Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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+;Dnmt3a+/+;MSCV_FLT3-ITD-GFP
strain
C57BL/6
chip antibody
Abcam ab8895

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
10766662
Reads aligned (%)
95.6
Duplicates removed (%)
22.4
Number of peaks
108 (qval < 1E-05)

mm9

Number of total reads
10766662
Reads aligned (%)
95.5
Duplicates removed (%)
22.4
Number of peaks
87 (qval < 1E-05)

Base call quality data from DBCLS SRA