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Sample GSM1963494 Query DataSets for GSM1963494
Status Public on Jan 24, 2017
Title corneal_endothelium_FECD_A61
Sample type RNA
 
Source name corneal endothelium FECD
Organism Homo sapiens
Characteristics gender: Female
age: 77
tissue: corneal endothelium with Descemet's membrane
group: Fuchs' endothelial corneal dystrophy
inheritance: not known
type of surgery: Descemet's stripping automated endothelial keratoplasty
phakic or pseudophakic: pseudophakic
time between cataract surgery and keratoplasty (in months): 44
Cause of death: n/a
number of cells per mm²: unknown
Extracted molecule total RNA
Extraction protocol The samples were collected in RNAlater. Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen, Hilden, Germany), without DNase treatment.
Label SYBR Green
Label protocol PCR assays were performed using two complementary Custom RT² Profiler PCR Arrays (CAPH10409 and CAPH104010, Qiagen) following the manufacturer's instructions. Reverse transcription was performed from 100 ng of total RNA per sample for each 96-well plate, using the RT² First Strand Kit (Qiagen). Quantitative real-time PCR was performed (7900 HT Fast Real-Time PCR System; Applied Biosystems, Carlsbad, California) with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds, using RT² SYBR Green ROX qPCR Mastermix (Qiagen).
 
Hybridization protocol n/a
Scan protocol n/a
Description FECD
total RNA (> 200 nucleotides)
Data processing Data analysis was done through the web portal of Qiagen, according to the manufacturers instructions: http://qiagen.com/geneglobe. The web-based software automatically performed all ΔΔCt based fold-change calculations from the uploaded raw threshold cycle data. For normalization it used the average arithmetic mean of Ct values from three reference genes: RPL13A, RPL19 and RPS5. To calculate p-values it used a two-sided t-statistic. Sample table reports normalized signal (against housekeeping genes). Fold Change file reports FECD/Control ratios.
 
Submission date Dec 03, 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 GPL21205
Series (2)
GSE75675 Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy [RT-qPCR array CAPH10410]
GSE75676 Identification of Circulating Fibrocytes and Dendritic Derivatives in Corneal Endothelium of Patients with Fuchs' Dystrophy

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
A01 11.630148
A02 4.261484
A03 11.630148
A04 7.252735
A05 8.147598
A06 5.985758
A07 7.965372
A08 7.606028
A09 9.789298
A10 5.913599
A11 4.297628
A12 11.630148
B01 5.984793
B02 5.365532
B03 9.800486
B04 8.228529
B05 10.886318
B06 11.630148
B07 11.071488
B08 11.630148

Total number of rows: 96

Table truncated, full table size 1 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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