Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Epidermis
Cell type
Squamous cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
SCC_1_shPixt1_K27Ac_ChIP
strain background
C57BL/6
tissue
skin
cell type
squamous cell carcinoma (SCC)
genotype/variation
shPitx1 lentiviruses
chip antibody
anti-H3K27Ac (Abcam, ab4729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from 1x10^6 SCC cells or2x10^6 sorted cells using the ChIPmentation protocol described in Schmidl et. al, Nat Methods. 2015 Oct; 12(10): 963–965, DOI: 10.1038/nmeth.3542 using 4ug of anti-Pitx1 (Santa Cruz, 18922), anti-Klf4 (R&D, AF3758) and anti-H3K27Ac (Abcam, ab4729). Library prep was performed acording to Schmidl et. al, Nat Methods. 2015 Oct; 12(10): 963–965, DOI: 10.1038/nmeth.3542, using Tn5 to tagment the DNA fragments previous elution of the DNA.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
15865560
Reads aligned (%)
98.6
Duplicates removed (%)
18.7
Number of peaks
512 (qval < 1E-05)

mm9

Number of total reads
15865560
Reads aligned (%)
98.5
Duplicates removed (%)
18.7
Number of peaks
509 (qval < 1E-05)

Base call quality data from DBCLS SRA