GEO DataSets

(Submitter supplied) We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.

Organism:

Picosynechococcus sp. PCC 7002

Type:

Other

Platform:

GPL21381

21 Samples

Download data: CSV, XLSX

(Submitter supplied) In this study, we performed RNA-sequencing on an E. coli model system to confirm known sites, identify novel targets, and determine the impact of RNase III cleavage events on transcript degradation and metabolic phenotypes. To find cleavage sites, we compared the abundance of sequencing reads across the transcriptome of a wild-type E. coli and an rnc- deletion mutant. The RNA-sequencing approach provided wider coverage and unprecedented resolution of mRNA abundance at each position in the transcriptome compared to prior studies that used qPCR, Northern blots, or microarrays. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

15 Samples

Download data: TXT

(Submitter supplied) Construction of a global gene co-expression network to determine gene relatedness and expand regulatory pathways in the model cyanobacterium Synechococcus 7002.

Organism:

Picosynechococcus sp. PCC 7002

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18074

8 Samples

Download data: TXT

(Submitter supplied) Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing the fast-growing response of Synechococcus sp. PCC 7002 response to variable irradience levels.

Organism:

Picosynechococcus sp. PCC 7002

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18074

6 Samples

Download data: TXT

(Submitter supplied) RNA samples from cells collected at twenty four time points in 48-hours diurnal cycles were analyzed, and they compared between each other for transcriptional profiles of global genes

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL21668

24 Samples

Download data: TXT

(Submitter supplied) Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the post-transcriptional regulation of gene expression. A key endoribonuclease in many bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria such as E. coli have evolved a tightly functioning feedback regulation of RNase E, which is mediated in cis by the rne 5′-untranslated region (5′UTR); however, the mechanisms involved in the control of RNase E in other bacteria have largely remained unknown. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL15867

8 Samples

Download data: TXT

(Submitter supplied) Neural-specific mRNA decay measurements by TU-Decay technique in control and Pumilio knockdown embryos

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL17080

15 Samples

Download data: TXT

(Submitter supplied) whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL6385

6 Samples

Download data: TXT

(Submitter supplied) In this study we conducted genome-wide mRNA decay analysis to get further insights into the physiology of Gluconobacter oxydans.

Organism:

Gluconobacter oxydans; Bacillus subtilis subsp. subtilis str. 168; Escherichia coli; Corynebacterium glutamicum; Gluconobacter oxydans 621H

Type:

Expression profiling by array

Platform:

GPL20268

12 Samples

Download data: GPR

(Submitter supplied) We used NEBNext Ultra Directional RNA Library Prep Kits to prepare RNA-seq libraries of total RNA from hnRNP A2/B1 and A1 depleted A549 cells. Pro-seq libraries were prepared from A549 cells using Illumina adapters

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: DIFF

(Submitter supplied) Cyanobacteria, photoautotrophic prokaryotes, contribute significantly to the global photosynthesis and require large amounts of the essential micronutrient iron in order to maintain their Fe-rich photosynthetic apparatus. Here we use the model organism Synechocystis sp. PCC 6803 (later referred to Synechocystis) in both, standard and iron stress conditions, to study transcription and post-transcription regulation in iron deprivation. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL23938

32 Samples

Download data: TXT