Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Neural
Cell type
Neuro-2a
Tissue
Brain
Cell Type
Neuroblast
Disease
Neuroblastoma

Attributes by original data submitter

Sample

source_name
mouse neuroblastoma N2a cells
tissue
neuroblastoma
cell line
N2a
chip antibody
H3K27me3 (Millipore,07-449)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of RIPA buffer( 50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate).The cells lysates was sonicated to generate DNA fragments of 200-500 bp, centrifuged for 10 min at 12,000 g, and the supernatant was directly used for immunoprecipitation. Place the tube containing the Pierce™ ChIP-grade Protein A/G Magnetic Beads on the magnetic ,then, discard the supernatant. Wash the beads for three times with 1ml 0.1M sodium phosphate Buffer . ChIP-seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer's instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing. ChIP-Seq sequencing was performed on NextSeq500 platform with 151 bp paired-end sequencing.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
34042884
Reads aligned (%)
79.3
Duplicates removed (%)
10.9
Number of peaks
415 (qval < 1E-05)

mm9

Number of total reads
34042884
Reads aligned (%)
79.2
Duplicates removed (%)
10.9
Number of peaks
405 (qval < 1E-05)

Base call quality data from DBCLS SRA