Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3

Cell type

Cell type Class
Bone
Cell type
HT-1080
Primary Tissue
Bone
Tissue Diagnosis
Fibrosarcoma

Attributes by original data submitter

Sample

source_name
HT1080 cells
cell line
HT1080 cells
treatment
3 uM CBL0137, 6 hours
antibody
H3 antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Samples for ChIP Sequencing were prepared using SimpleChIP Kit # 9003 from Cell Signaling Technology without modifications. Cells HT1080, tail fibroblasts from SSRP1 KO mice were grown to 80% confluence, fixed with 1% formaldehyde for 10 min and protocol for this kit was followed: chromatin was digested with Micrococcal Nuclease into 150-900 bp DNA/protein fragments, antibodies specific to H3 ( provided by kit) and to H3 acetyl K27 ( ab4729, Abcam) were added and the complex co-precipitated and was captured by protein G magnetic beads. Cross-links were reversed, and DNA was purified for sequencing. 20ng of Chromatin-immunoprecipitated (ChIP) DNA is used to generate a library for Next generation sequencing using the ThruPLEX DNA seq kit (Rubicon Genomics, Inc.) as per manufacturer's instructions.  ThruPLEX uses stem-loop adapters to construct high quality libraries in a fast and efficient workflow. In the first step, Template Preparation, the DNA is repaired and yields molecules with blunt ends. Next, stem-loop adaptors with blocked 5' ends are ligated with high efficiency to the 5' end of the genomic DNA, leaving a nick at the 3' end.  In the final step, the 3' ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. The library is quantitated using quantitative PCR (KAPA Biosystems), normalized, and pooled in an equimolar fashion.  Pooled libraries are loaded to an individual lane of a HiSeq High Output v3 flow cell, using an Illumina cBot, for 2 x 75 PE and 75bp single end sequencing on a NextSeq sequencer according to the manufacturer's recommended protocol (Illumina Inc.).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
29842103
Reads aligned (%)
98.2
Duplicates removed (%)
3.6
Number of peaks
752 (qval < 1E-05)

hg19

Number of total reads
29842103
Reads aligned (%)
97.3
Duplicates removed (%)
4.3
Number of peaks
455 (qval < 1E-05)

Base call quality data from DBCLS SRA