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Transcriptomicseif3k/WT polysome loading
To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the...
ORGANISM(S): Arabidopsis thaliana 
2011-03-29 | E-GEOD-28223 | biostudies-arrayexpress
GenomicsIn vivo probing of the DNA-binding Architecture by bacterial arginine repressor
Although DNA motifs recognized by the transcription factors (TFs) have been determined, challenges remain in probing in vivo architecture of TF-DNA complexes on a genome-wide scale. Here, we show in vivo architecture of Escherichia coli arginine repressor (ArgR)-DNA complexes using chromatin immunop...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2015-04-01 | E-GEOD-60546 | biostudies-arrayexpress
TranscriptomicsWhole transcriptome analyses of six thoroughbred horses before and after exercising using RNA-Seq
We sequenced the whole mRNA of six thoroughbred horse (Equus caballus) blood and muscle tissues before and after exercising, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters sp...
ORGANISM(S): Equus caballus 
2013-05-01 | E-GEOD-37870 | biostudies-arrayexpress
TranscriptomicsChIP-chip of E. coli K-12 MG1655 with antibody against RNA polymerase subunits, RpoB, RpoD, RpoS,RpoH, RpoN, FliA, and FecI
We investigate sigma factor binding regions for each sigma factor under various enviromental and/or genetic conditions. To measure sigma factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 wild type and its isogenic rpoS and rpoN knock-out s...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46541 | biostudies-arrayexpress
TranscriptomicsTranscriptome and translatome landscape of Streptomyces coelicolor M145
We have integrated nucleotide resolution genome-scale measurements of the transcriptome and translatome of the Streptomyces coelicolor A3(2), the model antibiotic-producing actinomycete. Our systematic study determined 3,473 transcription start sites, leading to discovery of a high proportion (~21%)...
ORGANISM(S): Streptomyces coelicolor 
2016-05-28 | E-GEOD-69350 | biostudies-arrayexpress
TranscriptomicsExpression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose
Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-de...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-05 | E-GEOD-46543 | biostudies-arrayexpress
TranscriptomicsGene expression profiles in the spinal cord below the lesion level and influence of treadmill locomotor training
Traumatic spinal cord injury (SCI) often leads to loss of locomotor function. Neuroplasticity of spinal circuitry underlies some functional recovery and therefore represents a therapeutic target to improve locomotor function following SCI. However, the cellular and molecular mechanisms mediating neu...
ORGANISM(S): Rattus norvegicus 
2013-11-27 | E-GEOD-52763 | biostudies-arrayexpress
TranscriptomicsNitric oxide(CysNO) mediated transcriptome profiling in Arabidopsis thaliana
This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants. 1mM CysNO Treatment to Leaf disc, Transcriptome profiling
ORGANISM(S): Arabidopsis thaliana 
2016-05-13 | E-GEOD-81361 | biostudies-arrayexpress
TranscriptomicsE14RNA-seq
Ctbp2 regulates exit from pluripotency via silencing of embryonic stem cell active genes during differentiation. Gene expression profiles were analyzed for wild-type and Ctbp2-knockdown ESCs at both fferentiated(+LIF) and undifferentiated(-LIF) state.
ORGANISM(S): Mus musculus 
2014-12-31 | E-MTAB-2030 | biostudies-arrayexpress
TranscriptomicsChIP-chip of E. coli K-12 MG1655 with antibody against ArcA-8myc or Fnr-8myc under various conditions.
Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a small fraction of the hundreds of genes that are regu...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-02-27 | E-GEOD-55366 | biostudies-arrayexpress
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