title: Participant ID and visit (v) # phchp131v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp128v1 Independent Test Cohorts (n=201) (505 visits)

status: Public on Mar 15 2019

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:
Yes
We used three independent cohorts: discovery (major psychiatric disorders with changes in state stress), validation (major psychiatric disorders with clinically severe trait and state stress), and testing (an independent major psychiatric disorders cohort for predicting state stress, and for predicting trait future hospitalization visits with stress as the primary reason)
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a self-report visual analog scale (1-100) for quantitatively assessing state stress at that particular moment in time (Simplified Stress Scale- SSS), which has 4-items (Life Stress, Financial Stress, Health Stress and Social Stress). We also administered the PTSD Checklist- Civilian Version (PCL-C) scale, which measures clinical severity of trait stress symptoms over the month preceding testing. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing

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

molecule: total RNA

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-BP

tag: vas stress score (1-100)

value: Independent Test cohort blood gene expression data


title: Participant ID and visit (v) # phchp131v1 Independent Test Cohorts (n=201) (505 visits)

value: F-SZ


title: Participant ID and visit (v) # phchp129v1 Independent Test Cohorts (n=201) (505 visits)

value: M-SZA


title: Participant ID and visit (v) # phchp127v3 Independent Test Cohorts (n=201) (505 visits)

description:
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-SZA


title: Participant ID and visit (v) # phchp127v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp120v2 Independent Test Cohorts (n=201) (505 visits)

value: M-SZ


title: Participant ID and visit (v) # phchp120v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp127v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp122v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp117v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp122v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp115v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp113v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp117v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp117v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp115v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp114v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp120v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp112v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp115v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp112v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp108v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp108v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp105v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp106v2 Independent Test Cohorts (n=201) (505 visits)

value: F-BP


title: Participant ID and visit (v) # phchp099v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp112v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp106v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp100v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp103v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp097v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp099v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp095v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp099v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp094v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp106v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp108v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp097v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp095v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp095v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp091v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp098v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp091v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp092v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp092v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp140v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp091v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp088v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp087v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp087v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp093v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp086v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp086v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp092v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp086v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp085v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp085v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp083v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp081v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp136v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp083v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp083v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp129v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp081v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp085v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp087v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp076v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp076v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp079v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp075v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp076v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp074v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp074v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp080v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp075v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp075v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp072v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp074v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp073v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp072v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp073v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp072v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp068v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp073v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp069v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp068v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp068v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp069v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp069v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp070v4 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc_neuron12

type: SRA

city: Worcester

first: Botao

last: Liu

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Ribosome protected footprints
qc_sample_ipsc_neuron12_reads_overlap_CDS.base
qc_sample_ipsc_neuron12_reads_overlap_CDS.length

library_source: transcriptomic

data_processing:
Basecallling and fastq file generation were performed by Illumina Basespace.
Individual samples were separated from the raw fastq files based on the barcode sequences. Barcode and UMI sequences were trimmed and moved to the read names. For QC samples, 1 million reads were randomly selected with fastq-tools (0.7) to calculate the GC contents and lengths of ribosome protected footprints. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1).
Trimmed reads were quality filtered and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9).
PCR duplicates were marked based on the UMI sequences and only uniquely mapped reads without duplicates were retained with samtools (0.0.19) for the downstream analysis. Reads mapped to CDS were extracted by intersecting Bam files with CDS bed annotation files with bedtools (2.22.0). The GC contents and lengths of readss were calculated with custom scripts.
Cleaned bam files of uniqly mapped reads without PCR duplicates were converted to fastq files with bedtools (2.22.0). Gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks.
Genome_build: mm10 / hg19
Supplementary_files_format_and_content: qc_sample_reads_overlap_CDS_base.tar.gz: Table of base composition at each position for reads mapped to CDS
Supplementary_files_format_and_content: qc_sample_reads_overlap_CDS_length.tar.gz: Table of length distribution for reads mapped to CDS

source_name: iPSC-derived neurons

growth_protocol: Human iPSC colonies were maintained in mTeSR1 medium (STEMCELL Technologies). Neural progenitor cells (NPCs) were derived from iPSCs using STEMdiff Neuron Differentiation Kit (STEMCELL Technologies) and mantained in STEMdiff Neural Progenitor Medium (STEMCELL Technologies). For the neural differentiation, NPCs were plated at 2X10^4 cells /cm2 onto Poly-L-Ornithine/laminin coated 15-cm dishes in neural differentiation medium (Neurobasal Medium, 1X N2, 1X B27, 1X GlutaMAX, 0.2uM L-Ascorbic acid, 1uM cAMP,10ng/ml BDNF, 10ng/ml GDNF) supplemented with 0.1uM Compound E  and 5uM ROCK inhibitor. Neural cultures were maintained in neural differentiation medium for 1 month before collection.

