Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
Flp-In T-REx 293 Cell Line
chip antibody
none
treatment
none
condition
Non Heat-Shock

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed using 1% methanol-free formaldehyde (CAT no) in DMEM (HEK293) or IMDM (K562) at room temperature for 10 minutes, followed by 5 minutes blocking in 0.125M glycine. Cells were washed twice with ice-cold PBS. Cell pellet was resuspended in Farnham Buffer (5 mM PIPES pH 8; 85 mM KCl; 0.5% Igepal). Cell suspensions were sonicated in 1ml Covaris tubes using Covaris S220 with the following settings: Peak Power=75; Duty Factor=2; Cycles/Burst=200. Sonication time varied from cell type to cell type; K562=~2.5minutes and HEK293=~3minutes. Isolated nuclei were washed with Farnham Buffer and suspended in shearing buffer (10 mM Tris-HCl pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared by sonication in 1ml Covaris tubes using the following settings: Peak Power=140; Duty Factor=5; Cycles/Burst=200, Time=25-30 minutes. Debris was removed by centrifugation. A DNA fragment-size distribution of 200-600bp was considered as ideal chromatin for ChIP. Chromatin was diluted 1:1 with IP buffer to achieve a final 0.05% SDS concentration. 200 μg of good quality chromatin was used for immunoprecipitation. Protein A or G magnetic beads (CAT) were incubated (rotated) with 5-10μg of antibody for 6h at 4ºC. This bead-antibody complex was then incubated overnight at 4ºC with chromatin.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
16686552
Reads aligned (%)
92.1
Duplicates removed (%)
2.1
Number of peaks
127 (qval < 1E-05)

hg19

Number of total reads
16686552
Reads aligned (%)
92.0
Duplicates removed (%)
2.1
Number of peaks
169 (qval < 1E-05)

Base call quality data from DBCLS SRA