Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
CD43- splenic B cells
strain
C57BL/6
cell population
CD43- splenic B cells
chip antibody
None (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Naïve resting B cells from splenocytes of 8 week old male C57BL6 mice were incubated with anti-CD43 beads (Miltenyi) and the negatively selected population isolated and confirmed as 95% CD19+ by flow cytometry (FACS Calibur). RNA libraries were prepared with the NuGEN Ovation RNA-Seq v2 library preparation kit, which amplifies both mRNA and non-polyadenylated transcripts. The resulting cDNA was fractionated by sonication and prepared using the Illumina TruSeq library preparation kit which was then multiplexed across single-end, 100bp (RNA), 50bp (ChIP and miRNA), lanes of an Illumina HiSeq2000 sequencer using the Illumina pipeline RTA version 1.12.4.2 and de-multiplexing with CASAVA v1.8.2. ChIP-seq was performed at NIH using an Illumina TruSeq ChIP library kit according to the manufacturer’s protocol followed by cluster generation with a TruSeq Cluster generation kit v5. ChIP libraries were sequenced on an Illumina Genome Analyzer (GA-II) with sequencing performed for 42 cycles using the Illumina RTA version1.8.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
27889802
Reads aligned (%)
97.4
Duplicates removed (%)
21.5
Number of peaks
474 (qval < 1E-05)

mm9

Number of total reads
27889802
Reads aligned (%)
97.2
Duplicates removed (%)
21.5
Number of peaks
499 (qval < 1E-05)

Base call quality data from DBCLS SRA