Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq

Cell type

Cell type Class
Digestive tract
Cell type
SNU-283
NA
NA

Attributes by original data submitter

Sample

source_name
Colon cancer cell line
histopathology
carcinoma
cell line
SNU283

Sequenced DNA Library

library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
Each genomic DNAs are obtained from other groups and extracted using Quiagen genomic DNA extraction Kit (69504) Entire amplicons obtained from eight rounds of multiplex PCR were pooled together in equal volumes. For sequencing library construction, we performed a series of enzymatic reactions such as 5’-end phosphorylation, adaptor ligation, and two additional cycles of PCR to attach barcode and other modules, as described elsewhere (Min et al., 2016). Every intermittent purification was conducted using ExpinTM PCR (GeneAll). The sequencing libraries were pooled with equal amount and applied to a multiple parallel sequencing in the same flow cell using Illumina Hi-seq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
1781805
Reads aligned (%)
0.0
Coverage rate (×)
0.0
Number of hyper MRs
0 (qval < 1E-05)

hg19

Number of total reads
1781805
Reads aligned (%)
90.4
Coverage rate (×)
0.0
Number of hyper MRs
532 (qval < 1E-05)

Base call quality data from DBCLS SRA