title: Participant ID and visit (v) # phchp323v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
74
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


title: 2days pbs line 3348A [D5-3]

status: Public on Mar 15 2019

type: SRA

city: Tel Aviv

first: Amit

last: Frishberg

address: Haim Levanon

department: Cell Research & Immunology

country: Israel

institute: Tel-Aviv University

description: processed data file: countsFinal.txt; countsNormFinal.txt

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4 software used for basecalling.
Reads were aligned using the HISAT aligner to the mouse reference genome (NCBI 37, mm9).
Expression levels of the list of mouse genes were then calculated and normalized by the total number of mapped reads per experiment, using HOMMER with the default parameters.
Recorded are those reads that were mapped to mouse gene exons (using the UCSC transcript annotation).
Reads that were mapped to multiple positions were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized reads by the total number of mapped reads per experiment

molecule: total RNA

organism: Mus musculus

source_name: 2days pbs_lungs

extract_protocol:
Murine lungs were harvested immediately after the time of sacrifice, sliced into small pieces, homogenized using BeadBlaster Microtube Homogenizer (90sec, 4000rpm) in the presence of QIAzol, and used for total RNA extraction using the miRNeasy Mini Kit.
For the preparation of RNA‐Seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95°C) treatment for 4:30 min (NEBNext Magnesium RNA Fragmentation Module). The 3′ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen). Strand‐specific cDNA was synthesized using a poly T‐VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double‐strand DNA was obtained using Second strand synthesis kit (NEB). DNA ends were repaired using T4 polynucleotide kinase and T4 polymerase (NEB‐Next). After the addition of an adenine base residue to the 5′ end using Klenow enzyme (NEB‐Next), a barcode Illumina compatible adaptor (IDT) was ligated to each fragment. The washed DNA fragment was amplified by PCR (12 cycles) using specific primers (IDT) to the ligated adaptors. The quality of each library was analyzed by TapeStation (Agilent).

tag: collaborative cross (cc) line

tag: infected with

value: PBS (control)

tag: weight loss

tag: viral load

tag: tissue

value: lungs

tag: time point

value: 48h after infection


title: 2days pbs line 2750A [D4-6]


title: 2days flu line 2750A [D5-1]

source_name: 2days flu_lungs

value: influenza virus (flu)


title: Participant ID and visit (v) # phchp313v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

type: RNA

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

country: USA

institute: Indiana University Medical School

description:
72
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

hyb_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

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.

label: Biotin

organism: Homo sapiens

source_name: Whole Blood

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.

extract_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.

tag: gender-diagnosis

value: M-PTSD

tag: vas stress score (1-100)


title: 2days flu line 2750A [D5-2]


title: Participant ID and visit (v) # phchp319v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
54
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


title: Participant ID and visit (v) # phchp316v6 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
56
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

value: M-BP


title: Participant ID and visit (v) # phchp313v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
77
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


title: 2days flu line 72A [D4-4]


title: Participant ID and visit (v) # phchp311v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

value: F-MDD


title: 2days flu line 72A [D4-3]


title: 2days pbs line 2750A [D4-5]


title: Participant ID and visit (v) # phchp299v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
66
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


title: Participant ID and visit (v) # phchp310v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
63
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

value: M-MOOD


title: Participant ID and visit (v) # phchp316v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
62
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


title: Participant ID and visit (v) # phchp299v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp289v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
53
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

value: F-PTSD


title: 2days pbs line 72A [D4-2]


title: 2days pbs line 72A [D4-1]


title: 2days pbs line 3912A [D3-6]


title: 2days pbs line 3912A [D3-7]


title: Participant ID and visit (v) # phchp296v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
55
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


title: Participant ID and visit (v) # phchp296v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
52
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


title: Participant ID and visit (v) # phchp307v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp299v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
64
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


title: 2days flu line 3912A [D3-5]


title: 2days flu line 3912A [D3-4]


title: Participant ID and visit (v) # phchp304v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
58
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

value: M-MDD


title: 2days pbs line 5004A [D3-3]


title: 2days flu line 5004A [D3-2]


title: 2days flu line 5004A [D3-1]


title: 2days pbs line 5022A [D2-4]


title: 2days flu line 5022A [D2-6]


title: 2days flu line 5022A [D2-5]


