|
| Status |
Public on Jun 14, 2016 |
| Title |
T47D_MK2206_H3K4me3_72 |
| Sample type |
SRA |
| |
|
| Source name |
T47D breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T47D
chip antibody: H3K4me3 Abcam (Ab8580)
treatment: MK2206
|
| Treatment protocol |
The medium was changed to medium containing either MK2206 or DMSO for 24 hours.
|
| Growth protocol |
Cells were maintained at 37oC and 5% CO2 in RPMI or DMEM + 10% FBS and Pen-Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked, lysed in SDS lysis buffer, and sonicated.
ThruPLEX-FD Prep kit, Rubicon Genomics
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed with FastQC version 0.10.0.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7.
Data were filtered according to mappable reads with 2 mismatches at most allowed.
Peaks were called using MACS version 2.0 with the following settings: band width (300), model fold (5, 50), qvalue cut-off (1*10e-2), range for calculating regional lambda (1000bps and 10000bps)
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using MACS version 2.0, scores represent -LOG10(qvalue)
|
| |
|
| Submission date |
Apr 22, 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 |
GPL11154 |
| Series (2) |
| GSE80592 |
Genome-wide H3K4me3 after MK2206/DMSO treatment of T47D cells |
| GSE80594 |
PI3K/AKT signaling regulates H3K4 methylation in breast cancer |
|
| Relations |
| BioSample |
SAMN04886752 |
| SRA |
SRX1721548 |
