Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX17

Cell type

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

Attributes by original data submitter

Sample

source_name
HEK 293T Cells
treatment
10 um CHIR for 24 hours
chip antibody
SOX17 R&D AF1924

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-Seq experiments, Total RNA was extracted using the Nucleospin RNA Extraction kit.For ChIP-Seq experiments, after differentiation to the desired stage, cells were dual crosslinked in plate with 1.5mM EGS and 1% formaldehyde. The fixation was then quenched with 125mM glycine. Cells were then washed twice and scraped in ice-cold PBS and resuspended in sonication buffer. For RNA-Seq experiments, 300ng of total RNA was poly-A selected and reverse transcribed using Illumina's TruSeq stranded mRNA library preparation kit (Illumina; 20020595). For ChIP-Seq experiments, DNA libraries were prepared using 1-5 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674) according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
101867077
Reads aligned (%)
83.5
Duplicates removed (%)
10.3
Number of peaks
41218 (qval < 1E-05)

hg19

Number of total reads
101867077
Reads aligned (%)
82.9
Duplicates removed (%)
10.6
Number of peaks
39999 (qval < 1E-05)

Base call quality data from DBCLS SRA