Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Blood
Cell type
Bone Marrow Cells
MeSH Description
Cells contained in the bone marrow including fat cells (see ADIPOCYTES); STROMAL CELLS; MEGAKARYOCYTES; and the immediate precursors of most blood cells.

Attributes by original data submitter

Sample

source_name
bone marrow
antibody
H3K27me3
type
MTF2 knockdown
cell sorting
CD34+/CD38-
status
Healthy

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Samples were sheared using a Covaris sonicator until DNA reached a final size of 100-300bp. 750ng of drosophila spike in chromatin (Active Motif) was added to each sonicated sample. 4ug of anti-H3K27me3 antibody (Cell Signaling, c36B11) or H3 (Abcam, ab1791) was bound to pre-blocked Protein A7 magnetic beads (Millipore) in combination with 2ug of Spike-in antibody (Active Motif) for 12 hours. The beads were then combined with sonicated sample containing Drosophila spike in chromatin and incubated overnight. After incubation, beads were collected and DNA-antibody complexes were eluted at 65 o C. Crosslinks were reversedovernight at 65 o C. Samples were treated with Proteinase K (Fisher Scientific) and RNaseA (Fisher Scientific) and DNA was purified using phenol-chloroform. All ChIP-seq experiments were cell number normalized and 150,000 cells per biological sample were used for each H3 and H3K27me3 ChIP experiment. For sequencing total ChIP DNA was used for library preparation (NextFlex Illumina Chip-seq kit).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
19815222
Reads aligned (%)
96.1
Duplicates removed (%)
11.2
Number of peaks
1057 (qval < 1E-05)

hg19

Number of total reads
19815222
Reads aligned (%)
95.3
Duplicates removed (%)
12.7
Number of peaks
881 (qval < 1E-05)

Base call quality data from DBCLS SRA