Antigen

Antigen Class

TFs and others

Antigen

Kdm3b

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

Total bone marrow

cell source

Total bone marrow

genotype

WT

ChIP

Anti-JMJD1B, Bethyl, Cat# A300-883A

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248) with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter). ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

49921707

Reads aligned (%)

94.9

Duplicates removed (%)

14.1

Number of peaks

549 (qval < 1E-05)

mm9

Number of total reads

49921707

Reads aligned (%)

94.6

Duplicates removed (%)

14.1

Number of peaks

626 (qval < 1E-05)