title: Placental tissue ID 660

value: Placenta

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: birth weight (gram)

value: Female

tag: gestational age (month)

tag: ethnicity

value: 0 (European)

tag: parity

value: 2 (2 children)

tag: maternal age (year)

value: 0 (never smoked)

tag: gestational weight gain (kilogram)

tag: gestational diabetes

tag: gestational hypertension


title: EXR-MBITZ1CTOT1SAMPB1A4-BS: CTOT04_01_Urine_1-4

status: Public on Mar 16 2019

type: SRA

city: Ann Arbor

first: Markus

last: Bitzer

state: MI

address: 1500 E Medical Center Dr SPC 5361

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

molecule: total RNA

organism: Homo sapiens

source_name: Urine

extract_protocol:
450 ul biofluid sample were mixed with 105 ul buffer P, digested with 28 ul Proteinase K working solution at 65C for 8 minutes, extracted with 517 ul ED2 working solution, cooled to 10C, phase separation was induced after adding 110 ul chloroform, approx. 600 ul aqueous supernatants were mixed with 1200 ul buffer VB2G, loaded on Zymo-I 96-well silica matrix plate, washed twice with 970 ul EWL, once with 970 ul 100% ethanol, twice with 500 ul 80% ethanol and eluted into 20 ul TrisHCl pH 7.5. Protocol was executed on epMotion 5075 liquid handling system. Low speed centrifugation (1200 g x 10 minutes) was performed for cell removal.
No Kit was used. Multiplexed Small RNA library preparation protocol developed by Tuschl lab. Adenylated DNA adapters each containing a unique 5-nt barcode sequence were ligated to the 3end of the RNA overnight at 4C.The barcoded adapters allow 24 individual RNA samples to be pooled into one lane.The pooled samples were purified on a 15% polyacrylamide gel and size-selection was guided by radiolabeled RNA markers corresponding to a sRNA size of 19-30 nt. Next, a 26-nt RNA adapter compatible with Illumina sequencing was ligated to the 5end of the RNA at 37C for 1 hour and samples were purified on a 12% polyacrylamide gel.  The cDNA libraries were then generated by reverse transcription and amplified using up to 20 PCR cycles, and the final libraries ranging from 90-101 nt were purified on a 2.5% agarose gel and sequenced in a single Illumina HiSeq lane.

tag: diagnosis

value: nephrotic syndrome

tag: tissue

value: urine

tag: condition

value: Transplanted kidney present

tag: anatomical location

value: Urinary system structure

tag: rna source

value: total cell-free biofluid RNA

tag: 3' adapter sequence

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: LT_FB_S_R3

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package v 2.1 of CLC Genomics Workbench Tool (v.9.5.2) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Lentinus tigrinus ALCF2SS1-6 v1.0 (Lenti6_1) JGI project ID: 1020066
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

molecule: polyA RNA

organism: Lentinus tigrinus

source_name: fruiting body, stipe

growth_protocol: Vegetative mycelia of Lentinus tigrinus RLP-9953-sp were maintained on MEA (20 g malt extract, 0.5 g yeast extract, 15 g agar for 1L). For fruiting a mycelial plug was placed (5 mm diameter) on modified sawdust-rice bran medium (1 part wheat bran and 2 parts aspen sawdust wetted to 65% moisture for 100 ml in a 250 ml beaker). The culture was incubated for 21 days at 30 °C in the dark, then placed in a moist growth chamber at 25 °C in a 12/12 hour light/dark cycle. Vegetative mycelia, stage 1 primordia, stage 2 primordia cap and stipe, young fruiting body cap and stipe and fruiting body cap and stipe tissues were harvested for RNA-Seq. Stage 1 primordium was defined as a 5-20 mm tall white stalk-structure without any differentiation of a cap initial, stage 2 primordium was defined as a 15 – 25 mm tall stalk-like structure with a brown apical pigmentation (cap initial), young fruiting body had and up to 5 mm wide brown cap initial with just barely visible gills on the bottom, growing on a 30-40 mm tall stipe, fruiting body was 50-70 mm tall, with fully flattened (but not funnel-shaped) cap.

