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Sample GSM4007375 Query DataSets for GSM4007375
Status Public on Nov 30, 2019
Title shARID1A-3
Sample type SRA
 
Source name A431 cells
Organism Homo sapiens
Characteristics cell line: A431
cell type: Human SCC cell
shRNA: shARID1A
Growth protocol Cells were cultured in DMEM medium supplemented with 10% FBS
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNA-seq libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) and validated using the 2100 Bioanalyzer (Agilent Technologies).
Libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, CA, USA).
After removing low-quality reads, clean reads were aligned to the human (hg37) genomes using HISAT2 (version 2.0.5).
Differential expression between ARID1A-depleted and control A431 cells was computed using the FPKM cultured by featureCounts (Version 1.5.0-p1).
Genome_build: hg37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Aug 05, 2019
Last update date Nov 30, 2019
Contact name Qingyu Luo
E-mail(s) 17710261112@163.com
Organization name Chinese Academy of Medical Sciences and Peking Union Medical College
Department State Key Laboratory of Molecular Oncology
Street address Panjiayuannanli No.17#, Chaoyang District
City Beijing
ZIP/Postal code 100021
Country China
 
Platform ID GPL24676
Series (1)
GSE131132 RNA-seq of A431 cells expressing control or ARID1A-targeting shRNAs
Relations
BioSample SAMN12496786
SRA SRX6656930

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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