cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000894
title: HIGHLY DIVERSE TCRalpha CHAIN REPERTOIRE OF PRE-IMMUNE CD8+ T CELLS REVEALS NEW INSIGHTS IN GENE RECOMBINATION

description: By sequencing tens of millions of TCRa chain transcripts from naïve mouse CD8+ T cells, we observed a hugely diverse repertoire, comprising nearly all possible TRAV-TRAJ combinations. Our findings are not compatible with sequential coordinate gene recombination, but rather with a model in which contraction and DNA looping in the TCRad locus provide equal access to TRAV and TRAJ gene segments, similar to that demonstrated for IgH gene recombination Overall design: High-throughput sequencing of entire TCRa repertoire from C57Bl/6 mice
DOI: 10.26036/cnphis0000895
title: Hoolock leuconedys Genome sequencing

description: The goal of this project is to generate whole genome sequence data for this species as part of the larger Gibbon Genome Sequence Project. The data for Hoolock leuconedys is intended as comparative sequence data, within the larger project Gibbon Genome Project that is based on the genome sequence and assembly of the Nomascus leucogenys genome.
DOI: 10.26036/cnphis0000896
title: Hylobates moloch Genome sequencing

description: The goal of this project is to generate whole genome sequence data for this species as part of the larger Gibbon Genome Sequence Project. The data for Hylobates moloch is intended as comparative sequence data, within the larger project Gibbon Genome Project that is based on the genome sequence and assembly of the Nomascus leucogenys genome.
DOI: 10.26036/cnphis0000897
title: Hylobates pileatus Genome sequencing

description: The goal of this project is to generate whole genome sequence data for this species as part of the larger Gibbon Genome Sequence Project. The data for Hylobates pileatus is intended as comparative sequence data, within the larger project Gibbon Genome Project that is based on the genome sequence and assembly of the Nomascus leucogenys genome.
DOI: 10.26036/cnphis0000155
title: CRC_BC Exome

description: Colorectal and Breast Cancer Whole Exome Sequencing
DOI: 10.26036/cnphis0000156
title: Mycobacterium africanum strain:D1 Transcriptome or Gene expression

description: M. africanum is most commonly found in West African countries, causing up to a quarter of cases of tuberculosis in countries such as the Gambia. It is an infection of humans only and is spread by an airborne route from individuals with open cases of disease. It has a similar degree of infectivity to the regular M. tuberculosis organism but is less likely to progress to clinical disease in an immunocompetent individual
DOI: 10.26036/cnphis0000157
title: Cynoglossus semilaevis Genome sequencing and assembly

description: The existance of male and females individuals, often strikingly different in morphology, reproductive strategies and behaviour, is one of the most widespread phenomena in biology. However, the genetic mechanisms used to generate this ubiquitous pattern are surprisingly diverse and do not at all follow a phylogenetic pattern. The tongue sole fish was selected to explain sex determination and sex chromosome evolution by whole genome sequence, because it offers the advantage of a relatively small genome and good karyological data with special ZW system and genomic resources as well as a molecular marker genetic map existed.
DOI: 10.26036/cnphis0000158
title: Homo sapiens Targeted Locus (Loci).SRP035336

description: A Novel Mutation in the TECTA Gene in a Chinese Family with Autosomal Dominant Nonsyndromic Hearing Loss
DOI: 10.26036/cnphis0000159
title: Gossypium barbadense Transcriptome or Gene expression

description: Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, is the most severe disease in cotton (Gossypium spp.), causing great lint losses worldwide.The objective of this study is to investigate the transcriptional profile in resistance cotton G. barbadense inoculated with V. dahliae. The infection samples at 2, 6, 12, 24, 48, and 72 hours, and one mock-inoculated sample were collected for the high throughput sequencing.about 200 million clean reads for each sample were generated with the quality control (Q=20).
DOI: 10.26036/cnphis0000160
title: GWAS for NPC

description: The susceptibility genes of nasopharyngeal carcinoma (NPC) and find a trim26 gene to study its function
DOI: 10.26036/cnphis0000161
title: Homo sapiens Exome.SRP035444

