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Sample GSM6809656 Query DataSets for GSM6809656
Status Public on Aug 01, 2023
Title B. fragilis - deoxycholate 20 min - rep 1
Sample type SRA
 
Source name bacterial cell
Organism Bacteroides fragilis
Characteristics strain: p207
cell type: bacterial cell
treatment: 20min_DC_exposure
Extracted molecule total RNA
Extraction protocol After treatment, culture was pelleted at 15,000 x g for 1 minute, supernatant was removed, and pellets were resuspended in 1 ml TRIzol and stored at -80°C. Samples were heated at 65°C for 10 min. Then, 200 µl chloroform was added, samples were vortexed, and incubated at room temperature for 5 min. Samples were centrifuged at 17,000 x g for 15 min at 4°C, then the upper aqueous phase was transferred to a fresh tube, an equal volume of 100% isopropanol was added, and samples were stored at -80°C overnight. Samples were centrifuged at 17,000 x g for 30 min at 4°C, the supernatant was removed, and the pellets were washed with cold 70% ethanol. Pellets were centrifuged again at 17,000 x g for 5 min at 4°C, supernatant was removed, and the pellet was allowed to dry before resuspension in 100 µl RNase-free water and incubation at 60°C for 10 min. Samples were treated with TURBO DNase and cleaned with RNeasy Mini Kit
 Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description SCR_385
Data processing Reads were mapped to B. fragilis p207 genome and normalized using default settings for RNA-seq workflow in CLC Genomics Workbench v 21
Supplementary files format and content: processed data file contains total count and normalized counts (CPM) for each annotated gene in B. fragilis p207
 
Submission date Dec 12, 2022
Last update date Aug 01, 2023
Contact name Sean Crosson
E-mail(s) [email protected]
Phone 5178845345
Organization name Michigan State University
Department Dept. Microbiology and Molecular Genetics
Street address 567 Wilson Rd
City East Lansing
State/province Michigan
ZIP/Postal code 48824
Country USA
 
Platform ID GPL32937
Series (1)
GSE220692 Measuring the effect of deoxycholate on Bacteroides fragilis gene expression
Relations
BioSample SAMN32164351
SRA SRX18644085

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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