Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HDAC9

Cell type

Cell type Class
Uterus
Cell type
SK-UT-1
Primary Tissue
Uterus
Tissue Diagnosis
Leiomyosarcoma

Attributes by original data submitter

Sample

source_name
SK-UT-1
cell type
Leiomyosarcoma cells
passages
below 20
strain
na
chip antibody
HDAC9 (Di Giorgio et al, 2019 NAR submitted)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies (2μg of anti-H3K27ac (Abcam ab4729) , 2.5 μg of anti-MEF2D (BD Bioscience), 4μg of anti-HDAC4 (Paroni et al, 2004) and anti-HDAC9 (home-made antibody) antibodies or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. 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. TruSeq ChIP Library

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
60482347
Reads aligned (%)
64.7
Duplicates removed (%)
31.4
Number of peaks
1244 (qval < 1E-05)

hg38

Number of total reads
60482347
Reads aligned (%)
67.0
Duplicates removed (%)
29.5
Number of peaks
1990 (qval < 1E-05)

Base call quality data from DBCLS SRA