description: Whole-exome sequencing for the identification of susceptibility genes of Kashin–Beck disease
DOI: 10.26036/cnphis0000163
title: Nipponia nippon Genome sequencing and assembly

description: Whole genome sequencing of Nipponia nippon
DOI: 10.26036/cnphis0000164
title: Egretta garzetta Genome sequencing.SRP035853

description: We sequenced the WGS of Egretta garzetta
DOI: 10.26036/cnphis0000898
title: White-cheeked gibbon genome sequencing

description: The <i>Nomascus leucogenys</i> genome has been sequenced to 5.6x coverage. The DNA for this genome sequencing project was derived from a female northern white-cheeked gibbon with karyotype 1a, 22a, 7b.
DOI: 10.26036/cnphis0000899
title: Symphalangus syndactylus Genome sequencing

description: The goal of this project is to generate whole genome sequence data for this species as part of the larger Gibbon Genome Sequence Project. The data for Symphalangus syndactylus is intended as comparative sequence data, within the larger project Gibbon Genome Project that is based on the genome sequence and assembly of the Nomascus leucogenys genome.
DOI: 10.26036/cnphis0000900
title: Whole Genome Shotgun (WGS) project of Aquilegia formosa

description: JGI is in the process of sequencing the genome of <i>Aquilegia formosa</i>. Having the sequence will help in better understanding of genome evolution particularly in reference to adaptations to different environments.
DOI: 10.26036/cnphis0000901
title: Genome-wide analysis of histone modification, protein-DNA binding, cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells

description: Genome-wide analysis of histone modification (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3), protein-DNA binding (TAF1, P300, Pou5f1 and Nanog), cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells We generated histone modification data (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3) and protein-DNA binding data (TAF1, P300, Pou5f1 and Nanog) using Chromatin Immunoprecipitation followed by short sequencing (ChIP-seq), cytosine methylation data using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq), transcriptome data with RNA short sequencing (RNA-seq) in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation. Overall design: Examination of 8 histone modifications, 4 protein-DNA binding, cytosine methylation and transcriptome in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation.
DOI: 10.26036/cnphis0000902
title: Heliconius melpomene melpomene Genome sequencing

description: a consortium we are currently collaborating to sequence the genome of a Heliconius species using a combination of 454 and Illumina sequencing technology, in collaboration with the Baylor Human Genome Sequencing Centre. See also recent Genomics posts for updates on progress. Why Heliconius? A major challenge in evolutionary biology is to identify the genes underlying the diversity of morphologies and adaptations within populations and among species. We would like to know how developmental pathways are modified to produce evolutionary novelty; which genes underlie evolutionary radiations or adaptive change and whether they share particular characteristics or modes of action. Examples of recent evolutionary novelty are also useful for studying genetic variation in the genome surrounding a locus under strong selection. Strong selection can reduce genetic variation in surrounding regions and might be an important cause of genetic drift . This signature of selection is used to detect genes in human disease gene association studies, but we are still lacking empirical studies of the expected pattern under different selection regimes. Butterfly wing patterns are excellent models of phenotypic adaptation, as they have a long history of field studies demonstrating their adaptive value, they are highly diverse even between very closely related taxa, and they are amenable to manipulation studies during development. In particular many species show striking convergence of pattern due to mimicry, which offers an opportunity to study how different species produce the same phenotype: how repeatable is adaptation in different genetic backgrounds? Heliconius butterflies are a long-standing example of mimicry adaptation in a group that are particularly well suited to this kind of study. The Mullerian co-mimics, H. melpomene and H. erato, are well known for precise mimicry between the two species but also a great diversity of geographic races. Thus, the two species look identical in any one site, but their pattern changes between geographic locations. We have recently found striking evidence for homology between a cluster of tightly linked patterning loci in H. melpomene and a region controlling similar phenotypic effects in H. erato. More surprisingly, the same locus is homologous to a single pattern switch gene in a third species, H. numata. The latter has a very different pattern of diversity with locally polymorphic populations having several divergent morphs flying
DOI: 10.26036/cnphis0000903
title: Snake venom-gland transcriptomics

description: This project consists of comparative venom-gland transcriptomics of various species of venomous snake.
DOI: 10.26036/cnphis0000904
title: Clinical isolate

