Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
PM154 organoids
tissue
PM154 organoids
chip antibody
MYCN (Santa Cruz, sc-53993)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were collected and crosslinked with 1% methanol-free formaldehyde for 10 minutes and fixation was quenched using 125 mM glycine for 8 minutes. The cell pellets were centrifuged and washed twice in cold PBS. Each pellet was resuspended in 1 ml of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors (Thermo Scientific)) and lysed for 20 minutes at 4°C. The nuclei were collected by centrifugation and resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors (Thermo Scientific)). The protein-bound chromatin was sheared by sonication (Diagenode, Bioruptor Pico). Input sheared chromatin was reserved as a control for downstream ChIP-seq analysis. Equal volumes of sheared chromatin were immunoprecipitated with specified antibodies. Libraries were generated using the Hyper Prep Kit (Kapa Biosystems) following the manufacturer's recommended protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
35771330
Reads aligned (%)
77.5
Duplicates removed (%)
4.4
Number of peaks
1259 (qval < 1E-05)

hg19

Number of total reads
35771330
Reads aligned (%)
77.0
Duplicates removed (%)
5.7
Number of peaks
1337 (qval < 1E-05)

Base call quality data from DBCLS SRA