Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Blood
Cell type
CD8+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Thymus
cell type
Thymocytes
Stage
CD8SP Innate Memory
strain
BALB/c
chip antibody
H3K4me3 (Merck, 17-614)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CD8SP from pooled thymus were isolated and crosslinked with formaldehyde 1% for 10min at room temperature before staining. Crosslinking was stopped with 0.125 M glycine. Cells then were washed twice by ice-cold PBS and sorted. Each sorted cell-population was resuspended with ChIP-lysis buffer (10mM Tris pH8, 140mM NaCl, 1mM EDTA, 1% Triton x-100, 0.5% SDS, 0.1% Na-Deoxycholate) for 10min on ice supplemented with PIC (proteinase inhibitors cocktail) and sheared to have a fragments size range between 200-600bp. After clearance by centrifugation at 4°C, sheared chromatin used for each immunoprecipitation of histone marks or transcription factors. For histones marks, library preparation was performed using TruSeq ChIP library Preparation kit using 3-6ng of ChIPed DNA. For transcription factors, the library preparation was done with MicroPlex Library Preparation kit with 0.5ng od ChIPed DNA

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
33743736
Reads aligned (%)
94.9
Duplicates removed (%)
43.8
Number of peaks
12805 (qval < 1E-05)

mm9

Number of total reads
33743736
Reads aligned (%)
94.6
Duplicates removed (%)
43.8
Number of peaks
12810 (qval < 1E-05)

Base call quality data from DBCLS SRA