Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SNAI2

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
CTR
cell line
CTR
chip antibody
Slug (C19G7) Rabbit mAb, CST 9585
enrichment target
SNAI2
mechanistic classifications of chip protein target
Transcription Factor
treatment
DMSO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[harvesting protocol] ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit). ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen). DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
49357743
Reads aligned (%)
69.8
Duplicates removed (%)
23.0
Number of peaks
1798 (qval < 1E-05)

hg38

Number of total reads
49357743
Reads aligned (%)
71.7
Duplicates removed (%)
21.5
Number of peaks
2098 (qval < 1E-05)

Base call quality data from DBCLS SRA