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Sample GSM2264592 Query DataSets for GSM2264592
Status Public on Mar 09, 2017
Title MCF7_H3K4me3_ShMEN1_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: ShMEN1
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 ShMEN1 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
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
BioSample SAMN05521667
SRA SRX2007553

Supplementary file Size Download File type/resource
GSM2264592_MCF7_H3K4me3_ShMEN1_2.bed.gz 302.3 Kb (ftp)(http) BED 73.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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