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| Status |
Public on Feb 24, 2017 |
| Title |
WTB_time2.5 |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organism |
Escherichia coli |
| Characteristics |
strain: MG1693
genotype/variation: wild type
time point: time2.5
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| Treatment protocol |
Cells were harvested after the addition of rifampicin (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples.
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| Growth protocol |
Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays)
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Adapters trimmed with Cutadapt (v1.12)
Aligned to NC_000913.3 with bwa version 0.7.7
Index and sort alignments with samtools version 1.2
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB
Gave a pseudocount of 0.01 to all values of 0
Genome_build: NC_000913.3
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes
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| Submission date |
Feb 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gina Gordon |
| E-mail(s) |
gcgordon@wisc.edu
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| Organization name |
University of Wisconsin Madison
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| Department |
Chemical and Biological Engineering
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| Lab |
Brian Pfleger Laboratory
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| Street address |
1415 Engineering Dr
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL18133 |
| Series (1) |
| GSE95318 |
RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA |
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| Relations |
| BioSample |
SAMN06444949 |
| SRA |
SRX2585938 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2507172_B3_c.txt.gz |
11.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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