|
| Status |
Public on Nov 05, 2020 |
| Title |
RI rep2 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Raw264.7
cell type: Monocyte-derived cell line
treatment: RANKL+Ibet
time point: 4 hours
|
| Treatment protocol |
Replicates were treated with RANKL, RANKL/I-BET, or I-BET for 4 hours.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were collected and washed at 500g at 40C for 5 min. The cells were resuspended in lysis buffer and immediately spun at 500g at 40C for 10 min. The nuclei were subjected to transposase reaction for 30 min at 37oC; termination of the reaction and DNA purification were performed using a MinElute Kit (Qiagen).
The purified DNA was amplified as described before with NEBNext High-Fidelity 2x PCR Master Mix (NEB). The PCR amplified product was cleaned with AMPure beads (Beckman).
The quality of the libraries was assessed with the Bioanalyser High Sensitivity DNA kit (Agilent). Libraries were quantified using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) on a StepOne Plus Real-Time PCR (Applied Biosystems). The libraries were sequenced at the Genomics Facility at MRC/LIMS of ICL using the Illumina HiSeq 2500 platform to obtain paired-end 100bp reads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality check using FastQC.
Reads trimming using cutadapt, reads aligned by bowtie2, duplicate marking using sambamba, bam cleaning/filtering using Picard.
Filter blacklist genes using bedtools, filter reads using samtools, convert to BED files using bedtools, Tn5 shifting to obtain awk files.
Tn5 tagAlign using BEDPE.
Peak calling using MACS2.
Subsampling.
Genome_build: mm10
Supplementary_files_format_and_content: *_peaks.narrowPeak: Peak files.
|
| |
|
| Submission date |
Nov 04, 2020 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Anastasios Karadimitris |
| E-mail(s) |
a.karadimitris@imperial.ac.uk
|
| Phone |
+44 20 3313 8438
|
| Organization name |
Imperial College London
|
| Department |
Department of Immunology and Inflammation
|
| Lab |
Karadimitris' Lab
|
| Street address |
Hammersmith Campus, Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE160835 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [ATAC-seq] |
| GSE160840 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development |
|
| Relations |
| BioSample |
SAMN16663168 |
| SRA |
SRX9432589 |
