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Sample GSM5345075 Query DataSets for GSM5345075
Status Public on Sep 27, 2021
Title A431-GOF-input1
Sample type SRA
 
Source name Skin squamous cell carcinoma
Organism Homo sapiens
Characteristics cell line: A431
cell type: Skin squamous cell carcinoma
treatment: None
Treatment protocol NR2F2 GoF induced cells were exposed to 1µg/mL Doxycycline for 48h.
Growth protocol Cells were grown in EMEM culture medium, with 10% FBS tetracycline-free.
Extracted molecule genomic DNA
Extraction protocol Chromatin was double fixed using DSG and Formaldehyde. Chromatin Shearing was performed using the ChIP-IT Express kit (Active Motif) according to the manufacturer's recommendations. Chromatin Immunoprecipitation was performed using Dynabeads Protein G (Invitrogen). Purification was performed using the iPure kit v2 (Diagenode).
NEB Next Ultra II DNA library Prep Kit for Illumina (Biolabs)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Adaptors sequences were removed with TrimmomaticPE using options “HEADCROP:10 CROP:65 ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50”
Reads were mapped against the human reference genome (hg38) using Bowtie2 using options “-X 2000 -q -p 6 -t --fr --very-sensitive --no-discordant --no-unal --no-mixed”.
Mitochondrial reads, reads from unmapped and random contigs, reads without unique alignment, reads with a mapping quality less than 20 and reads which are not properly mapped were removed using samtools
Duplicate reads were removed by Picard MarkDuplicates.
Peak calling was performed by macs2 (version 2.2.5) using options “-f BAMPE -g hs -p 0.01 --nomodel”.
Blacklisted regions are filtered out by bedtools (version 2.27.1).
Genome_build: hg38
Supplementary_files_format_and_content: .bed / Coordinate of called peaks
 
Submission date May 28, 2021
Last update date Sep 27, 2021
Contact name Yura Song
E-mail(s) yura.song@ulb.be
Organization name Université Libre de Bruxelles
Lab Laboratory of Stem Cells and Cancer
Street address 808, route de Lennik
City Bruxelles
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL24676
Series (2)
GSE164605 NR2F2 controls malignant squamous cell carcinoma state by promoting stemness and invasion and repressing differentiation
GSE175724 NR2F2 controls malignant squamous cell carcinoma state by promoting stemness and invasion and repressing differentiation IV
Relations
BioSample SAMN19402000
SRA SRX11014500

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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