Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Nerve tumor cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse nerve tumor cells
tissue
primary cultured nerve tumor cells
genotype
Lats1fl/fl;Lats2fl/+;CcGFPfl/+;Dhh-Cre

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Dissociated Lats1/2-deficient mouse tumor cells (∼50,000 cells) were spun down at 500 x g for 5 min at 4C, lysed in cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Afterspinning down at 500 x g for 10 min at 4C, nuclei were resuspended in transposition mix containing 25 μl TD (2x reaction buffer) 2.5 μl TDE1 (Nextera Tn5 Transposase), 22.5 μl Nuclease Free H2O, at 37°C for 30 min. Immediately following transposition, DNA were purified using a Qiagen MinElute PCR Purification Kit. Transposed DNA fragments were subsequently amplified and the amplified library was purified using Qiagen MinElute PCR Purification Kit. Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7–9 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14046054
Reads aligned (%)
80.7
Duplicates removed (%)
69.3
Number of peaks
11997 (qval < 1E-05)

mm9

Number of total reads
14046054
Reads aligned (%)
80.7
Duplicates removed (%)
69.3
Number of peaks
11951 (qval < 1E-05)

Base call quality data from DBCLS SRA