Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Pre-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
INPUT_C15-TCF3_CHA
cell type
pre-B cells Arf-/-
strain
C57BL/6
passages
TCF3-ZNF384 Fusion
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared as described (Zhang et.al, Nature Genetics, 2016). Breifly, 20 X 10^6 cells were crosslinked with 1% formaldehyde for 10 minutes. Cells were washed 3 times with PBS and lysed on ice for 10 minutes with lysis buffer. Chromatin was washed twice in wash buffer and once in shearing buffer before resuspending in 1ml of shearing buffer. Chromatin was sonicated with a Covaris E210 instrument and resuspended in dilution buffer. Finally, immunoprecipiation was performed with anti-HA antibody. To prepare ChIP-seq libraries, 10 ng of ChIP DNA was end repaired and adaptor ligation was performed using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs). Libraries were purified after 14 rounds of PCR amplification with Q5 DNA Hot-Start polymerase (New England BioLabs). Each ChIP-seq library underwent 50-cycle single-end sequencing using TruSeq SBS kit v3 on an Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
57574654
Reads aligned (%)
98.5
Duplicates removed (%)
17.2
Number of peaks
626 (qval < 1E-05)

mm9

Number of total reads
57574654
Reads aligned (%)
98.3
Duplicates removed (%)
17.2
Number of peaks
719 (qval < 1E-05)

Base call quality data from DBCLS SRA