Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MLXIP

Cell type

Cell type Class
Blood
Cell type
NALM-6
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
MondoA-IP from WT
cell type
B cell precursor leukemia
cell line
Human Pre-B Cell Line Nalm6
treatment
CRISPR/Cas9 control
genotype
MondoA-WT
chip antibody
MLXIP Rabbit Polyclonal antibody 13614-1-AP (Lot: 00042515)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with 1% formaldehyde for 9 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA), 6% of murine spike-in were added, and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 10-15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. NEBNext® Ultra II DNA Library Prep with Sample Purification Beads®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Sample Purification Beads. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
60420020
Reads aligned (%)
87.4
Duplicates removed (%)
37.8
Number of peaks
6718 (qval < 1E-05)

hg19

Number of total reads
60420020
Reads aligned (%)
86.7
Duplicates removed (%)
39.5
Number of peaks
6432 (qval < 1E-05)

Base call quality data from DBCLS SRA