extract_protocol:
After harvesting, samples were immediately placed on liquid nitrogen and stored at -80 °C until use.  50-75 mg frozen tissue was placed in a pre-chilled mortar and ground to a fine powder. RNeasy Midi Kit (QIAGEN) was used for RNA extraction according to manufacturer«s instructions.
Whole transcriptome sequencing was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent) and Qubit (ThermoFisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Backman Coulter). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent). Concentration of each library was determined using either the QPCR Quantification Kit for Illumina (Agilent) or the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)

tag: strain

tag: group

value: fruiting body, stipe


title: Placental tissue ID 652

type: RNA

city: Diepenbeek

first: Tim

middle: S

last: Nawrot

address: Agoralaan building D

department: Centre for Environmental Sciences

country: Belgium

institute: Hasselt University

hyb_protocol: Cyanine-3 labelled cRNA was hybridized onto Agilent Whole Human Genome 8 x 60K microarrays.

scan_protocol: Microarray signals were detected using the Agilent DNA G2505C Microarray Scanner (Agilent Technologies). Scan images were converted into TXT files using the Agilent Feature Extraction Software (Version 10.7.3.1, Agilent Technologies, Amstelveen, The Netherlands).

data_processing: An in-house developed quality control pipeline in R software was used to preprocess raw data as follows: local background correction, omission of controls, flagging of bad spots and spots with too low intensity, log2 transformation and quantile normalization using arrayQC. More information about the flagging and the R-scripts of the pipeline are available at https://github.com/BiGCAT-UM/arrayQC_Module . Further preprocessing included removal of probes showing >30% flagged data, merging of replicate probes based on the median, and imputation of missing values by means of K-nearest neighbor imputation (K = 15). Batch effects were corrected for by using an empirical Bayes method (ComBat) (Johnson et al., 2007). For genes with multiple probes, the probe with the largest interquartile range was selected. From the resulting 18,847 probes, only those with expression levels above 6 (in the log2 scale) in a minimum of 30 samples were kept, leaving 14,040 genes for further analysis.

source_name: Placental tissue

label_protocol: 0.2 μg total RNA was used to synthesize fluorescent cyanine-3-labeled cRNA following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies).

extract_protocol: Total RNA was extracted from one placental tissue biopsy using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s protocol. RNase-Free DNase treatment was performed on RNA samples according to the manufacturer’s instructions (Qiagen, Venlo, The Netherlands). RNA quantity and purity were assessed by spectrophotometry (Nanodrop 1000, Isogen Life Science, De Meern, the Netherlands) and RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). Samples with RNA Integrity Number below 6 were excluded from further analysis.

treatment_protocol: Placental tissue was collected within 1 hour after delivery. Four standardized biopsies were taken from the fetal side, at fixed locations across the middle point of the placenta around 4 cm distance from the umbilical cord (Janssen et al., 2017). The collected biopsies were stored in RNA later (ThermoFisher Scientific, Massachusetts, USA) at 4°C for at least 12 hours and maximally 24 hours, followed by storage at -20°C.

tag: labeling date

tag: hybridization date

tag: date delivery

tag: maternal pre-pregnancy bmi

tag: Sex

value: Male

tag: maternal smoking


title: HT1080-IFNg-3

first: Weimin

last: Wang

state: Michigan

address: 109 Zina Pitcher Place

department: Surgery

description: processed data file: mRNA_in_HT_Ctrl_vs_IFNg-RPKM.txt

data_processing:
Data was analyzed by the University of Michigan Bioinformatics Core. The quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.3).
The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, reads were aligned to the reference transcriptome (hg19) using TopHat (version 2.0.13) and a second round of quality control was performed after alignment. Cufflinks/CuffDiff (version 2.2.1) was used for expression quantitation, normalization, and differential expression analysis. Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Diagnostic plots were generated using the CummeRbund R package.
Different conditions were compared using ballgown R package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mRNA_in_HT_Ctrl_vs_IFNg-RPKM.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: HT-1080 cells

growth_protocol: HT-1080 cells were cultured routinely in EMEM (ATCC) medium.

extract_protocol:
Total RNA was isolated from cells by column purification (Direct-zol RNA Miniprep Kit, Zymo Research) with DNase treatment.
The Ribo-Zero Gold rRNA Removal Kit (Illumina) and TruSeq® Stranded Total RNA Library Prep Globin kit (Illumina) were used to prepare the library for RNA-sequencing. Sequencing was performed by the University of Michigan DNA Sequencing Core, using the Illumina Hi-Seq 4000 platform, paired end, 50 cycles.

