cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001171
title: RNA-sequencing of the human milk fat layer during colostrum, transitional, and mature stages of lactation

description: Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding ß-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans. Overall design: Milk fat mRNA profiles were generated from Day 2 and mature milk samples obtained from lactating mothers
DOI: 10.26036/cnphis0001172
title: Thelohanellus kitauei isolate:Wuqing Genome sequencing and assembly

description: Myxozoans (phylum myxozoa) are a diverse group of metazoan endoparasites, with characteristic multicellular spores, polar capsules and extrudible polar filament used in invasion of hosts. In the present work, we sequence and annotate the genome sequences of Thelohanellus kitauei, the first genome in Phylum myxozoa which will help us to get more insight into the unknown myxozoan biology and attempt to reveal its parasitic nutritional characterization. Also wish to find potential clues to control this severe fish parasitosis.
DOI: 10.26036/cnphis0001173
title: Aculeate systematics

description: Genomic and transcriptomic sequences were generated to determine the phylogenetic relationships among a number of Aculeate taxa.
DOI: 10.26036/cnphis0001174
title: Oryzias latipes strain:Hd-rR Epigenomics

description: SMRT Sequencing (by PacBioRS) of medaka fish and analyzing kinetics information (IPD ratio) to predict hypomethylated regions in medaka genome, while improving the draft genome.
DOI: 10.26036/cnphis0001175
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001176
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001849
title: Random survey sequencing of four dipteran flies; Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipalpis Random survey

description: Survey sequencing can serve as a method to quickly gain information on genome characteristics. We surveyed four dipteran taxa in an effort to assemble their mitochondrial genomes and to investigate transposable element content.
DOI: 10.26036/cnphis0001851
title: Characterization of the complete genome sequence of Barley yellow striate mosaic virus reveals an overprinted ancillary gene encoding a small hydrophobic protein

description: In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1. Overall design: Viral assembly from the BYSMV infected wheat plants to obtain the full lengh genome and characterise the viral siRNAs
DOI: 10.26036/cnphis0001852
title: Coturnix coturnix strain:HSR Genome sequencing

description: Analysis of two lines of Quail divergently selected on their social reinstatement behavior.
DOI: 10.26036/cnphis0001853
title: Genome sequencing for Pteropus vampyrus

description: The <i>Pteropus vampyrus</i> genome is being sequenced to ~2X coverage by the Human Genome Sequencing Center at the Baylor College of Medicine and the Broad Institute using a whole genome shotgun sequencing strategy.
DOI: 10.26036/cnphis0001854
title: Gymnodiptychus pachycheilus Transcriptome or Gene expression

description: Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation.
DOI: 10.26036/cnphis0001855
title: Exaiptasia pallida isolate:CC7 Genome sequencing and assembly

description: Coral reefs depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae of the genus Symbiodinium. Aiptasia, a globally distributed sea anemone, serves as a model system for cnidarian-dinoflagellate endosymbiosis.
DOI: 10.26036/cnphis0001856
title: Oryza sativa strain:Nipponbare Transcriptome or Gene expression

description: Strand-specific whole transcriptome RNA-Seq data of rice anthers, pistils, seeds 5DAP and shoots 14DAG.
DOI: 10.26036/cnphis0001857
title: Angiostrongylus cantonensis Genome sequencing and assembly

description: Angiostrongylus cantonensis is a bursate nematode parasite that causes eosinophilic meningitis (or meningoencephalitis) in humans. Its genome is needed for finding novel miRNAs and other gene products. We have sequenced, assembled and annotated the genome of A. cantonensis. The genome size is estimated to be 261 Mb, with 17,280 genomic scaffolds, 91X coverage and 93.15% of genome completeness. This draft genome is the first report for the Metastrongyloidea superfamily. It will facilitate the understanding of many unresolved issues on the parasite and the disorder it causes.
DOI: 10.26036/cnphis0001858
title: gold-monkey species Genome resequencing

description: Provide genome resequencing data of gold-monkey species
DOI: 10.26036/cnphis0000458
title: Macrotermes natalensis gut Metagenome

description: Metagenome sequencing of guts in queen, soldier and worker of Macrotermes natalensis.
DOI: 10.26036/cnphis0000462
title: CompleteGenomics sequencing of (PEL) Peruvian in Lima, Peru HapMap population. DNA for sequencing was extracted from whole blood

