Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Epidermis
Cell type
Epidermis
MeSH Description
The external, nonvascular layer of the skin. It is made up, from within outward, of five layers of EPITHELIUM: (1) basal layer (stratum basale epidermidis); (2) spinous layer (stratum spinosum epidermidis); (3) granular layer (stratum granulosum epidermidis); (4) clear layer (stratum lucidum epidermidis); and (5) horny layer (stratum corneum epidermidis).

Attributes by original data submitter

Sample

source_name
Mouse skin
strain
CD1 x FVB
gender
male
age
PD22-25
sorting markers
CD34+ / α6-integrin+
chip antibody
H3K4me3 (ActiveMotif)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
15-20 mice of CD1 x FVB wild-type strain between PD22-25 (early anagen, anagen I-IIIa) and PD38-44 (late catagen, catagen VII-VIII) were used. ~3-4 million bulge and non-bulge cell nuclei were isolated and treated with microccoccal nuclease (MNase) (50U, Affymetrix) (~12min, room temperature) to generate mono-nucleosomal fragments. Isolated chromatin was processed further for immunoprecipitation. Eluted ChIP DNA were used for sequencing library generation. ChIP DNA was quantified using Quant-iT dsDNA HS reagent (Invitrogen). Nanograms of ChIP DNA for each sample were processed using following steps: 1) end-repair using End-It DNA End-Repair Kit (Epicentre Biotechnologies), 2) addition of single A-base using Klenow Fragment (3’->5’ exo-) (New England Biolabs) and dATP (Invitrogen), 3) ligation of barcoded adapters to A-overhang (Enzymatics), 4) gel purification using SYBR gold (Invitrogen) and low Tm agarose gel, 5) PCR enrichment (13-14 cycles) using Phusion Polymerase (New England Biolabs), 6) PCR purify using AMPure kit (Agencourt), 7) native acrylamide gel purification, 8) PCIAA (Phenol-Chloroform-Isoamylalchol) extraction, and 9) ethanol precipitation. Purified DNA samples were measured in their quality and quantity using bioanalyzer before sequencing at the Cornell University Institute for Biotechnology.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
105859634
Reads aligned (%)
88.3
Duplicates removed (%)
67.6
Number of peaks
25214 (qval < 1E-05)

mm9

Number of total reads
105859634
Reads aligned (%)
88.1
Duplicates removed (%)
67.6
Number of peaks
25150 (qval < 1E-05)

Base call quality data from DBCLS SRA