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Sample GSM2264593 Query DataSets for GSM2264593
Status Public on Mar 09, 2017
Title MCF7_input_ShMEN1
Sample type SRA
Source name MCF-7 breast cancer cells
Organism Homo sapiens
Characteristics chip antibody: none
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 MiSeq
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 GPL15520
Series (1)
GSE85315 Genome-wide changes in H3K4me3 after MEN1 silencing in MCF-7 cells
BioSample SAMN05521666
SRA SRX2007554

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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