title: 2days flu line 57B [D2-2]


title: Participant ID and visit (v) # phchp237v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
79
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


title: Participant ID and visit (v) # phchp266v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
61
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


title: Participant ID and visit (v) # phchp234v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp231v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: 2days flu line 57B [D2-1]


title: Participant ID and visit (v) # phchp216v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
68
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


title: Participant ID and visit (v) # phchp291v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
51
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

value: F-SZ


title: Participant ID and visit (v) # phchp216v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
76
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


title: Participant ID and visit (v) # phchp286v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp205v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp215v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
78
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


title: Participant ID and visit (v) # phchp215v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
54
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


title: 2days pbs line 57B [D14-3]

description: processed data file: countsFinal.txt; countsNormFinal.txt


title: 2days flu line 5000A [D13-4]


title: 2days pbs line 57B [D14-4]


title: 2days pbs line 21B [D14-2]


title: 2days pbs line 5000A [D13-2]


title: 2days flu line 5000A [D13-3]


title: 2days pbs line 5000A [D13-1]


title: 2days pbs line 21B [D14-1]


title: 2days flu line 5023A [D12-6]


title: Pt-ptc + Pt-dpp double pRNAi embryo_1

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

description: There were no biological replicates.  This sample represents the same RNA used in GSM3070093.

hyb_protocol: cRNA probes were hybridized to a microarray in Hybridization buffer (5x SSC, 0.1% SDS, 10% formamide) at 42˚C for 16-20 h.

scan_protocol: Microarray slides were scanned using a GenePix 4000B Scanner (Molecular Devices).

data_processing: Obtained images were analyzed using an Array-Pro Analyzer Ver. 4.5 (Media Cybernetics, Inc.). The quantitative data were subjected to Loess normalization. The supplementary .xls files include both raw and normalized signal.

organism: Parasteatoda tepidariorum

source_name: pd-RNAi

label_protocol: cRNA labeled with Cy3 or Cy5 was prepared from 2 µg of total RNA using RNA Transcript SureLABEL Core Kit (Takara)

growth_protocol: Embryos were incubated at 25˚C.

extract_protocol: Total RNA was extracted from approximately 250 embryos of the same stage using MagExtractor (Toyobo). RNA integrity was examined with an Agilent Bioanalyzer 2100.

value: whole embryo

tag: developmental stage

value: late stage 5

tag: treatment

value: Pt-dpp + Pt-ptc double pRNAi

tag: treatment protocol

value: A mated female was injected with approximately 2.0µl of Pt-ptc and Pt-dpp dsRNA mixture (1µg/µl each) five times at 2-3 days intervals. Embryos derived from an egg sac produced by this female 25 days after the first injection of the dsRNA were used for RNA extraction.

source_name: normal

value: Embryos derived from a different egg sac produced by the same female one day before the first injection of the dsRNA were used for RNA extraction.


title: 2days flu line 5023A [D12-5]


title: Participant ID and visit (v) # phchp182v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
67
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


title: Participant ID and visit (v) # phchp167v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
70
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


title: Participant ID and visit (v) # phchp162v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp205v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp182v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
74
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


title: Participant ID and visit (v) # phchp155v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp205v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
56
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


title: Participant ID and visit (v) # phchp162v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
62
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


title: Participant ID and visit (v) # phchp150v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

value: M-SZA


title: Participant ID and visit (v) # phchp150v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: 2days pbs line 5023A [D12-4]

value: PBS (control)


title: Participant ID and visit (v) # phchp182v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
71
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


title: 2days pbs line 5023A [D12-3]

value: lungs


title: Participant ID and visit (v) # phchp150v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
60
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


title: 2days pbs line 5022A [D12-2]

value: 48h after infection


title: ΔTLR8 BlaER1 Ec KO 3

city: Heidelberg

first: Tatjana

last: Eigenbrod

address: Im Neuenheimer Feld 324

department: Department of Infectious Diseases

country: Germany

institute: Heidelberg University Hospital

description:
ΔTLR8 BlaER1 - E. coli ΔtrmH, sample 3
chip.microarray024.tsv

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and normalised to the respective non-trested control in Chipster

