Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

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
Primary Epidermal Keratinocyte - Differentiation Day 6
cell type
primary epidermal keratinocyte
differentiation state
Late differentiation (Day 6)
individual
Donor2
Sex
male
chip antibody
Smc1a (Bethyl, catalog# A300-055A, lot# A300-055-5)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an antibody. NEB Next ChIP-seq library prep kit was used.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
34111848
Reads aligned (%)
72.2
Duplicates removed (%)
4.6
Number of peaks
19577 (qval < 1E-05)

hg38

Number of total reads
34111848
Reads aligned (%)
73.6
Duplicates removed (%)
3.4
Number of peaks
19759 (qval < 1E-05)

Base call quality data from DBCLS SRA