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Sample GSM2041750 Query DataSets for GSM2041750
Status Public on Mar 03, 2016
Title PDPN- TMC, biological rep2
Sample type RNA
 
Source name PDPN- mesenchymal cells thymus
Organism Mus musculus
Characteristics strain: C57BL/6
age: 2 weeks
tissue: thymus
Treatment protocol Cell suspensions of thymus and lymph nodes were prepared with liberase TM (0.32 Wunsch U mL-1, Roche Diagnostics) and DNase I (50 Kunitz U mL-1, Sigma-Aldrich).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy Micro Kit (QIAGEN, Germantown, MD) according to manufacturer's instructions
Label biotin
Label protocol Isolated total RNA was reverse transcribed, amplified, fragmented and biotin-labelled using Ovation Pico WTA System V2 and Encore Biotin Module (NuGEN) according to manufacturer's protocol and hybridized to the Affymetrix Mouse Gene 1.1 ST Array at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany).
 
Hybridization protocol Affymetrix microarray hybridization was carried out at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany)
Scan protocol Microarray scanns were taken with GeneChip Scanner 3000 at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany)
Description Gene expression data from the PDGFRb+podoplanin(PDPN)-Ly51+ subset of thymic mesenchymal cells
Data processing Raw data was background corrected, normalized and summarized into probe sets using the RMA algorithm in the Affymetrix Expression Console software. Probe sets without annotation were removed from the dataset and only one copy was retained of multiple probe sets that represented the same gene and exhibited identical expression values on all arrays.
 
Submission date Jan 19, 2016
Last update date Mar 03, 2016
Contact name William Winston Agace
Organization name Technical University of Denmark
Department National Veterinary Institute, Section for Immunology and Vaccinology
Street address B├╝lowsvej 27
City Fredriksberg C
ZIP/Postal code 1870
Country Denmark
 
Platform ID GPL11533
Series (1)
GSE76974 Expression data from thymic and lymph node mesenchymal stromal subsets.

Data table header descriptions
ID_REF
VALUE log 2 GC-RMA signal

Data table
ID_REF VALUE
10496946 6.76
10378154 6.37
10537770 8.01
10514985 5.87
10514971 2.05
10540012 5.92
10600819 6.36
10605788 6.06
10363905 5.5
10594426 2.94
10585129 5.16
10368616 5.38
10386844 5.3
10412038 5.97
10507379 2.78
10580139 5.02
10478587 3.52
10484361 2.35
10478590 4.48
10549827 2.05

Total number of rows: 24758

Table truncated, full table size 335 Kbytes.




Supplementary file Size Download File type/resource
GSM2041750_A750_05_gp38neg_TH2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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