description: -
DOI: 10.26036/cnphis0000463
title: De novo assembly and characterization of Litchi fruit transcriptome.SRP020220

description: Litchi (Litchi chinensis Sonn.) is one of the most important tropical and subtropical fruit trees. There is a lack of transcriptomic and genomic information in public databases for understanding the molecular mechanisms underlying fruit set and development in litchi. High throughput transcriptome sequencing is a convenient technique to explore a large quantity of transcript sequences.
DOI: 10.26036/cnphis0000464
title: Cricetulus griseus strain:breed Genome sequencing and assembly

description: Cricetulus griseus Genome Sequencing assembly annotation and evolution.
DOI: 10.26036/cnphis0000465
title: CompleteGenomics sequencing of (CHS) Han Chinese population

description: -
DOI: 10.26036/cnphis0000467
title: CompleteGenomics sequencing of (LWK) Luhya HapMap population DNA for sequencing was extracted from whole blood

description: -
DOI: 10.26036/cnphis0000468
title: CompleteGenomics sequencing of (YRI) Yoruba HapMap population

description: -
DOI: 10.26036/cnphis0000469
title: CompleteGenomics sequencing of (YRI) Yoruba HapMap population. DNA for sequencing was extracted from whole blood

description: -
DOI: 10.26036/cnphis0000470
title: Phalaenopsis equestris Genome sequencing and assembly

description: Orchidaceae is one of the most diverse plant families and renowned for its spectacular flowers with highly evolved petals, labellum and fused androecium and gynoecium (gynostemium) to attract diverse pollinators for effective pollination. Because of these, and other specific reproductive and ecological adaptations, orchids are important species for evolutionary biology.
DOI: 10.26036/cnphis0001177
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001178
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001179
title: Mus musculus strain:black6 x castaneus Transcriptome or Gene expression

description: RNA-Seq of reciprocally crossed Black6 x CAST hybrid mouse tissues.
DOI: 10.26036/cnphis0001180
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001181
title: Asiatic Lion Mitochondrial Genome Sequencing [BIOWLT22E3], Project-151, Gujarat Genomics Initiative, GSBTM, DST, Gandhinagar, Gujarat, India

description: The Asiatic Lion exists as a single isolated population in India''s Gujurat State [IUCN]. The population of lions in Gir forests has gone up by nearly 14 per cent in last five years, with the latest census revealing the presence of 411 of the big cats as compared to 359 in the 2005 census [Forest Department, Government of Gujarat]. The aim of this study was to sequence the mitochondrial genome of Asiatic Lion. This study might have relevance in the field of evolutionary biology, conservation, breeding and biotechnology. Bio material ID: BIOWLT22E3
DOI: 10.26036/cnphis0001182
title: Anopheles christyi Genome sequencing project

description: None
DOI: 10.26036/cnphis0001183
title: Anopheles albimanus STECLA Genome sequencing project

description: None
DOI: 10.26036/cnphis0001184
title: Anopheles dirus WRAIR2 Genome sequencing project

description: None
DOI: 10.26036/cnphis0001185
title: Anopheles minimus MINIMUS1 Genome sequencing project

description: None
DOI: 10.26036/cnphis0001859
title: Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

description: DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4, 5. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. We show that DHS patterns at the single-cell level are highly reproducible among individual cells. Among different single cells, highly expressed gene promoters and enhancers associated with multiple active histone modifications display constitutive DHS whereas chromatin regions with fewer histone modifications exhibit high variation of DHS. Furthermore, the single-cell DHSs predict enhancers that regulate cell-specific gene expression programs and the cell-to-cell variations of DHS are predictive of gene expression. Finally, we apply scDNase-seq to pools of tumour cells and pools of normal cells, dissected from formalin-fixed paraffin-embedded tissue slides from patients with thyroid cancer, and detect thousands of tumour-specific DHSs. Many of these DHSs are associated with promoters and enhancers critically involved in cancer development. Analysis of the DHS sequences uncovers one mutation (chr18: 52417839G&gt;C) in the tumour cells of a patient with follicular thyroid carcinoma, which affects the binding of the tumour suppressor protein p53 and correlates with decreased expression of its target gene TXNL1. In conclusion, scDNase-seq can reliably detect DHSs in single cells, greatly extending the range of applications of DHS analysis both for basic and for translational research, and may provide critical information for personalized medicine. Overall design: Exploring the landscape of chromatin accessibility in single cells and clinical samples
DOI: 10.26036/cnphis0001860
title: The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

