|
| Status |
Public on Mar 03, 2016 |
| Title |
BP3+PDPN+ LNMC, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BP3+PDPN+ mesenchymal cells lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 2 weeks
tissue: pooled inguinal, axillary, brachial lymph nodes
|
| 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 PDGFRβ+podoplanin(PDPN)+BP3+ subset of lymph node 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 |
Bülowsvej 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. |
|
