Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Epidermis
Cell type
Keratinocytes
MeSH Description
Epidermal cells which synthesize keratin and undergo characteristic changes as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell.

Attributes by original data submitter

Sample

source_name
human keratinoctyes
cell type
primary human neonatal keratinocytes
chip antibody
J1 (gift from the Crabtree Lab (Khavari et al. Nature 1993))

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63. For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina were use for library construction

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
49085058
Reads aligned (%)
70.3
Duplicates removed (%)
28.5
Number of peaks
9361 (qval < 1E-05)

hg38

Number of total reads
49085058
Reads aligned (%)
71.8
Duplicates removed (%)
27.4
Number of peaks
9496 (qval < 1E-05)

Base call quality data from DBCLS SRA