|
| Status |
Public on Oct 16, 2017 |
| Title |
ATAC-seq_T47Dflp_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
T47D
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D Flp control cells
passages: <10
antibody: N/A
|
| Treatment protocol |
Cells were treated with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100), and then chromatin tagmentation was performed by Tn5 transposase (2.5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).
|
| Growth protocol |
Cells were grown on 15 cm plates in high glucose DMEM medium with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data files:
ATAC_T47Dflp.bigWig
|
| Data processing |
Reads were filtered based on a mean base quality score >20.
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. Reads were mapped to hg19 genome using Bowtie 0.12.8. The offset parameters suggested by Buenrostro et al (Nat. Methods, 2013) were applied to each mapped read. Unique reads (non- duplicate reads) were used for the subsequent analysis.
genome build: hg19
processed data files format and content: bigWig, bed, txt
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul A Wade |
| E-mail(s) |
wadep2@niehs.nih.gov
|
| Phone |
919-541-3392
|
| Organization name |
NIEHS
|
| Department |
Laboratory of Molecular Carcinogenesis
|
| Street address |
111 TW Alexander Drive
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE99479 |
A class of GATA3 mutation reprograms the breast cancer transcriptional network through gain and loss of function |
|
| Relations |
| BioSample |
SAMN07179315 |
| SRA |
SRX2871334 |