extract_protocol:
For the RNase titration experiments, frozen tissues were thawed in ice-cold polysome lysis buffer [20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100µg/ml cycloheximide, 25U/ml Turbo DNaseI (Ambion, #AM2238), 1% NP-40 in nuclease-free water] and lysed by trituration through a 25-G need for 10 times. After 10-min incubation on ice, lysates were clarified by centrifugation at 2000g 4 °C for 10min. The supernatants were collected and clarified again by centrifugation at 20,000g 4 °C for 10min. The supernatants were collected and the amounts of nucleic acids were measured with Nanodrop (Thermo Fisher Scientific) and Qubit HS assays (Invitrogen). Lysate containing 2µg RNA in 0.3ml was digested with 5-fold serial diluted RNase A (Ambion, #AM2270) and RNAse T1 (Thermo Fisher Scientific, #EN0542) at 25°C for 30min, including RNase1 (4.8ng RNase A + 0.6U RNase T1/µg RNA), RNase2 (24ng RNase A + 3U RNase T1/µg RNA), RNase3 (120ng RNase A + 15U RNase T1/µg RNA), RNase4(600ng RNase A + 75U RNase T1/µg RNA), and RNase5 (3000ng RNase A + 375U RNase T1/µg RNA). The digestion was stopped by adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694) and chilling on ice. Digested lysates were loaded on 10%-50% sucrose gradients prepared in 1Xpolysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100µg/ml cycloheximide in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection interval through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS. For other samples, RNase A+T1 or RNase I were added as indicated based on the A260 units in the lysates.
Libraries were prepared following the published protocols (Heyer et al., 2015; Ingolia et al., 2012). Briefly, rRNA was depleted from the purified monosomal RNA or cytoplasmic RNA samples with RiboZero (Illumina, #MRZG12324). For cyptoplamic RNA, RNA samples were fragmented in 1Xalkaline fragmentation solution at 95 °C for 15min. RNA samples were separated on a 15% TBU gel (National Diagnostics, #EC-833). Ribosome footprints were size-selected between 26-34nt, while cytoplamic RNAs were size-selected between 100-150nt.. RNA was eluted from the crushed gel pieces in RNA elution buffer (300mM NaOAc pH5.5, 1mM EDTA, 0.25% SDS) at RT overnight, filtered with Spin-X Centrifuge Tube Filters (Corning, #8162) and precipitated with equal volume of isopropanol. Recovered RNA was dephosphorylated with T4 Polynucleotide Kinase (NEB, #M0201S) and ligated with preadenylated adaptor in miRCat®-33 Conversion Oligos Pack (IDT) using T4RNL2Tr.K227Q ligase (NEB, #M0351L). Reverse transcription was performed with RT primers with 5nt-barcode and 5nt or 8nt unique molecular identifier (UMI) and SuperScript III (Invitrogen, #18080-044) in 1X first-strand buffer without MgCl2 (50 mM Tris-HCl, pH 8.3, 75 mM KCl). RT products were separated on a 10% TBU gel and the 130-140nt region was selected. cDNA was eluted in DNA elution buffer (10mM Tris pH 8.0, 300mM NaCl, 1mM EDTA) at RT overnight, filtered, and precipitated with isopropanol. Purified cDNA was circularized with CircLigase (Epicentre, #CL4115K). Optimal PCR cycle was determined empirically by test PCR reactions with titrated cycle numbers. Final PCR amplification was performed with KAPA Library Amplification Kit (Kapa Biosystems, #KK2611) and 180-190bp products were size-selected on an 8% TBE gel. DNA was eluted in DNA elution buffer and precipitated with isopropanol. The final library DNA was purified with AMPure XP beads (Beckman Coulter, #A63880).
Ribosome profiling

treatment_protocol: iPSCs and iPSC-neurons were treated with 100ug/ul cycloheximide at 37°C for 1min and then washed with ice-cold PBS with 100ug/ul cycloheximide. Cells were scraped off the plates in  ice-cold PBS with 100ug/ul cycloheximide, pelleted at 15,000g for 3min at °C, and snap-frozen in liquid nitrogen. Hippocampal tissues were collected and snap-frozen in liquid nitrogen.

tag: strain

value: Patient 2

tag: genotype

value: CRISPR-rescued

value: Ribosome profiling

tag: monosome rna yield (ug)

tag: rnase concentration

value: 100ng RNaseA + 60U RNase T1/A260


title: Participant ID and visit (v) # phchp067v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp067v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp065v3 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc_neuron11

description:
Ribosome protected footprints
qc_sample_ipsc_neuron11_reads_overlap_CDS.base
qc_sample_ipsc_neuron11_reads_overlap_CDS.length


title: qc_sample_ipsc_neuron7

description:
Ribosome protected footprints
qc_sample_ipsc_neuron7_reads_overlap_CDS.base
qc_sample_ipsc_neuron7_reads_overlap_CDS.length

value: Fragile X Syndrome


title: Participant ID and visit (v) # phchp065v2 Independent Test Cohorts (n=201) (505 visits)


title: A549 shCont, biological rep3

city: Lexington

first: Min

last: Chen

state: KY

address: 741 South Limestone

department: Toxicology and Cancer Biology

institute: University of Kentucky

description: Cells in regular culture for 3 days, 70% confluent. Cells were fed the day before harvesting.

