|
| Status |
Public on Jan 27, 2016 |
| Title |
Input_for_GATA3_ChIP-seq_PE_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: GATA3 expressed
passages: 3-7
antibody: N/A
|
| Treatment protocol |
ChIP-Seq: Cells were lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Bioruptor or Covaris. DNA was precipitated with antibody against each target protein.
MNase-seq: Cells were treated with a hypotonic buffer. Isolated nuclei were digested with MNase. DNA Mononucleosomal DNA was extracted by using a ZYMO RESEARCH cleanup column and QIAGEN Gel extraction kit.
ATAC-seq: 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 (5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).
|
| Growth protocol |
Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina or 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. The offset parameters suggested by Buenrostro et al were applied to each mapped read.
Peak calling was performed with HOMER v4.1 at default parameters. Peaks were then adjusted to 200-mers centered on the midpoint of the HOMER calls.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
All paired-end reads were converted to a single fragment. After normalization within each data set, bigWig files were generated to visualize the genomic coverage.
For RNA-seq data processing, read counts per gene per sample were collected by HTSeq-Count.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed
|
| |
|
| Submission date |
Aug 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul A Wade |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE72141 |
GATA3-mediated chromatin reprogramming in breast cancer cells |
|
| Relations |
| BioSample |
SAMN03998415 |
| SRA |
SRX1156480 |
