|
| Status |
Public on Jan 27, 2023 |
| Title |
MDA-MB-231 DSM OE |
| Sample type |
SRA |
| |
|
| Source name |
Triple negative breast
|
| Organism |
Homo sapiens |
| Characteristics |
strain: MDA-MB-231
tissue: Triple negative breast
genotype: DSM Overexpression
|
| Growth protocol |
The panel of MDA_MB-231 derived cell lines (control, WT DAXX OE, and DSM OE) were cultured in complete DMEM.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were resuspended in a swelling buffer in the presence of the protease inhibitor cocktail (Sigma) and then pelleted and resuspended in the SDS lysis buffer. The lysates were transferred to a Covaris microTUBE and sonicated with an E220 Covaris Ultrasonicator. Chromatin fragmentation (~500 bps) was verified through agarose gel electrophoresis. DNA was extracted using Qiagen mini prep based on manufacturer instructions.
DNA libraries were prepared for sequencing using standard ChIP Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq sequencing reads (Fastq files) were mapped to the human genome (GRCh37/hg19) using Bowtie2 (Langmead and Salzberg, 2012), where option –local was specified to trim or clip unaligned reads from one or both ends of the alignment. Genome browser BedGraph tracks and read density histograms were generated using SeqMINER. Peak finding and annotation to the nearest Refseq gene promoter was performed and de novo motif discovery was carried out using HOMER (Heinz et al., 2010).
Assembly: hg19
Supplementary files format and content: matrix table for peak distritbutions
Supplementary files format and content: matrix table for region distritbutions
|
| |
|
| Submission date |
Jan 26, 2023 |
| Last update date |
Jan 28, 2023 |
| Contact name |
Daiqing Liao |
| E-mail(s) |
dliao@ufl.edu
|
| Phone |
(352) 273-8188
|
| Organization name |
University of Florida
|
| Department |
Anatomy and Cell Biology
|
| Lab |
480E
|
| Street address |
2033 Mowry Rd
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE190783 |
DAXX genome binding/occupancy profiling by high throughput ChIP sequencing |
|
| Relations |
| SRA |
SRX19194568 |
| BioSample |
SAMN32944537 |
