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Sample GSM6341326 Query DataSets for GSM6341326
Status Public on Nov 17, 2022
Title DLPFC expression from sample 9-069
Sample type RNA
 
Source name postmortem dorsolateral prefrontal cortex tissue
Organism Homo sapiens
Characteristics sample: 9-069
diagnosis: CTL
dx: control
age: 65.4
Sex: M
ph: 6.47
pmi: 20.5
rin: 8.2
rin²: 67.24
suicide: N
type of death: Natural
c1: -0.0197608
c2: -0.00985686
c3: -0.00832127
c4: 0.00540537
sv1: 0.0415231959542387
adhd prs: -0.00250661553
bd prs: -0.00544818269
cdg prs: 0.00921865896
mdd-2018 prs: -0.000940875002
mdd-2019 prs: -0.00391757393
scz prs: -0.00263584522
ea prs: 3.42236966e-05
t2d prs: -0.00322130093
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 control 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

Data table header descriptions
ID_REF
VALUE Filtered and batch corrected RMA signal estimates from oligo 1.50.0 package in R 3.6.1

Data table
ID_REF VALUE
2315127 3.39418281184627
2315128 1.45158377528146
2315131 2.63770283220001
2315133 5.07287009861086
2315146 3.18313320132328
2315165 7.06020259031036
2315200 2.03614239329325
2315201 6.06927790374739
2315215 4.71924043151358
2315217 3.62439509514012
2315314 5.45787920899528
2315356 4.07852269959021
2315358 3.72720111958397
2315361 6.71873766259398
2315364 6.20356879391159
2315365 6.53181132154137
2315366 6.21755939708535
2315367 6.61103325991064
2315368 7.09775954652768
2315369 2.15262289168458

Total number of rows: 1097408

Table truncated, full table size 26673 Kbytes.




Supplementary file Size Download File type/resource
GSM6341326_9-069_HuEx-1_0-st-v2_.CEL.gz 22.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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