cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000922
title: Next generation sequencing reveals differentially expressed genes associated with development of PSE turkey meat.

description: The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR&lt;0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59±0.09, pH[normal] = 5.77±0.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect. Overall design: The mRNA profiles of normal and PSE turkey breast muscle were generated by deep sequencing using Illumina GAIIx platform. Multiplexing was performed (2 samples/lane). Afterwards, difference in gene expression between normal and PSE samples were tested.
DOI: 10.26036/cnphis0000923
title: Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila

description: The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally. Overall design: GSM914095: Fly genomic DNA sequencing. Sequenced on the Illumina GA II. GSM914102-GSM914113: Fly head nascent RNA profiles over 6 time points of a 12hr light:dark cycle in duplicate; sequenced on the Illumina GA II. GSM914114-GSM914119: Fly head nascent RNA profiles of yw, FM7, ADAR0 males in duplicate; sequenced on the HiSeq2000. GSM915213-GSM915214: Fly head mRNA profiles over 2 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II. GSM915215-GSM915220: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; paired-end sequenced on the Illumina GA II. GSM915221-GSM91526: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.
DOI: 10.26036/cnphis0000924
title: Syncerus caffer (cape buffalo) sequencing for SNP discovery

description: Cape Buffalo (Syncerus caffer) are one of the most ecologically important African bovids. In some areas they are the most important grazers and have a large impact on gassland management. In order to facilitate research into the genetics of cape buffalo populations we have sequenced the genomes of pooled DNA from 9 buffalo. The data were used to develop genotyping assays which will be used for further studies of buffalo populations.
DOI: 10.26036/cnphis0000925
title: Resequencing antibiotic-treated Brugia malayi

description: Resequencing antibiotic-treated Brugia malayi.
DOI: 10.26036/cnphis0000188
title: NJAU Transcriptome or Gene expression

description: Get the gene expression of Brassica campestris L.
DOI: 10.26036/cnphis0000189
title: exome sequencing data of posriasis

description: We sequenced the DNA of 1500 psoriasis patients
DOI: 10.26036/cnphis0000191
title: whole genome sequecing of two individuals

description: We sequenced the WGS of 2 patients
DOI: 10.26036/cnphis0000192
title: WES of 13 FFPE breast tumor samples and 13 corresponding frozen samples

description: We sequenced the exomes of 13 FFPE breast tumor samples and 13 corresponding frozen samples
DOI: 10.26036/cnphis0000193
title: Targeted Gene Correction

description: We performed whole-genome sequencing to evaluate the muta- tional load at single-base resolution in individual gene-corrected human induced pluripotent stem cell (hiPSC) clones in three different disease models
DOI: 10.26036/cnphis0000194
title: The Bactrian Camel Genome Sequencing Project

description: The Bactrian camel genome sequencing project is conducted by Inner Mongolia Agricultural University (IMAU) and BGI. The DNA extracted from blood sample of female Bactrian camel was sequenced using a whole genome shotgun strategy and the next-generation sequencing (NGS) technology on the Illumina HiSeq 2000 platform. The purpose of this project is to study camel desert adaption and genetic information of important economic traits, such as breeding and reproduction, disease, wool production, milk production, superior meat quality.
DOI: 10.26036/cnphis0000195
title: Vicugna pacos huacaya Genome sequencing and assembly

description: The Vicugna pacos genome sequencing project is conducted by Inner Mongolia Agricultural University (IMAU) and BGI. The DNA extracted from blood sample of female Vicugna pacos and sequenced by using the Illumina HiSeq 2000 platform. The purpose of this project is to do a comparsion analysis of the camelid.
DOI: 10.26036/cnphis0000196
title: Camelus dromedarius breed:Arabia Genome sequencing and assembly

description: Research on their evolution and desert adaptation
DOI: 10.26036/cnphis0000197
title: Genome sequecing of a Mongolian indivudual

