Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
tissue
Bone marrow
immunprecipitation
H3K9ac
mnase for chromatin digestion
High
treatment
DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mint-ChIP: Cells were lysed and native chromatin was digested using Mnase. Subsequently, nucleosomes were indexed by adapter ligation and pooled for immunoprecipiation of H3K9ac (Active Motif, 39917), H3K9me2 (Abcam, ab1220) and total H3 (Abcam, ab1791). Mint-ChIP: Immunoprecipitated DNA was amplified by in vitro transcription, followed by reverse transcription. Resulting fragments, tagged on both ends, were amplified by PCR using primers compatible with Illumina sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
8818226
Reads aligned (%)
91.1
Duplicates removed (%)
19.8
Number of peaks
2313 (qval < 1E-05)

hg19

Number of total reads
8818226
Reads aligned (%)
90.9
Duplicates removed (%)
19.9
Number of peaks
2344 (qval < 1E-05)

Base call quality data from DBCLS SRA