Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Blood
Cell type
Multipotent progenitors
NA
NA

Attributes by original data submitter

Sample

source_name
Multipotent Progenitor Cells (MPPs)
strain
C57BL/6
genotype
Jarid2-KO
age
8-weeks
cre-driver
Vav-CRE
chip antibody
H3K27me3 (Diagenode #pAb-069-050)
cell type
Multipotent Progenitor Cells (MPPs)
indexes
AGGCAGAA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
43543763
Reads aligned (%)
87.8
Duplicates removed (%)
15.1
Number of peaks
182 (qval < 1E-05)

mm9

Number of total reads
43543763
Reads aligned (%)
87.7
Duplicates removed (%)
15.1
Number of peaks
158 (qval < 1E-05)

Base call quality data from DBCLS SRA