Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
SW 1783
Primary Tissue
Brain
Tissue Diagnosis
Astrocytoma

Attributes by original data submitter

Sample

source_name
SW1783 cells
cell line
SW1783
treatment
IgG control (Cell signaling, #2729)
antibody
Rabbit IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The method for chromatin immunoprecipitation was described as ChIP assay kit (Cell Signaling Technology), while the agarose beads were replaced by magnetic beads. Indexed libraries were prepared from 6ng-20ng of Diagenode Biorupter sheared ChIP DNA using the KAPA Hyper Library Preparation Kit (Kapa Biosystems, Inc).  Libraries were amplified by 6 cycles of PCR then assessed for quality using the Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Advanced Analyticals) and quantified using the Qubit dsDNA HS Assay Kit (ThermoFisher).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
44694253
Reads aligned (%)
97.6
Duplicates removed (%)
5.0
Number of peaks
973 (qval < 1E-05)

hg19

Number of total reads
44694253
Reads aligned (%)
96.7
Duplicates removed (%)
7.0
Number of peaks
1021 (qval < 1E-05)

Base call quality data from DBCLS SRA