hyb_protocol: Samples were hybridized with GeneChip Human HTA2.0 Arrays (Affymetrix) and scanned at the UKHC Genomics Microarray Core Facility in the University of Kentucky.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Commend Console (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations at gene-level assembly, were performed using Partek Genomics Suite 6.0.

source_name: A549 cells stably expressing lentiviral control shRNA

label_protocol: Single-stranded cDNA was generated from the amplified cRNA and labeled using the WT Plus kit (ThermoFisher/Affymetrix).

growth_protocol: A549 shCont and shS100A4 cells are cultured in DMEM/F12 supplemented with 10% FBS and 1% penicillin, 1% streptomycin, and 1% of L-glutamine.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A549 shCont and shS100A4 cells were cultured for 2 days(about 70% confluent), fed the day before harvesting for total RNA extraction.

tag: cell line

tag: shRNA

value: lentiviral control shRNA


title: qc_sample_ipsc_neuron8

description:
Ribosome protected footprints
qc_sample_ipsc_neuron8_reads_overlap_CDS.base
qc_sample_ipsc_neuron8_reads_overlap_CDS.length


title: qc_sample_ipsc_neuron6

description:
Ribosome protected footprints
qc_sample_ipsc_neuron6_reads_overlap_CDS.base
qc_sample_ipsc_neuron6_reads_overlap_CDS.length

value: Patient 1


title: Participant ID and visit (v) # phchp065v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp062v3 Independent Test Cohorts (n=201) (505 visits)


title: A549 shS100A4, biological rep3

source_name: A549 cells stably expressing lentiviral shRNA targeting S100A4

value: lentiviral shRNA targeting S100A4


title: A549 shCont, biological rep2


title: qc_sample_ipsc_neuron5

description:
Ribosome protected footprints
qc_sample_ipsc_neuron5_reads_overlap_CDS.base
qc_sample_ipsc_neuron5_reads_overlap_CDS.length


title: qc_sample_ipsc_neuron10

description:
Ribosome protected footprints
qc_sample_ipsc_neuron10_reads_overlap_CDS.base
qc_sample_ipsc_neuron10_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp062v1 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc_neuron4

description:
Ribosome protected footprints
qc_sample_ipsc_neuron4_reads_overlap_CDS.base
qc_sample_ipsc_neuron4_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp062v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp061v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp061v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp061v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp060v1 Independent Test Cohorts (n=201) (505 visits)


title: A549 shCont, biological rep1


title: qc_sample_ipsc_neuron3

description:
Ribosome protected footprints
qc_sample_ipsc_neuron3_reads_overlap_CDS.base
qc_sample_ipsc_neuron3_reads_overlap_CDS.length


title: qc_sample_ipsc_neuron2

description:
Ribosome protected footprints
qc_sample_ipsc_neuron2_reads_overlap_CDS.base
qc_sample_ipsc_neuron2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp058v1 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc_neuron1

description:
Ribosome protected footprints
qc_sample_ipsc_neuron1_reads_overlap_CDS.base
qc_sample_ipsc_neuron1_reads_overlap_CDS.length


title: qc_sample_ipsc8_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc8_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc8_low_rnase_reads_overlap_CDS.length

source_name: iPSC

value: 20ng RNase A + 12U RNase T1/A260


title: Participant ID and visit (v) # phchp058v2 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc5_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc5_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc5_low_rnase_reads_overlap_CDS.length


title: qc_sample_ipsc6_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc6_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc6_low_rnase_reads_overlap_CDS.length


title: qc_sample_ipsc_neuron9

description:
Ribosome protected footprints
qc_sample_ipsc_neuron9_reads_overlap_CDS.base
qc_sample_ipsc_neuron9_reads_overlap_CDS.length


title: qc_sample_ipsc7_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc7_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc7_low_rnase_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp057v1 Independent Test Cohorts (n=201) (505 visits)

description:
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: qc_sample_ipsc4_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc4_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc4_low_rnase_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp058v3 Independent Test Cohorts (n=201) (505 visits)


title: scRNA-seq_pGBM2

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Sequencing (BCL) files were processed with the Cell Ranger 2.1.0 package (10xGenomics).
Genome_build: GRCh38 transcriptome

source_name: patient-derived xenograft

growth_protocol: Surgically resected tumor specimens from pediatric patients with newly diagnosed or recurrent GBM were obtained from the Clark H. Smith Neurologic and Pediatric Tumor and Related Tissue Bank within the Arnie Charbonneau Cancer Research Institute at the University of Calgary, Calgary, Canada. Tumor tissue was gently dissociated by trituration, filtered using a 0.7 µm filter, washed and resuspended in sterile DPBS (Gibco). Tumor cells were injected into the right striatum of the brains of CB17 SCID mice (Charles River Laboratory). Animals were monitored for tumor growth and tumors were isolated when signs of morbidity were observed.

