|
| Status |
Public on Nov 05, 2020 |
| Title |
INPUT Raw [ChIP-seq_BRD] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Raw264.7
cell type: Monocyte-derived cell line
treatment: Untreated
chip antibody: None
|
| Treatment protocol |
Replicates were treated with RANKL, RANKL/I-BET, or I-BET for 4 hours.
|
| Growth protocol |
Treated and untreated cells were cultured using DMEM medium. 10e7 cells per ChIP were cross-linked with 1% formaldehyde for 15min. The ChIP protocol was the same as for ChIP-qPCR until the elution.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP DNA was purified with AMPure beads (Beckman).
ChIP and input DNA libraries were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) following manufacturer’s protocols. The quantity was determined using the Qubit High Sensitivity DNA kit (Life Technologies) and library size was determined using the Bioanalyser High Sensitivity DNA kit (Agilent). Libraries were quantified using the Universal Library Quantification Kit for Illumina (Kapa Biosystems) and run on AB StepOne Plus Real-Time PCR (Applied Biosystems). Libraries were diluted to 2nM and sequenced at the MRC Imperial facility using the Illumina HiSeq 2500 platform to obtain single-end 50bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality check using FastQC.
Reads alignment using bowtie2 (2.3.4.1 64bit).
Subsampling based on the same INPUT file for BRD2, BRD3 and BRD4 samples.
Peak calling using MACS2 (VERSION 2.1.1.20160309) for subsamples.
MSPC used for filtering peaks, and then the peaks/tracks files were merged from subsamples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pileup track files (bigwig format) for merged subsamples.
Supplementary_files_format_and_content: Peak files (bed format) for merged subsamples.
|
| |
|
| 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) |
| GSE160838 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [BRD ChIP-seq] |
| GSE160840 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development |
|
| Relations |
| BioSample |
SAMN16663355 |
| SRA |
SRX9432533 |
