|
| Status |
Public on Mar 15, 2017 |
| Title |
MtbRaTopoI |
| Sample type |
SRA |
| |
|
| Source name |
Log/exponential phase Mtb H37Ra cells
|
| Organism |
Mycobacterium tuberculosis H37Ra |
| Characteristics |
chip antibody: anti-TopoI, monoclonal (generated in-house, lot# VNMNL2012)
growth phase: Exponential
|
| 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 H37Ra 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.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked bacteria cells were sonicated and protein-DNA complexes were isolated with No antibody (Mock) or anti-TopoI or anti-gyrA 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 |
Chromatin immunoprecipitation against Topoisomerase I
|
| Data processing |
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to M.tb H37Rv genome (NCBI accession NC_000962.2)
Mapping done using the Bowtie2 program (Version = 2.0.5) with default parameters
Coverage calculated using Bedtools (Version : 2.17.0)
Genome_build: M.tb H37Rv genome (NCBI accession NC_000962.2)
Supplementary_files_format_and_content: *.txt: Coverage calculated using Bedtools (Version : 2.17.0). Column 4: Genome coordinates, Column 5: Read depth.
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Valakunja Nagaraja |
| Organization name |
Indian Institute of Science (IISc)
|
| Department |
Department of Microbiology and Cell Biology
|
| Street address |
C V Raman Avenue
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560012 |
| Country |
India |
| |
|
| Platform ID |
GPL23183 |
| Series (1) |
| GSE85357 |
Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase |
|
| Relations |
| BioSample |
SAMN06605669 |
| SRA |
SRX2643411 |
