-Coupled Alternative Splicing

description: H3K36me3 has been reported to associate with active gene expression, and SETD2 is the mainly methyltransferase for H3K36me3. We identified SPOP which is a CUL3 family protein as a E3 ligase for SETD2. Genome wide analysis by using ChIPSeq and RNASeq demonstrate that SPOP specificly eliminate H3K36me3 modification at target genes and resulted in alternative splicing of those target genes. Overall design: RNA-Seq was perfomed in negative control(NC), siSPOP, siSEDT2, and SPOP/SETD2 double knock down cell lines. For alternative splicing events analysis illumina HiSeq4000 platform was used for sequencing with 150 paired end mode and sequencing reads range from 67 million to 90 million. H3K36me3 ChIP-Seq was performed in NC, siSPOP, siSETD2, SPOP and SETD2 double knock down cell lines. ChIP-Seq libraries were sequenced by HiSeq 2500 platform with single end 50bp mode.
DOI: 10.26036/cnphis0002281
title: Aves: Galliformes raw sequence reads

description: Phylogenetics of Galliformes inferred with ultraconserved elements
DOI: 10.26036/cnphis0002282
title: Shotgun sequencing of two Mycopsylla spp. - raw sequence reads

description: Identification of microsatellite markers and endosymbionts of two Mycopsylla spp.
DOI: 10.26036/cnphis0002283
title: Manatee rectal bacteria Metagenome

description: Manatee rectal bacteria metagenome
DOI: 10.26036/cnphis0002284
title: transcriptome of Canis lupus familiaris

description: transcriptome of Canis lupus familiaris
DOI: 10.26036/cnphis0002285
title: Necator americanus, Ascaris lumbricoides, Trichuris trichiura, Ancylostoma duodenale raw sequence reads

description: Sequencing aims to discover highly repetitive sequences within each organism. These sequences can be used for diagnostic development and evolutionary relationship characterization
DOI: 10.26036/cnphis0002286
title: Centropyge deborae genome sequencing

description: Samples of Centropyge deborae (voucher no. 373) were purchased from local aquarium and originally imported from Fiji. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002287
title: Centropyge nox genome sequencing

description: Samples of Centropyge nox (voucher no. 397) were purchased from local aquarium and originally imported from Bali, Indonesia. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002288
title: Oryctes borbonicus isolate:OB123 Genome sequencing and assembly

description: Genome of this beetle extends the possibilities to perform comparative genomic analysis of beetles and to study the interaction with nematodes such as Pristionchus pacificus
DOI: 10.26036/cnphis0001605
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001606
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001607
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001608
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001609
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001610
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001611
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001613
title: The Brain Transcriptome of the White-throated Sparrow, a Vertebrate Model of Inversion Polymorphism

description: Transcriptome sequencing of male and female brains. Female samples represent the ZAL2m/ZAL2m, ZAL2/ZAL2m and ZAL2/ZAL2 genotypes. Male samples represent the ZAL2/ZAL2m and ZAL2/ZAL2 genotypes.
DOI: 10.26036/cnphis0001614
title: Eyprepocnemis plorans plorans strain:Grasshopper Variation

description: Study of repeated sequences in the grasshopper Eyprepocnemis plorans
DOI: 10.26036/cnphis0002289
title: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

description: Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive diversification of lineages in New Guinea prior to its emergence as a landmass and long-distance dispersal to Africa or Asia when no dispersal corridors existed. However, these results may be flawed because the studies relied on unresolved phylogenetic relationships and a controversial biogeographic time calibration. Here, we combine the first genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide the first well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred after island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Although New Guinea presently contains high songbird species richness, our data unambiguously falsify the proto-Papuan hypothesis for early songbird diversification2,6 and suggest that New Guinea has, instead, served as an “evolutionary refuge” for Australian lineages that have diversified more recently within the island23. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.
DOI: 10.26036/cnphis0002290
title: Coturnix japonica strain:Cons DD Transcriptome or Gene expression

description: Transcriptome data generated for the annotation of the Japanese quail Coturnix japonica.
DOI: 10.26036/cnphis0002291
title: DNA repair in species with extreme lifespan differences

description: We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse. Overall design: Compare steady-state RNA levels from 3 samples each of adult liver tissue of human, naked mole rat, and mouse. Mouse samples available in the Short Reads Archive: SRX871336, SRX871370, SRX871395 (SRP053350) and BioProject PRJNA274780.
DOI: 10.26036/cnphis0002292
title: Aiptasia Raw sequence reads

description: The goal of this study was to investigate patterns of genome-wide polymorphism in Aiptasia sea anemones using low coverage genomic sequencing information from 10 individuals. Genomic DNA from 8 anemones harboring symbiotic algae (Symbiodinium sp.) and 2 anemones without symbiotic algae were sequenced.
DOI: 10.26036/cnphis0002293
title: Lycaon pictus Genome sequencing and assembly

description: Genome sequences of two wild dogs from separate populations (South Africa, Kenya) for population history reconstruction and scans for selection.
DOI: 10.26036/cnphis0002294
title: Single cell RNA sequencing of primary breast cancer.