label: biotin

source_name: Transdifferentiated BlaER1 cells

label_protocol: Biotinylated cRNA were prepared for Illumina arrays as described here: https://www.dkfz.de/gpcf/illumina_beadchips.html

growth_protocol: 10^6 BlaER1 B-cells were transdifferentiated in 3 ml RPMI1640 per well of a 6 well plate with 10 % FCS and 1 % Pen/Strep, supplemented with 10 ng/ml IL-3, 10 ng/ml M-CSF and 150 nM b-Estradiol and incubated at 37°C and 5 % CO2 for 7 days. At day 2 and 5 the medium was replaced with 3 ml RPMI 1640 with FCS, Pen/Strep, IL-3, M-CSF and b-Estradiol per well.

extract_protocol: Supernatant-free BlaER1 cells were lysed with 115 ml lysis buffer (supplemented with b -mercaptoethanol) per stimulation and three wells were pooled. RNA was isolated using RNeasy Mini Kit according to the manufacturer’s protocol, including on-column DNA digestion step. RNA was stored at -80°C until further analysis on Illumina HumanHT-12 v4 BeadChip microarray.

treatment_protocol: Stimuli were diluted in antibiotic-free RPMI1640 with 10 % FCS to a final concentration of 0.1 mg/ml for LPS and MOI 10 for bacteria. Antibiotic-free RPMI1640 served as a non-treated control. 2x10^5 BlaER1 cells were stimulated for 5 h at 37°C and 5 % CO2. Whenever bacteria were used, Pen/Strep at a final concentration of 10 mg/ml was added to all wells of the plate after 1.5 h of incubation.

tag: development stage

value: Macrophage-like

tag: transdifferntiation time

value: 7 days


title: ΔTLR8 BlaER1 Ec WT 2

description:
ΔTLR8 BlaER1 BlaER1 - E. coli WT, sample 2
chip.microarray020.tsv


title: Participant ID and visit (v) # phchp141v3 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

value: F-BP


title: ΔTLR8 BlaER1 Ec WT 1

description:
ΔTLR8 BlaER1 BlaER1 - E. coli WT, sample 1
chip.microarray019.tsv


title: Participant ID and visit (v) # phchp141v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
55
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


title: ΔTLR8 BlaER1 Ec KO 1

description:
ΔTLR8 BlaER1 - E. coli ΔtrmH, sample 1
chip.microarray022.tsv


title: 2days flu line 5001A [D11-5]

value: influenza virus (flu)


title: ΔTLR8 BlaER1 Ec KO 2

description:
ΔTLR8 BlaER1 - E. coli ΔtrmH, sample 2
chip.microarray023.tsv


title: 2days pbs line 5001A [D11-4]


title: ΔTLR8 BlaER1 LPS 3

description:
ΔTLR8 BlaER1 BlaER1 - LPS, sample 3
chip.microarray018.tsv


title: ΔTLR8 BlaER1 Ec WT 3

description:
ΔTLR8 BlaER1 BlaER1 - E. coli WT, sample 3
chip.microarray021.tsv


title: 2days pbs line 5001A [D11-3]

description: processed data file: countsFinal.txt; countsNormFinal.txt


title: ΔTLR8 BlaER1 LPS 1

description:
ΔTLR8 BlaER1 BlaER1 - LPS, sample 1
chip.microarray016.tsv


title: ΔTLR8 BlaER1 nt 2

description:
ΔTLR8 BlaER1 - non-treated, sample 2
chip.microarray014.tsv


title: 2days pbs line 5022A [D12-1]


title: Participant ID and visit (v) # phchp130v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
64
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

value: F-MDD


title: Participant ID and visit (v) # phchp133v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
73
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

value: M-SZ


title: 2days flu line 4438A [D11-2]


title: ΔTLR8 BlaER1 nt 1

description:
ΔTLR8 BlaER1 - non-treated, sample 1
chip.microarray013.tsv


title: Participant ID and visit (v) # phchp118v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
59
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


title: WT BlaER1 Ec WT 3

description:
WT BlaER1 - E. coli WT, sample 3
chip.microarray009.tsv


title: Participant ID and visit (v) # phchp119v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
58
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


title: 2days flu line 4438A [D11-1]


