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Sample GSM5502229 Query DataSets for GSM5502229
Status Public on Mar 01, 2022
Title Epi_YesFGF2_biological_rep1
Sample type RNA
 
Source name Organoids_YesFGF2
Organism Mus musculus
Characteristics age: E16
tissue: organoids
cell type: Epithelial
treatment: FGF2
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 9.101686728
AFFX-BioB-5_at 9.01531135
AFFX-BioB-M_at 9.478560284
AFFX-BioC-3_at 10.12325093
AFFX-BioC-5_at 10.30643564
AFFX-BioDn-3_at 11.75024943
AFFX-BioDn-5_at 11.32654761
AFFX-BkGr-GC03_st 1.920733066
AFFX-BkGr-GC04_st 1.753734089
AFFX-BkGr-GC05_st 1.787367476
AFFX-BkGr-GC06_st 1.800468284
AFFX-BkGr-GC07_st 1.828980029
AFFX-BkGr-GC08_st 1.886850419
AFFX-BkGr-GC09_st 1.964051197
AFFX-BkGr-GC10_st 2.107347384
AFFX-BkGr-GC11_st 2.303769242
AFFX-BkGr-GC12_st 2.656573451
AFFX-BkGr-GC13_st 3.176035221
AFFX-BkGr-GC14_st 3.928979377
AFFX-BkGr-GC15_st 4.606203973

Total number of rows: 29129

Table truncated, full table size 871 Kbytes.




Supplementary file Size Download File type/resource
GSM5502229_SL_04_F_Epi_1_10102019_Clariom_S_Mouse_.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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