Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
Tumor3
strain
C57BL/6
genotype
ThymoDp(A)/p(A)
chip antibody
none

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Tumor cells were cultured on OP9-DL1, aMEM 20% FBS, IL7, FLT3-L. Cells were harvested and immediately spun down, and resuspended in PBS. Cells were fixed with 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Fixed cells were stored at -80 degrees until use. 50000 cells were used for library preparation. Washed cells were resuspended in lysis buffer. After washing, cells were treated with transposition mix for 30 min at 37 degrees. Cycle of PCR amplification was determined by q-PCR. 100-800 bps of Libraries were selected from 2% agarose gel.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
60412537
Reads aligned (%)
94.5
Duplicates removed (%)
64.0
Number of peaks
38158 (qval < 1E-05)

mm9

Number of total reads
60412537
Reads aligned (%)
94.3
Duplicates removed (%)
64.1
Number of peaks
38232 (qval < 1E-05)

Base call quality data from DBCLS SRA