description: Here we provide a reference genome for Mongolians through whole genome sequencing and investigate the genetic imprints of Mongolians to other human populations.
DOI: 10.26036/cnphis0000198
title: Rsequencing of five pairs of Childhood B-ALL twins

description: We sequenced the WGS of five pairs of Childhood B-ALL twins
DOI: 10.26036/cnphis0000926
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000927
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000928
title: Bareilly outbreak

description: Genome sequencing project with two assemblies, a draft assembly from 454 reads (AOZS00000000) and a complete genome from PacBio data (CP006053-CP006054).
DOI: 10.26036/cnphis0000929
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000930
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000931
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000932
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000933
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000934
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000199
title: Nannochloropsis oceanica strain LAMB0001 genome sequencing

description: Nannochloropsis oceanica strain LAMB0001 genome sequencing project from College of Marine Life Sciences, Ocean University of China
DOI: 10.26036/cnphis0000200
title: Gossypium hirsutum WGS

description: Transcriptome analysis of Gossypium hirsutum
DOI: 10.26036/cnphis0000201
title: Escherichia coli strain:LCT-ECM001 Transcriptome or Gene expression

description: LCT-EC001 inoculated under stimulating microgravity in semi-solid BHI medium (Brain Heart Infusion + 0.6% low-melting agarose (invitrogen)) for about 15 days, at the same temperature intra the spacecraft.
DOI: 10.26036/cnphis0000202
title: Escherichia coli strain:LCT-ECS001 Transcriptome or Gene expression

description: LCT-EC001 inoculated in semi-solid BHI medium (Brain Heart Infusion + 0.6% low-melting agarose (invitrogen)), launched into space aboard the Shenzhou-X spacecraft for about 15 days.
DOI: 10.26036/cnphis0000203
title: Escherichia coli strain:LCT-ECG001 Transcriptome or Gene expression

description: LCT-EC001 inoculated in semi-solid BHI medium (Brain Heart Infusion + 0.6% low-melting agarose (invitrogen)) for about 15 days, under the same temperature intra the spacecraft.
DOI: 10.26036/cnphis0000204
title: whole genome sequencing of Capra aegagrus

description: We sequenced the WGS of Capra aegagrus
DOI: 10.26036/cnphis0000205
title: Nilaparvata lugens Genome sequencing and assembly

description: The genomes of the brown planthopper, Nilaparvata lugens. The Nilaparvata lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had been reared in rice seedlings (strain: TN1). One male and one female were isolated and mated to produce F1 progeny. A single pair was then selected for sibling inbreeding for 13 generations. Genomic DNA was extracted from adult females of the F13 generation.
DOI: 10.26036/cnphis0000206
title: Mus musculus strain:breed Transcriptome or Gene expression

description: By comparing the difference between the control group and experimental group, we want to find the key regulatory factors during development of palate, and then we can find the reason of occurrence of cleft palate.
DOI: 10.26036/cnphis0000208
title: RNA-SEQ Data of Cervical Cancer

description: We sequenced RNA of 11 patients of cervical cancer
DOI: 10.26036/cnphis0000935
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000936
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000937
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000938
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000939
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000940
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000941
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000943
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000209
title: HPV Capture Data of Cervical Cancer

description: We sequenced DNA of 135 patients of cervical cancer
DOI: 10.26036/cnphis0000210
title: WGS MHC typing

description: MHC typing for wgs and capture data
DOI: 10.26036/cnphis0000213
title: Pontibacter korlensis Transcriptome Sequencing

description: To compare gene expression under different UV radiation
DOI: 10.26036/cnphis0000214
title: Gut of Fat liver patients Metagenome

description: Fat liver vs microbe of gut
DOI: 10.26036/cnphis0000215
title: MHC target sequence for psoriasis study

description: we sequenced 20000+ samples in MHC region to take a Genome-wide Association Study for psoriaisis disease.
DOI: 10.26036/cnphis0000216
title: Sus scrofa Transcriptome or Gene expression

description: sus scrofa Transcriptome or Gene expression
DOI: 10.26036/cnphis0000217
title: Pooling of different fish and amphibian species Genome sequencing

description: Pooling of different fish and amphibian species to sequence their mitogenome
DOI: 10.26036/cnphis0000219
title: WGS of Jatropha curcas L.