title: WT BlaER1 Ec WT 1

description:
WT BlaER1 - E. coli WT, sample 1
chip.microarray007.tsv


title: WT BlaER1 LPS 2

description:
WT BlaER1 - LPS, sample 2
chip.microarray005.tsv


title: WT BlaER1 Ec KO 3

description:
WT BlaER1 - E. coli \delta trmH, sample 3
chip.microarray012.tsv


title: Participant ID and visit (v) # phchp118v4 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
52
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


title: ΔTLR8 BlaER1 nt 3

description:
ΔTLR8 BlaER1 - non-treated, sample 3
chip.microarray015.tsv


title: Participant ID and visit (v) # phchp116v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
57
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


title: WT BlaER1 LPS 3

description:
WT BlaER1 - LPS, sample 3
chip.microarray006.tsv


title: WT BlaER1 Ec WT 2

description:
WT BlaER1 - E. coli WT, sample 2
chip.microarray008.tsv


title: Participant ID and visit (v) # phchp102v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: WT BlaER1 LPS 1

description:
WT BlaER1 - LPS, sample 1
chip.microarray004.tsv


title: 2days pbs line 4438A [D10-6]

description: processed data file: countsFinal.txt; countsNormFinal.txt


title: Participant ID and visit (v) # phchp121v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

value: M-MOOD


title: 2days pbs line 4438A [D10-5]


title: WT BlaER1 Ec KO 2

description:
WT BlaER1 - E. coli \delta trmH, sample 2
chip.microarray011.tsv


title: siRNA-NC

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were pre-processed with trim galore for trimming Illumina adaptor sequences (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Expression level for all RefSeq genes was quantified using RSEM.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: CD87RNA-seq.TPM.matrix.txt: Tab-delimited text file includes abundance measurements.

source_name: Spermatogonial stem and progenitor cell (SSC)

extract_protocol:
Total RNA was isolated from sorted cells using the AllPrep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA) and subjected to Smart-seq2 protocol. In brief, the mixture of 1 µl of 10 mM oligo-dT30VN primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’), 1µl of 10mM dNTP mix and 10ng extracted RNA in 5ul reaction volume was incubated at 72˚C for 3 min. Then, 5 μl of the reverse transcription mixture (200U SuperScript II reverse transcriptase, 20U RNase inhibitor, 1x Superscript II first-strand buffer, 5 mM DTT, 1 M Betaine, 6mM MgCl2, 1µM TSO (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’) was added into the tube for RNA reverse transcription. The tubes containing total 10 µl mixture were put into ProFlex PCR System (Thermo Fisher Scientific) and the reaction condition was as follows: 42˚C for 90 min, followed by ten cycles of 50˚C for 2 min and 42˚C for 2 min. The final enzyme inactivation was performed at 70˚C for 15 min. After finishing the first-strand reaction, the 15µl PCR preamplification mix (1x KAPA HiFi HotStart ReadyMix, 0.1µM IS PCR primers (5’-AAGCAGTGGTATCAACGCAGAGT-3’)) was added into the tube containing 10µl of the first-strand reaction. PCR preamplification reaction was performed in ProFlex PCR System by using the following program: 98˚C for 3 min, 12 cycles of 98˚C for 20s, 67˚C for 15s and 72˚C for 6 min, with the final extension cycle of 72˚C for 5 min. Amplified cDNA was purified by using Ampure XP beads (1:1 ratio) according to the manufacturer’s manual and was eluted in 15 µl of ddH2O.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 using standard Illumina protocols.

tag: strain/background

tag: cell type

value: Oct4-GFP+ germ cell in vitro culture

tag: gender

value: male

tag: age

value: postnatal day 5.5


title: Oct4-GFP-high

value: Oct4-GFP+ germ cells


title: Participant ID and visit (v) # phchp101v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
67
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


title: 2days flu line 5021A [D10-4]

tag: collaborative cross (cc) line


title: WT BlaER1 nt 2

description:
WT BlaER1 - non-treated, sample 2
chip.microarray002.tsv


title: siRNA-Oct4


title: WT BlaER1 Ec KO 1

description:
WT BlaER1 - E. coli \delta trmH, sample 1
chip.microarray010.tsv


title: WT BlaER1 nt 1

description:
WT BlaER1 - non-treated, sample 1
chip.microarray001.tsv


title: Oct4-GFP-low


title: CD87+_group1

description: processed data file: CD87RNA-seq.TPM.matrix.txt


title: 2days flu line 5021A [D10-3]

