Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Cardiovascular
Cell type
AV cushion mesenchymal cells
NA
NA

Attributes by original data submitter

Sample

source_name
AVM cells 5.5mM Glucose
strain
H- 2Kb-tsA58 transgenic
cell type
AV cushion mesenchymal cells
passage
P6
glucose status
normal

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
54,000 AVM cells cultured in NG and HG for 48hrs were used for ATAC-sequencing. Similar to Buenrostro et al. (Nat Methods. 2013 Dec;10(12):1213-8), unfixed AVM cells were lysed and immediately transposed using Nextera DNA library preparation kit (FC-121-1030, Illumina) followed by column purification with MinElute Reaction cleanup kit (Qiagen). ATAC-seq libraries were generated from transposed and amplified DNA using Nextera index primers. The quality of the libraries was assessed using Agilent Bioanalyzer High Sensitivity DNA analysis kit and sent for 50bp paired-end sequencing on Illumina HiSeq 2000 platform to Epigentek Group Inc. (Farmingdale, NY).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
6648674
Reads aligned (%)
5.5
Duplicates removed (%)
25.4
Number of peaks
28 (qval < 1E-05)

mm9

Number of total reads
6648674
Reads aligned (%)
5.5
Duplicates removed (%)
25.4
Number of peaks
28 (qval < 1E-05)

Base call quality data from DBCLS SRA