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| Status |
Public on Jun 07, 2016 |
| Title |
WTRep1_2min |
| Sample type |
SRA |
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| Source name |
mg1655
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| Organism |
Escherichia coli |
| Characteristics |
genotype/variaion: WT
time point: 2 min
treatment: rifampicin
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| Treatment protocol |
Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition.
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| Growth protocol |
Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol.
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
WTRep1.csv
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| Data processing |
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2.
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: sam containing aligned sequences
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| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaowei Zhuang |
| E-mail(s) |
zhuang@chemistry.harvard.edu
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| Phone |
617-384-9818
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| Organization name |
Harvard University
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| Department |
Chemistry and Chemical Biology
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| Lab |
Zhuang
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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 |
GPL14548 |
| Series (1) |
| GSE75818 |
Spatial organization shapes the turnover of a bacterial transcriptome |
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| Relations |
| SRA |
SRX1471745 |
| BioSample |
SAMN04326732 |
| 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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