cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000778
title: Global Mapping of H3K4me1 and H3K4me3 in human CD4+CD25+FOXP3+ Treg cells

description: Regulatory T cells (Treg) contribute to the crucial immunological processes of self-tolerance and immune homeostasis. However, the mechanisms underlying Treg function and cell fate decisions to differentiate between Treg and conventional T cells (Tconv) remain to be fully elucidated, especially at the histone modification level. Covalent modifications of histones establish and maintain chromatin structure, and regulate gene transcription events by facilitating access to cis-elements by trans-acting factors during mammalian development and cellular differentiation. We aimed to investigate the role of the methylation form of histone modification as related to Treg function and phenotype. High-resolution maps of the genome-wide distribution of monomethylated histone H3 lysine 4, H3K4me1, and the trimethylated form H3K4me3 were generated for human activated conventional CD4+CD25+FOXP3- T cells (aTconv) and CD4+CD25+FOXP3+ regulatory T cells (Treg) by sequencing using the Solexa 1G Genetic Analyzer. We found 2115 H3K4me3 regions corresponding to proximal promoter regions; the genes associated with these regions in Treg cells included the crucial transcription factor forkhead box P3 (FOXP3) and the chemokine receptor CCR7. We also identified 41024 Treg cell type-specific H3K4me1 regions. The majority of the H3K4me1 regions differing between the Treg and aTconv cells were located at promoter-distal sites, some of which were selected and consolidated to further examine enhancer activity in in vitro reporter gene assays. The findings from our study provide a comprehensive genome-wide dataset of lineage-specific H3K4me1 and H3K4me3 patterns in Treg and aTconv cells, which may control the differentiation decision, lineage commitment and cell type-specific gene regulation. This basic principle is likely not confined to the two closely-related T cell populations, but may apply generally to somatic cell lineages in adult organisms. Overall design: Genome-wide distribution of monomethylated histone H3 lysine 4, H3K4me1, and the trimethylated form H3K4me3 in human activated conventional CD4+CD25+FOXP3- T cells (aTconv) and CD4+CD25+FOXP3+ regulatory T cells (Treg) (5 samples in total)
DOI: 10.26036/cnphis0000779
title: Mus musculus 129Sv/Jae genome sequencing

description: None
DOI: 10.26036/cnphis0000780
title: Clonorchis sinensis whole genome sequencing by Illumina technology

description: Clonorchis sinensis whole genome sequencing by Illumina technology
DOI: 10.26036/cnphis0001473
title: Quantitative assessment of single-cell RNA sequencing methods

description: We generated single-cell transcriptomes from a large number of single cells using several commercially available platforms, in both microliter and nanoliter volumes, and compared performance between them. We benchmarked each method to conventional RNA-seq of the same sample using bulk total RNA, as well as to multiplexed qPCR, which is the current gold standard for quantitative single-cell gene expression analysis. In doing so, we were able to systematically evaluate the sensitivity, precision, and accuracy of various approaches to single-cell RNA-seq. Our results show that it is possible to use single-cell RNA-seq to perform quantitative transcriptome measurements of individual cells, that it is possible to obtain quantitative and accurate gene expression measurements with a relatively small number of sequencing reads, and that when such measurements are performed on large numbers of cells, one can recapitulate the bulk transcriptome complexity, and the distributions of gene expression levels found by single-cell qPCR. Overall design: 109 single-cell human transcriptomes were analyzed in total; 96 using nanoliter volume sample processing on a microfluidic platform, Nextera library prep (biological replicates); 3 using the SMARTer cDNA synthesis kit, Nextera library prep (biological replicates); 3 using the Transplex cDNA synthesis kit, Nextera library prep (biological replicates); 7 using the Ovation Nugen cDNA synthesis kit (biological replicates) where 3 used Nextera library prep and 4 used NEBNext library prep. In addition, 4 bulk RNA samples were sequenced: bulk RNA generated using ~1 million pooled cells was used to make bulk libraries, 2 of which were made using SMARTer cDNA synthesis kit (technical replicates) and 2 made using Superscript RT kit with no amplification (technical replicates). All 4 bulk samples were made into libraries using Nextera.
DOI: 10.26036/cnphis0001474
title: Equus caballus Variation

