GSM3735446: HOTTIP-KO-MLL-ChIP-seq; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
KMT2A
Cell type
Cell type Class
Blood
Cell type
MOLM-13
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous
Attributes by original data submitter
Sample
source_name
MOLM13 leukemia cells
cell line
MOLM13
cell types
Human-derived acute myeloid leukemia cells
tissue origin
peripheral blood
genotype/variation
HOTTIP-KO
chip antibody
Anti-MLL, Millipore, #05-765
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA samples extracted with Trizol and treated with DNase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K27me3, H3K79me2 and MLL antibody (antibody: Anti-H3K4me3, Millipore, Cat No. 04-745; Anti-H3K27me3, Millipore, Cat No. 07-449; Anti-H3K79me2, Abcam, Cat No. ab3594.; Anti-MLL, Millipore, #05-765). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. CHIRP-seq library constructs with the Illumina TruSeq CHIP DNA library kit. HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030). RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq and CHIRP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.