|
| Status |
Public on Mar 09, 2017 |
| Title |
MCF7_H3K4me3_ShCtrl_2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3 antibody Abcam (Ab8580)
cell line: MCF-7
induced: ShCtrl
|
| Treatment protocol |
MCF-7 cells that had been lentivirally infected with constructs for inducible expression of small hairpin RNA's directed against the MEN1 mRNA (ShMEN1#1) or a control sequnece were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Expression of small hairpin RNA's was induced by adding 100 ng/ml for 72 hrs.
|
| Growth protocol |
Cells were maintained at 37oC and 5% CO2 in DMEM + 10% FBS and Pen-Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked, lysed in a buffer containing SDS and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-seq of H3K4me3 in ShCtrl treated cells, sample 2
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using Bowtie.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline at the DFCI
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Koen M.A. Dreijerink |
| E-mail(s) |
koendreijerink@yahoo.com
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE85315 |
Genome-wide changes in H3K4me3 after MEN1 silencing in MCF-7 cells |
|
| Relations |
| BioSample |
SAMN05521670 |
| SRA |
SRX2007550 |
