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
RAG-/-µ+ pre-B cells
strain
B6
tissue
Pre-B cells
genotype
RAG1-/-
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For bone marrow subset purification, B6.RAG-/- mice bearing a rearranged IgM transgene were used to obtain pre-B cells. For each sample 1 - 10 ng of IP material or input control sample was prepared into sequencing libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina following manufacturers protocol. Samples were amplified using 18 cycles of PCR and then size selected on 2% EX agarose gels (Thermo Fisher) and bands cut at 300bps (+ 25 bps) and cleaned up using DNA Clean & Concentrator-25 (Zymo Research). The prepared libraries were loaded onto an Illumina HiSeq2000 for single-end 100 base reads with 7 bases of the index read. Data was processed to generate Fastq files using CASAVA 1.8 and demultiplexed based on index sequences.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
103121230
Reads aligned (%)
96.8
Duplicates removed (%)
17.8
Number of peaks
617 (qval < 1E-05)

mm9

Number of total reads
103121230
Reads aligned (%)
96.6
Duplicates removed (%)
17.7
Number of peaks
697 (qval < 1E-05)

Base call quality data from DBCLS SRA