description: Mongolian horse (Equus caballus) is one of the most ancient horse breeds in the world and has been a key role in the Mongolian culture. They live in the Mongolian and inner Mongolian grasslands. With the expansion of the Mongolian Empire, this ancient breed has influenced other horse breeds of the northern European. Mongolian horse has many special attributesfeatures, such as endurance, disease resistance, and resistance to cold weather. Mongolian horse also has important means of agricultureand the genomic information could also benefit for breeding strategies.
DOI: 10.26036/cnphis0001475
title: Homo sapiens Genome sequencing of saliva sample

description: Whole-genome sequencing of saliva sample
DOI: 10.26036/cnphis0001476
title: Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior

description: Eusocial insects have evolved the capacity to generate adults with distinct morphological, reproductive and behavioural phenotypes from the same genome. Recent studies suggest that RNA editing might enhance the diversity of gene products at the post-transcriptional level, particularly to induce functional changes in the nervous system. Using head samples from the leaf-cutting ant Acromyrmex echinatior, we compare RNA editomes across eusocial castes, identifying ca. 11,000 RNA editing sites in gynes, large workers and small workers. Those editing sites map to 800 genes functionally enriched for neurotransmission, circadian rhythm, temperature response, RNA splicing and carboxylic acid biosynthesis. Most A. echinatior editing sites are species specific, but 8–23% are conserved across ant subfamilies and likely to have been important for the evolution of eusociality in ants. The level of editing varies for the same site between castes, suggesting that RNA editing might be a general mechanism that shapes caste behaviour in ants. Overall design: Analysis of genome-wide RNA editing in three different female castes of the the leaf-cutting ant Acromyrmex echinatior.
DOI: 10.26036/cnphis0001477
title: Notothenia coriiceps genome sequencing

description: whole genome and mitochondrial DNA
DOI: 10.26036/cnphis0001478
title: Aquila chrysaetos canadensis Genome sequencing and assembly

description: Aquila chrysaetos canadensis genome sequencing and assembly with ~40X coverage. A male golden eagle (subspecies A. c. canadensis, USFWS Band #0679-02608) was captured 6 December 2012 in the 71 California foothills of the southern Sierra Nevada, between the Central Valley and the Mojave 72 Desert (N 35 18 29.2 W 118 38 05.7).
DOI: 10.26036/cnphis0001479
title: Dermatophagoides farinae isolate:Derf Genome sequencing and assembly

description: Sequencing of the mite genome.
DOI: 10.26036/cnphis0001480
title: Panthera tigris altaica Transcriptome or Gene expression

description: Panthera tigris altaica lung transcriptome
DOI: 10.26036/cnphis0001481
title: Panthera tigris altaica whole Transcriptome

description: Panthera tigris altaica whole transcriptome
DOI: 10.26036/cnphis0001482
title: Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [RNA-Seq]

description: A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin. Overall design: Col-0 and edm2-4 total RNA are extracted from leaves and then polyA mRNAs are isolated for mRNA-seq.
DOI: 10.26036/cnphis0002161
title: Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin

description: Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible. Overall design: Sequencing of cfDNA libraries from healthy individuals, pooled healthy individuals and individuals with disease for the identification of nucleosomes and protection from other DNA binding proteins.
DOI: 10.26036/cnphis0002162
title: Class: Amphibia, Order: Anura. raw sequence reads

description: Mitochondrial genomes assembled from multiplex shotgun libraries.
DOI: 10.26036/cnphis0002163
title: Bovine genome assembly by Cattle Genome Sequencing International Consortium

description: The Cattle Genome Sequencing International Consortium, led by the Baylor College of Medicine, originally sequenced the Bos taurus genome at 6x coverage using a whole genome shotgun (WGS) strategy. The initial assembly (Btau_4.2) was later replaced by newer versions by incorporating high quality finished data, where available (Btau_4.6.1). The latest version takes the UMD 3.1 assembly contigs and scaffolds and incorporates ~19x Pacific Biosciences long-read data using the PBJelly method (English, Richards et al. 2012).
DOI: 10.26036/cnphis0002164
title: Arachis hypogaea cultivar:Tifrunner Transcriptome or Gene expression

description: RNA seq of 22 tissues and developmental stages for construction of a gene atlas
DOI: 10.26036/cnphis0002165
title: Salmonella enterica subsp. enterica serovar Enteritidis Genome sequencing and assembly

description: This study aims to find a genetic basis for phenotypical differences seen in 11 strains of Salmonella enterica subsp. enteritidis. It also increases the availability of draft genomes for comparison and larger statistical surveys of Salmonella genomes.
DOI: 10.26036/cnphis0002166
title: Adult mouse cortical cell taxonomy by single cell transcriptomics

