Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZFX

Cell type

Cell type Class
Prostate
Cell type
C4-2
Tissue
Prostate
Cell Type
Epithelial
Disease
Prostate Cancer

Attributes by original data submitter

Sample

source_name
Human prostate cancer cell line C42B
tissue
Human prostate cancer cell line C42B
cell line
C42B
chip antibody
ZFX
sirna
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol. For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts. RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA). ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX). NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
60538795
Reads aligned (%)
183.4
Duplicates removed (%)
6.4
Number of peaks
16095 (qval < 1E-05)

hg38

Number of total reads
60538795
Reads aligned (%)
184.0
Duplicates removed (%)
6.4
Number of peaks
15794 (qval < 1E-05)

Base call quality data from DBCLS SRA