cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001119
title: Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells (RNA-seq)

description: Aberrant DNA hypermethylation of CpG island (CGI) promoters are associated with transcriptional repression of many tumor suppressor genes and lead to tumor progression in many cancers. Most recently, one research group observed that aberrantly hypermethylated genes in multiple cancers are already repressed, but their promoters are maintained in a hypomethylated state in pre-cancerous tissues.Their studies didn''t provide a clue to explain by what mechanisms those genes were repressed in pre-cancerous tissues. Another research group found that many genes with de novo promoter hypermethylation in colon cancer were among the subset of genes "bivalently" marked in embryonic stem cells and adult stem/progenitor cells by repressive Polycomb group proteins (PcG), which are known for maintaining low, but poised, transcription.These observations provide a clue that CGI promoter hypermethylation in cancers is associated with PcG target genes in pre-cancerous tissues.we took advantage of ChIP-BS-seq technology and applied it to examine H3K27me3 and H3K4me3 profiles for one normal lymphoblastoid cell line (YH) and three cancer cell lines including one cervical cancer cell line (Hela) and two gastric cancer (GC) cell lines (BGC-823 and AGS). Overall design: We aplied ChIP-BS technology to examine H3K27me3 marks, which are catalyzed by the SET domain histone methyltransferase EZH2 and have a repressive function with 50bp pair-end sequencing. found H3K27me3 marks were enriched preferentially at CpG islands, (+/-500) transcription start sites (TSSs) and exons in two GC cell lines (BGC-823 and AGS). In YH cells, H3K27me3 marks were only preferentially enriched at CpG islands. In contrast, Hela cells presented a reverse pattern with highest H3K27me3 enrichment in intergenic regions. To confirm this result in Hela cells, we performed two independent replicates of ChIP-Seq and ChIP-BS-seq. Cause of useful was relative small. we still sequenced one 100bp pe reads replicate for H3K4me3 and two replicate for H3K27me3 ChIP-BS-seq.
DOI: 10.26036/cnphis0001120
title: Panthera tigris tigris Targeted Locus (Loci)

description: Mapping the white tiger gene.
DOI: 10.26036/cnphis0000403
title: Rhodiola crenulata Raw sequence reads

description: We sequenced RNA-Seq data of Rhodiola crenulata root, stem, leaf.
DOI: 10.26036/cnphis0000404
title: International Consortium on Evolution of Root Nodule Symbiosis

description: This project is to study the evolution of RNS by large-scale whole genome sequencing analysis from the FaFaCuRo clade, to explore the genetic diversification and specificity for the formation of nodule.
DOI: 10.26036/cnphis0000405
title: Acanthopagrus schlegelii Raw sequence reads.SRP100963

description: WGS of Acanthopagrus schlegelii
DOI: 10.26036/cnphis0000406
title: Prunus mume Genome sequencing and assembly

description: The Chinese plum, Prunus mume, as the important fruit and ornamental plant, domesticated in China more than 3,000 years ago. The genome was assembled by combination of 101 fold NGS data, and anchored 83.9% of the scaffolds onto 8 chromosomes.
DOI: 10.26036/cnphis0000407
title: Eleusine coracana Raw sequence reads

description: Finger millet is an important cereal crop in semi-arid regions of the world with excellent grain storage quality and high nutritional quality. To enhance crop improvement efforts, we generated whole genome and transcriptome sequences of finger millet genotype KNE796. For whole genome sequence, genomic DNA was extracted from 14-days old seedlings of KNE796. High molecular weight DNA was used to construct both mate-pair and paired end libraries for Illumina sequencing. For transcriptome sequencing, RNA was extracted from fresh tissues of leaves, flowers, stems, roots and seeds of well-watered and moisture stressed plants. RNA sequencing was also done using Illumina technology.
DOI: 10.26036/cnphis0000408
title: Pteropus alecto Genome sequencing and assembly

description: Whole genomic sequencing and assembly of Pteropus alecto.
DOI: 10.26036/cnphis0000409
title: Myotis davidii Genome sequencing and assembly

description: Whole genomic sequencing and assembly of Myotis davidii.
DOI: 10.26036/cnphis0000410
title: Male Infertility TRS

