|
| Status |
Public on Sep 16, 2023 |
| Title |
ChIP_Anti_MucR_Ba2308_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Brucella abortus 2308 |
| Characteristics |
cell type: Bacterial
genotype: wild type
treatment: Cells were growing in LB, fixed by 3% formaldehyde for 30min at room temperature
antibody: ChIP using anti-MucR antibodies
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wild type and mutant cells of Brucella abortus 2308 growing in LB were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1) by the hiclib pipline.
Assembly: B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.
|
| |
|
| Submission date |
Jun 14, 2023 |
| Last update date |
Sep 16, 2023 |
| Contact name |
Xindan Wang |
| E-mail(s) |
xindan@iu.edu
|
| Organization name |
Indiana University at Bloomington
|
| Department |
Biology
|
| Lab |
Biology Building 225
|
| Street address |
1001 E 3rd St
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL33491 |
| Series (1) |
| GSE234935 |
Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid  |
|
| Relations |
| BioSample |
SAMN35737118 |
| SRA |
SRX20681639 |