description: Nervous systems are composed of numerous cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. Overall design: Single-cell RNA-Seq of adult mouse primary visual cortex
DOI: 10.26036/cnphis0002167
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002168
title: Hymenolepis nana Raw sequence reads

description: Raw DNA sequence reads of malignantly transformed Hymenolepis nana and a reference H.nana specimen. Human reads have been removed.
DOI: 10.26036/cnphis0002169
title: Equus caballus genome sequencing

description: whole genome sequencing of horses
DOI: 10.5284/1049644
title: AD 410: The History and Archaeology of Late and Post-Roman Britain

description: As part of its centenary celebrations in 2010 the Roman Society organised a number of conferences across the UK exploring the theme of AD 410 and the 'End of Roman Britain'. This volume contains a selection of 16 papers delivered at these conferences, tackling the debate from different angles (historical, archaeological, literary) and setting out the current state of research.
DOI: 10.5284/1049645
title: Journal of Roman Studies Monographs

description: null
DOI: 10.26036/cnphis0000781
title: Primate exome sequencing reveals new targets of positive selection

description: Comparison of protein coding DNA sequences from diverse primates can provide insight into these species' evolutionary history and uncover the molecular basis for their phenotypic differences. Here we use targeted capture methods designed for human to sequence the protein coding regions, or exomes, of four non-human primate species (three Old World monkeys and one New World monkey) using massively parallel sequencing. Using this expanded set of primate sequences, we performed a genome-wide scan for genes experiencing positive selection and identified a novel class of adaptively evolving genes involved in the conversion of epithelial cells in skin, hair and nails to keratin. Interestingly, the genes we identify under positive selection also exhibit significantly increased allele frequency differences among human populations, suggesting that they play a role in both recent and long-term adaptation. We also identify several genes that have been lost on specific primate lineages, which illustrate the broad utility of this dataset for other evolutionary analyses.
DOI: 10.26036/cnphis0000782
title: Lottia digitalis Project

description: none provided
DOI: 10.26036/cnphis0000783
title: Genome sequencing for Lytechinus variegatus

description: None
DOI: 10.26036/cnphis0000784
title: Sorex araneus Genome sequencing and assembly

description: Sequence of the genome of a female European shrew
DOI: 10.26036/cnphis0001483
title: ESTABLISHMENT OF LUNG TRANSCRIPTOME OF NON INFECTED AND HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUS (HPAIV) INFECTED CROW USING NEXT GENERATION SEQUENCING (NGS)

description: The host-pathogen interaction and the molecular mechanisms underlying the pathophysiologic process of HPAIV infection in Crows or other wild birds is still remain largely unknown. Thus, as a first step to explore it, comprehensive global gene expression analysis performed in HPAIV infected and noninfected Crow lung tissue using high through put next generation sequencing.
DOI: 10.26036/cnphis0001484
title: Two bat species each sequenced separately:Lasiurus borealis and Lasiurus cinereus Genome resequencing for SSR discovery

description: This project uses whole genome re-sequencing and simple sequence repeat (SSR) bioinformatics search algorithms to develop a genome-wide set of microsatellite loci for bats in the genus Lasiurus. These markers greatly extend the genetic resources available for North American tree bats, and should be invaluable to conservation biologists studying environmental impacts on bat populations
DOI: 10.26036/cnphis0001485
title: Tissue-Resident Natural Killer (NK) Cells Are Cell Lineages Distinct From Thymic and Conventional Splenic NK Cells (part 1)

description: Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells. Overall design: Liver NK 1.1+CD49+, liver NK 1.1+CD49-, spleen NK 1.1+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads
DOI: 10.26036/cnphis0001486
title: human small RNA

description: small RNA in human serum infected with TB.
DOI: 10.26036/cnphis0001487
title: mRNA-sequencing of breast cancer subtypes and normal tissue