extract_protocol:
Xenograft tumor tissue was dissociated into single cells using the following protocol: 10 mL of ACCUTASETM (catalog # 07920) was added to tumor tissue for manual dissociation with surgical scissors. The sample was then incubated with sterile glass beads at 37°C, rotating continuously for 30 min. The glass beads were removed, and the sample was spun at 1000 rpm for 5 minutes at 25°C. The cell pellet was resuspended in neural stem cell media (NeuroCultTM NS-A Proliferation Kit (Human), catalog # 05751). Mouse cells were removed with the Miltenyi Biotec Mouse Cell Depletion Kit (catalog # 130-104-694) and the autoMACSâ Pro Separator and columns (catalog # 130-021-101). Protocol was followed as per manufacturers’ instructions. Viability and concentration of the purified human cells were quantified.
10xGenomics scRNA-seq with Chromium console
scRNA-seq

tag: tumor

value: pediatric GBM

tag: tumor type

value: second recurrence

tag: age


title: qc_sample_ipsc2_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc2_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc2_low_rnase_reads_overlap_CDS.length


title: qc_sample_ipsc1_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc1_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc1_low_rnase_reads_overlap_CDS.length


title: scRNA-seq_pGBM1

value: recurrence


title: Participant ID and visit (v) # phchp055v1 Independent Test Cohorts (n=201) (505 visits)

value: Independent Test cohort blood gene expression data


title: Participant ID and visit (v) # phchp053v3 Independent Test Cohorts (n=201) (505 visits)

value: M-BP


title: Participant ID and visit (v) # phchp055v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp053v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp055v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp053v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp049v2 Independent Test Cohorts (n=201) (505 visits)

value: M-SZA


title: Participant ID and visit (v) # phchp049v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp048v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp047v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp047v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp048v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp048v1 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ipsc3_low_rnase

description:
Ribosome protected footprints
qc_sample_ipsc3_low_rnase_reads_overlap_CDS.base
qc_sample_ipsc3_low_rnase_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp046v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp046v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp051v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp042v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp047v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp046v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp040v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp040v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp042v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp041v1 Independent Test Cohorts (n=201) (505 visits)

value: M-SZ


title: Participant ID and visit (v) # phchp042v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp039v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp033v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp038v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp027v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp030v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp038v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp040v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp031v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp038v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp025v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp030v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp026v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp031v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp026v1 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_hip_i_rpf

description:
Ribosome protected footprints
qc_sample_hip_i_rpf_reads_overlap_CDS.base
qc_sample_hip_i_rpf_reads_overlap_CDS.length

organism: Mus musculus

source_name: Hippocampus

value: Fmr1 -/y

value: 5U RNase I/A260


title: Participant ID and visit (v) # phchp026v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp031v2 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_hip_at_rpf

description:
Ribosome protected footprints
qc_sample_hip_at_rpf_reads_overlap_CDS.base
qc_sample_hip_at_rpf_reads_overlap_CDS.length


title: 314 organoids

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: CCO

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: cholangiocarcinoma organoids

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Total RNAs were extracted from tissues of organoids using miRVana isolation kit.

tag: source subject status

value: patients with biliary tract carcinomas

tag: tissue/cell type

value: cholangiocarcinoma organoids


title: NCC-CC1

source_name: cholangiocarcinoma cell line

value: cholangiocarcinoma cell line


title: qc_sample_ko_rna_batch4_rep2

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch4_rep2_reads_overlap_CDS.base
qc_sample_ko_rna_batch4_rep2_reads_overlap_CDS.length

value: RNA-seq


title: Participant ID and visit (v) # phchp021v2 Independent Test Cohorts (n=201) (505 visits)


title: 314 tissue

source_name: cholangiocarcinoma xenograft tissue

value: cholangiocarcinoma xenograft tissue


title: Participant ID and visit (v) # phchp022v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp022v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp024v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp021v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp021v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp020v3 Independent Test Cohorts (n=201) (505 visits)


title: A549 shS100A4, biological rep1

description: Cells in regular culture for 3 days, 70% confluent. Cells were fed the day before harvesting.


title: qc_sample_ko_rna_batch4_rep1

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch4_rep1_reads_overlap_CDS.base
qc_sample_ko_rna_batch4_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rna_batch3_rep2