description: We sequenced the DNA of Jatropha curcas L.
DOI: 10.26036/cnphis0000944
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000945
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000946
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000947
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000948
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000949
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000950
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000951
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000952
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000220
title: Personal haplotypes and recombination activity in an Asian

description: Low coverage whole genome sequencing of single sperm cell to accomplished haplotyping, and identified rare structural variants contained within rare haplotype blocks in an Asian male.
DOI: 10.26036/cnphis0000221
title: Sequencing and analyzing of hypervariable region 6 of 16S rRNA gene of endophytic bacteria from Noni

description: We collected five sites of Noni (roots, branches, leaves, fruits and seeds) ,sequenced hypervariable region 6 of 16S rRNA gene and analyzed. Targeted Locus (Loci)
DOI: 10.26036/cnphis0000223
title: Human Herpes Virus 6B Infection

description: detect the pathogen
DOI: 10.26036/cnphis0000224
title: Papilio xuthus isolate:ya''a_city_454_Px Genome sequencing and assembly

description: Whole genome project to do comparative analysis for Papilio xuthus and Papilio machaon. and a good resource for genome research
DOI: 10.26036/cnphis0000225
title: Papilio machaon isolate:ya''a_city_454_Pm Genome sequencing and assembly

description: Whole genome project to do comparative analysis for Papilio xuthus and Papilio machaon. and a good resource for genome research.
DOI: 10.26036/cnphis0000226
title: Litchi chinensis cultivar:Wuye Transcriptome or Gene expression

description: RNA-seq profiling approach was used to discovering the differentially expressed genes (DEGs) under the girding plus defoliation (GPD) treatment for 2, 4 and 7 d in litchi trees (Litchi chinensis Sonn. cv. Wuye).
DOI: 10.26036/cnphis0000227
title: A metagenome-wide association study of gut microbiota in type 2 diabetes.

description: Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.
DOI: 10.26036/cnphis0000228
title: Hordeum vulgare L. var. nudum WGS

description: We did whole genome sequencing of hulless barley.
DOI: 10.26036/cnphis0000229
title: Cucumis sativus Genome sequencing

description: A high-density cucumber genetic map is constructed by sequencing a RIL population to facilitate the molecular breeding and biology studies in cucumber.
DOI: 10.26036/cnphis0000953
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000954
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000955
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000956
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000957
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000958
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000959
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000960
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000961
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000231
title: Turnip Yellow Mosaic Virus Raw sequence reads

description: Mutational Bias of Turnip Yellow Mosaic Virus in the Context of Host Anti-viral Gene Silencing
DOI: 10.26036/cnphis0000232
title: The origin of Aboriginal Australian

description: We present the first Aboriginal Australian genomic sequence, obtained from a lock of hair donated by an Aboriginal man living in South-Western Australia in the early 20th century. The genome was sequenced to an average depth of 11x, showing no evidence of European admixture, and an estimated contamination level of &lt; 0.5%. It represents the first high-depth ancient genome sequence from outside the permafrost regions. Using population genetic approaches based on whole genome data, we find evidence that: i) all non-African populations diverged from West Africans at the same time; ii) Aboriginal Australians were the first to separate from this ancestral non-African gene pool some 50-60 thousand years ago, 10-25 thousand years prior to the split between Europeans and Asians; iii) Aboriginal Australians received substantial gene flow from Asians at a later date, suggesting that the Neanderthal genetic signal in the Aboriginal Australian genome, similar to that found in Eurasians, may be secondarily derived. Our findings imply that current views on the population history of Aboriginal Australian based on uniparental markers and SNP chip data are over simplistic. As such our understanding of modern human evolutionary history will likely benefit from being revisited using ancient and modern human genomics.
DOI: 10.26036/cnphis0000234
title: WGS of Ophisaurus gracilis

