|
| Status |
Public on Dec 01, 2012 |
| Title |
Input_DNA2 |
| Sample type |
SRA |
| |
|
| Source name |
Stat phase Mtb H37Rv cells
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: H37Rv
chip antibody: none
growth phase: stationary phase
|
| Treatment protocol |
M. tuberculosis cultures, either in exponential or stationary phase, were cross-linked with 1% formaldehyde for ten minutes at 37°C.
|
| Growth protocol |
Mycobacterium tuberculosis H37Rv was grown at 37°C in 7H9 broth (Difco) supplemented with 0.2% glycerol, 0.05% Tween 80 and 10% albumin-dextrose-catalase (ADC, Middlebrook) or on 7H10 plates supplemented with 0.5% glycerol and 10% oleic acid-albumin-dextrose-catalase (OADC, Middlebrook). Logarithmic-phase cultures (exponential phase) were harvested at an optical density (OD600) of 0.4-0.6, stationary phase cultures were collected four weeks later.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with either anti-RpoB or anti-NusA antibodies. 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 |
input DNA
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2) using the Bowtie v0.11.3 with parameters -S -n 3 --best --strata --solexa1.3-quals -a -m 10
Genome_build: NC_000962.2
Supplementary_files_format_and_content: Reads mapping to the forward and reverse strands were shifted by 80bp and merged to generate a single ChIP-seq profile, represented as a bedgraph file
|
| |
|
| Submission date |
Sep 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Swapna Uplekar |
| Organization name |
EPFL
|
| Street address |
Station 19, EPFL-GHI-UPCOL
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL15138 |
| Series (2) |
| GSE40845 |
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (ChIP-seq) |
| GSE40862 |
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis |
|
| Relations |
| SRA |
SRX186562 |
| BioSample |
SAMN01173979 |
