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Sample GSM5502227 Query DataSets for GSM5502227
Status Public on Mar 01, 2022
Title Epi_NoFGF2_biological_rep2
Sample type RNA
 
Source name Organoids_NoFGF2
Organism Mus musculus
Characteristics age: E16
tissue: organoids
cell type: Epithelial
treatment: control
Treatment protocol Grown with or without FGF2 containing media
Growth protocol Organoids were cultured for 7 days with a 4 day media change
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini-Kit (Qiagen), then cDNA synthesis and amplification (Clariom D Kit)
Label biotin
Label protocol Samples were enzymatically fragmented and biotinylated by terminal deoxynucleotidyl transferase (TdT) (Clariom D Kit)
 
Hybridization protocol Samples were hybridized to the Affymetrix Clariom D Assay, Mouse for 16-18 h at 45°C.
Scan protocol Microarrays were scanned using GeneChip® Scanner 3000
Description Epithelial portion of organoids grown for 7 days
Data processing Data were processed using Transcriptome Analysis Console software and R/Rstuio. The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method. Values are presented according to log2 RMA signal intensity. We defined the genes with a fold-change of more than 1.99 or less than 1.99 and a p-value of less than 0.05 as different expression genes
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps
 
Submission date Aug 03, 2021
Last update date Mar 01, 2022
Contact name Nicholas Moskwa
E-mail(s) nmoskwa@albany.edu
Organization name University at Albany
Street address 1400 Washington Avenue
City Albany
State/province New York
ZIP/Postal code 12222
Country USA
 
Platform ID GPL23038
Series (2)
GSE181423 Expression data from E16 mouse embryonic organoids - grown with epithelium and stroma in the presence or absence of FGF2 [Epi]
GSE181430 Single-cell sequencing reveals PDFGRα+ stromal cell subpopulations that promote proacinar differentiation in embryonic salivary gland organoids

Data table header descriptions
ID_REF
VALUE RMA signal estimates from Transcriptome Analysis Console software and R/Rstudio.

Data table
ID_REF VALUE
AFFX-BioB-3_at 9.235526991
AFFX-BioB-5_at 9.026734327
AFFX-BioB-M_at 9.544625267
AFFX-BioC-3_at 10.17232431
AFFX-BioC-5_at 10.33332181
AFFX-BioDn-3_at 11.71879723
AFFX-BioDn-5_at 11.35754827
AFFX-BkGr-GC03_st 1.942244037
AFFX-BkGr-GC04_st 1.868851667
AFFX-BkGr-GC05_st 1.904163143
AFFX-BkGr-GC06_st 1.89614411
AFFX-BkGr-GC07_st 1.940828221
AFFX-BkGr-GC08_st 1.978494379
AFFX-BkGr-GC09_st 2.023045632
AFFX-BkGr-GC10_st 2.228365681
AFFX-BkGr-GC11_st 2.384522774
AFFX-BkGr-GC12_st 2.648140563
AFFX-BkGr-GC13_st 3.247035694
AFFX-BkGr-GC14_st 4.010113686
AFFX-BkGr-GC15_st 4.674679061

Total number of rows: 29129

Table truncated, full table size 871 Kbytes.




Supplementary file Size Download File type/resource
GSM5502227_SL_02_Epi_2_10102019_Clariom_S_Mouse_.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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