|
| Status |
Public on Feb 15, 2022 |
| Title |
Clone EM2 replicate 2 (ATAC-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Clone EM2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ER-/PR- IBC
cell line: SUM149PT_EM2
cell line origin: SUM149PT
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Grown according to ATCC recommendations
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei extracted and tagmented per the Buenrostro ATAC-seq protocol
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/
Libraries constructed per the Buenrostro ATAC-seq protocol
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Tn5 fragmented genomic DNA
EM2_rep2
|
| Data processing |
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v1.9.1) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters “-X 2000 -k 2”
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs, which were converted to tagAlign format and reads were shifted +4 bp and -5 bp on the + and – strands, respectively.
Peaks were called using MACS2 (v2.1.1) callpeak command with parameters “--shift -75 --extsize 150 --nomodel --keep-dup all --call-summits -p 1.0E-10” and filtered against the ENCODE hg38 blacklist
Irreproducible Discovery Rate (IDR) method was applied, retaining peaks IDR threshold of 0.05
IDR peak sets were merged across samples to create a consensus peak set. reads falling within the consensus peak set in each sample were counted using featureCounts.
BAM files for sample replicates were merged using Picard MergeSamFiles before create of BigWig files
Counts per million (CPM) normalized tn5 insertion signal tracks were generated using deepTools8 (v3.4.3) bamCoverage command with parameters “--binSize 5 --normalizeUsing CPM --effectiveGenomeSize 2913022398 --ignoreForNormalization chrX” on the position-shifted BAM files
Genome_build: hg38
Supplementary_files_format_and_content: matrix of raw read counts in txt format
Supplementary_files_format_and_content: Normalized tn5 insertion signal tracks in BigWig format
Supplementary_files_format_and_content: peak files in BED format
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Diwakar Pattabiraman Pattabiraman |
| E-mail(s) |
Diwakar.R.Pattabiraman@Dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Molecular and Systems Biology
|
| Lab |
Pattabiraman lab
|
| Street address |
1 Medical Center Drive
|
| City |
LEBANON |
| State/province |
NH |
| ZIP/Postal code |
03765 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE172608 |
Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer [ATAC-seq] |
| GSE172613 |
Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer |
|
| Relations |
| BioSample |
SAMN18823525 |
| SRA |
SRX10654376 |
