|
| Status |
Public on Nov 17, 2022 |
| Title |
DLPFC expression from sample MU_9_082 |
| Sample type |
RNA |
| |
|
| Source name |
postmortem dorsolateral prefrontal cortex tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample: MU_9_082
diagnosis: MDD
dx: case
age: 50.8
Sex: F
ph: 6.85
pmi: 50.5
rin: 7.4
rin²: 54.76
suicide: Y
type of death: Non-violent
c1: 0.00870016
c2: 0.0236119
c3: 0.000194327
c4: 0.0150924
sv1: 0.0281148957035356
adhd prs: -0.00282841606
bd prs: -0.00541135181
cdg prs: 0.00935705341
mdd-2018 prs: -0.00106861209
mdd-2019 prs: -0.00405459153
scz prs: -0.00269858387
ea prs: 3.73076989e-05
t2d prs: -0.00317392006
tissue: postmortem dorsolateral prefrontal cortex (DLPFC)
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Subjects were refrigerated within 5 hours of being found. Brodmann area 9 (BA 9) was taken from the lateral surface of the frontal lobe from an area comprising the middle frontal superior gyrus to the inferior frontal sulcus of the left hemisphere. After removal at autopsy, brain tissue was rapidly processed and frozen at -70°C using a standardized procedure that minimizes autolytic effects.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ∼100 mg frozen gray matter using 1.0 ml TRIzol reagent (Life Technologies). After homogenization and phase separation, an equal volume of 70% ethanol was added to the aqueous phase. RNA isolation was performed using RNeasy minikits (Qiagen), and all samples were treated with DNase by column digestion. RNA quantity and quality were analyzed by spectrophotometry with NanoDrop (Thermo Fischer Science) and by determination of RNA integrity numbers (RINs) using an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples with RIN ⩾ 6.00 were used for further analysis with Affymetrix Human Exon 1.0 ST v2 arrays (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Labeling was performed by the Australian Genome Research Facility (AGRF; Melbourne, Australia), which performed cRNA labeling of the samples with biotin using the Affymetrix Synthesis and Labeling Kit.
|
| |
|
| Hybridization protocol |
Hybridization was conducted by the Australian Genome Research Facility (AGRF; Melbourne, Australia), which prepared samples for hybridization with a standard probe cocktail and hybridized them overnight in an Affymetrix Human Exon 1.0 ST v2 Array.
|
| Scan protocol |
Scanning of the arrays was carried out by the Australian Genome Research Facility (AGRF; Melbourne, Australia) according to the protocol provided by Affymetrix.
|
| Description |
DLPFC expression case sample
|
| Data processing |
Data were processed using the oligo package version 1.50.0 in R 3.6.1. Oligo’s Robust Multichip Average (RMA) algorithm was used for background adjustment, quantile normalisation and summarization (using median-polish) at the probeset level. Probesets that did not contain start or stop information, were labelled as controls in the current NetAffx annotation for Affymetrix’s HuEx 1.0 ST v2 array, were cross-hybridized (number_cross_hyb_probes ≥ 1), or were located on X, Y and M chromosomes were removed from the data set. The SVA package version 3.34.0 in R was used for batch correction of known and hidden batches.
HuEx-1_0-st-v2.r2.pgf
|
| |
|
| Submission date |
Jul 17, 2022 |
| Last update date |
Nov 17, 2022 |
| Contact name |
Karolina Worf |
| E-mail(s) |
karolina.worf@gmail.com
|
| Organization name |
Helmholtz Zentrum Muenchen
|
| Department |
Computational Health
|
| Street address |
Ingolstaedter Landstr. 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE208338 |
Expression data from postmortem human dorsolateral prefrontal cortex - psychiatric disorders & healthy controls |
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