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| Status |
Public on Mar 10, 2020 |
| Title |
DwoC_2318_30mM (SC.132) |
| Sample type |
RNA |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Lymphoblastoid cell line
|
| Treatment protocol |
All lymphoblastoid cell lines were maintained in conventional lymphocyte cell culture conditions of RPMI 1640 with 10% FBS in a 25-cm2 cell culture flask. The cells were incubated at 370C in 5% CO2 and the media was changed twice each week. Prior to the experiments (below), lymphoblastoid cells following serum starvation were passaged for a minimum of one week in either standard (SG) RPMI 1640 (11mM glucose) or high glucose (HG) RPMI media (30mM glucose)
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| Growth protocol |
Lymphoblastoid cell lines were thawed and cultured in RPMI and 10% FBS until they reached over 85% cell viability. Cells were seeded in a T25 flask. Two replicates were performed per cell line. Cells were counted every day or every other day for five to ten days and recorded.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Quality control from RNA extraction was performed using the Agilent bio-analyzer.
|
| Label |
biotin
|
| Label protocol |
Samples were processed using the Illumina™ TotalPrep™-96 RNA Amplification Kit (ThermoFisher 4393543)
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| |
|
| Hybridization protocol |
Hybridizationwas done to Illumina HT12v4 microarrays (Catalog number: 4393543)
|
| Scan protocol |
Scanned on an Illumina HiScan scanner
|
| Description |
SC.132
|
| Data processing |
Analysis of the gene expression data was performed as follows. For a given individual Si (i= 1,…,22) and gene Gk (k= 1,...,15591), we calculated ∆i,k= HGi,k - SGi,k, where ∆ is response to glucose RG, HG is gene expression in high glucose culture, and SG is gene expression in standard glucose culture. All replicate data was fit using a mixed model that accounted for the correlation between repeated measures within individuals. We built a design matrix using the model.matrix function, and accounted for correlation between biological triplicates using limma’s duplicatecorrelation function. A mixed linear model was then fit that incorporates this correlation and ∆i,k (where ∆ is response to glucose, RG = HGi,k - SGi,k) using the lmFit function. The analysis was performed using the R package limma
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| |
|
| Submission date |
Mar 09, 2020 |
| Last update date |
Mar 10, 2020 |
| Contact name |
Michael Grassi |
| Organization name |
University of Illinois at Chicago
|
| Department |
Department of Ophthalmology and Visual Sciences
|
| Lab |
Retina Chemical Genomics Lab
|
| Street address |
1855 West Taylor Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612-7244 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE146615 |
Mendelian randomization identifies FLCN expression as a mediator of diabetic retinopathy |
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