tag: infected with


title: CD87+_group2


title: 2days flu line 5010A [D1-5]

tag: weight loss


title: ΔTLR8 BlaER1 LPS 2

description:
ΔTLR8 BlaER1 BlaER1 - LPS, sample 2
chip.microarray017.tsv


title: Participant ID and visit (v) # phchp089v4 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
50
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


title: CD87-_group2


title: 2days pbs line 5010A [D1-3]

tag: viral load


title: Participant ID and visit (v) # phchp084v4 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
61
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


title: 2days pbs line 5021A [D10-1]

tag: tissue


title: 2days flu line 5010A [D1-4]

tag: time point


title: CD87-_group1


title: Oct4-GFP-mid


title: Participant ID and visit (v) # phchp096v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

tag: gender-diagnosis


title: Fadu_TP63 shRNA SCC 1

city: Aurora

first: Maranke

last: Koster

address: 12800 E19th Avenue

department: Dermatology

description: Human HNSCC cells implanted into mouse tongue

data_processing:
Illumina Real-Time Analysis (RTA) was used for base calling
Adapter sequences were trimmed using Trimmomatic and RNA-seq reads were mapped to the human genome (hg19) using STAR
DESeq2 was used to obtain differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including basemean, log2FoldChange,IfCSE,stat, pvalue, padj were obtained for  TP63 shRNA SCCs (n=3) compared to NS shRNA SCCs (n=3)

source_name: Tongue

extract_protocol:
RNA from xenograft SCCs was extracted using the mini-RNeasy kit according to the manufacturer’s (Qiagen) protocol.
Sequencing libraries for RNA-Seq was prepared by Genomics and Microarray Core Facility at University of Colorado-Anschutz Medical Campus

value: Human HNSCC cell line

tag: genotype/variation

value: TP63 knockdown


title: Fadu_TP63 shRNA SCC 2

institute: University of Colorado-Anschutz Medical Campus


title: FaDu_NS shRNA SCC 2

value: NS shRNA


title: FaDu_NS shRNA SCC 3


title: Participant ID and visit (v) # phchp362v3 Independent Discovery Cohort (n=36) (91 visits)

description:
Discovery Cohort Blood Gene Expression
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

value: M-MDD

tag: vas stress score (1-100)


title: Participant ID and visit (v) # phchp361v3 Independent Discovery Cohort (n=36) (91 visits)

value: F-PTSD


title: Participant ID and visit (v) # phchp361v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp351v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp351v1 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp340v3 Independent Discovery Cohort (n=36) (91 visits)


title: DKO_YFP_pos_3

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

description:
Raw_counts_mesenteric.csv.gz
TPM_counts_mesenteric.csv.gz

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped against the UCSC mouse genome mm9 using TopHat2 (v2.1.1) with the parameters: "-p 16 -N 2 --max-multihits 1 --read-gap-length 1 --transcriptome-index". The RefSeq gene anotation was obtained from ucsc Genome Bioinformatics database.
Exons from all isoforms of a gene were merged to create one meta-transcript, using featureCounts 52 (subread-1.4.3-p1) with the following parameters “-g gene_name -s 2”
Transcripts per million counts were calculated by normalizing the size of the meta-transcript (in kilobases),by 1,000,000 ("per million" scaling factor) and by the library size.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated values delimited file that include TPM values for each sample (columns) or the raw counts per gene per sample (column)

source_name: Mesenteric lymph nodes

extract_protocol:
CD4+Foxp3+ Treg cells and CD4+Foxp3- T cells were sorted from mesenteric lymph nodes from either WT or Tet2/3fl/flFoxp3Cre mice and total RNA were extracted using Qiagen RNeasy plus mini kit
Libraries were constructed using Illumina TruSeq stranded mRNA library prep kit

tag: strain

value: 14 weeks old

tag: genotype

value: Tet2/3 DKO

value: CD4+Foxp3+ Treg cells


title: 5b_NKG2DLneg

city: Basel

first: Claudia

last: Lengerke

address: Hebelstr. 20

department: Department of Biomedicine

country: Switzerland

institute: University Hospital Basel and University of Basel

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression W ash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies).