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Paratyphi C str. SARB49</b>. <i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Paratyphi C str. SARB49 was isolated from the blood of a patient in Santiago, Chile. This genome is part of the Comparative Genomics in the Enterobacteriaceae Project.
DOI: 10.26036/cnphis0000906
title: Strain for comparative analysis

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Enteriditis str. 48-0811</b>. This genome is part of the Comparative Genomics in the Enterobacteriaceae Project.
DOI: 10.26036/cnphis0000165
title: Aptenodytes forsteri Genome sequencing and assembly

description: Whole genome sequencing of Aptenodytes forsteri
DOI: 10.26036/cnphis0000166
title: Pygoscelis adeliae Genome sequencing and assembly

description: Whole genome sequencing of Pygoscelis adeliae
DOI: 10.26036/cnphis0000167
title: Zootermopsis nevadensis Transcriptome or Gene expression

description: Zootermopsis nevadensis transcriptome sequencing of different development stages and castes.
DOI: 10.26036/cnphis0000172
title: whole genome sequecing of one individual

description: We sequenced the genome of a patient
DOI: 10.26036/cnphis0000173
title: Ooceraea biroi Genome sequencing and assembly

description: The genome of the clonal raider ant Cerapachys biroi
DOI: 10.26036/cnphis0000174
title: Yersinia pestis Genome sequencing

description: we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives
DOI: 10.26036/cnphis0000175
title: YH_exome

description: WES data for the establishment of OTG-snpcaller
DOI: 10.26036/cnphis0000176
title: Human papillomavirus Genome sequencing

description: The original data of 18 cases of type HPV11 samples
DOI: 10.26036/cnphis0000178
title: Gossypium arboreum Genome sequencing

description: Genome assembly and study.
DOI: 10.26036/cnphis0000905
title: Salmonella enterica subsp. enterica serovar Enteritidis str. SARB19 Genome sequencing

description: This genome is part of the Comparative Genomics in the Enterobacteriaceae Project.
DOI: 10.26036/cnphis0000908
title: Transcriptome sequencing of Foxtail millet Setaria italica for different tissues

description: Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues. Overall design: Four RNA pools were created corresponding to four different tissues: root, leaf, stem, spica (tassel) at developmental stage, then each pool was sequenced.
DOI: 10.26036/cnphis0000909
title: Digital Marine Bioprospecting

description: Mining for bioactive compounds in hexacoral transcriptomes
DOI: 10.26036/cnphis0000910
title: Salmonella enterica subsp. enterica serovar Rissen str. 150 Genome sequencing and assembly

description: This project is for an outbreak isolate.
DOI: 10.26036/cnphis0000911
title: Salmonella enterica subsp. enterica serovar Enteritidis str. 18569 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar <i>Enteritidis</i> str. 18569</b>. This genome will be used for comparative analysis.
DOI: 10.26036/cnphis0000912
title: Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq

description: Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes. Overall design: We get transcriptome of 124 individual cells from human pre-implantation embryos and human embryonic stem cells by applying single cell RNA-seq technique we recently developed[1][2][3][4]. We did in-depth bioinformatic analysis to these data and found very dynamic expression of protein-coding genes. [1] Tang, F. et al. (2010a) Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis. Cell Stem Cell 6, 468-478. [2] Tang, F. et al. (2010b) RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protocols 5, 516-535. [3] Tang, F. et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Meth 6, 377-382. [4] Tang, F. et al. (2011) Development and applications of single-cell transcriptome analysis. Nat Meth 8, S6-S11.
DOI: 10.26036/cnphis0000913
title: Salmo salar Genome sequencing

