|
| Status |
Public on Jul 08, 2024 |
| Title |
ATAC, Dox, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
4D6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 4D6
cell type: thymic epithelial cells
genotype: WT AIRE
treatment: Dox 24hr
|
| Treatment protocol |
4D6 stable cells were seeded on 150mm plates with or without Dox and grown for 24 hrs.
|
| Growth protocol |
4D6 cells were maintained in RPMI supplemented with 10% FBS, 1% L-glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
100,000 cells were used for each replicate.
ATAC-seq libraries were prepared using ATAC-seq library prep kit (Active Motif) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3). Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly) using bwa (v0.7.17). The resulting SAM files were converted to BAM files, sorted and indexed, and reads mapped to mitochondrial DNA were removed using Samtools (v1.6).
Read fragment sizes were checked using the ATACseqQC R package (v3.19). Post PCR duplicate removal, reads were shifted +4bp and –5bp for positive and negative strand respectively, and were further split into nucleosome-free regions (NFR), mono- or di-nucleosome regions using the alignmentSieve function in deepTools (v3.5.1).
Peak calling was performed on bam files containing reads mapped to NFR using MACS2 (v2.2.7.1).
Assembly: hg38
Supplementary files format and content: bigwig files contain nucleosome-free regions
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Qianxia Zhang |
| E-mail(s) |
qianxia.zhang@childrens.harvard.edu
|
| Phone |
9018345955
|
| Organization name |
Boston Children's Hospital
|
| Street address |
3 Blackfan Circle, RM 3117.16
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (2) |
| GSE243825 |
Mechanism for controlled assembly of transcriptional condensates by Aire |
| GSE267525 |
Mechanism for controlled assembly of transcriptional condensates by Aire [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN41402203 |
| SRA |
SRX24558051 |
