NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3566128 Query DataSets for GSM3566128
Status Public on Mar 15, 2019
Title Participant ID and visit (v) # phchp181v3 Independent Test Cohorts (n=201) (505 visits)
Sample type RNA
 
Source name Whole Blood
Organism Homo sapiens
Characteristics gender-diagnosis: F-BP
vas stress score (1-100): Independent Test cohort blood gene expression data
Extracted molecule total RNA
Extraction protocol Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture. PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion. A second centrifugation step will be done to remove residual cell debris. After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column. The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps. The RNA is then eluted using DEPC-treated water.
Label Biotin
Label protocol Sample Labeling: Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps: 1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence. 2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. 3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription. 4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step. 5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.
 
Hybridization protocol Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.
Scan protocol Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values
Description Yes
We used three independent cohorts: discovery (major psychiatric disorders with changes in state stress), validation (major psychiatric disorders with clinically severe trait and state stress), and testing (an independent major psychiatric disorders cohort for predicting state stress, and for predicting trait future hospitalization visits with stress as the primary reason)
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a self-report visual analog scale (1-100) for quantitatively assessing state stress at that particular moment in time (Simplified Stress Scale- SSS), which has 4-items (Life Stress, Financial Stress, Health Stress and Social Stress). We also administered the PTSD Checklist- Civilian Version (PCL-C) scale, which measures clinical severity of trait stress symptoms over the month preceding testing. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing
Data processing The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis. We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.
 
Submission date Jan 16, 2019
Last update date Mar 15, 2019
Contact name Dr. Alexander B. Niculescu
E-mail(s) anicules@iupui.edu
Phone 317-274-6544
Organization name Indiana University Medical School
Department Psychiatry
Lab Neuroscience Building Room 203
Street address 320 W. 15th Street
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL570
Series (1)
GSE125216 Towards Precision Medicine for Stress Disorders: Diagnostic Biomarkers and Targeted Drugs ( Molecular Psychiatry, under review)

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
1007_s_at 161.3643421
1053_at 67.56026116
117_at 713.7910491
121_at 391.8807782
1255_g_at 8.593739228
1294_at 251.1591457
1316_at 70.78388296
1320_at 19.86522185
1405_i_at 3975.333001
1431_at 17.79144766
1438_at 49.76763757
1487_at 172.0776598
1494_f_at 88.68910607
1552256_a_at 102.1864432
1552257_a_at 102.4044075
1552258_at 64.02644487
1552261_at 25.80740183
1552263_at 381.4999347
1552264_a_at 642.6453581
1552266_at 8.149519501

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM3566128_phchp181v3.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap