|
| Status |
Public on Nov 05, 2020 |
| Title |
RANKL rep3 [ChIP-seq_H3K27ac] |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Raw264.7
cell type: Monocyte-derived cell line
treatment: RANKL
time point: 4 hours
chip antibody: H3K27ac
|
| 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.
Peak calling using MACS2.
Subsampling.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peaks files (broadpeak format).
|
| |
|
| 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) |
| GSE160839 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [H3K27ac ChIP-seq] |
| GSE160840 |
Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development |
|
| Relations |
| BioSample |
SAMN16663361 |
| SRA |
SRX9432544 |