description: An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome “shock” and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, mainly siRNAs and miRNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid (genome: AB) and its allotetraploid (genome: AABB) between Brassica rapa (?) and Brassica nigra (?) in the present study.The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The high-throughput sequencing results obtained for the small RNAs showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, 320 known and 52 novel miRNAs were obtained from the parents in both the allodiploid and allotetraploid. However, quantitative real-time polymerase chain reaction (qRT PCR) analysis showed that the expression levels of the targets genes were negatively corrected with the expressed miRNAs.The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids. Overall design: High throughput sequence of the parents (Brassica rapa and Brassica nigra) and their hybrids (allodiploid and allotetraploid)
DOI: 10.26036/cnphis0001861
title: Genome sequencing of the Darwin''s Finch species

description: Study of the evolutionary history of Darwin''s Finches
DOI: 10.26036/cnphis0001863
title: Sus scrofa strain:Duroc, Landrace, Yorkshire Metagenome

description: We used the three most common purebred lines of pigs (Duroc, Landrace and Yorkshire), known for their favourable characteristics and profitability. And we examined the effects of a 12-week cohabitation period on the microbiotas of these genetically distinct breeds, using 16S rRNA gene pyrosequencing.
DOI: 10.26036/cnphis0001865
title: Random survey sequencing of nine crocodilians - Alligator sinensis, Caiman latirostris, Ca. yacare, Crocodylus acutus, Cr. niloticus, Mecistops cataphractus, Melanosuchus niger, Osteolaemus tetraspis, and Tomistoma schlegelii Random survey

description: We conducted random survey sequencing of nine crocodilians to complement and enhance whole genome analyses of three other crocodilians, whose genomes were fully sequenced. The survey sequences were used to estimate transposable element diversity within the Order Crocodylia.
DOI: 10.26036/cnphis0001866
title: Anas platyrhynchos Transcriptome or Gene expression

description: The goal of this project is to identify the key transcripts controlling feed conversion and breast yield traits
DOI: 10.26036/cnphis0001867
title: Hoplostethus atlanticus population genomics sequencing

description: Our goal was to develop a SNP array to survey stock structure in orange roughy populations.
DOI: 10.26036/cnphis0001868
title: Oncorhynchus tshawytscha Genome sequencing

description: The purpose of this study was to characterize a putative sex determining gene (sexually dimorphic on the Y chromosome; sdY) in Chinook Salmon and develop a method to test genomic DNA (gDNA) samples for genetic sex assignment.
DOI: 10.26036/cnphis0000466
title: CompleteGenomics sequencing of (LWK) Luhya HapMap population

description: -
DOI: 10.26036/cnphis0000471
title: Prunus persica Genome sequencing.SRP021175

description: To dissect the genetic basis of peach domestication, here we report the resequencing data of 10 wild and 74 cultivated peach accessions to an average of 3.2× depth.
DOI: 10.26036/cnphis0000472
title: CompleteGenomics sequencing of (PUR) Puerto Rican in Puerto Rico HapMap population DNA for sequencing was extracted from whole blood

description: -
DOI: 10.26036/cnphis0000474
title: Morus notabilis Genome sequencing and assembly

description: We applied a whole genome shotgun sequencing (WGS) strategy to the species Morus notabilis, here we provide the sequencing data for the project.
DOI: 10.26036/cnphis0000475
title: Noninvasive prenatal detection for pathogenic CNVs related with fetal monogenetic diseases

description: Noninvasive prenatal detection for pathogenic CNVs related with fetal monogenetic diseases using target region capture sequencing.
DOI: 10.26036/cnphis0000476
title: Homo sapiens Exome.SRP019719

description: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be.
DOI: 10.26036/cnphis0000477
title: Human gut bacterial Targeted Locus (Loci)

