GEO DataSets

(Submitter supplied) While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23073

4 Samples

Download data: XLSX

(Submitter supplied) Transcriptional analysis of the effects of the deletion of the sRNAs glmY and glmZ in EHEC

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of the Expression Change of RyhB Regulon in RyhB-deleted Mutant Strains.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by array

Platform:

GPL9864

3 Samples

Download data: TXT

(Submitter supplied) 89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions.

Organism:

Rhizobium etli CFN 42

Type:

Non-coding RNA profiling by genome tiling array; Expression profiling by genome tiling array

Platform:

GPL9409

5 Samples

Download data: GFF, TXT

(Submitter supplied) The transcriptional changes in Escherichia coli upon induction of the SOS response are investigated by utilizing custom designed oligonucleotide microarrays. Keywords: Gene expression during the SOS response in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL7714

10 Samples

Download data: CEL

(Submitter supplied) The differentiation of activated B cells into antibody secreting plasma cells (PCs) is governed by a strict regulatory network that results in expression of specific transcriptomes along the continuum. In vitro models resulting in PCs that are phenotypically identical to the in vivo state permit investigation of molecules, transcripts, pathways, and metabolomes not previously identified in the differentiation process. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied)  Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: TXT