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Sample GSM3832912 Query DataSets for GSM3832912
Status Public on May 31, 2019
Title 100Pa_SAHA_rep2
Sample type SRA
 
Source name MCF10A mammary epithelial cells
Organism Homo sapiens
Characteristics treatment: SAHA
stiffness: 100Pa
tissue culture substrate: 3D matrix
cell line: MCF10A
Treatment protocol Some groups were treated with 1 uM suberoylanilide hydroxamic acid
Growth protocol MCF10A cells were grown in alginate-recombinant basement membrane hydrogels of 100 Pa or 2000 Pa elastic modulus, or on 2D polyacrylamide (100 Pa) or on tissue culture plastic. Standard MCF10A growth media was used.
Extracted molecule genomic DNA
Extraction protocol Cells were extracted from matrices by incubating gels in ice cold 50 mM EDTA in PBS for 10 minutes with pipette mixing. The suspensions were centrifuged at 500 g at 4oC for 10 mins to pellet cells. The pellets were incubated in 1 ml of 0.25% trypsin/2.21 mM EDTA at 37oC for 5 minutes to digest any remaining rBM, then centrifuged at 500 g for 10 mins again.
Libraries were prepared using Illumina Nextera Tn5 Transposase (FC-121-1030)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description MCF10A cells cultured in soft 3D matrices, treated with SAHA
tagAlign.counts.for.naive.overlap.merged.peaks.txt
saha_100Pa_ppr.IDR0.1.filt.narrowPeak.gz
saha_100Pa_ppr.naive_overlap.filt.narrowPeak.gz
100Pa_saha_1_TAAGGCGA_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
100Pa_saha_1_TAAGGCGA_R1.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig
Data processing FASTQ files for each sample were processed through the ENCODE DCC ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline/) version 1.3.0
A merged peak set was generated by concatenating the optimal naive overlap peaks for all samples, truncating the concatenated peak set to 200 bp around the summit, sorting and merging the resulting peaks. This yielded a merged peak set of 221,510 peaks.
Read counts for each replicate for each peak were obtained by running bedtools coverage on the the filtered tagAlign file generated by the ENCODE DCC pipeline over the set of 221,510 merged peaks.
Differential accessibility across each pair of samples was obtained via DESeq2 on the count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: fold change bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: pval bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: Tab-delimited text file including un-normalized read counts from each replicate for each peak in the merged naive overlap peak set.
Supplementary_files_format_and_content: Naive overlap optimal narrowPeak calls
 
Submission date May 30, 2019
Last update date May 31, 2019
Contact name Carlos Aguilar
E-mail(s) caguilar@umich.edu
Organization name University of Michigan - Ann Arbor
Department Dept. of Biomedical Engineering & Biointerfaces Institute
Lab NANO-OMIC-BIO-ENGINEERING-LAB
Street address 300 Pasteur Dr
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL16791
Series (1)
GSE131968 Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility
Relations
BioSample SAMN11893204
SRA SRX5933506

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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