description: Atlantic salmon is one of 68 closely related species of salmonids which comprise eleven genera that include salmon, trout, charr, freshwater whitefishes, ciscos and graylings. Atlantic salmon are of considerable economic, social and environmental importance. Salmonids contribute to local and global economies through aquaculture, wild stock fisheries and recreational sport fisheries. In addition, they are a traditional food source for aboriginal peoples and play a central role in their culture. Salmon and trout are sentinel species for monitoring the aquatic environment, and therefore they are used extensively for eco-toxicology studies. Importantly, the common ancestor of salmon and trout experienced a whole genome duplica­tion (60-100MYA), and modern species may be considered pseudo­ tetraploid as they are well along the process of reverting to a stable diploid state. There is a large salmonid research community working on the biology, life histories, population dynamics, biogeography, phylogenetic relationships, physiology and nutrition of salmonids. No other species group of fishes receives such comprehensive commercial and scientific attention. p An International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG), representing researchers, funding agencies and industry from Canada, Chile and Norway, was formed to undertake a comprehensive genome sequence that would benefit all salmonids. p Note: Double haploid individual chosen for sequencing.
DOI: 10.26036/cnphis0000915
title: Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing

description: The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Overall design: Examination of 7 small RNA libraries in spike tissues during cold and control condition
DOI: 10.26036/cnphis0000916
title: Whole Genome SNP Discovery and Analysis of Genetic Diversity in Turkey (Meleagris gallopavo)

description: Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, and subsequent analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles.
DOI: 10.26036/cnphis0000917
title: Staphylococcus aureus subsp. aureus Genome Sequencing

description: Despite its clinical importance, the evolution of the EMRSA-16 clone, in addition to the molecular basis for its success are poorly understood. Here we employ a phylogenomic approach to examine the diversity of the EMRSA-16 clone relative to other CC30 pandemic clones. The results represent a high resolution insight into the emergence, expansion and transmission of a major clone of MRSA, revealing novel molecular correlates for its hospital association. 22 strains within S. aureus clonal complex 30 were sequenced.
DOI: 10.26036/cnphis0000179
title: Ovis aries breed:Texel Genome sequencing and assembly

description: WGS assembly of the genome from a male and a female Texel sheep.
DOI: 10.26036/cnphis0000180
title: Heterocephalus glaber genome sequencing

description: Genome sequencing of a male naked mole-rat using Illumina reads, with a sequencing depth of &gt;20x. The animal is from a captive breeding colony at the University of Illinois, Chicago.
DOI: 10.26036/cnphis0000181
title: Nanorana parkeri isolate:BGI_ZX_2015 Genome sequencing and assembly

description: -
DOI: 10.26036/cnphis0000182
title: Triticum urartu Genome sequencing and assembly

description: Wheat A Genome Sequencing.
DOI: 10.26036/cnphis0000183
title: Aegilops tauschii cultivar:AL8/78 Genome sequencing and assembly

description: We uploaded the genome sequence and annotation for Aegilops tauschii genome sequencing project here.
DOI: 10.26036/cnphis0000185
title: Pseudosciaena crocea BAC

description: We sequenced the BAC of Pseudosciaena crocea
DOI: 10.26036/cnphis0000186
title: Homo sapiens Targeted Locus (Loci).SRP041218

description: We want to find the evolution history of EPAS1 gene from Tibetan
DOI: 10.26036/cnphis0000187
title: Bacterial community in liquor fermentation process

description: Bacterial diversity in liquor fermentation process characterized by 16S rDNA sequencing
DOI: 10.26036/cnphis0000918
title: Metaseiulus occidentalis genome sequencing project

description: The <i>Metaseiulus occidentalis</i> genome was sequenced by the Baylor College of Medicine using the 454 XLR sequencing platform. Genomic DNA was prepared from an inbred line to facilitate assembly.
DOI: 10.26036/cnphis0000919
title: Chrysemys picta bellii Genome sequencing

description: The Chrysemys picta bellii, the painted turtle, whole genome shotgun project. Specimen collected in Grant Co, WA, from a small lake 1.3 miles south of potholes reservoir.
DOI: 10.26036/cnphis0000920
title: m6A mapping in human RNA (untreated)

description: We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Overall design: Identification of m6A modified sequences in HepG2 cells.
DOI: 10.26036/cnphis0000921
title: Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

description: The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. To identify smRNA targets in the wheat TGMS line, we applied the degradome sequencing method, which globally and directly identifies the remnants of smRNA-directed target cleavage. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Overall design: Examination of 2 mRNA degradome libraries in spike tissues during cold and control condition