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Sample GSM7622414 Query DataSets for GSM7622414
Status Public on May 01, 2024
Title alpha-MSH 2
Sample type RNA
 
Source name cell treated with 200nM of α-MSH
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 α-MSH 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 (http://www.affymetrix.com). 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
E-mail(s) mariembejaoui.mb@gmail.com
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
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
AFFX-BkGr-GC03_st 6.78137 0.78515
AFFX-BkGr-GC04_st 6.63913 0.994174
AFFX-BkGr-GC05_st 6.76026 0.998969
AFFX-BkGr-GC06_st 6.51292 0.9995
AFFX-BkGr-GC07_st 5.27364 0.998098
AFFX-BkGr-GC08_st 4.45052 0.994717
AFFX-BkGr-GC09_st 3.81238 0.992303
AFFX-BkGr-GC10_st 3.65427 0.976607
AFFX-BkGr-GC11_st 3.34415 0.952447
AFFX-BkGr-GC12_st 3.27863 0.889568
AFFX-BkGr-GC13_st 2.98487 0.928884
AFFX-BkGr-GC14_st 2.91453 0.90927
AFFX-BkGr-GC15_st 2.80802 0.902734
AFFX-BkGr-GC16_st 2.98005 0.855819
AFFX-BkGr-GC17_st 3.10671 0.819657
AFFX-BkGr-GC18_st 3.53189 0.74266
AFFX-BkGr-GC19_st 5.909 0.638931
AFFX-BkGr-GC20_st 6.04636 0.628657
AFFX-BkGr-GC21_st 6.04178 0.622845
AFFX-BkGr-GC22_st 6.2399 0.617907

Total number of rows: 28846

Table truncated, full table size 1045 Kbytes.




Supplementary file Size Download File type/resource
GSM7622414_alpha-MSH_2.CEL.gz 1.0 Mb (ftp)(http) CEL
GSM7622414_alpha-MSH_2.CHP.gz 320.2 Kb (ftp)(http) CHP
Processed data included within Sample table

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