description: A studied short-term effects of preoperative antibiotics on the intestinal microbiota of three undergone thyroidectomy patients who were treated with a dose of cephazoline preoperative and a patient who was not treated.
DOI: 10.26036/cnphis0000478
title: Homo sapiens Genome sequencing.SRP022372

description: Whole genome resequencing data of imatinib sensitive and resistent tumor of one DFSP patient.
DOI: 10.26036/cnphis0000479
title: RNA-Seq of Thermoanaerobacter tengcongensis MB4

description: We sequenced the RNA of Thermoanaerobacter tengcongensis MB4 in four different temperatures (i.e. 55?, 65?, 75?, 80?).
DOI: 10.26036/cnphis0000480
title: Whole genome sequencing of 4 pairs of HCCs and lung metastases

description: We sequenced the whole genomes of 4 HCC patients with lung metastases.
DOI: 10.26036/cnphis0000481
title: A copy number variation detection methods based on low coverage sequencing

description: We developed an sensitively and reliably detect CNVs method using low coverage or even ultra-low coverage data through population-scale sequencing.
DOI: 10.26036/cnphis0001186
title: Anopheles stephensi SDA500 Genome sequencing project

description: None
DOI: 10.26036/cnphis0001187
title: Anopheles atroparvus EBRO Genome sequencing project

description: None
DOI: 10.26036/cnphis0001188
title: Anopheles funestus FUMOZ Genome sequencing project

description: None
DOI: 10.26036/cnphis0001189
title: Anopheles maculatus Genome sequencing project

description: None
DOI: 10.26036/cnphis0001190
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001191
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001192
title: Anopheles 15 Genomes

description: None
DOI: 10.26036/cnphis0001193
title: Genome sequencing of Drosophila Outgroups (Diptera)

description: Whole-genome sequencing of several dipteran species: Drosophila busckii (Drosophilidae), Phortica variegata (Drosophilidae), Sarcophaga bullata (grey flesh fly, Sarcophagidae), Bactrocera oleae (olive fly, Tephritidae) and Hermetia illucens (black soldier fly, Stratiomyidae).
DOI: 10.26036/cnphis0001194
title: Whole genome shotgun (WGS) project for Drosophila pseudoobscura strain MV2-25

description: The <i>Drosophila pseudoobscura</i> genome was sequenced by the Human Genome Sequencing Center at Baylor College of Medicine (BCM-HGSC) using a whole genome shotgun (WGS) approach. The estimated 131 Mb euchromatic portion of the genome was sequenced to approximately 9-fold coverage. This WGS project represents Baylor release Dpse_2.0, and has the project accession AADE00000000. The current version of the project (01) has the accession number AADE01000000, and consists of sequences AADE01000001-AADE01012826. Gene annotation is provided by FlyBase.
DOI: 10.26036/cnphis0001869
title: Helicoverpa assulta Transcriptome or Gene expression

description: Data for manuscirpt: " Chemosensory Receptor Genes in Oriental Tobacco Budworm Helicoverpa assulta"
DOI: 10.26036/cnphis0001870
title: Struthio camelus Transcriptome

description: We sequenced the transcriptome from Struthio camelus in order to analyze the gene Expression of the serine/Threonine kinase 33 in the class Aves.
DOI: 10.26036/cnphis0001871
title: Operophtera brumata isolate:WM2013NL Genome sequencing and assembly

description: The goal of this project is to create an annotated reference genome for the Winter Moth (Operophtera brumata), which is studied for its adaptation to climate change.
DOI: 10.26036/cnphis0001872
title: Aphalara itadori strain:Hokkaido Genome sequencing

description: Identify polymorphic SNP loci for genotyping and identification of individuals of A. itadori collected on Hokkaido and Kyushu for release in the United States and Canada for the biological control of Japanese Knotweed
DOI: 10.26036/cnphis0001873
title: Bos taurus Transcriptome or Gene expression

description: mRNA was isolated from 79 different tissues from Dominette, the animal used for the original Bos taurus genome sequence. MRNA was also isolated from four tissues from Dominette''s daughter, three tissues from Dominette''s male fetus and ten tissues from SuperBull 99375. MRNA was isolated from each of these 96 tissue samples and sequenced by Illumina HiSeq 2000.
DOI: 10.26036/cnphis0001874
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001875
title: Foodborne Pathogen Survey

description: Genome Sequencing Project