GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3484585 Query DataSets for GSM3484585
Status Public on Nov 21, 2018
Title C7_24h
Sample type SRA
Source name AGS-BX1 cells
Organism Homo sapiens
Characteristics cell type: EBV-positive gastric carcinoma cells
Treatment protocol C7 10mM
Growth protocol F-12, 10% FBS
Extracted molecule total RNA
Extraction protocol RNeasy® Plus Mini Kit (Qiagen)
Indexed sequencing library construction was carried out using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). The libraries were denatured and diluted to optimal concentration before applying to cluster generation in the flow cell. Cluster generation was carried out using the HiSeq PE Cluster Kit v3 cBot (Illumina). Pair-end sequencing of 101 bp was carried out in the Illumina HiSeq 1500 in CGS, HKU with the Illumina HiSeq SBS Kit v3.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Reads from sequencing were assigned to samples using CASAVA, and adapter sequences, reads with more than 5 % unknown bases and reads with more than 50 % bases of quality score lower than or equal 10 were filtered.
Sequence alignment, expression quantification and differential expression analysis were performed with the CLC Genomics Workbench Version 7.0.4 (CLC bio).
Reads after filtering were aligned to the human genome (hg19) first with default parameters except for similarity fraction (set to 0.9), length fraction (set to 0.8) and strand specific (set to reverse).
The unmapped read were then aligned to the EBV genome (NC_007605).
Expression quantification was performed separately for human and EBV genes and differential expression analysis was performed with Kal’s test with Bonferroni correction.
Genome_build: hg19 and NC_007605.1
Supplementary_files_format_and_content: CLC files of differential expression analysis were generated using CLC Genomics Workbench Version 7.0.4 (CLC bio).
Submission date Nov 20, 2018
Last update date Nov 21, 2018
Contact name Kwai Fung Hui
Phone 39179361
Organization name HKU
Department Paediatrics and Adolescent Medicine
Lab Alan KS Chiang
Street address L7-01, Laboratory Block, FMB, 21 Sassoon Road, Pokfulam
City Hong Kong
State/province Hong Kong
ZIP/Postal code NA
Country Hong Kong
Platform ID GPL18460
Series (1)
GSE122751 RNA sequencing data in AGS-BX1 cells treated with C7
BioSample SAMN10453390
SRA SRX5029604

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap