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| Status |
Public on Aug 01, 2023 |
| Title |
B. fragilis - deoxycholate 20 min - rep 2 |
| Sample type |
SRA |
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| Source name |
bacterial cell
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| Organism |
Bacteroides fragilis |
| Characteristics |
strain: p207
cell type: bacterial cell
treatment: 20min_DC_exposure
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
SCR_386
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| 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
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| Submission date |
Dec 12, 2022 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Sean Crosson |
| E-mail(s) |
[email protected]
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| Phone |
5178845345
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| Organization name |
Michigan State University
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| Department |
Dept. Microbiology and Molecular Genetics
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| Street address |
567 Wilson Rd
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| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL32937 |
| Series (1) |
| GSE220692 |
Measuring the effect of deoxycholate on Bacteroides fragilis gene expression |
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| Relations |
| BioSample |
SAMN32164350 |
| SRA |
SRX18644086 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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