Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

Cell type

Cell type Class
Blood
Cell type
MOLM-14
NA
NA

Attributes by original data submitter

Sample

source_name
MOLM-14_Veh (DMSO)
cell line
MOLM-14
cell type
Human AML Cells
treatment
Veh (DMSO)
chip antibody
MED1 (CRSP1/TRAP220) (Bethyl, cat# A300-793A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA for RNA-Seq was extracted from treated MOLM-14 cells using a Qiagen RNeasy Kit with on-column Dnase treatment. For ChIP-Seq, genomic DNA was precipitated using lysate from treated MOLM-14 cells and purified using a Qiagen PCR Purification Kit. For RNA-Seq, RNA samples were normalized to 250ng each, based on picogreen quantitation, and ERCC RNA controls were incorporated into each sample. Samples then went through ribosomal RNA reduction and subsequently fragmented and primed with random hexamers to produce first strand cDNA. During second strand cDNA synthesis, RNA templates were removed and replaced with cDNA strands containing dUTP. The ds-cDNA was then purified using Beckman Coulter AMPure XP beads. Libraries were created from the cDNA by attaching an adenosine to the 3' end and ligating unique adapters to the ends. The ligated products were then amplified. The resulting libraries were quantitated using a NanoDrop spectrophotometer and fragment size assessed with the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 Quantitative PCR instrument and a Library Quantification Kit (KAPA, KK4824). All samples were pooled equimolarly and quantitated by qPCR, and also assessed on the Bioanalyzer. ChIP-Seq library prep was done using a ThruPLEX DNA-Seq 6S Kit (Takara Bio) following the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
69671357
Reads aligned (%)
87.8
Duplicates removed (%)
10.1
Number of peaks
1350 (qval < 1E-05)

hg38

Number of total reads
69671357
Reads aligned (%)
90.0
Duplicates removed (%)
8.6
Number of peaks
1798 (qval < 1E-05)

Base call quality data from DBCLS SRA