Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
Thymic epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
cTEClo
strain
C57BL/6
genotype
wild-type
sample type
input
cell type
cTEClo
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from single cells using the SMART-seq2 protocol. TEC for ChIP-seq and ATAC-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215 RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq, ATAC-seq and ChIP-seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
80747172
Reads aligned (%)
96.0
Duplicates removed (%)
27.7
Number of peaks
62539 (qval < 1E-05)

mm9

Number of total reads
80747172
Reads aligned (%)
95.8
Duplicates removed (%)
27.8
Number of peaks
63174 (qval < 1E-05)

Base call quality data from DBCLS SRA