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| Status |
Public on Mar 01, 2017 |
| Title |
Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 299) |
| Sample type |
SRA |
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| Source name |
Sig70 in E. coli_exponential aerobic growth_no rifampicin
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| Organism |
Escherichia coli |
| Characteristics |
growth condition: Exponential + O2
treated with: none
replicate: 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The samples were sonicated for a total of 16 minutes and 50 uL protein A/G sepharose. All reactions are performed in an Eppendorf ThermalMixerR while being mixed at 1.4k x rpm. After each reaction, the sepharose was washed with 1 mL of each of the following buffers, leaving 50-100 uL buffer above the sepharose in-between each wash : 1x TE : 10mM Tris-HCl, pH 8.0 + 1 mM EDTA ; 1 x High Salt - 1M NaCl (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 1M NaCl) ; 1x Wash Buffer 2 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 0.5M NaCl) ;1x Wash Buffer 3 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 1.0% sodium deoxycholate, 0.25 M LiCl, 1% NP-40, and 10 mM Tris-HCl, pH 8.0) ; 1x TE : 10mM Tris-HCl, pH 8.0 + 1mM EDTA.
The ChIP-exo experiments were generated by following the steps presented by Rhee and Pugh, 2011.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
E1-1
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| Data processing |
library strategy: ChIP-exo
Samples 931, 933, 935 and 937 were aligned with bowtie (V 1.1.2) with parameters --wrapper basic-0 -q -m 1 -l 55 -k 1 -5 3 -3 40 --best -S -p 24, and samples 1311, 1314, 1317 and 1320 were aligned with bowtie (V 1.1.2) with paramters --wrapper basic-0 -q -m 1 -v 2 --best -p 24 -S
Genome_build: K12 - MG1655
Supplementary_files_format_and_content: Each wig file contains the alignd reads of each ChIP-exo sample.
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| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rene Welch |
| E-mail(s) |
welch@stat.wisc.edu
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| Phone |
6088861033
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| Organization name |
University of Wisconsin-Madison
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| Department |
Statistics
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| Lab |
Keles
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| Street address |
626 Johnson St.
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53703 |
| Country |
USA |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE84830 |
Data Exploration, Quality Control and Statistical Analysis of ChIP-exo/nexus Experiments |
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| Relations |
| BioSample |
SAMN05521730 |
| SRA |
SRX2007579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2251955_edsn931_Sig70.sort.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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