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Sample GSM2357380 Query DataSets for GSM2357380
Status Public on Dec 19, 2016
Title MCF10a_rep6
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
E-mail(s) guertin@virginia.edu
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
Relations
BioSample SAMN05932795
SRA SRX2255552

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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