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| Status |
Public on Sep 22, 2020 |
| Title |
PCDH_mRNA_rep1 |
| Sample type |
SRA |
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| Source name |
SK-Hep1
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| Organism |
Homo sapiens |
| Characteristics |
cell lines: SK-Hep1
treament: PCDH
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
PCDH control replicate 1
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| 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
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| Submission date |
Sep 25, 2017 |
| Last update date |
Sep 22, 2020 |
| Contact name |
zhiwei Guo |
| E-mail(s) |
gzw188@126.com
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| Organization name |
Southern medical university
|
| Street address |
NO.1838 Guangzhou Road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510515 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN07693680 |
| SRA |
SRX3214395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2792919_PCDH_rep1.txt.gz |
242.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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