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch3_rep2_reads_overlap_CDS.base
qc_sample_wt_rna_batch3_rep2_reads_overlap_CDS.length

value: wild-type


title: qc_sample_wt_rna_batch4_rep2

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch4_rep2_reads_overlap_CDS.base
qc_sample_wt_rna_batch4_rep2_reads_overlap_CDS.length


title: qc_sample_wt_rna_batch3_rep1

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch3_rep1_reads_overlap_CDS.base
qc_sample_wt_rna_batch3_rep1_reads_overlap_CDS.length


title: qc_sample_ko_rna_batch1_rep1

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch1_rep1_reads_overlap_CDS.base
qc_sample_ko_rna_batch1_rep1_reads_overlap_CDS.length


title: qc_sample_ko_rna_batch1_rep2

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch1_rep2_reads_overlap_CDS.base
qc_sample_ko_rna_batch1_rep2_reads_overlap_CDS.length


title: qc_sample_ko_rna_batch3_rep1

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch3_rep1_reads_overlap_CDS.base
qc_sample_ko_rna_batch3_rep1_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp019v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp020v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp019v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp019v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp017v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp019v5 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_wt_rna_batch2_rep1

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch2_rep1_reads_overlap_CDS.base
qc_sample_wt_rna_batch2_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rna_batch1_rep1

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch1_rep1_reads_overlap_CDS.base
qc_sample_wt_rna_batch1_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rna_batch2_rep2

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch2_rep2_reads_overlap_CDS.base
qc_sample_wt_rna_batch2_rep2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp016v3 Independent Test Cohorts (n=201) (505 visits)

description:
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: qc_sample_wt_rna_batch1_rep2

description:
Cytoplasmic mRNA
qc_sample_wt_rna_batch1_rep2_reads_overlap_CDS.base
qc_sample_wt_rna_batch1_rep2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp020v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp017v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp016v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp016v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp014v1 Independent Test Cohorts (n=201) (505 visits)

value: M-PSYCH


title: Participant ID and visit (v) # phchp013v3 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_ko_rpf_batch3_rep2

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch3_rep2_reads_overlap_CDS.base
qc_sample_ko_rpf_batch3_rep2_reads_overlap_CDS.length

value: Ribosome profiling

value: 100ng RNaseA + 60U RNase T1/A260


title: qc_sample_ko_rpf_batch3_rep1

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch3_rep1_reads_overlap_CDS.base
qc_sample_ko_rpf_batch3_rep1_reads_overlap_CDS.length


title: qc_sample_ko_rpf_batch4_rep2

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch4_rep2_reads_overlap_CDS.base
qc_sample_ko_rpf_batch4_rep2_reads_overlap_CDS.length


title: qc_sample_ko_rpf_batch2_rep1

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch2_rep1_reads_overlap_CDS.base
qc_sample_ko_rpf_batch2_rep1_reads_overlap_CDS.length


title: qc_sample_ko_rpf_batch1_rep2

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch1_rep2_reads_overlap_CDS.base
qc_sample_ko_rpf_batch1_rep2_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch4_rep1

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch4_rep1_reads_overlap_CDS.base
qc_sample_wt_rpf_batch4_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch4_rep2

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch4_rep2_reads_overlap_CDS.base
qc_sample_wt_rpf_batch4_rep2_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch3_rep2

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch3_rep2_reads_overlap_CDS.base
qc_sample_wt_rpf_batch3_rep2_reads_overlap_CDS.length


title: qc_sample_ko_rpf_batch4_rep1

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch4_rep1_reads_overlap_CDS.base
qc_sample_ko_rpf_batch4_rep1_reads_overlap_CDS.length


title: qc_sample_ko_rpf_batch1_rep1

description:
Ribosome protected footprints
qc_sample_ko_rpf_batch1_rep1_reads_overlap_CDS.base
qc_sample_ko_rpf_batch1_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch3_rep1

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch3_rep1_reads_overlap_CDS.base
qc_sample_wt_rpf_batch3_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch2_rep2

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch2_rep2_reads_overlap_CDS.base
qc_sample_wt_rpf_batch2_rep2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp010v2 Independent Test Cohorts (n=201) (505 visits)


title: qc_sample_wt_rpf_batch1_rep1

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch1_rep1_reads_overlap_CDS.base
qc_sample_wt_rpf_batch1_rep1_reads_overlap_CDS.length


title: qc_sample_wt_rpf_batch1_rep2

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch1_rep2_reads_overlap_CDS.base
qc_sample_wt_rpf_batch1_rep2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp010v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp012v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp013v1 Independent Test Cohorts (n=201) (505 visits)


title: rnase5

description:
Ribosome profiling
Ribosome protected footprints
3000ng RNase A + 375U RNase T1/µg RNA
processed data file: rnase.titration.rpf.rsem.gene.counts.txt
processed data file: rnase.titration.rpf.rsem.gene.tpm.txt

