Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
Thymus
cell type
Leukemic cells
cell surface marker
CD4+;CD8+
genotype
Mx1-cre+;Dnmt3af/f;MSCV_FLT3-ITD-GFP
strain
C57BL/6
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
2 million FACS-sorted cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was terminated by addition of 0.125M glycine and washed with ice-cold PBS containing protease inhibitor cocktail (PIC, Roche). Samples were sonicated to 200-500bp fragments for 8 cycles at 5 minutes each (Biorupter, Diagenode). Sheared chromatin were incubated with antibodies and Protein A (Dynabeads, Invitrogen). Antibodies used were against H3K27ac (ab4729; Abcam), H3K4me1 (ab8895; Abcam). Chromatin were reverse crosslinked at 68°C for 3 hours at mixed in Elution buffer (1M Tris pH 7.5, 0.5M EDTA, 5M NaCl, 10% SDS, Proteinase K) at 1100rpm. DNA was purified by MiniElute PCR Purification Kit (Qiagen) and eluted in 22μL EB buffer. Purified DNA was used to generate libraries with the ThruPLEX-FD preparation kit (Rubicon)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
9111466
Reads aligned (%)
86.6
Duplicates removed (%)
28.0
Number of peaks
268 (qval < 1E-05)

mm9

Number of total reads
9111466
Reads aligned (%)
86.4
Duplicates removed (%)
28.1
Number of peaks
247 (qval < 1E-05)

Base call quality data from DBCLS SRA