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TranscriptomicsTranscription profiling of human synovial fibroblasts from rheumatoid arthritis and osteoarthritis patients
mRNA expression levels in synovial fibroblasts in 6 rheumatoid arthritis patients versus 6 osteoarthritis patients. Experiment Overall Design: Synovial tissue was obtained from open joint replacement surgery or Experiment Overall Design: arthroscopic synovectomy. Patients with RA or OA (n = 6 each...
ORGANISM(S): Homo sapiens 
2009-04-28 | E-GEOD-7669 | biostudies-arrayexpress
TranscriptomicsTranscriptomic profiling of a fission yeast cross in response to oxidative stress
A total of 130 strains from a three parental fission yeast cross were grown with and without additional H2O2 treatment. The samples were harvested, processed and subjected to RNA-sequencing.
ORGANISM(S): Schizosaccharomyces pombe 
2023-05-10 | E-MTAB-12930 | biostudies-arrayexpress
GenomicsH2A.Z (pht1) ChIP-seq data in 968, Y0036, and swc5-del strains
After finding a QTL hotspot in a fission yeast cross of strains 968xY0036 that was apparently driven by frame shift mutation in swc5 (swc5-fs), we have determined the genome-wide occupancy of the histone variant H2AZ (PhT1). Indeed swc5 has been shown to affect H2AZ occupancy. To test the impact of ...
ORGANISM(S): Schizosaccharomyces pombe 
2014-12-04 | E-MTAB-2650 | biostudies-arrayexpress
TranscriptomicsRNA sequencing of 968xY0036 fission yeast recombinant library
We generated the first recombinant strain library for fission yeast and conducted an RNA-seq based QTL study of the coding, non-coding, and antisense transcriptomes. We cross the lab strain 968 with the lab strain Y0036 to generate segregant. We used RNA-seq for both expression profiling and gentoyp...
ORGANISM(S): Schizosaccharomyces pombe 
2014-12-04 | E-MTAB-2640 | biostudies-arrayexpress
TranscriptomicsRIP-chip by array of mouse undifferentiated and neural cells to identify mRNAs associated with SRp20 and SRp75
Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs is unknown, and comprehensive knowledge of endogenous mRNA targets is lack...
ORGANISM(S): Mus musculus 
2010-07-20 | E-MEXP-2637 | biostudies-arrayexpress
TranscriptomicsRNAi profiling by array of mouse P19 cells to investigate how SR proteins coordinate gene expression programs
Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs has been largely unexplored, and comprehensive knowledge of endogenous mRN...
ORGANISM(S): Mus musculus 
2010-07-20 | E-MEXP-2640 | biostudies-arrayexpress
ModelsAho2010_RefRec_S_cerevisiae
This model is described in the article: Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network Aho T, Almusa H, Matilainen J, Larjo A, Ruusuvuori P, Aho K-L, Wilhelm T, Lähdesmäki H, Beyer A, Harju M, Chowdhury S, Lei...
2005-01-01 | MODEL3883569319 | BioModels
TranscriptomicsIntegration of transcriptome, proteome and phoshpoproteome data elucidates the genetic control of molecular networks
150 cultures of 112 Saccharomyces cerevisiae strains (BYxRM cross) were grown in full medium and harvested in log phase. RNA was isolated and quantified via RNAseq. The reads were subsequently mapped against strain-specific genomes. The same cultures were also characterized on the proteomic and phos...
ORGANISM(S): Saccharomyces cerevisiae 
2022-02-02 | E-MTAB-8146 | biostudies-arrayexpress
TranscriptomicsThe footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus
We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distri...
ORGANISM(S): Arabidopsis thaliana x Arabidopsis halleri 
2016-06-01 | E-GEOD-80462 | biostudies-arrayexpress
TranscriptomicsTranscriptional signatures of regulatory and toxic responses to benzo(a)pyrene exposure in murine Hepa1c1c7 cells
Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is important for understanding secondary effects of drugs and for eluci...
ORGANISM(S): Mus musculus 
2011-12-31 | E-GEOD-29188 | biostudies-arrayexpress
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