Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Adipocyte
Cell type
Adipose Tissue
MeSH Description
Encapsulated adipose tissue.

Attributes by original data submitter

Sample

source_name
Adipose
strain
C57BL/6
genotype
WT
stimulus
N/A
sample type
chromatin

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Adipocyte nuclei were isolated according to methods previously described (Church 2014). Briefly, 250,000 cells from filtered adipocyte suspension were washed once with PBS prior to addition of cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. For SVF, 50,000 cells were used for nuclei isolation according to standard protocol. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 10x concentration Tn5 (Nextera) for primary adipose and standard concentration for SVF. All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 100-1000bp, were quantified with qPCR and Qubit, and sequenced 50bp, single-end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14705945
Reads aligned (%)
86.6
Duplicates removed (%)
20.5
Number of peaks
4496 (qval < 1E-05)

mm9

Number of total reads
14705945
Reads aligned (%)
86.5
Duplicates removed (%)
20.6
Number of peaks
4409 (qval < 1E-05)

Base call quality data from DBCLS SRA