Transcription profiling by array of chicken anterior wing buds treated with retinoic acid at stage HH20 and later harvested at stage HH24
Ontology highlight
ABSTRACT: RNA transcripts were compared between 5 replicates of anterior wing bud thirds from stage HH24 chicken embros that had been treated with retinoic acid at HH20, using chicken Affymetrix chips. Data collected with Affymetrix scanner was normalized using the Plier algorithm within the expression console package from Affymetrix and log2 transformed. Please note that samples in this experiment can be compared against wild-type, untreated counterparts previously deposited at ArrayExpress under accession number E-MTAB-309 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-309 ).
Project description:As part of cross-platform comparisons of microarray and RNA-seq, the current experiment using the Illumina NextSeq 500 and MGI DNBSEQ-G400RS aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpress; E-MTAB-2874) and Affymetrix Human Transcriptome Array 2.0 (archived in ArrayExpress; E-MTAB-11080).
Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The present accession presents the data from the adult chicken of the first (parental) generation.To access data for the young chicken of the first (parental) generation see accession E-MTAB-924. The male offspring of the birds of the first (parental) generation is also available in ArrayExpress with accession E-MTAB-925.
Project description:This is a replication study of E-MTAB-3562 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3562/ ) and complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ )
Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The data for the offspring of the birds in this experiment is available in ArrayExpress with accession E-MTAB-925.
Project description:Lack of comprehensive genome structural- and functional-annotation significantly prevents researchers from exploiting the full potential of the chicken genome model system for comparative and functional genomic studies. Comprehensive genome structural- and functional-annotation must be made easily accessible for the chicken genome sequence to reach its full potential to contribute to human health and well-being. To this end we collected a variety of tissues from 2 (1 male, 1 female) healthy 2-year-old red jungle fowls. We performed mRNA sequencing, small RNA sequencing, proteomics and proteogeomic mapping on each of these tissues to further elucidate tissue and sex specific expression and to improve upon current gene models. Results of small RNA sequencing have also been deposited at ArrayExpress under accession number E-MTAB-1826 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1826/ ).
Project description:Transgenerational effects of early experience on behavioural, hormonal and gene expression responses to acute stress in the precocial chicken. The data for the parental stressed and control birds is available in ArrayExpress with accession E-MTAB-924, while this experiment only concerns their offspring that never been exposed to early life stress.
Project description:The expression data for this study can be found here:
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1088/
and its SNP6 data can be found here:
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1087/
Project description:Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) and partially fragmented NSF-HA (fNSF-HA) on the transcriptome of IMR90 cells. Related RNA-Seq datasets are deposited in ArrayExpress (E-MTAB-8943).
Project description:Relative levels of RNA transcripts were compared between anterior and posterior wing bud thirds from stage HH24 normal and talpid3 mutant chicken embryos using chicken Affymetrix chips. Data collected with Affymetrix scanner was normalized using the Plier algorithm within the expression console package from Affymetrix and log2 transformed. 5 replicates of anterior third normal wing buds, 4 replicates of posterior third of normal wing buds and 4 replicates each of anterior and posterior thirds of talpid3 wing buds at stage HH24 were examined.