Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
CD34 Hematopoietic stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
Bone marrow
cell type
HSCe (CD34+, CD38-,Lineage-)
donor age
73
donor sex
female
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Micro-ChIPseq was performed using the True MicroChIP (Diagenode, #C01010130) kit and antibodies that had been validated for specificity and reactivity using the MODified Histone Peptide Array (Active Motif, #13001). The following antibodies were used, 1 g H3K27me3 (Millipore, #07-449, Lot: 21494165), 1 g H3K4me3 (Abcam, #ab8580, Lot: GR164207-1), 0.5 g H3K4me1 (Diagenode, #C15410194, Lot: A1862D), or 0.5 g H3K27ac (Abcam, #ab4729, Lot: GR155970-2). ChIP-seq libraries were prepared using the V1 MicroPlex Library Preparation kit (Diagenode, #C05010011). For the PCR amplification, a total of 16 amplification cycles was used. Libraries were purified using a 1:1 Ampure bead cleanup and eluted in 16 uL of Tris-HCl ph 8.0. Only libraries with enrichment at targeted sites by QPCR were used for sequencing. Libraries were multiplexed and sequenced using an Illumina Hi-Seq-2500 with 50bp single end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
38276362
Reads aligned (%)
98.4
Duplicates removed (%)
5.1
Number of peaks
1275 (qval < 1E-05)

hg19

Number of total reads
38276362
Reads aligned (%)
97.6
Duplicates removed (%)
6.4
Number of peaks
1204 (qval < 1E-05)

Base call quality data from DBCLS SRA