data_processing:
Library strategy: Ribo-Seq
Basecallling and fastq file generation were performed by Illumina Basespace.
Individual samples were separated from the raw fastq files based on the barcode sequences. Barcode and UMI sequences were trimmed and moved to the read names. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1).
Trimmed reads were quality filtered and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9).
PCR duplicates were marked based on the UMI sequences and only uniquely mapped reads without duplicates were retained with samtools (0.0.19) for the downstream analysis.
Cleaned bam files of ribosome footprints were converted to fastq files with bedtools (2.22.0). Gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rnase.titration.rpf.rsem.gene.counts.txt: Tab-delimited text file includes raw counts from RSEM.
Supplementary_files_format_and_content: rnase.titration.rpf.rsem.gene.tpm.txt: Tab-delimited text file includes TPM values from RSEM.

extract_protocol:
Hippocampal tissues were collected and snap-frozen in liquid nitrogen. Frozen tissues were thawed in ice-cold polysome lysis buffer [20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100µg/ml cycloheximide, 25U/ml Turbo DNaseI (Ambion, #AM2238), 1% NP-40 in nuclease-free water] and lysed by trituration through a 25-G need for 10 times. After 10-min incubation on ice, lysates were clarified by centrifugation at 2000g 4 °C for 10min. The supernatants were collected and clarified again by centrifugation at 20,000g 4 °C for 10min. The supernatants were collected and the amounts of nucleic acids were measured with Nanodrop (Thermo Fisher Scientific) and Qubit HS assays (Invitrogen). Lysate containing 2µg RNA in 0.3ml was digested with 5-fold serial diluted RNase A (Ambion, #AM2270) and RNase T1 (Thermo Fisher Scientific, #EN0542) at 25°C for 30min, including RNase1 (4.8ng RNase A + 0.6U RNase T1/µg RNA), RNase2 (24ng RNase A + 3U RNase T1/µg RNA), RNase3 (120ng RNase A + 15U RNase T1/µg RNA), RNase4 (600ng RNase A + 75U RNase T1/µg RNA), and RNase5 (3000ng RNase A + 375U RNase T1/µg RNA). The digestion was stopped by adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694) and chilling on ice. Digested lysates were loaded on 10%-50% sucrose gradients prepared in 1X polysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100µg/ml cycloheximide in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection interval through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS.
Libraries were prepared following the published protocols (Heyer et al., 2015; Ingolia et al., 2012). Briefly, rRNA was depleted from the purified monosomal RNA samples with RiboZero (Illumina, #MRZG12324). Remaining RNA samples were separated on a 15% TBU gel (National Diagnostics, #EC-833) and the ribosome footprints were size-selected based on the 26 and 34nt markers. RNA was eluted from the crushed gel pieces in RNA elution buffer (300mM NaOAc pH5.5, 1mM EDTA, 0.25% SDS) at RT overnight, filtered with Spin-X Centrifuge Tube Filters (Corning, #8162) and precipitated with equal volume of isopropanol. Recovered RNA was dephosphorylated with T4 Polynucleotide Kinase (NEB, #M0201S) and ligated with preadenylated adaptor in miRCat®-33 Conversion Oligos Pack (IDT) using T4RNL2Tr.K227Q ligase (NEB, #M0351L). Reverse transcription was performed with RT primers with 5nt-barcode and 5nt or 8nt unique molecular identifier (UMI) and SuperScript III (Invitrogen, #18080-044) in 1X first-strand buffer without MgCl2 (50 mM Tris-HCl, pH 8.3, 75 mM KCl). RT products were separated on a 10% TBU gel and the 130-140nt region was selected. cDNA was eluted in DNA elution buffer (10mM Tris pH 8.0, 300mM NaCl, 1mM EDTA) at RT overnight, filtered, and precipitated with isopropanol. Purified cDNA was circularized with CircLigase (Epicentre, #CL4115K). Optimal PCR cycle was determined empirically by test PCR reactions with titrated cycle numbers. Final PCR amplification was performed with KAPA Library Amplification Kit (Kapa Biosystems, #KK2611) and 180-190bp products were size-selected on an 8% TBE gel. DNA was eluted in DNA elution buffer and precipitated with isopropanol. The final library DNA was purified with AMPure XP beads (Beckman Coulter, #A63880).

tag: strain/background

tag: genotype/variation

tag: tissue

value: Hippocampus


title: Participant ID and visit (v) # phchp012v2 Independent Test Cohorts (n=201) (505 visits)

description:
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) # phchp009v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp006v2 Independent Test Cohorts (n=201) (505 visits)


title: rnase3

description:
Ribosome profiling
Ribosome protected footprints
120ng RNase A + 15U RNase T1/µg RNA
processed data file: rnase.titration.rpf.rsem.gene.counts.txt
processed data file: rnase.titration.rpf.rsem.gene.tpm.txt


title: Participant ID and visit (v) # phchp009v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp012v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp006v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp005v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp010v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp005v3 Independent Test Cohorts (n=201) (505 visits)


title: A549 shS100A4, biological rep2

description: Cells in regular culture for 3 days, 70% confluent. Cells were fed the day before harvesting.

