Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Blood
Cell type
CD4 CD8 double negative cells
NA
NA

Attributes by original data submitter

Sample

source_name
in-vitro DN2 cells
strain
C57BL/6
genotype
ThymoD+/p(A)
chip antibody
CTCF (Millipore, 07-729, 262833)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Cells were fixed with PBS containing 1% formaldehyde. Formaldehyde was quenched with 0.2 M glycine for 10 min. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS. Fixed cells were stored at -80 degrees until use. Libraries were prepared with NEBNext primer set. Fragment size was selected with AMPure beads (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
40176579
Reads aligned (%)
93.8
Duplicates removed (%)
29.7
Number of peaks
29866 (qval < 1E-05)

mm9

Number of total reads
40176579
Reads aligned (%)
93.5
Duplicates removed (%)
29.7
Number of peaks
29848 (qval < 1E-05)

Base call quality data from DBCLS SRA