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
Trametinib 100 nM

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
47528995
Reads aligned (%)
55.6
Duplicates removed (%)
36.9
Number of peaks
1278 (qval < 1E-05)

hg38

Number of total reads
47528995
Reads aligned (%)
56.9
Duplicates removed (%)
35.9
Number of peaks
1414 (qval < 1E-05)

Base call quality data from DBCLS SRA