description: Goal: To define the digital transcriptome of three breast cancer subtypes (TNBC, Non-TNBC, and HER2-positive) using RNA-sequencing technology. To elucidate differentially expressed known and novel transcripts, alternatively spliced genes and differential isoforms and lastly expressed variants in our dataset. Method: Dr. Suzanne Fuqua (Baylor College of Medicine) provided the human breast cancer tissue RNA samples. All of the human samples were used in accordance with the IRB procedures of Baylor College of Medicine. The breast tumour types, TNBC, Non-TNBC and HER2-positive, were classified on the basis of immunohistochemical and RT-qPCR classification. Results: Comparative transcriptomic analyses elucidated differentially expressed transcripts between the three breast cancer groups, identifying several new modulators of breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We also report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. Additionally we describe novel SNPs and INDELs in cancer relevant genes with no prior reported association of point mutations with cancer Overall design: mRNA profiles of 17 breast tumor samples of three different subtypes (TNBC, non-TNBC and HER2-positive) and normal human breast organoids (epithelium) samples (NBS) were sequenced using Illumina HiSeq.
DOI: 10.26036/cnphis0002170
title: Aspidoscelis inornata, Sceloporus cowlesi fosmid sequencing and assembly

description: Aspidoscelis inornata, Sceloporus cowlesi fosmid sequencing and assembly
DOI: 10.26036/cnphis0002171
title: GenomeTrakr Project: Maryland Department of Health and Mental Hygiene

description: Whole genome sequencing of cultured Salmonella enterica as part of the FDA GenomeTrakr surveillance project for rapid source tracking of foodborne illness outbreaks.
DOI: 10.26036/cnphis0002172
title: Microbiome analysis complements fecal occult blood test for improved detection

description: Using microbiome-based models to differentiate healthy patients from those with colonic lesions.
DOI: 10.26036/cnphis0002173
title: Evolution of the activation steps in the vertebrate phototransduction cascade analysed using agnathan eye transcriptomes

description: Vertebrate phototransduction represents the best understood example of response activation in a G protein cascade. Not only have the protein components been characterised comprehensively, but in addition the molecular mechanisms that mediate high amplification and rapid response kinetics are understood in sufficient detail to predict the onset phase of the response to light absorption. Although the phylogeny of the phototransduction proteins has been studied extensively in jawed vertebrates (gnathostomes), there is a paucity of information about the corresponding proteins in the jawless branch of vertebrates (agnathans), from which gnathostomes diverged around 500 million years ago. The only surviving jawless vertebrates are lampreys (around 40 species) and hagfish (around 80 species). We have applied high-throughput sequencing to eye tissue from one species of hagfish, two species of lamprey and five species of gnathostome fish, to obtain mRNA sequences for the components of the phototransduction cascade
DOI: 10.26036/cnphis0002174
title: Hybridization and the origin of contagious asexuality in Daphnia pulex

description: To understand the origin of obligate asexuality in Daphnia pulex
DOI: 10.26036/cnphis0000785
title: Spermophilus tridecemlineatus genome sequencing

description: None
DOI: 10.26036/cnphis0000786
title: Genome-wide sequencing small RNAs in response to powdery mildew and heat stress in wheat

description: To test whether non-coding RNAs play roles in regulating response to powdery mildew infection and heat stress in wheat, by using Solexa high-throughput sequencing and computational analysis and experimental approach we cloned the small RNAs and identified 125 putative long npcRNAs from wheat leaves infected by preponderant physiological strain Erysiphe graminis f. sp. tritici (Egt) or by heat stress treatment. Among long non-coding RNAs, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP) 7S RNA variants, and three were characterized as U3 snoRNAs. Wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress. Overall design: Examination non-coding RNAs of 2 near isogenic lines 8866 (Susceptible) and Pm30 (Resistant) in response to powdery milew and two genotypes CK (insensitive) and TAM107 (insensitive) to heat. CK and TAM107 represent the same material in different treatments (no heat stress or 1hour after heat stress).
DOI: 10.26036/cnphis0000787
title: Eucidaris tribuloides genome sequencing project

description: None
DOI: 10.26036/cnphis0000788
title: Genome sequencing of Echinops telfairi

description: The <i>E. telfairi</i> genome has been sequenced at 2-fold coverage.
DOI: 10.26036/cnphis0000789
title: Mayetiola destructor genome sequencing project

description: None
DOI: 10.26036/cnphis0001488
title: Neocaridina denticulata Genome sequencing

description: Cherry Shrimp (Neocaridina denticulata) Genome sequencing
DOI: 10.26036/cnphis0001489
title: Carassius auratus Transcriptome or Gene expression

description: Filter difference gene between male and female Carassius auratus
DOI: 10.26036/cnphis0001491
title: GenomeTrakr Project: Minnesota Department of Health

description: None