Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
LSK cells
NA
NA

Attributes by original data submitter

Sample

source_name
ExSed_LSK
strain
C57BL/6
age
7-8 weeks
sample group
access to exercise wheels for 6 wks followed by a 3 wks wheel withdrawal (ExSed).
tissue
all long bones including pelvic bone
cell type
sorted LSK cells
markers
CD3- CD4- CD8- CD49b- CD90.2- CD19- B220- NK1.1- Ter119- CD11b- CD11c- Gr1- Sca-1+ ckit+

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Sorted LSKs underwent ATAC-seq. 20.000 sorted LSK cells were initially resuspended in lysis buffer and centrifuged. The nuclei pellets were then subjected to transposition reaction using the Nextera Tn5 transposase enzyme (Illumina). Tagmented DNA was purified with the MinElute PCR Purification Kit and eluted in 10L of elution buffer (Qiagen). Barcoded libraries were prepared and PCR amplified. Double-sided bead purification was performed using AMPure XP beads to remove primer dimers and large >1,000 bp fragments. Libraries were sequenced 50 bp paired end on an Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
33196977
Reads aligned (%)
93.6
Duplicates removed (%)
30.8
Number of peaks
1138 (qval < 1E-05)

mm9

Number of total reads
33196977
Reads aligned (%)
93.5
Duplicates removed (%)
30.9
Number of peaks
1120 (qval < 1E-05)

Base call quality data from DBCLS SRA