Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Spi1

Cell type

Cell type Class
Blood
Cell type
WEHI-279
Tissue
Bone Marrow
Cell Type
B Lymphocyte
Disease
Lymphoma

Attributes by original data submitter

Sample

source_name
WEHI-279 mouse lymphoma cells
transcription factor
PU.1
antibody
Monoclonal ANTI-FLAG M2 (F3165 SIGMA)
sample type
ChIP chromatin

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell lysates were sonicated for 30 minutes and PU.1/Spi-B-DNA complexes were isolated with an anti-FLAG antibody. Fragmented DNA was quantified using 2100 Bioanalyzer (Agilent Technologies). Libraries were generated robotically with 10 ng of fragmented DNA (range 100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold, the size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies) whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LaChip GX (PerkinElmer) instrument. Libraries were sequenced on a SR100 run on a HiSeq2000 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
139027982
Reads aligned (%)
82.2
Duplicates removed (%)
51.4
Number of peaks
3570 (qval < 1E-05)

mm9

Number of total reads
139027982
Reads aligned (%)
82.1
Duplicates removed (%)
51.5
Number of peaks
3649 (qval < 1E-05)

Base call quality data from DBCLS SRA