value: lentiviral shRNA targeting S100A4


title: rnase4

description:
Ribosome profiling
Ribosome protected footprints
600ng RNase A + 75U RNase T1/µg RNA
processed data file: rnase.titration.rpf.rsem.gene.counts.txt
processed data file: rnase.titration.rpf.rsem.gene.tpm.txt


title: Participant ID and visit (v) # phchp004v4 Independent Test Cohorts (n=201) (505 visits)

value: Independent Test cohort blood gene expression data


title: rnase1

description:
Ribosome profiling
Ribosome protected footprints
4.8ng RNase A + 0.6U RNase T1/µg RNA
processed data file: rnase.titration.rpf.rsem.gene.counts.txt
processed data file: rnase.titration.rpf.rsem.gene.tpm.txt


title: rnase2

description:
Ribosome profiling
Ribosome protected footprints
24ng RNase A + 3U RNase T1/µg RNA
processed data file: rnase.titration.rpf.rsem.gene.counts.txt
processed data file: rnase.titration.rpf.rsem.gene.tpm.txt


title: input DNA_wash

city: Bristol

first: Caroline

middle: Alison

last: Rivers

address: Dorothy Hodgkin Building, Whitson Street

department: Translational Health Sciences

country: United Kingdom

institute: Bristol University

library_source: genomic

data_processing:
Library strategy: ChIP-nexus
Illumina NextSeq Control Software (NCS) was used for base-calling and quality score assignment using RTA v2,
Quality filter – average read quality <20 trimmed, reads <29 bp dropped, reads trimmed to 59 bp.
Reads were mapped to mm10 mouse reference genome using Bowtie2.
Mapped reads were filtered for mapping quality >20.
Peaks were called using MACS2 callpeak version macs2 2.1.1.20160309 with FDR <0.05, peak width 100 bp for each GR/MR ChIP-nexus treatment using combined mapped input DNA data for each treatment.
MACE border pairs were defined using MACE: Model based Analysis of ChIP-exo v1.2 (Wang et al., 2014) for each GR/MR ChIP-nexus treatment and for combined input control data for each treatment.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated from Bowtie2 mapped data; MACS2 ChIP binding site scores represent chr, start, end, name, length, -log10(pvalue), fold_enrichment, -log10(qvalue); MACE ChIP binding site scores represent chr, start, end, label, pvalue.

molecule: genomic DNA

source_name: Neuro2A cells

growth_protocol: Neuro2A cells were routinely cultured in DMEM supplemented with 7.5% FBS, cysteine.HCl 0.3 mM, L-alanine 0.4 mM, asparagine 0.45 mM, L-aspartic acid 0.4 mM, L-proline 0.4 mM and L-glutamate 0.4 mM (Oortgiesen 1989) up to passage 20 in a 5% CO2 humidified incubator at 37oC.

extract_protocol:
Cells were formaldehyde fixed and chromatin lysates were prepared by sonication (4x10s in Bioruptor) and benzonase-treatment (16U, 15 mins, 25oC).
ChIP-nexus was performed as in published protocol (He et al., 2015). Briefly, samples were end-repaired, dA-tailed, adapters were ligated, 5' overhangs were filled in, 5' ends trimmed, lambda-exonuclease treated, RecJ exonuclese digested, DNA was eluted, DNA was circularized, oligos annealed, BamHI digested and enriched by PCR-amplification for 18 cycles. PCR-amplification introduced bar-coded using NEBNext primers for Illumina  indexes 1 to 18. Input samples were prepared with NEBNext Ultra II DNA Library Prep with NEBNext Multiplex Oligos for Illumina (set 1 and 2, indexes 1 to 18). Sequencing was performed with NextSeq 500 Hi-Output Kit v2 (75 Cycles).

treatment_protocol: Neuro2A cells were seeded, at 6 million per 15 cm plate, in DMEM supplemented with 7.5% charcoal-stripped serum (CSS), cysteine.HCl 0.3 mM, L-alanine 0.4 mM, asparagine 0.45 mM, L-aspartic acid 0.4 mM, L-proline 0.4 mM and L-glutamate 0.4 mM (Oortgiesen 1989), incubated overnight, transfected using a ratio of 1:2 (w/v) DNA to jetPRIME® (Polyplus) following the manufacturer’s instructions.

