Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Kidney
Cell type
G-401
Primary Tissue
Kidney
Tissue Diagnosis
Wilms' tumor

Attributes by original data submitter

Sample

source_name
MRT cells
transfection
SNF5
cell line
G401
passage
ten-thirty
antibody
MYC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq experiments, chromatin was clarified from sonicated nuclear preps and antibodies were added. For ATAC-seq, nuclei were extracted wtih non-ionic detergent in hypotonic buffer and treated with transposase. For RNA-seq, RNA was extracted by Trizol method, for PRO-seq, nuclei were extracted through hypotonic lysis with a low amount of non-ionic detergent. For ChIP-seq experiments, libraries were made using NEBnext Ultra II DNA library Prep and NEBNext Multiplex Oligos for Illumina, for ATAC-seq libraries were made using transposed DNA made Illumina Nextera DNA kit, NEBNext High-Fidelity 2x PCR Master Mix, and Nextera based primers ordered from IDT, for RNA-seq, libraries were made at Genewiz using their standard methods, and for PRO-Seq, libraries were made using RNA that was made through a biotin-run on reaction.Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
78693413
Reads aligned (%)
71.5
Duplicates removed (%)
26.7
Number of peaks
1628 (qval < 1E-05)

hg38

Number of total reads
78693413
Reads aligned (%)
74.0
Duplicates removed (%)
24.8
Number of peaks
2210 (qval < 1E-05)

Base call quality data from DBCLS SRA