Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

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

Attributes by original data submitter

Sample

source_name
HEK293
perturbation/epigenome editor
pLV dCas9-KRAB
grna
control
assay
ChIP-seq
chip epitope
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were crosslinked in 1% formaldehyde at 37C for 10min, quenched with glycine, lysed on ice in buffer containing 1% SDS, diluted to a final concentration of 0.3% SDS and sonicated for 5 minutes total time at ~10W power. Sonicated chromatin was incubated with the relevant antibody overnight at 4C with rotation after dilution to 0.1% SDS. ChIP-seq library prep: Performed as previously described using 5 ng (CTCF and H3K27ac), or 20 ng (H3K9me3) of ChIP DNA input. ChIP-seq sequencing: Paired-end 38 bp reads were generated on a NextSeq500 (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
12000000
Reads aligned (%)
178.0
Duplicates removed (%)
9.0
Number of peaks
43306 (qval < 1E-05)

hg38

Number of total reads
12000000
Reads aligned (%)
179.0
Duplicates removed (%)
8.9
Number of peaks
43488 (qval < 1E-05)

Base call quality data from DBCLS SRA