treatment_protocol: Recombinant IFNg 10 ng/ml treated for 8h.

tag: cell line

tag: cell type

value: fibrosarcoma cell line from ATCC

tag: genotype/variation

value: WT

tag: treatment

value: IFNg


title: HT1080-Ctrl-3

value: PBS


title: EXR-MBITZ1CTOT1SAMPB1A3-BS: CTOT04_01_Urine_1-3

tag: diagnosis

tag: tissue

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 36: M8

type: genomic

city: Beijing

first: Hongying

last: Ma

address: yuanmingyuan road NO.2

country: China

institute: China agriculture university

description: Genomic DNA extracted from blood was genotyped with the Illumina Equine SNP70 Bead Array

hyb_protocol: Not provided

scan_protocol: After allele-specific staining BeadChip arrays  and scanned on  Illumina BeadScand..

data_processing:
Genomic DNA extracted from blood was genotyped using the Illumina Equine SNP70 Bead Array.
Image data was analyzed using GenomeStudio Software.

label: not provided

molecule: genomic DNA

organism: Equus caballus

source_name: Kazakh horse

label_protocol: Not provided

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction. Integrity and purity of DNA verified by agarose gel electrophoresis and A260/280 ratio.

treatment_protocol: The samples were obtained following the principles approved by the Animal Care and Use Committee of China Agricultural University (Permit Number: XK257)

tag: gender

value: unknown

value: blood

tag: age

value: 3 years


title: Chinese horse breeds_Series 35: M7


title: HT1080-Ctrl-1


title: LT_FB_L_R3

source_name: fruiting body, lamellae

value: fruiting body, lamellae


title: LT_FB_S_R2


title: LT_FB_S_R4


title: HT1080-Ctrl-2


title: EXR-MBITZ1CTOT1SAMPB1A2-BS: CTOT04_01_Urine_1-2

value: nephrotic syndrome

tag: condition

tag: anatomical location

tag: rna source

tag: 3' adapter sequence

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Chinese horse breeds_Series 34: M6


title: HT1080-IFNg-1


title: LT_FB_L_R1

tag: strain

tag: group


title: LT_FB_C_R2

source_name: fruiting body, cap

value: fruiting body, cap


title: LT_FB_C_R3


title: Chinese horse breeds_Series 33: M5


title: Chinese horse breeds_Series 37: M9-1


title: Chinese horse breeds_Series 31: M3


title: Chinese horse breeds_Series 30: M2


title: LT_YFB_S_R3

source_name: young fruiting body, stipe

value: young fruiting body, stipe


title: EXR-MBITZ1CTOT1SAMPB1A1-BS: CTOT04_01_Urine_1-1

value: urine

value: Transplanted kidney present

value: Urinary system structure

value: total cell-free biofluid RNA

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: LT_YFB_S_R2


title: LT_YFB_S_R1


title: Chinese horse breeds_Series 28: NQ29

source_name: Naqu horse


title: LT_YFB_C_R2

source_name: young fruiting body, cap

value: young fruiting body, cap


title: EXP19NG2: Treated prostate benign epithelium sample 9

city: Portland

first: Ryan

last: Gordon

state: OR

address: 3181 SW Sam Jackson Park Road, BRB519

institute: Oregon Health & Science University

description:
Prostate benign epithelium treated samples 9 and 10
raw_data_file: EXP19NG2_EXP24NG_raw.txt

hyb_protocol: Cy3- and Cy5-conjugated cDNA targets were then purified by QIAquick PCR purification columns, combined, vacuum-concentrated, and diluted to 55 µl with hybridization solution containing final concentrations of 50% formamide, 4.1x Denhardts, and 4.4x SSC. To reduce nonspecific hybridization, the hybridization solution also contained final concentrations of 15 µg human Cot1 DNA (Invitrogen), 12µg poly-deoxyadenylate, and 5 µg of yeast tRNA (Sigma). After clarification by centrifugation, the cDNA/hybridization solution was applied to DNA microarrays and incubated at 42ºC for 16-20 h.