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.6 (both Agilent Technologies), Excel 2010 (Microsoft) and the IMGM internal tool marfin v1.9 were used for quality control, statistical data analysis, filtering of differentially expressed transcript, RNA annotation and visualization.

source_name: CD34 non-expressing AML, sorted fraction: NKG2DLneg

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies). All steps were carried out according to manufacturer’s instructions. cRNA concentration (ng/μl), RNA absorbance ratio (A260nm/A280nm) and Cyanine-3 dye concentration (pmol/μl) were recorded for all cRNA samples using NanoDrop ND-1000 UV- VIS spectrophotometer. Yield and specific activity of each reaction were determined. The RNA 6000 Nano LabChip Kit (Agilent Technologies) was used on the 2100 Bioanalyzer to analyze the quality of labeled non-fragmented cRNA.

growth_protocol: Standard protocol for primary human tissue

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and RNA concentration and purity determined on the NanoDrop ND-1000 spectral photometer (peqlab). The 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano as well as the 6000 Pico LabChip Kit (Agilent Technologies) were used to analyze RNA integrity.

treatment_protocol: For simultaneous staining of all NKG2DL, a recombinant NKG2D-Fc chimera (fusion protein) and the corresponding isotype control were purchased from R&D (Minneapolis, MN, USA) and biotinylated with the One-step biotinylation kit (MACS Miltenyi) according to manufactures instructions. Prior to staining, cells were blocked with human IgG (Sigma-Aldrich) and washed. Then biotinylated fusion protein or control (10µg/ml each) were added followed by two washing steps. Afterwards streptavidin-PE (LifeTechnologies, Carlsbad, CA, USA) and selection antibodies were further added prior to sorting into NKG2DLpos and NKG2DLneg fractions

tag: origin

value: AML, peripheral blood, CD33+

tag: sorted fraction


title: 5c_NKG2DLneg


title: FaDu_NS shRNA SCC 1


title: Participant ID and visit (v) # phchp362v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp333v4 Independent Discovery Cohort (n=36) (91 visits)

value: M-PTSD


title: Participant ID and visit (v) # phchp340v1 Independent Discovery Cohort (n=36) (91 visits)

value: F-MDD


title: DKO_YFP_pos_1


title: Fadu_TP63 shRNA SCC 3


title: DKO_YFP_neg_3

value: CD4+Foxp3- T cells


title: 5c_NKG2DLpos

source_name: CD34 non-expressing AML, sorted fraction: NKG2DLpos


title: 5a_NKG2DLneg


title: DKO_YFP_pos_2


title: DKO_YFP_neg_2


title: Participant ID and visit (v) # phchp333v3 Independent Discovery Cohort (n=36) (91 visits)


title: DKO_YFP_neg_1


title: 5a_NKG2DLpos


title: 5b_NKG2DLpos


title: 4b_NKG2DLneg


title: WT BlaER1 nt 3

description:
WT BlaER1 - non-treated, sample 3
chip.microarray003.tsv

tag: development stage

value: Macrophage-like

tag: transdifferntiation time

value: 7 days


title: Participant ID and visit (v) # phchp329v3 Independent Discovery Cohort (n=36) (91 visits)

value: M-SZA


title: WT_YFP_pos_3

value: WT

tag: cell type


title: 4c_NKG2DLpos


title: WT_YFP_pos_2

tag: age


title: 4c_NKG2DLneg


title: 4a_NKG2DLneg


title: Participant ID and visit (v) # phchp329v2 Independent Discovery Cohort (n=36) (91 visits)


title: WT_YFP_pos_1


title: WT_YFP_neg_3


title: Participant ID and visit (v) # phchp333v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp333v1 Independent Discovery Cohort (n=36) (91 visits)


title: WT_YFP_neg_2


title: Participant ID and visit (v) # phchp302v5 Independent Discovery Cohort (n=36) (91 visits)

value: M-BP


title: 4a_NKG2DLpos


title: 3b_NKG2DLneg

source_name: CD34 expressing AML, sorted fraction: NKG2DLneg


title: Participant ID and visit (v) # phchp302v3 Independent Discovery Cohort (n=36) (91 visits)


