|
| Status |
Public on Jan 24, 2017 |
| Title |
corneal_endothelium_control_A28 |
| Sample type |
RNA |
| |
|
| Source name |
corneal endothelium control
|
| Organism |
Homo sapiens |
| Characteristics |
rna integrity number: 7.90
gender: male
age: 54 years
tissue: corneal endothelium with Descemet's membrane
group: donor cornea as normal control
number of cells per mm²: 2500
Cause of death: cerebrovascular accident
|
| Biomaterial provider |
University Hospitals Leuven (Belgium), Department of Ophthalmology
|
| Treatment protocol |
The sample was collected in RNAlater.
|
| Growth protocol |
The donor cornea was provided in storage medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen), without DNase treatment.
|
| Label |
biotin
|
| Label protocol |
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
|
| Scan protocol |
To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
|
| Description |
corneal endothelium control
|
| Data processing |
Data were processed with RMA (as implemented in the XPS package of Bioconductor). Reported values are on log2-scale.
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
Jan 24, 2017 |
| Contact name |
Joost J van den Oord |
| E-mail(s) |
joost.vandenoord@med.kuleuven.be
|
| Phone |
+32 16 33 65 91
|
| Organization name |
KU Leuven
|
| Department |
Department of Imaging & Pathology
|
| Lab |
Translational Cell & Tissue Research
|
| Street address |
Minderbroedersstraat 12, block q, box 1032
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE74123 |
Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy [microarray expression analysis] |
| GSE75676 |
Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy |
|
