|
| Status |
Public on May 30, 2023 |
| Title |
BOV_1929(D55E)_output_2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial
|
| Organism |
Brucella ovis |
| Characteristics |
cell type: bacterial
chip antibody: anti-FLAG
|
| Treatment protocol |
none
|
| Growth protocol |
Cells were grown on TSA blood plates supplemented with 30 µg/ml oxytetracycline
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with formaldehyde for 10 minutes and quenched with glycine. After sonication, lysates were applied to pre-washed anti-FLAG magnetic beads and incuated for 3h. After washed, beads were washed and DNA-protein complex were eluted. After reverse crosslinking and proteinase K treatment at 65˚C overnight, ChIP DNA was cleaned up using Zymo ChIP DNA clean & concentrator kit.
ChIP-seq libaray was prepared using Illumina DNA prep kit and IDT 10bp UDI indices
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
cenR_D55E_2.csv
|
| Data processing |
ChIP-seq analysis was done on Galaxy
Output and input sequences were first mapped to the reference genome (Brucella ovis ATCC 25840, Genbank accessions NC_009504 and NC_009505) using bowtie2
Genrich was performed using the output file and its corresponding input file with parameters set as maximum q-value = 0.05, and minimum AUC (area under the curve) = 20. PCR duplicates were removed. bamCoverage was used to create bigwig files for each replicate.
Assembly: NC_009504 and NC_009505
Supplementary files format and content: bigWig for output files
|
| |
|
| Submission date |
Apr 06, 2023 |
| Last update date |
May 30, 2023 |
| Contact name |
Sean Crosson |
| E-mail(s) |
[email protected]
|
| Phone |
5178845345
|
| Organization name |
Michigan State University
|
| Department |
Dept. Microbiology and Molecular Genetics
|
| Street address |
567 Wilson Rd
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL33317 |
| Series (2) |
| GSE229120 |
A unique mode of cross regulation in a cell envelope stress signaling system [ChIP-seq] |
| GSE229183 |
A unique mode of cross regulation in a cell envelope stress signaling system |
|
| Relations |
| SRA |
SRX19898290 |
| BioSample |
SAMN34103459 |
