|
| 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
|
| |
|
| 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 |
