Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
Primary neonatal human foreskin fibroblasts (HFF)
cell type
neonatal human foreskin fibroblasts (primary culture cells)
treatment
transduced with MycER and control shRNA, treated with 4-hydroxytamoxifen (4-OHT)
chip antibody
anti-MYC N262 (Santa Cruz Biotechnology, catalog number sc-764)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPed DNA was extracted by phenol-chloroform and isopropanol precipitation. DNA samples were provided by the user. Input samples correspond to balanced blends of inputs from selected samples. 20ng of DNA, as quantitated by fluorometry, was resolved by electrophoresis and fractions of 50-250bp were extracted. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
20609251
Reads aligned (%)
65.9
Duplicates removed (%)
29.8
Number of peaks
686 (qval < 1E-05)

hg38

Number of total reads
20609251
Reads aligned (%)
67.4
Duplicates removed (%)
28.6
Number of peaks
654 (qval < 1E-05)

Base call quality data from DBCLS SRA