|
| Status |
Public on Sep 02, 2024 |
| Title |
mESC to CM Day 1 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
A2lox.cre mouse embryonic stem cell line under cardiac differentiation
|
| Organism |
Mus musculus |
| Characteristics |
cell line: A2lox.cre
cell type: intermediate of cardiac differentiation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted by deteregent lysis. Transposition was carried out at 37C for 30 minutes.
Libraries were prepared with Illumina’s Nextera DNA Library Prep kit (Illumina 15028212).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
transposase-accessible genomic DNA
D1_FE.bw
D1_peaks.narrowPeak
|
| Data processing |
Mapping reads to mm10; Adapter sequences were clipped from reads using Cutadapt version 2.10 (cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 4 -m 10) , then aligned to UCSC mouse genome mm10 with bowtie2 version 2.3.2 with default settings.
Filtering for quality reads; Low quality reads ( q < 30 ) and reads mapping to blacklisted regions were removed using samtools version 1.5. Duplicated reads were marked and removed with picard tool MarkDuplicates version 2.8.1.
Peak calling; Accessible regions were identified using MACS2 version 2.1.1 grouping replicates together. (macs2 callpeak -f BAMPE -g mm –keep-dup all -B --SPMR ).
Generating fold enrichment tracks; Fold enrichment tracks were generated with MACS2 bdgcmp ( -m FE). Bedgraph files from MACS2 were converted to bigwig format with UCSC tool bedGraphToBigWig version 4.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are aligned to the mm10 genome. NarrowPeak files are called ATAC-seq peaks in the mm10 genome.
|
| |
|
| Submission date |
Sep 09, 2021 |
| Last update date |
Sep 02, 2024 |
| Contact name |
Megan J Rowton |
| Organization name |
University of Chicago
|
| Department |
Human Genetics and Genetic Medicine
|
| Lab |
Moskowitz
|
| Street address |
900 East 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE183767 |
Cardiac differentiation of mESCs and analysis of chromatin accessibility time series |
|
| Relations |
| BioSample |
SAMN21368202 |
| SRA |
SRX12121239 |
