Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Epidermis
Cell type
Interfollicular epidermis cells
NA
NA

Attributes by original data submitter

Sample

source_name
Back skin inetrfollicular epidermis
treatment
tissue stretching
strain
CD1

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4ºC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37ºC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

mm10

Number of total reads
109031667
Reads aligned (%)
54.8
Duplicates removed (%)
47.7
Number of peaks
39918 (qval < 1E-05)

mm9

Number of total reads
109031667
Reads aligned (%)
54.8
Duplicates removed (%)
47.7
Number of peaks
39901 (qval < 1E-05)

Base call quality data from DBCLS SRA