|
| Status |
Public on Sep 01, 2018 |
| Title |
Normal Differentiated Mesodermal Cells (NDMCs) type 2, biological rep1 [exon] |
| Sample type |
RNA |
| |
|
| Source name |
Normal Differentiated Mesodermal Cells type 2 (NDMC2) , biological rep1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NDMC2
ID: 13
gender: Female
|
| Treatment protocol |
For each gram of minced tissue, 2 mL of HEPES buffer containing 1.25 mg/ mL of Collagenase I (Sigma Aldrich, CAT#C6885-1G) was added. This was incubated for 30 – 45 min at 37ºC before being diluted 1:9 with additional HEPES buffer. The mixture was passed through a 250 micron mesh before being centrifuged at 300 rcf for 6 minutes at room temperature. The top layer was removed and the NDMCs collected for snap-freezing in liquid nitrogen.
|
| Growth protocol |
Tissue was collected from the site of surgical incision and a sample snap frozen in liquid nitrogen. Samples of each tissue were weighed and minced with surgical scissors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from NDMC samples following the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat#74804). The protocol was followed exactly except that homogenisation used the probe tissue ruptor for NDMCs, and on-column DNase digestion was carried out. RNA quality and quantity were determined on the Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the Ramachiotti Center for Gene Function Analysis, UNSW, Australia.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the standard Affymetrix protocol at the Ramachiotti Center for Gene Function Analysis, UNSW, Australia.
|
| Scan protocol |
Human Transciptome arrays were scanned using a GC3000 scanner at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Kensington, NSW, Australia), according to the manufacturers instructions.
|
| Description |
Global gene expression measured in NDMC2.
|
| Data processing |
The data were RMA normalized Using Expression Console (from Affymetrix and the library files on the Affymetrix website). rma-alt-splice.summary.txt.
|
| |
|
| Submission date |
Jun 05, 2015 |
| Last update date |
Sep 01, 2018 |
| Contact name |
Timothy John Peters |
| E-mail(s) |
t.peters@garvan.org.au
|
| Phone |
+61292958325
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Immunology
|
| Lab |
Immunogenomics
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17585 |
| Series (1) |
| GSE69598 |
Transcriptome profiling of purified normal differentiated mesodermal cells (NDMCs) using Affymetrix Human Transcriptome Array 2.0 |
|
| Relations |
| Reanalyzed by |
GSM1704482 |
