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Sample GSM6341444 Query DataSets for GSM6341444
Status Public on Nov 17, 2022
Title DLPFC expression from sample MU_9_111
Sample type RNA
 
Source name postmortem dorsolateral prefrontal cortex tissue
Organism Homo sapiens
Characteristics sample: MU_9_111
diagnosis: SCZ
dx: case
age: 41.5
Sex: M
ph: 6.64
pmi: 52
rin: 7.3
rin²: 53.29
suicide: Y
type of death: Violent
c1: -0.0074683
c2: -0.00867939
c3: 0.0137439
c4: 0.0123957
sv1: 0.188083149460482
adhd prs: -0.00266201891
bd prs: -0.00557981271
cdg prs: 0.0091838949
mdd-2018 prs: -0.00100787165
mdd-2019 prs: -0.00399081227
scz prs: -0.0026201159
ea prs: 2.25474211e-05
t2d prs: -0.00346083657
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

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 2.43128925416626
2315128 1.69405787368327
2315131 2.79081364745487
2315133 5.43090223597856
2315146 3.7445751713013
2315165 7.31161342126857
2315200 2.33727856023677
2315201 4.81947217122273
2315215 4.85202109956818
2315217 3.15140586251218
2315314 6.12297129966379
2315356 4.35279552104423
2315358 1.7435502261132
2315361 4.34113374319515
2315364 6.17954283843031
2315365 6.29183970120412
2315366 5.61001171515269
2315367 6.35460287199859
2315368 6.48922953813881
2315369 2.28897608870095

Total number of rows: 1097408

Table truncated, full table size 26673 Kbytes.




Supplementary file Size Download File type/resource
GSM6341444_MU_9_111_HuEx-1_0-st-v2_.CEL.gz 21.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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