Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
MLL-AF9 leukemic cell
NA
NA

Attributes by original data submitter

Sample

source_name
AML cells; MLL-AF9/NrasG12D
tissue
peripheral blood
cell type
expected ckit+, Mac1-, Gr1- genotype: NRasG12D; MLL-AF9
chip antibody
none
treatment
Dox inducible knockdown of Setd2; shSetd2.1638

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-Seq: Total RNA was isolated using Qiagen Rneasy kit. ChIP-Seq: Lysates were clarified from sonicated nuclei and chromatine was isolated with indicated antibody. RNA-Seq: TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer) ChIP-Seq: Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) ChIP-Rx (ChIP-seq, samples spiked in with Dropsophila Melanogaster Chromatin (S2 cell line))

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
66415658
Reads aligned (%)
93.8
Duplicates removed (%)
17.0
Number of peaks
627 (qval < 1E-05)

mm9

Number of total reads
66415658
Reads aligned (%)
93.5
Duplicates removed (%)
17.0
Number of peaks
698 (qval < 1E-05)

Base call quality data from DBCLS SRA