Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Thymus
NA
NA

Attributes by original data submitter

Sample

source_name
Thymus
strain
C57BL/6
genotype
Aire+/+
cell type
MECs
antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as MECs. Chromatin IPed with specific Abs was eluted from the Protein-G beads, treated with 1µg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample.

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
10440531
Reads aligned (%)
98.0
Duplicates removed (%)
14.2
Number of peaks
99 (qval < 1E-05)

mm9

Number of total reads
10440531
Reads aligned (%)
97.9
Duplicates removed (%)
14.2
Number of peaks
71 (qval < 1E-05)

Base call quality data from DBCLS SRA