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Sample GSM2228891 Query DataSets for GSM2228891
Status Public on Dec 07, 2016
Title AGS Non-Targeting Control RNA treated biological replicate 1
Sample type RNA
Source name AGS cell line (Gastric adenocarcinoma)_control RNA
Organism Homo sapiens
Characteristics cell line: AGS
tissue: Stomach
cell type: gastric cancer
Treatment protocol In AGS cells, anti-miR miR-25-3p inhibitor or non targeting control RNA was transfected with oligofectamine transfection reagent (invitrogen). AGS cells were transfected with miRNA inhibitor at 70 % confluency. 24 hrs after transfection, cells were transfected again with miRNA inhibitor or non targeting control RNA . After 48 hrs of first transfection, cells were harvested and total RNA was isolated.
Growth protocol AGS cells were grown in DMEM (F12/HAM) media with 10% FBS and 2mM Glutamine. The cells were incubated at 37ºC with 5%CO2 and 95% humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the instructions provided by the manufacturer.
Label Biotin
Label protocol Biotin was labelled to the single stranded cDNA fragments prepared from 500 ng of total RNA. The steps were followed as per the instructions in the user manuals of Ambion® WT Expression Kit, GeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix).
Hybridization protocol The biotin labelled single stranded cDNA was hybridized with the probes on Human Gene 1.0 ST Array for 16 hrs at 45ºC using GeneChip Hybridization Oven 640. GeneChips were stained with Phycoerythrin and washed using GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned using GeneChip® Scanner 3000 7G system.
Description mRNA profile of AGS cells treated with non targeting control RNA
Data processing The CEL files were subjected to RMA normalization at exon level using Expression Console (EC) software of Affymetrix. The CHP files were analysed for differential gene expression in Transcriptome Analysis Console (TAC) software of Affymetrix.
Submission date Jul 08, 2016
Last update date Dec 07, 2016
Contact name Kumaresan Ganesan
Organization name Madurai Kamaraj University
Department Genetics
Street address School of Biological Sciences,
City Madurai
State/province Tamil Nadu
ZIP/Postal code 625021
Country India
Platform ID GPL10739
Series (1)
GSE84196 mRNA profiling in gastric cancer cell line AGS upon miR-25-3p silencing

Data table header descriptions
VALUE RMA normalized log2 Signal intensity

Data table
7892501 4.28
7892502 3.32
7892503 2.77
7892504 7.65
7892505 2.73
7892506 3.8
7892507 4.54
7892508 3.41
7892509 12.03
7892510 2.42
7892511 2.42
7892512 6.73
7892513 2
7892514 9.62
7892515 8.7
7892516 3.02
7892517 2.68
7892518 2.68
7892519 5.16
7892520 8.4

Total number of rows: 257430

Table truncated, full table size 3254 Kbytes.

Supplementary file Size Download File type/resource
GSM2228891_AGS-NTC_1.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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