Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
cell type
AML cell line
translocation
MLL-AF9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from cell lines was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014). Total RNA was extracted with TRIzol (Invitrogen) or RNAsol (GenDepot), treated with DNase on column (Qiagen) and analyzed by strand specific sequencing. ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, AF9, AF4, and RUNX1, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the Genome Analyzer (Illumina) or HiSeq 2000 (Illumina). For RNA-seq 250 ng of RNA was used for ribosomal RNA depletion with RiboZero (Illumina) and subsequent strand specific (USER) library preparation. 4C-seq libraries were prepared as previously described (Van de Werken, Nat. Meth., 2012)

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
30652636
Reads aligned (%)
97.2
Duplicates removed (%)
51.7
Number of peaks
1074 (qval < 1E-05)

hg19

Number of total reads
30652636
Reads aligned (%)
96.6
Duplicates removed (%)
52.8
Number of peaks
1094 (qval < 1E-05)

Base call quality data from DBCLS SRA