Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1083308 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-sequencing data to inversigate the effects of DMRT1-distruption at E6 and 1W time points in male and female chickens.
2021-08-28 | GSE150339 | GEO
Project description:This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens. 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection. A piece of skin (8 mm in diameter) from the left back was collected . Total RNA was extracted from the sample using Trizol reagent . Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The sequencing of the library was performed using an Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China). According the result of sequencing, some colored gene expressions were validated using Real time quantitative polymerase chain reaction (qPCR).
2015-05-20 | E-GEOD-68460 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the differentially expressed genes between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Genome Analyzer IIx. Results: Through raw data processed, 49,979,648 and 43,704,401 clean reads with an average length of 101 bp, which represented total residues of 4,859,084,087 and 4,238,826,168 bp, were obtained for WRR- and WRR+ libraries, respectively. Subsequently, the clean reads in the two libraries were assembled. Altogether, 121,493 contigs were assembled with an average length of 927 bp (ranged from 300 bp to 23,402 bp), leading to generation of 82,829 unigenes. The length of unigenes varied from 351 bp to 28,928 bp, with an average length of 1,155 bp. Based on the FPKM value of each gene, 252 DEGs were identified by DEGseq package using Benjamini-q-value of 0.05 as a cut-off. In ALV-J infected spleens, 90 genes showed up-regulated and 162 showed down-regulated expression when compared to uninfected samples. Conclusions: Our study represents the first time to elucidate the ALV-J infected chickens’spleens at the transcription level by RNA-seq technology. A total of 252 genes were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These genes can be considered as candidates for further study ALV-J invasion. Spleen mRNA profiles of 140-day-old ALV-J infected (WRR+) and uninfected (WRR-) female chickens of White Recessive Rock were generated by deep sequencing, using Illumina Genome Analyzer IIx.
2014-11-15 | E-GEOD-63226 | biostudies-arrayexpress
Project description:Here, we report on a novel chicken comb phenotype, designated Antler-comb. Using a 600K Axiom® Genome-Wide Chicken Genotyping Array, we separately genotyped 12 and 24 female Hetian Wildtype-comb and Antler-comb chickens, respectively. Meanwhile, we sequenced the genomes of 10 Hetian Antler-comb and 10 Wildtype-comb chickens to interrogate the GWAS results and explore the potential genetic variants underlying this phenotype. After conducting a genome-wide association study (GWAS), a 36.5-kb candidate genomic region (chromosome 19:757,754-794,200) related to the Antler-comb phenotype was identified, which wholly and partially encompassed heat shock factor 5 (HSF5) and ring finger protein 43 (RNF43), respectively. HSF5 was ectopically expressed and RNF43 was up-regulated in Antler-comb chickens at embryo ages 7 and 9 (E7 and E9). We further genotyped the most significant single-nucleotide polymorphism (SNP) site, Chr19:794200, across 222 chickens of 16 breeds. We found that the major allele G in Antler-comb chickens remained highly significant across different breeds, and each Antler-comb chicken harbored an allele G. Whole-genome re-sequencing (WGS) involving 10 Hetian Antler-comb and 10 Wildtype-comb chickens reaffirmed the 36.5-kb candidate genomic region, and revealed a genomic duplication, which was 15.7 kb in length and pertained to the 5’-untranslated region and 5’-flanking region of HSF5 (Chr19:784,335-800,034), suggesting its possible role in inducing ectopic expression of HSF5 and altering expression of RNF43 during comb development (E7 and E9). The present study furthers our understanding of this novel chicken comb phenotype, and likely gives another example regarding interactions between genetic variation and phenotype.
2023-12-31 | GSE145948 | GEO