title: WT_YFP_neg_1


title: Participant ID and visit (v) # phchp285v3 Independent Discovery Cohort (n=36) (91 visits)

value: F-BP


title: 3c_NKG2DLneg


title: 3a_NKG2DLneg


title: Participant ID and visit (v) # phchp302v1 Independent Discovery Cohort (n=36) (91 visits)


title: 4b_NKG2DLpos


title: Line 5023A - No treatment [T7_6]

data_processing:
Reads were aligned using the bowtie2 aligner to the mouse reference genome (NCBI 37, mm9).
Expression levels of the list of mouse genes were then calculated and normalized as FPKM, using RSEM with the default parameters.
Recorded are those reads that were mapped to mouse gene exons (using the UCSC transcript annotation).
Reads that were mapped to multiple positions were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized reads by the total number of mapped reads per experiment

source_name: Collaborative Cross mice strain

value: Lungs

tag: condition

value: No treatment


title: Line 111A - No treatment [T19_1]


title: 3c_NKG2DLpos

source_name: CD34 expressing AML, sorted fraction: NKG2DLpos


title: Line 1912A - No treatment [T13_2]


title: Participant ID and visit (v) # phchp292v2 Independent Discovery Cohort (n=36) (91 visits)


title: Participant ID and visit (v) # phchp292v1 Independent Discovery Cohort (n=36) (91 visits)


title: Line B6 - No treatment [T36_1]

source_name: C57BL/6 mouse


title: Line 2750A - No treatment [T21_5]


title: 2b_NKG2DLneg


title: 3a_NKG2DLpos


title: Participant ID and visit (v) # phchp282v1 Independent Discovery Cohort (n=36) (91 visits)

value: M-SZ


title: 2c_NKG2DLneg


title: Participant ID and visit (v) # phchp279v3 Independent Discovery Cohort (n=36) (91 visits)


title: 3b_NKG2DLpos


title: Participant ID and visit (v) # phchp279v2 Independent Discovery Cohort (n=36) (91 visits)


title: Tet2/3_DKO_CD4+Foxp3-_replicate1

description:
TPM_counts.csv
Raw_counts.csv
CD4_DKO_E2_1

data_processing:
Bcl2fastq v2.20.0.442 was used to obtain fastq files from Illumina
Sequenced reads were trimmed for adaptor sequence, and mapped against the UCSC mouse genome mm9 using TopHat2 (v2.1.1) with the parameters: "-p 16 -N 2 --max-multihits 1 --read-gap-length 1 --transcriptome-index". The RefSeq gene anotation was obtained from ucsc Genome Bioinformatics database.
Exons from all isoforms of a gene were merged to create one meta-transcript, using featureCounts 52 (subread-1.4.3-p1) with the following parameters “-g gene_name -s 2”
Transcripts per million counts were calculated by normalizing the size of the meta-transcript (in kilobases),by 1,000,000 ("per million" scaling factor) and by the library size.
Genome_build: mm9
Supplementary_files_format_and_content: comma separated values delimited file that include TPM values for each sample (columns)
Supplementary_files_format_and_content: Raw abundance counts
Supplementary_files_format_and_content: Transcripts per million abundance counts

source_name: Spleen+peripheral lymph nodes

extract_protocol:
CD4+Foxp3+ Treg cells and CD4+Foxp3- T cells were sorted from the spleen and peripheral lymph nodes from either WT or Tet2/3fl/flFoxp3Cre mice and total RNA were extracted using Qiagen RNeasy plus mini kit
Libraries were constructed using Illumina TruSeq stranded mRNA library prep kit


title: Participant ID and visit (v) # phchp285v1 Independent Discovery Cohort (n=36) (91 visits)


title: WT_CD4+Foxp3-_replicate2

description:
TPM_counts.csv
Raw_counts.csv
CD4_WT_E2_2


title: Participant ID and visit (v) # phchp282v5 Independent Discovery Cohort (n=36) (91 visits)


title: 2a_NKG2DLneg


title: Participant ID and visit (v) # phchp279v1 Independent Discovery Cohort (n=36) (91 visits)


title: Line 2126A - No treatment [T17_3]


title: 2c_NKG2DLpos


title: 2b_NKG2DLpos


title: Participant ID and visit (v) # phchp279v4 Independent Discovery Cohort (n=36) (91 visits)


