|
| Status |
Public on May 31, 2019 |
| Title |
2D_Soft_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A mammary epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: None
stiffness: 100Pa
tissue culture substrate: 2D 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 4000 |
| |
|
| Description |
MCF10A cells cultured on soft 2D matrices
tagAlign.counts.for.naive.overlap.merged.peaks.txt
2D_soft_ppr.IDR0.1.filt.narrowPeak.gz
2D_soft_ppr.naive_overlap.filt.narrowPeak.gz
2D_Soft_CAGAGAGG_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
2D_Soft_CAGAGAGG_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 |
GPL20301 |
| Series (1) |
| GSE131968 |
Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility |
|
| Relations |
| BioSample |
SAMN11893192 |
| SRA |
SRX5933518 |
