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| Status |
Public on Jan 19, 2022 |
| Title |
Brain, AD_TilingArray_M05 |
| Sample type |
RNA |
| |
|
| Source name |
human brain tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Alzheimer's disease (AD)
tissue: brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by Trizol™ method (Invitrogen, Karlsruhe, Germany). 100mg deeply frozen human brain tissue (temporal cortex) was homogenized in the presence of 1ml Trizol in a glass-Teflon™ homogenizer. The homogenate was transferred to a microtube and after adding chloroform, samples were centrifuged at 15 000 g (4 °C) for 15min and the supernatant transferred to a fresh tube. Samples were mixed with equal amounts of isopropanol and centrifuged at 12 000 g (4 °C) for 15min to precipitate the RNA. After washing, the pellet was air-dried and dissolved in water. RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis, by spectrophotometry (scanning at 220−320 nm) and by analysis using Agilent 2100 bioanalyzer. Only samples with RIN > 5 were further processed. The RNA concentration was estimated spectrophotometrically by absorbance at 260 nm, concentration was adjusted to 1mg/ml and RNA was stored at −80 °C until use.
|
| Label |
biotin
|
| Label protocol |
The Affymetrix Human Whole Genome Tiling Array 1.0 Set consisting of 14 arrays was used according to the manufacturer’s instructions, except that separate labeling reactions were used for each array starting from 10 μg pooled total RNA.
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| |
|
| Hybridization protocol |
Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.
|
| Scan protocol |
Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.
|
| Description |
AD_E
|
| Data processing |
We used the TileShuffle algorithm (Otto C, Reiche K, Hackermuller J. Detection of differentially expressed segments in tiling array data. Bioinformatics 2012; 28: 1471–1479) to determine expressed and differentially expressed genomic intervals. Affymetrix Human Whole Genome Tiling Array 1.0 Set raw signal intensities were mapped to human genome version NCBI36 using Affymetrix BPMAP files. Expressed segments were detected with the TileShuffle parameter settings: window size = 200, the window score was defined as the arithmetic mean trimmed by the maximal and minimal values over signal intensities of all probes in a window, number of permutations = 10 000 and number of GC classes = 4. All windows with an adjusted p < 0.05 according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995) were defined to be significantly expressed. DE-TARs are differentially expressed TileShuffle intervals with adjusted p < 0.05 (window size = 200, the window score was defined as the logfold-change discarding all probes with converse behavior as observed for the relevant significantly expressed windows, number of permutations = 100 000 and number of GC classes = 1). Finally, the genome coordinates of all significantly expressed and all significantly differentially expressed segments were lifted over to GRCh37 (hg19) using liftOver (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver).
[additional results files] Ueberham_AD_K_highdiff3.bed: significantly differentially expressed segments (adjusted p<0.05)
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| |
|
| Submission date |
Sep 30, 2019 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Kristin Reiche |
| E-mail(s) |
kristin.reiche@izi.fraunhofer.de
|
| Organization name |
Fraunhofer Institute for Cell Therapy and Immunology
|
| Department |
Diagnostics
|
| Street address |
Perlickstr. 1
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6160 |
| Series (2) |
| GSE138214 |
Transcriptome-wide expression analysis of pooled brain samples of patients with Alzheimer's disease compared to controls |
| GSE138261 |
Alzheimer-related genes show accelerated evolution |
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