Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Thymocytes
MeSH Description
HEMATOPOIETIC PROGENITOR CELLS that have migrated to the THYMUS where they differentiate into T-LYMPHOCYTES. Thymocytes are classified into maturational stages based on the expression of CELL SURFACE ANTIGENS.

Attributes by original data submitter

Sample

source_name
thymocytes, blt/blt, input
strain/background
C57BL/6
genotype/variation
blt/blt
cell type
total thymocytes
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sonicated nuclei were cleared by centrifugation and incubated overnight with anti-Zfp335 bound to Dynabeads. Beads were washed in low-salt buffer, high-salt buffer, LiCl buffer and TE buffer. Protein/DNA complexes were eluted, reverse-crosslinked overnight at 65°C and treated with RNase A and proteinase K. ChIP DNA was purified using QIAquick PCR Purification kit (Qiagen). 7-10 ng ChIP DNA and 10 ng input DNA were used for library preparation, performed according to Illumina's TruSeq protocol with some modifications. DNA clean-up, removal of adapter dimers and size selection (300-500 bp) were done using Agencourt AMPure XP beads (Beckman Coulter). Libraries were checked for quality using the High Sensitivity DNA Bioanalyzer kit (Agilent Technologies), quantified with the Qubit dsDNA HS Assay kit (Life Technologies), and sequenced as 50 bp single-end reads on the Illumina HiSeq 2000 platform.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
26493787
Reads aligned (%)
83.4
Duplicates removed (%)
27.1
Number of peaks
509 (qval < 1E-05)

mm9

Number of total reads
26493787
Reads aligned (%)
83.0
Duplicates removed (%)
27.1
Number of peaks
555 (qval < 1E-05)

Base call quality data from DBCLS SRA