Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
SMS-KCNR
NA
NA

Attributes by original data submitter

Sample

source_name
Neuroblastoma line KCNR
cell line
KCNR
cell type
Neuroblastoma
antibody
none
enrichment target
input
target function
input
treatment
Ethanol

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
harvesting protocol: ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit). ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen). DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
46643358
Reads aligned (%)
90.9
Duplicates removed (%)
10.8
Number of peaks
4270 (qval < 1E-05)

hg19

Number of total reads
46643358
Reads aligned (%)
89.0
Duplicates removed (%)
15.0
Number of peaks
3111 (qval < 1E-05)

Base call quality data from DBCLS SRA