|
| Status |
Public on Jan 11, 2018 |
| Title |
MCF7_PMA_TGF_LSD1_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: PMA/TGFb
cell line: MCF7
antibody: LSD1
|
| Treatment protocol |
Cells were left or stimulated with PMA (1.29ng/ml) with a recombinant TGF-beta1 (5 ng/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 10^6 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 10 μg of anti-LSD1 (ab17721; Abcam) antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research).
TruSeqLT paired end
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
Adapters stripped using Trimmomatic
Reads mapped with Bowtie2 using global alignment. --no-unal -q -I 100 -X 500 --fr -x
Duplicates removed using Picard
bedgraph files from HOMER, reads extended 200bp.
Peaks called with HOMER against TI -style histone -F 4 -size 300 -minDist300 and filtered on >=12.2 normalised tag count
Genome_build: hg19
Supplementary_files_format_and_content: bed files show enriched regions.
|
| |
|
| Submission date |
Oct 10, 2017 |
| 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 |
GPL18573 |
| Series (2) |
| GSE104754 |
LSD1 activation promotes inducible EMT programs and modulates the tumour microenvironment in breast cancer |
| GSE104755 |
The role of LSD1 in Epithelial to Mesenchymal Transition: gene expression profiling and ChIP-seq |
|
| Relations |
| BioSample |
SAMN07765803 |
| SRA |
SRX3265285 |
