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| Status |
Public on Mar 08, 2021 |
| Title |
wildtype_glucose_B |
| Sample type |
SRA |
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| Source name |
Bacterial culture
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| Organism |
Vibrio cholerae |
| Characteristics |
strain: O1 biovar El Tor 484 N16961 deltatcpA
genotype: wildtype
carbon source: glucose
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| Growth protocol |
Cells from LB-agar plates were used to inoculate 2 mL of 1X M9 minimal medium supplementedwith 0.1% (wt/vol) trace metals (5% MgSO4, 0.5% MnCl2, 0.5% FeCl3, 0.4% nitrilotriacetic acid) and 0.4% glucose or fructose (w/v). Overnight cultures were diluted into 2 mL fresh 1X M9 medium (+ trace metals) with 0.4% glucose or fructose (starting OD600 ~ 0.05) and grown to an OD600 ~0.30.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The entire culture was harvested (8,000 x g, 5 min, 4 °C) and the RNA was purified from the cells using the Direct-zol RNA Miniprep kit (Zymo Research) following the manufacturer’s instructions. Eluted samples were treated with DNase at 37 °C for 30 minutes, twice, using Turbo DNA-free (Ambion), according to the manufacturer’s protocol. RNA integrity was initially analyzed by agarose gel electrophoresis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Fastq files were mapped to the V. cholerae biovar El Tor str. N16961 genome (NCBI accession GCA_000006745.1) using the bwa-mem algorithm in BWA version 0.7.12
Aligned reads were counted with htseq-count version 0.11.2 with the intersection-strict argument
Counts were imported into R version 3.6.2 and differential expression was assessed with DEseq2 version 1.26.0
Genome_build: GenBank assembly accession: GCA_000006745.1
Supplementary_files_format_and_content: counts
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| Submission date |
Jan 05, 2021 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Daniel Stoebel |
| E-mail(s) |
[email protected]
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| Organization name |
Harvey Mudd College
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| Department |
Biology
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| Street address |
301 Platt Blvd
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| City |
Claremont |
| State/province |
CA |
| ZIP/Postal code |
91711 |
| Country |
USA |
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| Platform ID |
GPL27062 |
| Series (1) |
| GSE164298 |
Effect of Cra and carbon sources on global transcription |
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| Relations |
| BioSample |
SAMN17218416 |
| SRA |
SRX9786173 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5006012_WT_G_B_counts_strict.txt.gz |
15.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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