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Sample GSM6341398 Query DataSets for GSM6341398
Status Public on Nov 17, 2022
Title DLPFC expression from sample a-42-94.101
Sample type RNA
 
Source name postmortem dorsolateral prefrontal cortex tissue
Organism Homo sapiens
Characteristics sample: a-42-94.101
diagnosis: CTL
dx: control
age: 50.2
Sex: M
ph: 6.4
pmi: 65
rin: 8.8
rin²: 77.44
suicide: N
type of death: Natural
c1: -0.0063902
c2: 0.0103871
c3: -0.00379128
c4: 0.00152099
sv1: -0.00928537516910005
adhd prs: -0.00253645129
bd prs: -0.00565632455
cdg prs: 0.00917514508
mdd-2018 prs: -0.000995040359
mdd-2019 prs: -0.00407500771
scz prs: -0.00259876675
ea prs: 5.50858989e-06
t2d prs: -0.00319872175
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 3.73301903534947
2315128 1.89553444301551
2315131 3.08340250419388
2315133 5.03565641505409
2315146 3.4788717419106
2315165 7.3269733028314
2315200 1.71389848493313
2315201 6.03936887799419
2315215 3.72917364216159
2315217 2.48000154525187
2315314 5.56242114158781
2315356 4.88842503491297
2315358 4.24721534149191
2315361 6.85161139648671
2315364 5.63076397304671
2315365 6.60474047264086
2315366 5.8271783695516
2315367 6.93979255073108
2315368 8.12875001012059
2315369 1.53513698362354

Total number of rows: 1097408

Table truncated, full table size 26673 Kbytes.




Supplementary file Size Download File type/resource
GSM6341398_afae2196-42-94.101-150709.CEL.gz 20.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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