Antigen

Antigen Class

Input control

Antigen

Input control

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

HOXA9 IDH1 R132H

cell type

HOXA9 immortalized bone marrow

treatment

Vitamin C

vector genotype

IDH1 R132H

chip antibody

None

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Frozen cell pellets (10e7 cells) were cross-linked by formaldehyde (1% final concentration) and washed by PBS. Cells were lysed and chromatin was Covaris E-220 Sonicator (Covaris). Chromatin fragments were incubated with protein G and A Sepharose beads (GE Healthcare) for two hours at 4oC to eliminate non-specific binding. Unbound chromatin fragments were separated from the beads and incubated with no antibody at 4oC overnight in IP buffer (10mM Tris-HCl pH 7.5, 2mM EDTA, 90mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate, 0.1% SDS). After incubation, IPs were washed twice with ChIP wash buffer (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and once with final ChIP wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). IPs were eluted in elution buffer (1% SDS, 100mM Sodium Bicarbonate) and incubated at 68oC for 2 hours to reverse crosslinks. DNA fragments were stripped from histones and purified using QIAquick PCR Purification Kit (Qiagen) and subjected to 8 cycles of paired-end indexing PCR. Illumina sequencing libraries were generated as previously described. Libraries were PCR amplified and sequenced on the Illumina NextSeq 500 platform following the manufacturer’s protocols (Illumina, Hayward CA.) Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

22065955

Reads aligned (%)

97.7

Duplicates removed (%)

9.2

Number of peaks

145 (qval < 1E-05)

mm9

Number of total reads

22065955

Reads aligned (%)

97.5

Duplicates removed (%)

9.4

Number of peaks

125 (qval < 1E-05)