Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Zbtb17

Cell type

Cell type Class
Blood
Cell type
P6D4
NA
NA

Attributes by original data submitter

Sample

source_name
P6D4 ChIP-Seq Miz1
cell line
P6D4
cell type
SCID.adh murine thymic lymphoma
development stage
DN3
chip antibody
rabbit anti-Miz-1
chip antibody vendor
Santa Cruz Biotechnology

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies) For ChIP-Seq experiments, sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS. For RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
76577795
Reads aligned (%)
90.0
Duplicates removed (%)
39.7
Number of peaks
692 (qval < 1E-05)

mm9

Number of total reads
76577795
Reads aligned (%)
89.8
Duplicates removed (%)
39.9
Number of peaks
662 (qval < 1E-05)

Base call quality data from DBCLS SRA