title: Tet2/3_DKO_CD4+Foxp3-_replicate2

description:
TPM_counts.csv
Raw_counts.csv
CD4_DKO_E2_2


title: WT_CD4+Foxp3-_replicate1

description:
TPM_counts.csv
Raw_counts.csv
CD4_WT_E2_1


title: 2a_NKG2DLpos


title: Participant ID and visit (v) # phchp274v3 Independent Discovery Cohort (n=36) (91 visits)


title: 1c_NKG2DLneg


title: Participant ID and visit (v) # phchp274v4 Independent Discovery Cohort (n=36) (91 visits)


title: 1a_NKG2DLneg


title: Participant ID and visit (v) # phchp274v1 Independent Discovery Cohort (n=36) (91 visits)


title: Tet2/3_DKO_Treg_replicate2

description:
TPM_counts.csv
Raw_counts.csv
Treg_DKO_E2_2


title: 1b_NKG2DLneg


title: Tet2/3_DKO_Treg_replicate1

description:
TPM_counts.csv
Raw_counts.csv
Treg_DKO_E2_1


title: WT_Treg_replicate2

description:
TPM_counts.csv
Raw_counts.csv
Treg_WT_E2_2


title: WT_Treg_replicate1

description:
TPM_counts.csv
Raw_counts.csv
Treg_WT_E2_1


title: Participant ID and visit (v) # phchp258v3 Independent Discovery Cohort (n=36) (91 visits)


title: YeO:8 (8081v) 37°C stationary growth phase, not enriched 2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

description: not enriched for primary transcripts

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: NC_008800.1 Yersinia enterocolitica subsp. enterocolitica 8081; CP030980/CP030981 Yersinia enterocolitica subsp. Y1
Supplementary_files_format_and_content: *.tab files: CSV format with raw read counts per gene; tar-Archive DESeq2_results.tar.gz with  DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

organism: Yersinia enterocolitica

source_name: in vitro culture

growth_protocol: bacteria were grown in LB medium

extract_protocol:
total RNA was isolated using hot phenol extraction
cDNA libraries were constructed using NEBNext Multiple Small RNA Library Prep Set (New England Biolabs)

treatment_protocol: Purification of mRNA was done using human/mouse/rat ScriptSeq complete kit (Illumina). Following the purification, the RNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).

tag: grwoth condition

value: 25C, exponential growth phase


title: YeO:8 (8081v) 37°C stationary growth phase, enriched 2

description: enriched for primary transcripts


title: YeO:8 (8081v) 37°C exponential growth phase, not enriched 2

description: not enriched for primary transcripts


title: RNA-Seq Dnmt1 KO2

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

data_processing:
For RRBS data, the adapter sequences and low quality base calls (< 30) were trimmed from the 3’ end using Trim_Galore program with –rrbs option.
The bisulfite converted sequencing reads were then aligned to the mouse reference genome (mm10) using Bismark program.
For mRNA-Seq data, adaptor and lower-quality bases were trimmed with Trim-galore.
Reads were aligned to the Gencode mouse genome (GRCm38) using STAR-2.4.1d.
Read counts for each sample was obtained using HTSeq-0.6.1 (htseq-count).
Genome_build: mm10
Supplementary_files_format_and_content: RRBS: Bismark coverage file, mRNA-Seq: HTSeq count file

source_name: Six2+ cells from kidney

extract_protocol:
Genomic DNA was extracted from whole kidneys using Puregene Core Kit A (Qiagen). RNA was isolated using RNeasy mini kit (Qiagen).
Genome wide DNA methylome analysis was performed of using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode) following manufacturer’s instruction. 200ng total RNA was used to isolate poly A purified mRNA using the Illumina TruSeq RNA Preparation Kit.

value: kidney

value: Six2Cre Dnmt1 f/f


title: YeO:8 (8081v) 37°C exponential growth phase, enriched 2

description: enriched for primary transcripts


title: RNA-Seq Dnmt1 KO3


title: RNA-Seq Dnmt1 KO1


title: YeO:8 (8081v) 25°C stationary growth phase, not enriched 2

description: not enriched for primary transcripts


title: Participant ID and visit (v) # phchp274v2 Independent Discovery Cohort (n=36) (91 visits)