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Sample GSM5502232 Query DataSets for GSM5502232
Status Public on Mar 01, 2022
Title Mes_NoFGF2_biological_rep1
Sample type RNA
 
Source name Organoids_NoFGF2
Organism Mus musculus
Characteristics age: E16
tissue: organoids
cell type: Stromal
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 Stromal 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
MTA-1_0.r3.pgf
MTA-1_0.r3.Psrs.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 GPL20775
Series (2)
GSE181424 Expression data from E16 mouse embryonic organoids - grown with epithelium and stroma in the presence or absence of FGF2 [Mes]
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-BkGr-GC03_st 1.242469511
AFFX-BkGr-GC04_st 1.380552539
AFFX-BkGr-GC05_st 1.377509329
AFFX-BkGr-GC06_st 1.390467539
AFFX-BkGr-GC07_st 1.404298758
AFFX-BkGr-GC08_st 1.484306392
AFFX-BkGr-GC09_st 1.525465199
AFFX-BkGr-GC10_st 1.669686404
AFFX-BkGr-GC11_st 1.849628058
AFFX-BkGr-GC12_st 2.117305501
AFFX-BkGr-GC13_st 2.593690087
AFFX-BkGr-GC14_st 3.328616869
AFFX-BkGr-GC15_st 4.014236474
AFFX-BkGr-GC16_st 4.845599655
AFFX-BkGr-GC17_st 5.426809901
AFFX-BkGr-GC18_st 5.967027664
AFFX-BkGr-GC19_st 6.43662515
AFFX-BkGr-GC20_st 6.806883234
AFFX-BkGr-GC21_st 7.118187859
AFFX-BkGr-GC22_st 7.662584529

Total number of rows: 72688

Table truncated, full table size 2143 Kbytes.




Supplementary file Size Download File type/resource
GSM5502232_ML_01_Exp131_Mes_noFGF2_Control_06042019_MTA-1_0_.CEL.gz 24.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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