Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Blood
Cell type
RAMOS
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

source_name
ChIP-seq HA-WT-3E7-MYC
cell line
Ramos
cell type
Burkitt's lymphoma cell line
genotype/variation
Myc WT-HA
treatment
20 nM 4-OHT for 24 hours
chip antibody
HA (C29F4 from Cell Signaling)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was clarified from sonicated cells and protein-DNA complexes were isolated with antibody. ChIP libraries were prepared according to New England Biolabs instructions accompanying the NEBNext Ultar II DNA Library Prep Kit for Illumina (Part# E7645S). After adapter ligation DNA was PCR amplified with NEBNext Multiplex Oligos for Illumina (Part# E7335S and E7500S) for 16 cycles (HA ChIP) or 15 cycles (WDR5 ChIP). For RNA-seq, libraries were prepared using Poly-A selected 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.RNA libraries were prepared using Poly-A selected RNA.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
56793135
Reads aligned (%)
85.0
Duplicates removed (%)
6.1
Number of peaks
7856 (qval < 1E-05)

hg38

Number of total reads
56793135
Reads aligned (%)
86.6
Duplicates removed (%)
4.9
Number of peaks
8027 (qval < 1E-05)

Base call quality data from DBCLS SRA