|
Status |
Public on Feb 07, 2019 |
Title |
20w BcorWT KL Chip-seq Input |
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: none
|
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 |
20wInput
|
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 |
SAMN10881079 |
SRA |
SRX5342439 |