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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
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
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
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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