description: the aim of the study is to identify the genomic components that are associated with male infertility. We select genomic regions and genes that have been reported to be related to infertility and STSs regions in Y chromosome to do high throughput sequencing.
DOI: 10.26036/cnphis0000411
title: Glycine max Transcriptome or Gene expression

description: Comparative Transcriptome Analysis of Soybean Response to Bean Pyralid Larvae
DOI: 10.26036/cnphis0000412
title: Homo sapiens Genome sequencing.SRP014833

description: The data included raw reads of the long insert sized mate paired library sequencing with the Yanhuang cell line generated on the Illumina sequencing platform in this project. The insert size of these libraries ranged with 2kb, 5kb, 10kb, 20kb and 35kb length.
DOI: 10.26036/cnphis0001122
title: Gene expression profilling of six species of Brassica and early four generation of resynthesized B. napus (F1-F4)

description: Analysis of the different gene expression profiles of natural and resynthesized Brassica polyploids with Illumina deep sequencing technology could help to improve our knowledge of polyploid genome evolution. We obtained approximately 6 million sequence tags per sample,and 6018254, 5930726, 6022170, 5950123, 5991210, 5798939, 5823113, 5772449,5858527 and 5657697 clean tags were obtained in libraries of B. rapa, B. oleracea, B. napus-F1, B. napus-F2, B. napus-F3, B. napus-F4, natural B. napus, B. nigra, B. juncea and B. carinata, respectively.16574, 15970, 22059, 18155, 16479, 18196, 17448, 13867, 19424 and 16645 genes of B. rapa genome were unambigously mapped by sequence tags of these ten DGE libraries, respectively. Differentially expressed genes during polyploidization were broadly discovered by comparing the tetraploids with their progenitors. Overall design: mRNA obtained from young leaves of 28-days-old seedlings were compared during polyploidization.
DOI: 10.26036/cnphis0001123
title: Glossina pallidipes Genome sequencing and assembly

description: The tetse fly Glossina pallidipes is a vector of pathogenic trypanosomes which cause trypanosomiasis in humans and animals in Africa. In particular it is a major vector of Trypanosome brucei brucei, the causative agent of nagana or African Animal Trypanosomiasis. Glossina pallipides is also a minor vector of Trypanosome brucei rhodesiense, the causative agent of an acute form of Human African Trypanosomiasis (sleeping sickness). The sequence of this Glossina species will contribute to the understanding of typanosomiasis transmission and inform vector control efforts.
DOI: 10.26036/cnphis0001124
title: Taenia solium Genome sequencing and assembly

description: Genomic Analysis of Taenia solium.
DOI: 10.26036/cnphis0001125
title: Ornithorhynchus anatinus Genome sequencing

description: Genome sequencing of Ornithorhynchus anatinus male and female individuals.
DOI: 10.26036/cnphis0001126
title: The evolution of lncRNA repertoires and expression patterns in tetrapods

description: Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. We identify ~11,000 primate- specific lncRNA families, which show evidence for selective constraint during recent evolution, and ~2,400 highly conserved lncRNAs (including ~400 genes that likely originated more than 300 million years ago). We find that lncRNAs, in particular ancient ones, are generally actively regulated and may predominantly function in embryonic development. lncRNA X-inactivation patterns reveal an extremely female-biased monotreme-specific lncRNA, which may partially compensate X-dosage in this lineage. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but global patterns like tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network, which surprisingly contains many lncRNA hubs, suggests potential functions for lncRNAs in fundamental processes like spermatogenesis or synaptic transmission, but also in more specific mechanisms such as placenta growth suppression through miRNA production. Overall design: [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.
DOI: 10.26036/cnphis0001127
title: Zea mays Variation

description: Profiling transcription levels across many parental inbreds from the maize nested association mapping population.
DOI: 10.26036/cnphis0001128
title: Azumapecten farreri Genome sequencing

description: Whole genome shotgun sequencing of Azumapecten farreri.
DOI: 10.26036/cnphis0001129
title: Translational landscape of photomorphogenic Arabidopsis

