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Sample GSM7622416 Query DataSets for GSM7622416
Status Public on May 01, 2024
Title 5 OL-2
Sample type RNA
Source name cell treated with 5 µM of OL
Organism Mus musculus
Characteristics cell type: murine melanoma cells
cell line: B16F10
Treatment protocol After the 24 hour seeding in 6-well plates, cells were treated with 0 (Control), 200nM α-MSH (Positive control), and 5µM of OL, and OC for 24 hours
Growth protocol B16F10 cells were purchaced from RIKEN and were maintained in RPMI1640
Extracted molecule total RNA
Extraction protocol For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added to each sample well and then the total RNA sample in 70% ethanol was stored at -20℃ until use.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA
Hybridization protocol Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Clariom_S_Mouse Array. GeneChips were washed and stained in the GeneAtlas® Fluidics Station
Scan protocol GeneChips were scanned using the GeneAtlas Imaging Station
Description Gene expression data from 5 µM of OL treated for 24 hours
Data processing The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm ( Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Genes with a linear fold change >1.5 and p-value < 0.05(one-way between-subjects ANOVA) were considered as differentially expressed genes(DEGs). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software.
algorithm: RMA
Submission date Jul 17, 2023
Last update date May 01, 2024
Contact name Meriem Bejaoui
Organization name University of Tsukuba
Street address 1 Chome-1-1 Tennodai
City Tsukuba,
State/province Ibaraki
ZIP/Postal code 305-8577
Country Japan
Platform ID GPL23038
Series (1)
GSE237508 Expression data from OL and OC treated B16F10 cells

Data table header descriptions
VALUE Quantification

Data table
AFFX-BkGr-GC03_st 6.56673 0.792699
AFFX-BkGr-GC04_st 6.60501 0.982245
AFFX-BkGr-GC05_st 6.77893 0.995243
AFFX-BkGr-GC06_st 6.03713 0.998589
AFFX-BkGr-GC07_st 4.88167 0.996455
AFFX-BkGr-GC08_st 4.03517 0.992846
AFFX-BkGr-GC09_st 3.63206 0.984918
AFFX-BkGr-GC10_st 3.46186 0.965565
AFFX-BkGr-GC11_st 3.15021 0.931563
AFFX-BkGr-GC12_st 3.05872 0.865608
AFFX-BkGr-GC13_st 2.7627 0.916796
AFFX-BkGr-GC14_st 2.70199 0.89384
AFFX-BkGr-GC15_st 2.64872 0.89698
AFFX-BkGr-GC16_st 2.7764 0.855398
AFFX-BkGr-GC17_st 2.90345 0.826524
AFFX-BkGr-GC18_st 3.31582 0.748997
AFFX-BkGr-GC19_st 5.93797 0.621129
AFFX-BkGr-GC20_st 6.08049 0.608584
AFFX-BkGr-GC21_st 6.1412 0.605397
AFFX-BkGr-GC22_st 6.27624 0.602675

Total number of rows: 28846

Table truncated, full table size 1056 Kbytes.

Supplementary file Size Download File type/resource
GSM7622416_5_OL-2.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM7622416_5_OL-2.CHP.gz 320.7 Kb (ftp)(http) CHP
Processed data included within Sample table

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