|
| Status |
Public on Mar 10, 2016 |
| Title |
MDAMB231_TotalInput |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
cell line: MDA-MB-231
chip antibody: none
|
| Treatment protocol |
Cells were left untreated or stimulated with PMA (1.3ng/ml) for 60h.
|
| Growth protocol |
Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 5 x 106 cells were cross-linked with formaldehyde (1%, 10 min) then quenched with glycine (125mM). Fixed cells were lysed in SDS lysis buffer and chromatin-bound DNA sheared by sonication with a Misonix Sonicator S-4000. ChIP samples were incubated overnight at 4°C with Protein A Magnetic Beads (Millipore) and 5 μg of either H3K4me1 (ab8895; Abcam) or H3K27ac (ab4729; Abcam) antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research).
Libraries were prepared from ChIP DNA (10ng) using the NEBNext® ChIP-Seq Library for Illumina (New England Biolabs) and Ampure XP Bead clean-up.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Total Input
MDA_TI
|
| Data processing |
Adapters stripped using cutadapt
Reads mapped with Bowtie2 using global alignment. Only uniquely mapped reads used.
Duplicates removed using Picard
bedgraph files from HTSEQ, reads extended 200bp.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files show tag densities for the different treatments (NS and ST) and cell type for ChIP
|
| |
|
| Submission date |
Jan 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kristine Hardy |
| E-mail(s) |
kristine.hardy@anu.edu.au
|
| Organization name |
University of Canberra
|
| Lab |
Cytokine Gene Expression
|
| Street address |
University of Canberra
|
| City |
Bruce |
| State/province |
ACT |
| ZIP/Postal code |
0200 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE76732 |
Identification of enhancers in EMT and breast cancer stem cell formation |
|
| Relations |
| BioSample |
SAMN04395836 |
| SRA |
SRX1527008 |
