Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Umbilical cord blood
NA
NA

Attributes by original data submitter

Sample

source_name
Umblical Cord Blood Cells Undergoing Differentiation
time-point
D12

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Mononuclear cells was isolated from the buffy coat layer of the corb blood by the Ficoll-Paque layering assay. Cells were then cultured with erythrobalst differentiation medium. Single cell suspensions were collected at the respective time points and the live cells were enriched by Dead Cell Removal Kit (Miltenyi). The enriched cells were then harvested for STAR Scripts run using C1 Fluidigm Open App chips (10-17um). The open chromatin was transposed by Tn5 transposase. Cell specific barcode was integrated to tagmented DNA of each cell by PCR amplification with indexed primer. The amplified PCR produced was purified by Ampure XP beads and the purified ATACseq library was sent for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
27819535
Reads aligned (%)
97.8
Duplicates removed (%)
87.3
Number of peaks
10 (qval < 1E-05)

hg19

Number of total reads
27819535
Reads aligned (%)
96.9
Duplicates removed (%)
87.7
Number of peaks
13 (qval < 1E-05)

Base call quality data from DBCLS SRA