|
| Status |
Public on Mar 20, 2017 |
| Title |
IP_vjbR |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Brucella abortus |
| Characteristics |
strain: DvjbR
chip antibody: Anty-VjbR
|
| Treatment protocol |
Bacteria were shifted to minimal medium MM1 pH 5.5 in the presence of Urocanic acid for 3 h
|
| Growth protocol |
Bacteria were growth in bacteriological rich medium (TSB) until optical density of 1.0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
VjbR-DNA complexes were isolated with the anti-VjbR antibody and protein G magentic beads
total RNA was isolated using MasterPure RNA Purification Kit (Epicentre) and then treated with TURBO DNAse (Ambion – Life Technologies)
Samples were submitted to Illumina TruSeq library preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Immunoprecipitated chromatin
|
| Data processing |
Low-quality reads were removed using Trimmomatic v0.32
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
Bigwig files were generated with custom bash scripts and BEDtools
ChIP-seq peaks were called using MACS2
RNA-seq differential expression analysis was performed using DESeq
Supplementary_files_format_and_content: narrowPeak files generated by MACS2 provide genomic coordinates, signal value (ChIP-seq) enrrichment, p-, and q-values for each detected ChIP-seq peak.
Supplementary_files_format_and_content: tsv file generated by DESeq provides gene ID, base mean reads, fold-change, log2 fold-change, p-value and adjusted p-value for the expression of each gene, baseMeanA represents wild type samples and baseMeanB represents mutant samples
|
| |
|
| Submission date |
Mar 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sieira Rodrigo |
| E-mail(s) |
[email protected]
|
| Organization name |
Fundacion Instituto Leloir
|
| Street address |
Av. Patricias Argentinas 435
|
| City |
Buenos Aires |
| ZIP/Postal code |
C1405 BWE |
| Country |
Argentina |
| |
|
| Platform ID |
GPL23154 |
| Series (1) |
| GSE95722 |
ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network |
|
| Relations |
| BioSample |
SAMN06481638 |
| SRA |
SRX2614389 |