scan_protocol: After hybridization, microarray slides were washed by immersion in 2X SSC, 0.1%SDS for 5 min at room temperature, 1X SSC, 0.01% SDS for 5 min at room temperature, and 0.2X SSC for 2 min at room temperature. The microarrays were dried by centrifugation for 5 min at 1000 rpm and scanned immediately with a ScanArray 4000 confocal laser system (Perkin-Elmer).

data_processing: Fluorescent intensities were background subtracted, and normalization and filtering of the data were performed using the QuantArray software package (Perkin-Elmer). When comparing gene expression between different groups, genes were Z-normalized and rank ordered, and outliers identified and selected for further consideration based upon previously reported criteria, including Student’s t-test P-value </= 0.003 between indicated groups, fold difference >/= 1.8 fold, and for at least one of the groups, expression 2 fold above background.

source_name: Prostate benign epithelium treated with genistein

label_protocol: To generate fluorescently-labeled single-stranded cDNA target, 40µg of total RNA was incubated with 2µg of anchored oligodeoxythymidylate primer in a total volume of 30µl at 70ºC for 10 min and chilled on ice. To each sample was added 10X first strand buffer (6µl), 0.1M DTT (6µl), 20X aminoallyl-dNTP mix (3µl; 10mM dATP, 10mM dCTP, 10mM dGTP, 6mM dTTP, and 4mM aminoallyl-dUTP), RNase inhibitor (0.5µl) (RNasin, Promega), and StrataScript reverse transcriptase (3µl; 50U/µl). After incubation at 48ºC for 60 min, an additional 50 units (1µl) of StrataScript was added to the samples and incubated for an additional 60 min. The reaction was stopped by adding 12 µl of 0.5M EDTA (pH 8). Residual RNA was hydrolyzed by adding 12 µl of 1M NaOH to the mixture followed by incubation at 65ºC for 15 min and cooled to room temperature. The reaction was neutralized with 16.8µl of 1N HCl. First-strand cDNA was purified from unicorporated amino allyl-dUTPs on QIAquick PCR purification columns (Qiagen) according to manufacuter’s protocols, except that QIAquick wash buffer was replaced with 5 mM potassium phosphate buffer (pH 8.5) containing 80% ethanol, and cDNA was eluted with 4 mM potassium phosphate buffer (pH 8.5) and vacuum-dried. cDNA was resuspended in 10 µl 0.05 M Na2CO3 buffer (pH 9), mixed with either Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia), and incubated for 90 min in the dark at room temperature.

extract_protocol: Prostate tissue was collected following radical prostatectomy, samples were snap frozen within 30 minutes of the procedure.  6-μm serial cryosections were cut and sections were processed immediately prior to LCM, normal epithelial or cancer cells were micro-dissected on a PixCell II LCM Workstation (Arcturus), total RNA extracted using a PicoPure RNA Extraction kit (Arcturus), RNA integrity analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies), and RNA liner amplification performed.

treatment_protocol: Patients with localized, biopsy-proven adenocarcinoma of the prostate who had been scheduled for radical prostatectomy, had a Gleason's score of 6 or 7, a prostate-specific antigen level of less than 20 ng/mL, clinical stage T1 or T2 cancer, and intact end organ function, and were not on other therapy were accrued onto a Northwestern University Institutional Review Board–approved protocol, after they provided verbal and written informed consent. The trial was registered with the National Cancer Institute (PDQ Registration No. NCT00058266). Patients were randomly assigned to genistein treatment or no treatment in a 1:1 ratio, before radical prostatectomy. Patients received 150-mg gel cap pills of Genistein or a mock control daily for four weeks prior to surgery.

tag: sample

value: Genistein 150mg/d for 4 weeks


title: EXP24NG: Treated prostate benign epithelium sample 10

value: Prostate benign epithelium treated with genistein


title: LT_YFB_C_R3


title: EXP18NG: Treated prostate benign epithelium sample 7

description:
Prostate benign epithelium treated samples 7 and 8
raw_data_file: EXP18NG_EXP19NG_raw.txt


title: EXP19NG: Treated prostate benign epithelium sample 8


title: LT_FB_C_R1


title: EXP16NG: Treated prostate benign epithelium sample 6

description:
Prostate benign epithelium treated samples 5 and 6
raw_data_file: EXP9NG_EXP16NG_raw.txt


