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Sample GSM5502228 Query DataSets for GSM5502228
Status Public on Mar 01, 2022
Title Epi_NoFGF2_biological_rep3
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 8.901251027
AFFX-BioB-5_at 8.682555394
AFFX-BioB-M_at 9.255599719
AFFX-BioC-3_at 9.898502411
AFFX-BioC-5_at 10.04971073
AFFX-BioDn-3_at 11.55746844
AFFX-BioDn-5_at 11.08774781
AFFX-BkGr-GC03_st 1.822505957
AFFX-BkGr-GC04_st 1.780061481
AFFX-BkGr-GC05_st 1.821067156
AFFX-BkGr-GC06_st 1.818167234
AFFX-BkGr-GC07_st 1.873374015
AFFX-BkGr-GC08_st 1.914830527
AFFX-BkGr-GC09_st 1.979225537
AFFX-BkGr-GC10_st 2.175250025
AFFX-BkGr-GC11_st 2.256202466
AFFX-BkGr-GC12_st 2.554966268
AFFX-BkGr-GC13_st 3.065962072
AFFX-BkGr-GC14_st 3.756488051
AFFX-BkGr-GC15_st 4.432052977

Total number of rows: 29129

Table truncated, full table size 871 Kbytes.




Supplementary file Size Download File type/resource
GSM5502228_SL_03_Epi_3_10102019_Clariom_S_Mouse_.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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