|
| Status |
Public on Feb 07, 2019 |
| Title |
BcorΔE9-10KrasG12D ubChIP-seq (3) |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid Progenitor Cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: scl-Cre-ERT +; Bcorfl/y;KrasG12D/WT
tissue: Bone Marrow
cell type: Myeloid Progenitor Cells
chip antibody: H2AK119ub (Cell Signalling Technology, 8240S, lot 2)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Donor-derived 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 |
BK3
|
| Data processing |
Sample QC was first 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(v2.3.3) to the mouse reference genome (GRCm38/mm10)
Read counting over genomic regions, filtering, normalisation and computation of statistical significance was performed with R package Csaw (v1.10.0). TDF files were generated with IGVTools (v2.3.95)
Genome_build: mm10
Supplementary_files_format_and_content: Browser viewable TDF 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) |
| GSE126177 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [BcorKrasChIP-seq] |
| GSE126264 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis |
|
| Relations |
| BioSample |
SAMN10881440 |
| SRA |
SRX5342469 |
