|
| Status |
Public on Sep 30, 2018 |
| Title |
Vav-Jarid2-KO HSC H3K27me3-ChIP 1 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic Stem Cell (HSC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Jarid2-KO
age: 8-weeks
cre-driver: Vav-CRE
chip antibody: H3K27me3 (Diagenode #pAb-069-050)
cell type: Hematopoietic Stem Cell (HSC)
indexes: TAAGGCGA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1.0x104 HSCs were sorted into PBS+10% FBS, and then crosslinked at room temperature for 8 minutes using 1% paraformaldehyde (VWR #J531). Chromatin was sheared using a Covaris E220 Focused-ultrasonicator until the DNA fragments were between 200 – 700 base pairs. Chromatin samples were incubated overnight at 4°C with either the H3K27me3 antibody (Diagenode # pAb-195-050). Following overnight incubation, protein G dynabeads (Life Technologies #130-099-508) were added for 2-hours at 4°C. The beads were washed, and tagmented for 10-minutes at 37°C using the Nextera DNA Library Preperation Kit (Illumina #FC-121-1030). After additional washes, an overnight decrosslinking was performed immunoprecipiated DNA was isolated using Ampure XP beads.
2xKapa HiFi HotStart Ready Mix (Kapa #KB KK2601), along with Nextera custom primers, was used for library amplification of the ChIP DNA(12 cycles of PCR as determined by qPCR). Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
For ChIP-seq reads were aligned to the mm10 using Bowtie2 v1.2.1.1
For ChIP-seq peak calling was performed with hiddenDomains v3.0
ChIPQC v3.6 was used for QC
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for H3K27me3
|
| |
|
| Submission date |
Sep 27, 2018 |
| Last update date |
Sep 30, 2018 |
| Contact name |
Hamza CELIK |
| E-mail(s) |
[email protected]
|
| Phone |
314-362-0986
|
| Organization name |
Washington University in St Louis
|
| Department |
Internal Medicine
|
| Lab |
Challen Lab
|
| Street address |
660 S Euclid Ave
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE120595 |
Jarid2 Functions as a Tumor Suppressor in Myeloid Neoplasms by Repressing Self-Renewal in Hematopoietic Progenitor Cells |
|
| Relations |
| BioSample |
SAMN10140259 |
| SRA |
SRX4746911 |
