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Sample GSM2131193 Query DataSets for GSM2131193
Status Public on Jun 14, 2016
Sample type SRA
Source name T47D breast cancer cells
Organism Homo sapiens
Characteristics cell type: T47D
chip antibody: KDM5A #1416 (gift Kaelin Lab DFCI)
treatment: DMSO
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 NextSeq 500
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
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 (2)
GSE80593 Genome-wide KDM5A occupancy after MK2206/DMSO treatment of T47D cells
GSE80594 PI3K/AKT signaling regulates H3K4 methylation in breast cancer
BioSample SAMN04886753
SRA SRX1721564

Supplementary file Size Download File type/resource
GSM2131193_T47D_DMSO_KDM5A.bed.gz 78.0 Kb (ftp)(http) BED 346.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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