Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SSRP1

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_CBL0137
cell line
HT1080
treated with
CBL0137
concentration
3uM
time of treatment
1.5 hr
chip antibody
SSRP1 antibody
chip antibody vendor
BioLegend
chip antibody clone
10D1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-with SSRP1 antibody 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 100 PE sequencing on a HiSeq2500 sequencer according to the manufacturer's recommended protocol (Illumina Inc.).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
80674562
Reads aligned (%)
154.4
Duplicates removed (%)
21.1
Number of peaks
9110 (qval < 1E-05)

hg38

Number of total reads
80674562
Reads aligned (%)
155.4
Duplicates removed (%)
20.9
Number of peaks
9776 (qval < 1E-05)

Base call quality data from DBCLS SRA