description: We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER+ and HER2+); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2+); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. We separated these single cells into epithelial tumor and tumor-infiltrating immune cells using inferred CNVs from RNA-seq. The refined single cell profiles for the tumor and immune cells provide key expression signatures of breast cancer and the surrounding microenvironment. Overall design: All single-cell mRNA expression profiles were acquired from eleven patients (BC01-BC11) including two lymph node metastases (BC03LN, BC07LN) (549 samples). We applied four filtering criteria so as to remove samples with low sequencing quality and finally obtained 515 single cell sequencing data. Matched bulk tumor tissues and/or pooled cells were also sequenced and analyzed by the single cell RNA-seq pipeline (14 samples). Bulk tumor transcriptomes showed significant correlations with the average of single cell transcriptomes.
DOI: 10.26036/cnphis0002296
title: Leuciscus idus Raw sequence reads

description: GBS reads : Leucicus idus from anadromous and non-migrating populations
DOI: 10.26036/cnphis0002297
title: Snapshot and temporal scRNA-seq of progenitor cells to dissect human embryonic stem cells entry into endoderm progenitors

description: Human pluripotent stem cells (hPSCs) offer a unique cellular model to study lineage specifications of the primary germ layers during human development. We profiled single-cell RNA-seq (scRNA-seq) on four lineage-specific progenitor cells derived from hESCs. Our scRNA-seq analyses revealed each type of progenitors display various extend of heterogeneity. Specifically, definitive endoderm cells (DECs) not only show a greater degree of heterogeneity, but are also enriched in metabolic signatures. Followed by detailed temporal scRNA-seq profiling along DEC differentiation, we reconstructed a differentiation trajectory using a novel statistical pipeline named Wave-Crest. Wave-Crest further identifies candidate regulators during the transitioning phase from Brachyury (T)+ mesendoderm towards CXCR4+ DEC state. To functionally test identified novel regulators; we generated a live cell monitoring system, a T-2A-EGFP knock-in reporter cell line via CRISPR/CAS9. We demonstrated that, among the top candidate genes, KLF8 plays a pivotal role modulating mesendoderm to DEC differentiation. In this submission, 1810 raw fastq files are provided; 212 are re-analysis from GSE64016. Four expected count matrices are provided - 1) 1018 single cells from snapshot progenitors; 2) 758 single cells from time couse profiling; 3) 19 bulk RNA-seq sample from snapshot progenitors; 4) 15 bulk RNA-seq sample from time course profiling. Overall design: Total 1018 single cells from snapshot progenitors and 758 single cells from time couse profiling. Matchd population bulk RNA-seq samples for both the progenitors snapshot (19 samples) and time course profiling (15 samples) also included in this submission. These data set are used to detect the transitioning phase from mesendoderm to definitive endoderm.
DOI: 10.26036/cnphis0002298
title: Galaxea fascicularis Genome sequencing

description: Samples of Galaxea fascicularis (voucher no. 467) were collected from Hainan island, China. Total genomic DNA was extracted and paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq platform (2X300bp).
DOI: 10.26036/cnphis0001612
title: Onthophagus taurus Genome sequencing

description: Whole genome assembly of Onthophagus taurus (Bull-headed Dung beetle) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001616
title: Reorganization of enhancer patterns in transition from naïve to primed pluripotency (RNA-seq)

description: Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even in the absence of other differentiation cues, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a large subset of primed pluripotency-associated genes and redirect Oct4 to thousands of previously inaccessible sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to function as pioneers is highly context-dependent Overall design: transcription profile of ESCs and EpiLCs to analzye changes during differentiation and the effect of Otx2 loss and overexpression on the differentiation properties
DOI: 10.26036/cnphis0001617
title: Cimex lectularius Genome sequencing

description: Whole genome assembly of Cimex lectularius (Bed Bug) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001618
title: Fasciola hepatica isolate:Oregon Genome sequencing and assembly

description: Fasciola hepatica is a parasitic fluke that lives in the liver. In addition to humans it infects cows and sheep. It is known as the sheep or common liver fluke and causes a disease called fascioliasis. Fasciola hepatica is found in areas where cattle and sheep are raised. Adults reach a length of 3 cm and 1 cm width. Fascioliasis is caused by Fasciola species (F. hepatica and F. gigantica), where infection arises from ingestion of metacercariae on water plants such as watercress. Note that the physical sample for this Fasciola hepatica BioSample (SAMN02780903) was found to contain a Neorickettsial endosymbiont, so the physical sample was assigned a second BioSample accession (SAMN04272095) for the endosymbiont record.
DOI: 10.26036/cnphis0001619
title: Pacific Biosciences Model Organism Genome Sequencing

