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Sample GSM2792924 Query DataSets for GSM2792924
Status Public on Sep 22, 2020
Title siGFP_rep2
Sample type SRA
 
Source name SK-Hep1
Organism Homo sapiens
Characteristics cell lines: SK-Hep1
treament: siGFP
Treatment protocol NA
Growth protocol NA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy kit (Qiagen, GE) as recommended by the manufacturer. Polyadenylated RNA was isolated from total RNA using standard protocols (Dynabeads mRNA Direct Micro Kit, Ambion/Life Technologies, USA) starting with 5 μg total RNA.
Library preparation for NGS using Ion Torrent technology (Life Technologies, USA) was carried out according to the manufacturers recommendations (Ion Total RNA-Seq Kit v2, Ion torrent/Life Technologies, USA), and sequenced using an Ion Proton system (Life Technologies, USA). Quality control, quantification of RNA and libraries was carried out using using Agilent RNA 6000 Nano Kit or Agilent High Sensitivity DNA kit and Agilent Bioanalyzer (Agilent Technologies, USA). In brief, approximately 50 ng polyA RNA was fragmented down to 100-300 base fragments using RNaseIII for 1-3 min followed by adapter ligation, amplification for 9-14 cycles and barcoding using Ion Express RNA-Seq Barcode kit (Ion Torrent/Life Technologies, USA). The final library fragment size and concentration was determined by Agilent Bioanalyzer analysis followed by template preparation using Ion PI Template OT2 200 Kit v3 (Life Technologies, USA) and Ion One Touch System followed by NGS on an Ion Proton system using Ion PI™ Chip Kit v2. In general two transcriptome libraries were barcoded and analyzed on one Ion PI v2 chip.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description si GFP control replicate 2
Data processing Ion Proton software was used for basecalling
Sequencing reads were mapped to hg19 and bioinformatics analysis was conducted using TAMP and life default RNA-Seq analysis plugin of Life technology for expression analyses
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Sep 25, 2017
Last update date Sep 22, 2020
Contact name zhiwei Guo
E-mail(s) gzw188@126.com
Organization name Southern medical university
Street address NO.1838 Guangzhou Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510515
Country China
 
Platform ID GPL17303
Series (1)
GSE104226 Translated Long Non-Coding Ribonucleic Acid ZFAS1 Promotes Cancer Cell Migration by Elevating Reactive Oxygen Species Production in Hepatocellular Carcinoma
Relations
BioSample SAMN07693685
SRA SRX3214400

Supplementary file Size Download File type/resource
GSM2792924_siGFP_rep2.txt.gz 242.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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