|
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)
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|
|
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
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|
|
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 |