description: DNA from three model organisms (Yeast, Flowering plant, and Fruit Fly) have been sequenced and de novo assembled using the PacBio RS II insrument
DOI: 10.26036/cnphis0001620
title: Diuraphis noxia strain:RWA2 Genome sequencing and assembly

description: <i>Diuraphis noxia<i> Kurdjumov, AKA “Russian wheat aphid”, is a major pest of wheat and barley throughout the semi-arid climatic regions of world. This phytotoxic aphid damages cereals and wild grasses during feeding by inducing red and white leaf streaking, leaf rolling, plant stunting and death. Such damage causes over $100 million in yield losses annually in the United States alone. This genome sequencing project was undertaken to aid in the development of a phytotoxic aphid model that will lead to an understanding of how this aphid overcomes resistance genes in wheat, how new virulent biotypes evolve, how phytotoxic aphid-plant interactions progress, and how genomic structure and content differs among aphids differing in host associations, as well as provide new approaches for aphid control.</i></i>
DOI: 10.26036/cnphis0001621
title: Small RNAs from four Drosophila melanogaster-subgroup species

description: Curration of small RNAs from four melanogaster-subgroup species (Drosophila simulans, Drosophila sechellia, Drosophila erecta, and Drosophila yakuba) for the purpose of non-coding RNA annotation and comparative genomics assessment. Overall design: Non-replicated small RNA samples from four melanogaster-subgroup species.
DOI: 10.26036/cnphis0001622
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001623
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002299
title: Porites lutea Genome sequencing

description: Samples of Porites lutea (voucher no. 466) were collected from Hainan island, China. Total genomic DNA was extracted and paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq platform (2X300bp).
DOI: 10.26036/cnphis0002300
title: Paragonimus heterotremus strain:LC Genome sequencing and assembly

description: The human lung fluke Paragonimus heterotremus represents one of the food-borne helminths infecting humans. These flukes cause paragonimiasis in people and other crab-eating mammals in Asia, parts of West Africa, and South and Central America
DOI: 10.26036/cnphis0002301
title: Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells

description: We were interested in how the complex mammalian transcriptomes were established. Using spermatogenesis as a model system, we address this question first by profiling the mRNAs, lncRNAs and circRNAs and examining their relative abundances in 4 types of SPCs (priSG-A, plpSC, pacSC, rST). Overall design: F1 pups of DBA/2 and C57BL6 mice were used for cell isolation and SSC culture. priSG-A, plpSC and pacSC were isolated from prepubertal mice undergoing the first wave of spermatogenesis while rST were from 60 dpp adult mice.
DOI: 10.26036/cnphis0002303
title: Hypsibius dujardini Genome sequencing and assembly

description: The goal of the study was to sequence and assemble the genome of the tardigrade (water bear) Hypsibius dujardini. No published genome exists for the entire phylum tardigrada and thus this project is relevant for studies addressing the evolution, development, and physiology of these organisms.
DOI: 10.26036/cnphis0002304
title: Whole exome sequencing for primary breast cancer and lymph node metastasis samples

description: We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER and HER2 ); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2 ); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. We separated these single cells into epithelial tumor and tumor-infiltrating immune cells using inferred CNVs from RNA-seq. The refined single cell profiles for the tumor and immune cells provide key expression signatures of breast cancer and the surrounding microenvironment. Overall design: All single-cell mRNA expression profiles were acquired from eleven patients (BC01-BC11) including two lymph node metastases (BC03LN, BC07LN) (549 samples). We applied four filtering criteria so as to remove samples with low sequencing quality and finally obtained 515 single cell sequencing data. Matched bulk tumor tissues and/or pooled cells were also sequenced and analyzed by the single cell RNA-seq pipeline (14 samples). Bulk tumor transcriptomes showed significant correlations with the average of single cell transcriptomes.
DOI: 10.26036/cnphis0002305
title: Globodera rostochiensis Raw sequence reads

description: genome assembly
DOI: 10.26036/cnphis0002306
title: Paulownia fortunei Raw sequence reads

description: Paulownia witches' broom mechanism study
DOI: 10.26036/cnphis0002307
title: Hypophthalmichthys nobilis Transcriptome or Gene expression

description: the liver transcriptomes of two groups (F and S) of bighead carp within a full-sib family with significant differences in growth rate were sequenced using Illumina RNA-Seq
DOI: 10.26036/cnphis0002308
title: Athlete Microbiome Project (AMP)

description: Metagenomic sequencing to identify and measure the abundances of microorganisms present in stool samples from athletes
DOI: 10.26036/cnphis0001624
title: GenomeTrakr Project: USDA - Food Safety and Inspection Service

description: CDC isolated strains of Salmonella enterica