Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sox2

Cell type

Cell type Class
Epidermis
Cell type
Squamous cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
squamous cell carcinoma
strain
C57BL/6
tissue
skin
antibody
anti-Sox2 (R&D, AF2018), 4ug
condition
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from 2x10^7 SCC cells or 1x10^6 sorted cells using the ChIP-IT High Sensitivity kit (53040, Active Motif) according to manufacturers instructions. Library prep was performed with ThruPLEX DNA-seq kit (Rubicon Genomics, R400427) using 200pg of ChIP DNA or KAPA Hyper Prep kit (KAPA, KK8505) using 1ng of ChIP DNA

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
40472943
Reads aligned (%)
91.0
Duplicates removed (%)
51.7
Number of peaks
2081 (qval < 1E-05)

mm9

Number of total reads
40472943
Reads aligned (%)
90.9
Duplicates removed (%)
51.8
Number of peaks
2111 (qval < 1E-05)

Base call quality data from DBCLS SRA