Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Satb1

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
CD4 thymocyte
cell type
CD4 thymocyte
antibody
SATB1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with anti-SATB1 antibody (Abcam, ab70001) that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified. Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

mm10

Number of total reads
17352525
Reads aligned (%)
97.6
Duplicates removed (%)
20.0
Number of peaks
13695 (qval < 1E-05)

mm9

Number of total reads
17352525
Reads aligned (%)
97.4
Duplicates removed (%)
20.1
Number of peaks
13793 (qval < 1E-05)

Base call quality data from DBCLS SRA