description: We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings Overall design: Examine steady-state mRNA and ribosome-protected mRNA abundance in 4-day-old etiolated seedlings with/without 4-h light treatment
DOI: 10.26036/cnphis0001807
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001808
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001809
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001810
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001811
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001812
title: Trichinella nativa Genome sequencing and assembly

description: The Trichinella nativa genome sequencing project.
DOI: 10.26036/cnphis0000413
title: Setaria italica Raw sequence reads.SRP102814

description: To identify QTLs (quantitative trait locus) associated with hulled kena lcolor in foxtail millet, a F2 population of 144 plants from the cross between Heizhigu and Changnong 35 was used to construct a high density linkage map based on RAD-seq and to map QTLs for Setaria italica hulled kenal color. The map contained 1694 Bin markers from 46256 SNPs (Single Nucleotide Polymorphism) spanning 1542.87 cM. A hulled kenal colorr QTLs were detectedover the 6 chromosomes using Composite Interval Mapping (CIV),between M33926512-M34281352 , explaining 80.26% of phenotypic variation (PV),, In addition, we argued that the candidate genes for the hulled kenal color QTLs
DOI: 10.26036/cnphis0000414
title: Setaria italica Raw sequence reads.SRP103192

description: To identify QTLs (quantitative trait locus) associated with agronomy traits in foxtail millet, a F2 population of 543 plants from the cross between Aininghuang and Jingu 21 was used to construct a high density linkage map based on RAD-seq and to map QTLs for 12 various agronomy traits: Number of tillers (NT), panicle neck length (PNL), plant height (PH), panicle length (PL), panicle diameter (PD), first internode diameter (FID), second internode diameter (SID), panicle weight (PW), thousand grain weight (TGW), grain weight (GW), hull color(HC) and panicle type (PT). The map contained 3129 Bin markers from 48790 SNPs (Single Nucleotide Polymorphism) spanning 1460.996 cM. A total of 63 QTLs containing eight QTLs for PD, PNL and PT, seven QTLs for PH, six QTLs for NT and PW, five QTLs for TGW and HC, four QTLs for SID and GW, two QTLs for FID, respectively, explaining 0.38-30.52 % of phenotypic variation (PV), were detected on 9 chromosomes using Composite Interval Mapping (CIM), and surprisingly, none QTL for PL was detected. Among them, five major QTLs explaining =10 % of PV containing qPH5-2 for PH, qPD5-2 for PD, qPW5-1 for PW, and qHC7-1 and qHC7-2 for HC were detected, and other 58 QTLs could explain 0.38-9.82 % of PV. In addition, we argued that the candidategenes for the five major QTLs. These results suggested that it was effective to mapping QTL by RAD-seq using larger F2 population and this paper offered valuable insights into the genetic basis of quantitative traits in foxtail millet.
DOI: 10.26036/cnphis0000415
title: Advanced Whole Genome Sequencing and Analysis of Fetal Genomes from Amniotic Samples

description: Amniocentesis is a procedure that collects cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single to multi-base defects. However, it is blind to birth defects known to be caused by single to megabase scale changes in thousands of different genes and chromosomal regions. In an effort to improve the detection of the number of birth defects by this test we apply whole genome sequencing to 30 amniocentesis samples. For all samples cell free DNA (cfDNA), isolated from the amniotic fluid, and DNA isolated from the cell pellet, were sequenced to ~50X genome coverage using complete genomics nanoarray platform. In a subset of the samples, Long Fragment Read (LFR) libraries were generated from DNA isolated from cells and sequenced to ~100X genome coverage. DNA isolated from the blood of each parent was sequenced to ~50X on the same platform for all amniotic samples. In total... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000416
title: Complete Genomics LFR technology paper

description: Data from the Complete Genomics LFR technology paper in Nature.
DOI: 10.26036/cnphis0000417
title: Homo sapiens Genome sequencing.SRP014997

description: Nomal individual sequencing.
DOI: 10.26036/cnphis0000418
title: Verticillium dahliae Genome sequencing

description: Verticillium dahilae resequencing.
DOI: 10.26036/cnphis0000419
title: Fusarium oxysporum f. sp. cubense race 1 Genome sequencing and assembly

