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Sample GSM3985179 Query DataSets for GSM3985179
Status Public on Jun 05, 2020
Title HGC-27 siNC_1
Sample type SRA
 
Source name HGC-27 cells
Organism Homo sapiens
Characteristics tissue: gastric cancer cell line
differentiated level: undifferented
cell line: HGC-27
Treatment protocol Cells were treat with siSTRN3 mixture or negative control siRNA using RNAIMAX (Thermo) reagent for 72 hours
Growth protocol Cells were incubated with RPMI 1640 medium with 10% FBS in CO2 incubators at 37℃.
Extracted molecule total RNA
Extraction protocol Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
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 Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCh38.p10 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: xls file includes RPKM values for each Sample.
 
Submission date Jul 30, 2019
Last update date Jun 05, 2020
Contact name yang tang
E-mail(s) tangyang2013@sibcb.ac.cn
Organization name Shanghai Institute of Biochemistry and Cell Biology
Street address Yueyang Road 320
City shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL24676
Series (1)
GSE135085 Whole transcriptomes analyses of gastric cancer HGC-27 cell line treated with siSTRN3 mixture or negative control siRNA
Relations
SRA SRX6614703
BioSample SAMN12414605

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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