Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SNAI1

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa cell
cell line
HeLa
chip antibody
Snail

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 1 x 107 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against Snail, MTA1, or PRMT5. The DNA was purified with a Qiagen PCR purification kit Libraries were prepared according to Illumina's instructions. The NEBNext Ultra DNA Library Prep Kit for Illumina was used for DNA library construction. After adapter ligation DNA PCR was amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from the agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced following the manufacturer protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
18255261
Reads aligned (%)
76.4
Duplicates removed (%)
17.0
Number of peaks
196 (qval < 1E-05)

hg38

Number of total reads
18255261
Reads aligned (%)
77.6
Duplicates removed (%)
16.7
Number of peaks
445 (qval < 1E-05)

Base call quality data from DBCLS SRA