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Series GSE106338 Query DataSets for GSE106338
Status Public on Nov 01, 2018
Title Gene expression profiling study by RNA-seq in PDX model based diffuse type gastric cancers.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out RNA-seq based transcriptome profiling using 15 stomach samples including three PDX lines (HGC-3, HGC-8, and HGC-20) and normal-looking surrounding tissues. Via comparative analysis between cells and tissues, we identified significant gene set associated with each cell and observed that genes involved in AKT signalling pathway were commonly associated with all PDX lines.
 
Overall design RNA-seq data of 15 gastric samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using Hiseq-2500 (Illumina).
 
Contributor(s) Kim J, Kim S, Bae D, Kim Y, Fukamachi H
Citation(s) 30866995, 31773340
Submission date Oct 30, 2017
Last update date Mar 18, 2020
Contact name Seon-Kyu Kim
E-mail(s) seonkyu@kribb.re.kr
Phone +82-42-879-8107
Organization name Korea Research Institutue of Bioscience & Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
City Daejeon
ZIP/Postal code 305-806
Country South Korea
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (15)
GSM2836244 surrounding normal 04002179N
GSM2836245 surrounding normal 04351995N
GSM2836246 surrounding normal 04500663N
Relations
BioProject PRJNA416330
SRA SRP122939

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE106338_RAW.tar 2.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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