Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

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
GSK LSD1
cell type
Normal Human Epidermal Keratinocyte
passages
6-8
treatment
GSK-LSD1 (2 mM) for 2 days
chip antibody
Rabbit polyclonal anti-Kdm1a (Abcam, Cat# ab17721) RRID: AB_443964

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as described previously (Capell et al., 2016; Lin-Shiao et al., 2018). Briefly, keratinocytes cultured in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min, and fixation was quenched with the addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and washed twice in 1× PBS before storage at −80°C. ChIP extracts were sonicated for 15 minutes in a Covaris sonicator. All ChIPs were performed using 500 µg of extract and 2 µg of antibody per sample. Thirty microliters of Protein G Dynabeads was used per ChIP. Libraries were prepared according to NEBNext Ultra DNA library preparation kit for Illumina instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
40322656
Reads aligned (%)
84.2
Duplicates removed (%)
9.2
Number of peaks
936 (qval < 1E-05)

hg38

Number of total reads
40322656
Reads aligned (%)
85.7
Duplicates removed (%)
8.2
Number of peaks
1024 (qval < 1E-05)

Base call quality data from DBCLS SRA