Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Biotin

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
murine primary activated B cells
experiment type
ChIP-Seq
chip antibody
Streptavidin beads
chip antibody manufacturer
Invitrogen
activation protocol
LPS/IL4
precipitated ctcf genotype
mZF8

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells (10-20 x 10^6 cells) were crosslinked for 10min at 37C with 1% (vol/vol) formaldehyde, followed by quenching with 0.125 M glycine (final concentration). Crosslinked cell samples were then sonicated with a Covaris sonicator to obtain DNA fragments 200-300 bp in length. Biotinylated samples were incubated with 40ul of Dynabeads M-280 Streptavidin Beads (Invitrogen) overnight at 4C in RIPA buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 0.1% (wt/vol) SDS, 0.1% (wt/vol) sodium deoxycholate and 1% (vol/vol) Triton X-100). Beads were washed twice with Wash buffer1 (2% (vol/vol) SDS), once with Wash buffer2 (0.1% (vol/vol) deoxycholate, 1% (vol/vol), once with Wash buffer3 (250 mM LiCl, 0.5% (vol/vol) NP-40, 0.5% (vol/vol) deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and then twice with TE buffer (10 mM Tris-HCl (pH 7.5) and 1 mM EDTA). ChIP DNA was then extracted for 4h at 65C in Tris-EDTA buffer with 0.3% (wt/vol) SDS and proteinase K (1 mg/ml). Library preparation followed standard protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42209040
Reads aligned (%)
74.7
Duplicates removed (%)
25.3
Number of peaks
45330 (qval < 1E-05)

mm9

Number of total reads
42209040
Reads aligned (%)
74.4
Duplicates removed (%)
25.3
Number of peaks
45387 (qval < 1E-05)

Base call quality data from DBCLS SRA