Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

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.

Sample

source_name

Fetal bone marrow

gestational age

17 weeks

tissue

fetal bone marrow

population

ProB-progenitors

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

The protocol for ATAC-Sequencing was adapted for small cell number from Corces et al26. 2000 PreProB and ProB-progenitors (n=3); and 5000 Lin+ mononuclear cells were sorted directly into 25uL of transposase mix (Tn5 enzyme, 2X TD buffer and 0.01% digitonin, Promega) at 4°C. Immediately following sorting, samples were incubated at 37°C for 30 minutes at 300 rpm agitation. Transposed DNA was immediately purified using a Qiagen MinElute kit and eluted in 10uL pre-warmed EB. Transposed fragments were amplified by PCR as previously described27. Libraries were quantified by qPCR (NEBNext Library Quant for Illumina kit) before sequencing using a 75-cycle paired-end kit on the NextSeq Illumina platform.

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

43882592

Reads aligned (%)

95.6

Duplicates removed (%)

64.6

Number of peaks

32072 (qval < 1E-05)

hg19

Number of total reads

43882592

Reads aligned (%)

94.9

Duplicates removed (%)

65.1

Number of peaks

31958 (qval < 1E-05)