description: We sequenced the DNA of Ophisaurus gracilis
DOI: 10.26036/cnphis0000235
title: The insect gut bacteria Raw sequence reads

description: Study about the insect gut bacteria
DOI: 10.26036/cnphis0000236
title: Habropoda laboriosa Genome sequencing and assembly

description: The overarching goal of this project is to identify the genomic signatures of social evolution.
DOI: 10.26036/cnphis0000237
title: Clupea harengus WGS

description: Whole genome sequencing of Clupea harengus
DOI: 10.26036/cnphis0000238
title: Eufriesea mexicana isolate:0111107269 Genome sequencing and assembly

description: The overarching goal of this project is to identify the genomic signatures of social evolution.
DOI: 10.26036/cnphis0000239
title: Dufourea novaeangliae isolate:0120121106 Genome sequencing and assembly

description: The overarching goal of this project is to identify the genomic signatures of social evolution.
DOI: 10.26036/cnphis0000962
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000963
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000964
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000965
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000966
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000967
title: Junco hyemalis Transcriptome

description: From one adult male and one adult female dark-eyed junco (Junco hyemalis carolinensis), we extracted RNA from 14 tissues (whole brain, gonad, liver, pectoralis muscle, syrinx, beak, eye, gizzard, heart, kidney, lung, preen gland, skin, and tongue). We then sequenced a normalized library from each individual (all tissues pooled) using Roche/454 pyrosequencing. This sequencing effort adds to the growing store of genomic-level data available for ecological-model species that have historically lacked genomic tools.
DOI: 10.26036/cnphis0000968
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000969
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000970
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000971
title: Bareilly outbreak

description: Genome sequencing project
DOI: 10.26036/cnphis0000240
title: Melipona quadrifasciata isolate:0111107301 Genome sequencing and assembly

description: The overarching goal of this project is to identify the genomic signatures of social evolution.
DOI: 10.26036/cnphis0000241
title: Anser cygnoides domesticus breed:Zhedong Genome sequencing and assembly

description: Goose (Anser cygnoides) is one of the oldest poultry that has undergone a long domesticated history, and possesses some special biological characteristics such as fast-growing, disease resistance, rough feeding resistance and high capacity for fatty liver production. In order to reveal the molecular basis of these special characteristics of goose, we sequenced and analyzed the genome of goose. This research can enhance the discovery of genetic variations underlying economically important quantitative traits. Moreover, relevant findings on geese disease resistance and hepatic lipid metabolism may have important implications for understanding waterfowl unique immune or disease-resistant mechanisms, as well as research on human liver lipid metabolism related diseases.
DOI: 10.26036/cnphis0000244
title: Genomic sequencing of Pediatric Rhabdomyosarcoma

description: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood accounting for approximately 350 newly diagnosed cases yearly in the United States. With the development of multimodal chemotherapy regimens, relapse-free survival rates have improved to 70-80% in patients with localized disease albeit with significant toxicity. Unfortunately, despite aggressive treatment, patients with metastatic or recurrent disease continue to suffer from high mortality. Further characterization of the genetic events underlying this tumor type is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. In a collaborative effort between the National Cancer Institute, the Children''s Oncology Group, and the Broad Institute, we use a combination of whole-genome and whole-exome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs.
DOI: 10.26036/cnphis0000245
title: RNA_seq of venom gland from Chinese yellow catfish

description: We sequenced the transcripts of venom gland from 24 Chinese yellow catfish
DOI: 10.26036/cnphis0000246
title: Prunus persica Genome sequencing.SRP057585

description: To dissect the genetic basis of peach domestication, here we report the resequencing data of 40 peach accessions to an average of 3.2× depth.
DOI: 10.26036/cnphis0000247
title: nonhuman primate WES

description: We introduced a new method to resequence the exome of Non-human primates (NHP) species by a designed capture approach specifically targeted to the NHP