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| Status |
Public on Jul 30, 2010 |
| Title |
time point 2 |
| Sample type |
SRA |
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| Source name |
Escherichia coli
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| Organism |
Escherichia coli |
| Characteristics |
strain: DY330 (W3110)
treatment group: rifampicin time point 2
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| Treatment protocol |
At time point 0, rifampicin was added to a final concentration of 500ug/ml. Samples were collected at 0, 2, 4, 6, and 8 minutes.
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| Growth protocol |
E.coli strain, DY330, was grown at 30C in M9 media supplemented with 0.4% glucose, vitamins and amino acids.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from lysates by phenol/chloroform method. rRNA was first removed using MICROBExpress following manufacturer’s protocol, except RNA was collected using Zymo’s RNA columns. A second rRNA removal step was performed following the protocol described in Affymetrix Expression Handbook, substituting enzymes MMLV (Ambion), RNase H (NEB), and DnaseI (Amplification grade, Invitrogen).
The RNA was fragmented using Ambion’s Fragmentation Reagent at 70°C for 5 min, and collected by Zymo’s RNA columns. RNA seq libraries were prepared according to Illumna’s protocol, using NEB enzymes and barcoded adapters (Integrated DNA Technologies). The libraries were pooled and sequenced with an Illumina GA II machine (Center for Systems Biology, Harvard University).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
cDNA from time point 2
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| Data processing |
Sequence reads were obtained and mapped to the W3110 genome (NCBI) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Repeated sequences were ignored (rRNA). The counts in each sample was normalized by ssrA RNA and then converted to logarithmic values. A value of 1 was added to every count before the logarithmic conversion to avoid an undefined logarithm of 0. The lifetime was determined from the inverse of the slope of a linear fit to the logarithmic values.
The measured lifetime of mRNA is available as a supplementary file (real_rna_life.txt) on the Series record.
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| Submission date |
Apr 14, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Huiyi Chen |
| E-mail(s) |
hchen@fas.harvard.edu
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| Phone |
617-496-8654
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| Organization name |
Harvard University
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| Department |
Chemistry
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| Lab |
Sunney Xie
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| Street address |
12 Oxford St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL10328 |
| Series (1) |
| GSE21341 |
genome-wide measurement of mRNA lifetime in Escherichia coli |
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| Relations |
| SRA |
SRX022144 |
| BioSample |
SAMN00015193 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM533305_GG_s7table.txt.gz |
18.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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