Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MAF1

Cell type

Cell type Class
Blood
Cell type
THP-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
THP-1 cells, - PMA exposure, MAF1 ChIP
cell line
THP-1
pma exposure
( - PMA )
cell type
monocytes
chip antibody
anti-MAF1 (Santa Cruz sc-365312 lot # G1411)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Equal numbers of THP-1 monocytes and THP-1 derived macrophages were collected (~10 million cells per ChIP experiment) and resuspended in growth media at 1 x 10^6 cells/mL and cross-linked with rotation at room temperature in 1% formaldehyde for 10 minutes. Cross-linking was quenched with the addition of 200 mM glycine and an additional 5 minutes of rotation at room temperature. Cross-linked cells were then spun down and resuspended in 1x RIPA lysis buffer, followed by chromatin shearing via sonication (3 cycles using a Branson sonicator: 30 seconds on, 60 seconds off; 15 additional cycles on a Bioruptor sonicator: 30 seconds on, 30 seconds off). Individual ChIP experiments were performed on pre-cleared chromatin using antibody-coupled Dynabead protein G (ThermoFisher) magnetic beads. Anti-histone H3 (acetyl K27) antibody was obtained from Abcam (ab4729), POLR3D antibody was obtained from abcam (ab86786; Lot# GR267691-1). 3-5 ug of antibody per ChIP was coupled to 18 uL beads and rotated overnight with sheared chromatin at 40 C. Beads were then washed 5x in ChIP wash buffer (Santa Cruz), 1x in TE, and chromatin eluted in TE + 1% SDS. Cross-linking was then reversed by incubation at 65C overnight, followed by digestion of RNA (30 min RNase incubation at 37C) and digestion of protein (30 min proteinase K incubation at 45C). ChIP DNA was then purified on a minElute column (Qiagen) Libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
41057078
Reads aligned (%)
14.2
Duplicates removed (%)
76.3
Number of peaks
208 (qval < 1E-05)

hg38

Number of total reads
41057078
Reads aligned (%)
15.1
Duplicates removed (%)
75.1
Number of peaks
236 (qval < 1E-05)

Base call quality data from DBCLS SRA