tag: cell type

value: Neuroblast

tag: transfected proteins

value: eGFP-GR + mCherry-MR

tag: chip antibody

tag: treatment

value: cort, 2 x wash, 40 mins CSS media


title: Participant ID and visit (v) # phchp008v1 Independent Test Cohorts (n=201) (505 visits)

tag: gender-diagnosis

value: M-SZ

tag: vas stress score (1-100)


title: qc_sample_wt_rpf_batch2_rep1

description:
Ribosome protected footprints
qc_sample_wt_rpf_batch2_rep1_reads_overlap_CDS.base
qc_sample_wt_rpf_batch2_rep1_reads_overlap_CDS.length

tag: strain

tag: genotype

tag: monosome rna yield (ug)

tag: rnase concentration


title: input DNA_cort

value: cort 100 nM 20 mins


title: input DNA_vehicle

value: vehicle


title: GR_ChIP-nexus_cort+wash

value: GFP


title: GR_ChIP-nexus_cort


title: Participant ID and visit (v) # phchp039v1 Independent Test Cohorts (n=201) (505 visits)

value: M-BP


title: GR_ChIP-nexus_vehicle


title: Participant ID and visit (v) # phchp004v1 Independent Test Cohorts (n=201) (505 visits)

value: M-SZA


title: Participant ID and visit (v) # phchp004v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp003v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp003v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp359v3 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: F-PTSD


title: Participant ID and visit (v) # phchp005v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp003v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp003v2 Independent Test Cohorts (n=201) (505 visits)


title: MR_ChIP-nexus_cort+wash

value: RFP


title: MR_ChIP-nexus_cort


title: Participant ID and visit (v) # phchp363v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
69
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 111A [D9-6]

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

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

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

value: lungs

tag: time point

value: 48h after infection


title: Participant ID and visit (v) # phchp368v2 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

value: F-MDD


title: Participant ID and visit (v) # phchp003v5 Independent Test Cohorts (n=201) (505 visits)

value: Independent Test cohort blood gene expression data


title: Participant ID and visit (v) # phchp004v3 Independent Test Cohorts (n=201) (505 visits)


title: MR_ChIP-nexus_vehicle

value: Neuroblast


title: 2days flu line 111A [D9-5]

source_name: 2days flu_lungs

value: influenza virus (flu)


title: 2days flu line 21B [D9-2]


title: qc_sample_ko_rna_batch2_rep1

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch2_rep1_reads_overlap_CDS.base
qc_sample_ko_rna_batch2_rep1_reads_overlap_CDS.length

value: Fmr1 -/y

value: RNA-seq


title: 2days pbs line 21B [D9-3]


title: 2days flu line 111A [D9-4]


title: 2days flu line 2513A [D8-5]


title: Participant ID and visit (v) # phchp341v2 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: Participant ID and visit (v) # phchp342v1 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: 2days flu line 21B [D9-1]


title: Participant ID and visit (v) # phchp337v3 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: M-PTSD


title: Participant ID and visit (v) # phchp345v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
75
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: qc_sample_ko_rna_batch3_rep2

description:
Cytoplasmic mRNA
qc_sample_ko_rna_batch3_rep2_reads_overlap_CDS.base
qc_sample_ko_rna_batch3_rep2_reads_overlap_CDS.length


title: Participant ID and visit (v) # phchp345v3 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 2513A [D8-4]


title: 2days pbs line 2513A [D8-2]


title: 2days pbs line 2513A [D8-3]


title: Participant ID and visit (v) # phchp341v3 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 flu line 1488A [D8-1]


title: 2days pbs line 5003A [D7-4]


title: 2days flu line 5003A [D7-5]


title: 2days pbs line 1912A [D7-2]


title: Participant ID and visit (v) # phchp323v3 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) # phchp328v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
83
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 5003A [D7-3]


title: Participant ID and visit (v) # phchp325v2 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


title: Participant ID and visit (v) # phchp320v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: Participant ID and visit (v) # phchp320v3 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 1912A [D7-1]


title: Participant ID and visit (v) # phchp328v1 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


title: Participant ID and visit (v) # phchp334v1 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

value: F-BP


title: 2days flu line 5003A [D7-6]


title: Participant ID and visit (v) # phchp320v2 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) # phchp323v2 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
84
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) # phchp319v6 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)


title: 2days pbs line 2126A [D6-4]

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


title: 2days flu line 1912A [D6-5]


title: Participant ID and visit (v) # phchp319v2 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 2126A [D6-3]


title: 2days flu line 1912A [D6-6]


title: 2days flu line 2126A [D6-2]


title: Participant ID and visit (v) # phchp316v5 Independent Validation Cohort with Clinically Severe Stress(n=48) (75 visits)

description:
85
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 [D5-4]


title: 2days flu line 2126A [D6-1]


title: 2days flu line 3348A [D5-6]


title: 2days flu line 3348A [D5-5]


title: Participant ID and visit (v) # phchp313v2 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