Broiler chicken Iso-Seq Testes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25378 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Iso-Seq with 5' cap selection and normalization on adult chicken spleen tissue.
| PRJEB25379 | ENA
Project description:Sex chromosomes are characterized by a non-random content of genes with preferential expression in one sex. The mechanisms which are responsible for this phenomenon are, however, largely unresolved. To elucidate selective forces shaping the Z chromosome gene content in chicken, we analyzed microarray data from adult and embryonic gonads (the latter already available in GEO Series GSE8693). Experiment Overall Design: Total RNA from gonads of 8 males and 8 females was used for hybridization to Affymetrix GeneChip® Chicken Genome Arrays. Prior to hybridization the samples were combined in equal quantities into 4 pools (4 testes/ovary samples in each pool), 2 of them representing testis and 2 ovary. Experiment Overall Design: All four GeneChips met Affymetrix quality control criteria. Furthermore, all chips were checked by methods based on probe level robust linear model fitting provided by "affyPLM" package (Bolstad, 2007). None of the chips showed any signs of abnormality.
2009-12-14 | E-GEOD-14013 | biostudies-arrayexpress
Project description:To realize the gene expression in response to acute heat stress in chicken testis, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Male B strain Taiwan country chickens were subjected to acute heat stress (38℃) for 4 h, and then exposed to 25℃, with testes collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed roosters as a control group (n = 3 roosters per group). Based on a chicken 44K oligo microarray, 163 genes significantly differed in the testes of the heat-stressed chickens from those of the control chickens. The mRNA expressions of upregulated genes, including HSP25, HSP90AA1, HSPA2, and LPAR2, and downregulated genes, including CDH5, CTNNA3, EHF, CIRBP, SLA, and NTF3, were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).
2015-01-27 | GSE65279 | GEO
Project description:To realize the gene expression in response to acute heat stress in chicken testis, we have employed whole genome microarray expression profiling as we have employed whole genome microarray expression profiling as a tool to identify genes response to acute heat stress. Male B strain Taiwan country chickens were subjected to acute heat stress (38M-bM-^DM-^C) for 4 h, and then exposed to 25M-bM-^DM-^C, with testes collected 0, 2, and 6 h after the cessation of heat stress, using non heat-stressed roosters as a control group (n = 3 roosters per group). Based on a chicken 44K oligo microarray, 163 genes significantly differed in the testes of the heat-stressed chickens from those of the control chickens. The mRNA expressions of upregulated genes, including HSP25, HSP90AA1, HSPA2, and LPAR2, and downregulated genes, including CDH5, CTNNA3, EHF, CIRBP, SLA, and NTF3, were confirmed through quantitative real-time polymerase chain reaction (qRT-PCR). Acute heat stress induced testicular gene experssion in B strain Taiwan country chicken was measured at 0, 2, and 6 h of recovery after 4 h of 38 degree acute heat stress.
2015-01-27 | E-GEOD-65279 | biostudies-arrayexpress
Project description:One of the most regulated steps of translation initiation is the recruitment of an mRNA by the translation machinery. In eukaryotes, this step is mediated by the 5M-BM-4end cap-binding factor eIF4E bound to the bridge protein eIF4G and forming the eIF4F complex. In plants, different isoforms of eIF4E and eIF4G form the antigenically distinct eIF4F and eIF(iso)4F complexes proposed to mediate selective translation. Using a microarray analysis of polyribosome- and non-polyribosome-purified mRNAs from 15 day-old Arabidopsis thaliana wild type [WT] and eIF(iso)4E knockout mutant [AteIF(iso)4E-1] seedlings we found 79 transcripts shifted from polyribosomes toward non-polyribosomes, and 47 mRNAs with the opposite behavior in the mutant. The translationally decreased mRNAs were overrepresented in root-preferentially expressed genes and proteins from the endomembrane system, including several transporters such as the phosphate transporter PHOSPHATE1 (PHO1), Sucrose transporter 3 (SUC3), the ABC transporter-like with ATPase activity (MRP11) and five electron transporters, as well as signal transduction-, protein modification- and transcription-related proteins. For transcriptional analysis used total RNA of AteIF(iso)4E-1 seedlings of 15 days old to known the changes on transcripts leves by the eIF(iso)4E absence, using as control Wt seedlings. The experiments were performed in duplicate, and swap analysis were done. For translational analysis, used non-polysomal and polysomal RNA of AteIF(iso)4E-1 seedlings of 15 days old in order to known the transcripts that are modified in their translational levels by the eIF(iso)4E absence, using as control non polysomal and polysomal RNA of Wt seddlings.
2013-07-26 | E-GEOD-29386 | biostudies-arrayexpress
Project description:Broiler chicken cecum raw sequence reads
| PRJNA663615 | ENA
Project description:To reannotate the genome of Zymoseptoria tritici IPO323, RNA-Seq and Iso-Seq runs were performed on different growth media to provide new source of evidence for gene model predictors. New gene models were predicted and combined with existing annotation releases. Finally, selection of best gene models was done by congruence with evidence data like transcript assembled from RNA-Seq, Iso-Seq cDNA and fungal proteins from databases.
2023-07-04 | GSE218898 | GEO