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Series GSE227248 Query DataSets for GSE227248
Status Public on Mar 20, 2023
Title Transcript degradation profiling for Mycolicibacterium smegmatis in log phase, hypoxia, and RNase E knock down conditions.
Organism Mycolicibacterium smegmatis
Experiment type Other
Expression profiling by high throughput sequencing
Summary We calculated transcriptome-wide mRNA half-life using RNAseq to characterize the mRNA stability in log phase and hypoxia, as well as the impact of RNase E on mRNA degradation.
 
Overall design mRNA abundance were measured at multiple time points after rifampicin treatment using Mycolicibacterium smegmatis in log phase, hypoxia, and RNase E knockdown condition. Three RNAseq replicates were used for each time point.
 
Contributor(s) Shell SS, Zhou Y, Sun H, Vargas-Blanco DA
Citation(s) 37802316
Submission date Mar 13, 2023
Last update date Nov 02, 2023
Contact name Scarlet Shell
E-mail(s) sshell@wpi.edu
Organization name Worcester Polytechnic Institute
Department Biology & Biotechnology
Lab Shell Lab
Street address 60 Prescott Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL25202 Illumina NextSeq 500 (Mycolicibacterium smegmatis)
Samples (96)
GSM7093795 Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 1
GSM7093796 Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 2
GSM7093797 Control strain in the absence of ATc at 0 minutes after rifampicin treatment replicate 3
Relations
BioProject PRJNA944224

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE227248_RNaseE_cleavageSite_normalized_coverage.txt.gz 228.1 Mb (ftp)(http) TXT
GSE227248_mRNA_halfLife_normalized_log2_coverage.txt.gz 1.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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