Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
FDC-P1
Tissue
Bone Marrow
Disease
Normal

Attributes by original data submitter

Sample

source_name
FDC-P1 wt
cell line
FDC-P1
infection
GFP
chip antibody
Rabbit IgG (ab37415, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the EZ-ChIP Kit (Upstate/Millipore) on murine FDCP1 cells. After chromatin-crosslinking with 1% formaldehyde, cells were lysed and nuclei were isolated by centrifugation. Chromatin was extracted from the isolated nuclei and fragmented by sonication to an average length of 200–500 bp. Material from 1x10e7 cells was pre-cleared with protein-G agarose beads to reduce non-specific background. Chromatin immunoprecipitation was performed with either rabbit anti-Runx1 antibody, generated against a C-terminal peptide,2 or rabbit IgG (Abcam). Bound protein-DNA complexes were captured with Protein G Sepharose 4 Fast Flow (GE Healthcare) and chromatin eluted according to the manufacturer’s protocol. Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts >70 bps. DNA fragments between 200-400 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 2100 using a High Sensitivity DNA Kit (Agilent)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
37450098
Reads aligned (%)
95.9
Duplicates removed (%)
54.8
Number of peaks
277 (qval < 1E-05)

mm9

Number of total reads
37450098
Reads aligned (%)
95.6
Duplicates removed (%)
54.8
Number of peaks
335 (qval < 1E-05)

Base call quality data from DBCLS SRA