Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM28

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293T
cell line
HEK293T
cell type
Human embryonic kidney cell
genotype
KO-WTcomp
chip antibody
anti-KAP1 antibody (Abcam cat. no. ab10483 RRID:AB_297222)

Sequenced DNA Library

library_name
GSM6619991
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each HEK293T cell sample, 107 cells grown in 10-cm plates were fixed for 15 min at room temperature with 1% formaldehyde, added directly to the DMEM media (GIBCO). The 10x formaldehyde stock solution was freshly prepared with molecular biology-grade reagents and contained 11% formaldehyde (Sigma-Aldrich, cat. no. F-8775), 50 mM HEPES pH 7.9, 0.1 M NaCl, and 1 mM EDTA. Fixation was quenched by adding 120 mM glycine (Sigma cat. no. G-7403) from a 20x stock solution and incubating for 5 min at room temperature. The cells were washed twice by centrifugation (800 g, 4˚C, 10 min) and resuspension in PBS, 0.5% IGEPAL CA-630 (Sigma-Aldrich, cat. no. I-8896), 0.1 mM phenylmethylsulfonyl fluoride (PMSF). Cell pellets were then frozen and shipped in dry ice to Active Motif for chromatin preparation, immunoprecipitation with anti-KAP1 antibody (Abcam cat. no. ab10483 RRID:AB_297222) ChIP-Seq libraries were generated by Active Motif from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
57336201
Reads aligned (%)
98.7
Duplicates removed (%)
31.3
Number of peaks
1593 (qval < 1E-05)

hg19

Number of total reads
57336201
Reads aligned (%)
98.0
Duplicates removed (%)
32.7
Number of peaks
1421 (qval < 1E-05)

Base call quality data from DBCLS SRA