|
| Status |
Public on Dec 12, 2022 |
| Title |
Brain_EOAD_BK709 |
| Sample type |
RNA |
| |
|
| Source name |
Frozen prefrontal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
sample group: EOAD
tissue/cell type: Frozen prefrontal cortex
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
Human frozen prefrontal cortex from the Neurological Tissue Bank of IDIBAPS-Hospital Clínic of Barcelona. Lymphoblastoid cell lines immortalized with Epstein Barr virus, cultivated in suspension and maintained with RPMI-1640 GlutaMAX medium supplemented with 10% inactivated FBS and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from frozen tissue was performed using RNeasy Lipid Tissue Mini Kit (Qiagen) using 20 mg of cortex samples. RNA extraction from LCLs was performed using Allprep DNA/RNA/Protein Mini Kit (Qiagen) following the manufacturer’s protocol.
|
| Label |
Biotin
|
| Label protocol |
In this procedure, the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labling Reagent that is covalently linked to biotin. 5.5 ug of single-stranded cDNA is required for fragmentation and labeling.
|
| |
|
| Hybridization protocol |
Fragmentation, labelling and hybridization were performed according to the instructions described in the GeneChip WT Pico Reagent Kit Manual (from ThermoFisher Scientific). Instruments employed were a hybridization oven model 645 (Thermo Fisher) and a Fluidics Station 450 module. Arrays were washed before scanning using the FS450_0001 protocol, as stated in the aforementioned protocol.
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 System according to the instructions detailed in the GeneChip Command Console User Guide.
|
| Description |
AD.MF.B2
|
| Data processing |
The data were processed and analyzed separately for each tissue. Raw expression values were obtained directly from .CEL files and were processed using the Robust Multiarray Average (RMA) algorithm to get normalized expression values (log2 scale) summarized at the gene level. Different quality checks were performed before and after normalization to ensure that samples were suitable for differential expression analysis. Samples AD.MF.L3 and FTD.M2.B1 were identified as putative outliers during quality control and were therefore excluded from the analysis prior to normalization. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis. Statistical language R (version 3.6.0) and Bioconductor associated packages were used to process and analyze the data.
probe group file: Clariom_D_Human.r1.pgf
meta-probeset file: Clariom_D_Human.r1.mps
|
| |
|
| Submission date |
Feb 01, 2022 |
| Last update date |
Dec 12, 2022 |
| Contact name |
Anna Antonell |
| E-mail(s) |
antonell@clinic.cat
|
| Organization name |
Fundacio Clinic per a la Recerca Biomèdica
|
| Department |
Neurosciences
|
| Lab |
Alzheimer's disease and other cognitive disorders Unit
|
| Street address |
C/Casanova, 143
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE195872 |
Differential gene expression in sporadic and genetic forms of Alzheimer’s disease and frontotemporal dementia in brain tissue and lymphoblastoid cell lines. |
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