|
| Status |
Public on Feb 07, 2019 |
| Title |
20w BcorΔE9-10 H2AK119ub Chip-seq (1) |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid Progenitor Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: scl-Cre-ERT +; Bcorfl/y
tissue: Bone Marrow
cell type: Myeloid Progenitor Cells
treatment: Tamoxifen IP
chip antibody: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)
|
| Treatment protocol |
Mice aged 3-6 months were administered 1mg tamoxifen for 5 consecutive days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lin-cKIT+Sca-1- myeloid progenitor cells were isolated from the BM of experimental mice by FACS. Nuclei were isolated from cross-linked cells and sonicated to shear chromatin, then histone-DNA complexes were immunoprecipitated using relevant antibodies.
DNA libraries were prepared using the KAPA Hyper Prep Kit for Illuminaplatforms (Kapa Biosystems) and the SeqCap Adapter Kit (Roche) following vendor’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H2AK119ubB1
|
| Data processing |
Sample QC was performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The ChIP-sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using bowtie2 to the mouse reference genome (GRCm38/mm10)
Peak calling was performed with MACS (v2.1.1) and BigWigs were created with deeptools(v2.5.3)
Normalisation, enrichment over genomic regions, and computation of statistical significance were performed with R package Csaw (v1.10.0).
Genome_build: mm10
Supplementary_files_format_and_content: Peaks files
Supplementary_files_format_and_content: bigWig Files
|
| |
|
| Submission date |
Feb 06, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Madison Kelly |
| E-mail(s) |
mjk4002@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
413 E69th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE126173 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [20wChiP-seq] |
| GSE126264 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis |
|
| Relations |
| BioSample |
SAMN10881097 |
| SRA |
SRX5342424 |
