|
Status |
Public on Apr 02, 2012 |
Title |
EspR_ChIP-Seq_2 |
Sample type |
SRA |
|
|
Source name |
log phase_Mtb H37Rv_EspR_ChIP
|
Organism |
Mycobacterium tuberculosis |
Characteristics |
strain: H37Rv growth phase: mid-log chip antibody: rat anti-EspR
|
Treatment protocol |
Bacteria cells were treated with formaldehyde (final concentration 1%) for 10 min at 37°C
|
Growth protocol |
Mtb H37Rv cultures (50 ml) were grown to OD600 0.4-0.6 in complete 7H9 medium
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with an anti-EspR antibody. Libraries were prepared according to Illumina's instructions.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
Chromatin IP against EspR The rat anti-EspR antibody was produced by our collaborator Ida Rosenkrands at the STATENS SERUM INSTITUT (Danemark).
|
Data processing |
Alignment: Sequence reads were aligned to the Mtb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie software Reads from the two experimental replicates were pooled together as they showed a high level of correlation. Reads mapped to the forward and reverse strands were shifted (by 80 bp) and combined together to generate a single merged profile ["EspR_merged.bed" available as a Series Supplementary file]. In order to estimate the binding location in the enriched regions, we used a deconvolution algorithm that models the expected tag distribution on both strands. Genome Build: EspR2.bed: NC_000962.2
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|
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Submission date |
Jan 17, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Benjamin Blasco |
E-mail(s) |
benjamin.blasco@epfl.ch
|
Organization name |
EPFL
|
Department |
SV-GHI
|
Lab |
UPCOL
|
Street address |
Station 19
|
City |
Lausanne |
ZIP/Postal code |
1015 |
Country |
Switzerland |
|
|
Platform ID |
GPL15138 |
Series (1) |
GSE35149 |
Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein |
|
Relations |
SRA |
SRX116268 |
BioSample |
SAMN00773669 |