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TranscriptomicsNext Generation Metatranscriptome Sequencing of an Anaerobic Hexadecane-Degrading Microbial Consortia
Purpose: Identification of transcriptionally active genes in the unculturable community constituent, Smithella, during hexadecane degradation; Differential gene expression analysis of hexadecane-relevant genes acoss three different conditions; Extension of metatranscriptomic datasets to other commun...
ORGANISM(S): mixed culture KAZ_0815 
2013-10-29 | E-GEOD-49830 | biostudies-arrayexpress
TranscriptomicsChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions.
We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the PurR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring PurR-8myc under various con...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2011-06-14 | E-GEOD-26589 | biostudies-arrayexpress
TranscriptomicsChIP-chip of MG1655 with antibody against E. coli RNAP beta subunit under various conditions
We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under m...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2009-11-03 | E-GEOD-15588 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of E. coli MG1655
Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine. An eight chip study with two different strains under two separate culture conditions.
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2011-06-14 | E-GEOD-26588 | biostudies-arrayexpress
TranscriptomicsChIP-chip of E. coli K-12 MG1655 with antibody against ArgR-8myc, Lrp-8myc, and TrpR-8myc under various conditions.
We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArgR, Lrp, and TrpR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring ArgR-8myc, L...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2011-12-01 | E-GEOD-26054 | biostudies-arrayexpress
TranscriptomicsRibosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose
Ribosome profiling was performed on E. coli wild type cells. All replicates were grown to an OD of ~0.4 in MOPS rich Media with 0.2% glucose supplemented, aerobically in shake flasks. Cultures were treated with chloramphenicol 2 min prior to harvest. Two biological replicates
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2015-06-09 | E-GEOD-63858 | biostudies-arrayexpress
TranscriptomicsRNA-seq for Thermotoga maritima MSB8 glucose evolved cultures
RNA-seq was performed on T. maritima wild type, three glucose evolved cultures, and three glycerol adapted cultures. Wild type and glucose evolved strains were grown on glucose minimal media and glycerol evolved cultures were grown on glycerol minimal media. All samples were harvested in exponential...
ORGANISM(S): Thermotoga maritima MSB8 
2015-06-09 | E-GEOD-63141 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of E.coli MG1655 under multiple growth conditions
Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition. A fourteen chip study using total RNA recovered from four separa...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2009-11-03 | E-GEOD-15534 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of Geobacter sulfurreducens under multiple growth conditions
Investigation of comprehensive information about the transcripts (boundary, level, etc.) across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode. A five array study using total RNA recovered from two separate culture conditions of G. sulfurred...
ORGANISM(S): Geobacter sulfurreducens PCA 
2010-07-01 | E-GEOD-22497 | biostudies-arrayexpress
TranscriptomicsChIP-chip of Geobacter sulfurreducens PCA with antibody against RNAP and RpoD under various conditions
We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A 21 C...
ORGANISM(S): Geobacter sulfurreducens PCA 
2010-07-01 | E-GEOD-22503 | biostudies-arrayexpress
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