description: Whole genomic sequencing of Fusarium oxysporum f. sp. cubense tropical race 1.
DOI: 10.26036/cnphis0000420
title: Fusarium oxysporum f. sp. cubense race 4 Genome sequencing and assembly

description: Whole genomic sequencing of Fusarium oxysporum f. sp. cubense tropical race 4.
DOI: 10.26036/cnphis0001121
title: Foodborne Pathogen Survey

description: De novo assembly of Salmonella Javiana genome.
DOI: 10.26036/cnphis0001130
title: Pinctada maxima Variation

description: Pearl oysters are extensively cultured for the production of gemstone quality pearls and are rapidly becoming model organisms for investigating genetic mechanisms of biomineralization. However, despite their economic and scientific importance, limited genomic resources are available for this important group of bivalves (i.e. genetic marker resources, dense genetic maps, or quantitative trait loci), limiting our understanding of the quantitative genetic basis underlying commercial traits and hampering the instigation of molecular informed breeding techniques into the pearling industry. The objective of this study was to develop and validate a large number of genome wide SNPs for Pinctada maxima suitable for high-throughput genotyping assays.
DOI: 10.26036/cnphis0001131
title: Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq cells)

description: Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNA-seq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially post-meiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis. To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA-Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of &gt;60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells. Overall design: RNA-Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa
DOI: 10.26036/cnphis0001132
title: Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq organs)

description: Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNA-seq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially post-meiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis. To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA-Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of &gt;60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells. Overall design: RNA-Seq of brain, liver and the whole testis
DOI: 10.26036/cnphis0001133
title: Salmonella enterica subsp. enterica serovar Heidelberg str. 41578 Genome sequencing

description: Genome sequencing project
DOI: 10.26036/cnphis0001134
title: Midgut symbiotic microorganisms of Plutella xylostella Targeted Locus (Loci)

description: None
DOI: 10.26036/cnphis0001135
title: 454 pyrosequencing based whole transcriptome analysis of the poultry red mite Dermanyssus gallinae

description: Background The poultry red mite Dermanyssus gallinae (De Geer, 1778) is a serious problem in poultry farming causing substantial economic losses every year. Although this mite is the most important ectoparasite in poultry farming, nucleotide data are rare in the public databases. Therefore, de novo sequencing covering the transcriptome of D. gallinae was carried out. Results The obtained ~1.5 million 454 pyrosequencing reads were clustered and assembled to 232,097 singletons and 42,130 contiguous sequences (contigs) which were subsequently clustered into 24,140 isogroups consisting of 35,788 isotigs. Sequences possibly originating from undesired contaminating organisms like those of bacteria and the host Gallus gallus (Linnaeus, 1758), were identified and subtracted from the data sets. In total 267,471 sequences (231,663 singletons, 56 contigs and 35,752 isotigs) remained for further analyses. Of these, 11.2% showed sequence homology to proteins derived from other organisms. To gain functional knowledge about identified D. gallinae proteins, sequences were assigned to Gene Ontology (GO) terms resulting in 15,482 annotated sequences (8,034 singletons, 18 contigs and 7,430 isotigs). GO mapping underlined biological characteristics on the genetic level in terms of response to environmental stimuli, development and growth. Additionally, GO annotation suggested vector competence of the poultry red mite for the avian leukosis virus. Furthermore, D. gallinae sequences were mapped to 127 pathway maps and analyzed for functional protein domains. Conclusions De novo 454 pyrosequencing of the poultry red mite has made a large transcriptome dataset available. It provides new insights in general mite genetics and helps to understand the biology of the parasitic mite D. gallinae. Furthermore, it lays a foundation for future studies on stage-specific transcriptomics as well as genomic, proteomic, and metabolomic explorations and might provide new perspectives to control this parasitic mite by identifying possible drug targets or vaccine candidates.
DOI: 10.26036/cnphis0001136
title: Apis mellifera syriaca strain:Varroa resistant strain Genome sequencing

description: Apis mellifera syriaca is the native honey bee subspecies of Jordan and much of the Middle East. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp "Vespa orientalis" and in most cases it is resistant to varroa mites.