Antigen

Antigen Class

DNase-seq

Antigen

DNase-Seq

Cell type

Cell type Class

Blood

Cell type

Hematopoietic Stem Cells

MeSH Description

Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Sample

source_name

HSC

strain

C57BL/6

tissue

Bone marrow

dilution setting

Dnase 1:20 dilution

antibody

NULL

Sequenced DNA Library

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

For Hi-C, five thousands to millions cells were stained with Biotin anti-CD45.2 antibody. Cells were bound to biotin binder (Dynabeads Biotin Binder, Cat#11047, Invitrogen) and cross-link with 1% formaldehyde. Biotin binders were blocked by 0.5mM biotin solution. Cells were lysed and digested with CviQ I + CviA II + Bfa I for 20min. For DNase-Seq, 1000 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 3mM MgCl2) and digested with 8ul of DNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EDTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For MNase-Seq, 100 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 2mM CaCl2) and digested with 8ul of MNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EGTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For RNA-Seq, 2ng of total RNA were extracted miRNeasy Micro Kit (50) from Qiagen (Cat # 217084). The Hi-C samples were processed following the Hi-C protocol (PMID 19815776) with modifications briefly described as follows: DNA end were marked by biotin-14-dATP with Klenow(larg) for 1hrs at 37°C. Blunt-end DNA were ligated with T4 DNA Ligase for overnight at 16°C. DNA were reverse cross-linked and purified by phenol/chloroform extraction. Biotin were removed from unligated DNA-ends by T4 DNA polymerase for 2hrs at 12°C. DNA were purified by phenol/chloroform. DNA were sheared to 300-500bps by sonication and flowed by DNA-end repair and add”A”34. Biotin labeled DNA were pull-downed by streptavidin beads and then flowed by illumine adapter ligation and PCR amplification. Library construction protocals for DNase-Seq, MNase-Seq and RNA-Seq follow that described in (PMID 26605532), (PMID 18329373) and (PMID 24056875), respectively.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

18134194

Reads aligned (%)

92.7

Duplicates removed (%)

8.2

Number of peaks

9062 (qval < 1E-05)

mm9

Number of total reads

18134194

Reads aligned (%)

92.6

Duplicates removed (%)

8.3

Number of peaks

9065 (qval < 1E-05)