Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Others
Cell type
Palatal shelve mesenchymeS
NA
NA

Attributes by original data submitter

Sample

source_name
Mesenchymal cells from palatal shelves
age
E14.5
strain
C57BL/6
tissue
mesenchyme

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Isolated cells were lysed with 50 µL cold lysis buffer (10 mM Tris-­HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40; all components purchased from Sigma) in a centrifuge at 500 x g for 15 minutes at 4°C. Pelleted nuclei were resuspended in 50 µL tagmentation reaction mix (25 µL Nextera TD Buffer, 2.5 µL Nextera TD Enzyme, and 22.5 µL H2O, all from the Nextera DNA Sample Preparation Kit (Illumina). Immediately after Tn5 tagmentation, DNA samples were purified and indexed using NEBNext® High-Fidelity 2x PCR Master Mix (New England Biolabs) with a customized Nextera PCR primer pair, according to the following program: 72°C for 5 minutes; 98°C for 30 seconds; 11 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute; and hold at 4°C. All DNA libraries that exhibited a nucleosome pattern in the BioAnalyzer 2100 Assay passed the pre-sequencing QC process and were pooled for high-throughput sequencing.

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
103954615
Reads aligned (%)
51.5
Duplicates removed (%)
27.5
Number of peaks
10912 (qval < 1E-05)

mm9

Number of total reads
103954615
Reads aligned (%)
51.5
Duplicates removed (%)
27.5
Number of peaks
10875 (qval < 1E-05)

Base call quality data from DBCLS SRA