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Sample GSM2357376 Query DataSets for GSM2357376
Status Public on Dec 19, 2016
Title MCF10a_rep1
Sample type SRA
Source name mammary epithelial cell line
Organism Homo sapiens
Characteristics cell line: MCF10a
cell type: mammary epithelial cell line
cell status: Healthy cells with passage number < 30
Treatment protocol baseline
Growth protocol MCF10A cells were cultured in Dulbecco’s modified Eagle’s medium DMEM (Invitrogen) with 5% horse serum (Invitrogen), 1% penicillin/streptomycin (Invitrogen), 20 ng/ml EGF (Peprotech), 0.5 μg/ml hydrocortisone(Sigma), 100 ng/ml cholera toxin (Sigma) and 10 μg/ml insulin (Sigma) . Cells were grown in a humidified incubator at 37°C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cell lysis in hypotonic solution
nextera kit
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Data processing library strategy: ATAC-seq
Align with bowtie2
Merge bam files for all replicates
Normalize and create BedGraph, bigWig
Peak calling with hotspot (standard paramters)
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph and bigWig file for merged replicates, hotspot file with spots calculated by hotspot with fdr <0.01
Submission date Oct 20, 2016
Last update date May 15, 2019
Contact name Michael Guertin
Organization name University Of Virginia
Street address 1340 Jefferson Park Ave
City Charlottesville
State/province Virginia
ZIP/Postal code 22908
Country USA
Platform ID GPL18573
Series (1)
GSE89013 Identification of Breast Cancer Associated Variants That Modulate Transcription Factor Binding
BioSample SAMN05932794
SRA SRX2255548

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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