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| Status |
Public on Apr 19, 2017 |
| Title |
WT_ac |
| Sample type |
SRA |
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| Source name |
whole cells, acetate
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| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth carbon source: acetate
strain: wild-type
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| Growth protocol |
Cells were grown under conditions of aerobic, exponential phase growth on M9 minimal medium containing either 4 g/L glucose, 4 g/L xylose, 4 g/L acetate, or 0.2% (v/v) glycerol.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested using the Qiagen RNA-protect bacteria reagent according to the manufacturer’s specifications. Prior to RNA extraction, pelleted cells were stored at -80°C, then thawed and incubated with lysozyme, SuperaseIn, protease K, and 20% sodium dodecyl sulfate for 20 min at 37°C. Total RNA was isolated and purified using Qiagen’s RNeasy mini kit column according to the manufacturer’s specifications. Ribosomal RNA (rRNA) was removed using Epicentre’s Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit was used to generate paired-end, strand-specific RNA sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Read quality was examined with FastQC and reads were trimmed with FASTX Trimmer as necessary.
RNAseq reads were aligned to the E. coli genome using bowtie2.
FPKM values were calculated with cufflinks.
Sample normalization was performed with cuffnorm.
Differential expression levels were quantified via cuffdiff.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: *txt: Tab-delimited text files present per-gene FPKM values.
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| Submission date |
Apr 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Troy E Sandberg |
| E-mail(s) |
tsandberg@ucsd.edu
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| Organization name |
UCSD
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| Department |
Bioengineering
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| Lab |
Palsson
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL15010 |
| Series (1) |
| GSE97944 |
E. coli evolution to alternating substrate conditions |
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| Relations |
| BioSample |
SAMN06764639 |
| SRA |
SRX2744800 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2582324_18.txt.gz |
130.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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