title: Chinese horse breeds_Series 27: NQ28


title: LT_P2_S_R3

source_name: stage 2 primordium, stipe

value: stage 2 primordium, stipe


title: EXP9NG: Treated prostate benign epithelium sample 5


title: Chinese horse breeds_Series 25: NQ25

value: unknown


title: Chinese horse breeds_Series 26: NQ27

value: blood


title: Chinese horse breeds_Series 32: M4

value: 3 years


title: EXP8NG: Treated prostate benign epithelium sample 4

description:
Prostate benign epithelium treated samples 3 and 4
raw_data_file: EXP4NG_EXP8NG_raw.txt


title: EXP2NG: Treated prostate benign epithelium sample 2

description:
Prostate benign epithelium treated samples 1 and 2
raw_data_file: EXP1NG_EXP2NG_raw.txt

source_name: Prostate adenocarcinoma

value: Prostate adenocarcinoma


title: Chinese horse breeds_Series 24: NQ24


title: LT_P2_S_R1


title: LT_P2_S_R2


title: LT_P2_C_R3

source_name: stage 2 primordium, cap

value: stage 2 primordium, cap


title: Chinese horse breeds_Series 29: NQ30


title: Chinese horse breeds_Series 23: NQ23


title: LT_P2_C_R1


title: EXP1NG: Treated prostate benign epithelium sample 1


title: Chinese horse breeds_Series 22: NQ22


title: LT_P2_C_R2


title: Chinese horse breeds_Series 21: NQ21


title: LT_YFB_C_R1


title: Chinese horse breeds_Series 20: NQ20


title: LT_P1_R3

source_name: stage 1 primordium

value: stage 1 primordium


title: Chinese horse breeds_Series 19: NQ19


title: LT_P1_R2


title: EXP16T: Prostate adenocarcinoma sampel 10

description:
Prostate adenocarcinoma samples 9 and 10
raw_data_file: EXP14T_EXP16T_raw.txt

value: Mock


title: Chinese horse breeds_Series 18: NQ18


title: EXR-MBITZ1CTOT1SAMPB3A2-BS: CTOT04_01_Urine_3-2

value: nephrotic syndrome

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: EXP23T: Prostate adenocarcinoma sampel 8

description:
Prostate adenocarcinoma samples 7 and 8
raw_data_file: EXP13T_EXP23T_raw.txt


title: Chinese horse breeds_Series 17: NQ17


title: EXP5T: Prostate adenocarcinoma sampel 6

description:
Prostate adenocarcinoma samples 5 and 6
raw_data_file: 34902T_EXP5T_raw.txt


title: LT_VM_R3

source_name: vegetative mycelium

value: vegetative mycelium


title: EXP4NG: Treated prostate benign epithelium sample 3


title: EXP13T: Prostate adenocarcinoma sampel 7


title: Chinese horse breeds_Series 16: NQ16


title: LT_VM_R2


title: EXP14T: Prostate adenocarcinoma sampel 9


title: Chinese horse breeds_Series 15: NQ15


title: 34902T: Prostate adenocarcinoma sampel 5


title: LT_VM_R1


title: Chinese horse breeds_Series 14: NQ14


title: LT_P1_R1


title: 34939T: Prostate adenocarcinoma sampel 4

description:
Prostate adenocarcinoma samples 3 and 4
raw_data_file: 34931T_34939T_raw.txt


title: Chinese horse breeds_Series 13: NQ13


title: 34931T: Prostate adenocarcinoma sampel 3


title: CC_FB_S_R3

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.3). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.1 of CLC Genomics Workbench Tool (v. 9.5.3) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Coprinopsis cinerea AmutBmut pab1-1 v1.0 (Copci_AmutBmut1) JGI Project Id: 1004746
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Coprinopsis cinerea

growth_protocol: For fruiting Coprinopsis cinerea strain #326 (A43mut B43mut pab 1-1) an agar disk (5 mm in diameter) was placed on the center of YMG/T agar media (4 g yeast extract, 10 g malt extract, 4 g glucose, 10 g agar media with 100 mg tryptophane added after cooling at 37 °C for five days in the dark. When the colonies reached the 1-2 mm distance from the edge of Petri dishes they were placed into 25 °C for one week in a 12 hrs light/12 hrs dark cycle for fruiting

extract_protocol:
After harvesting, samples were immediately placed on liquid nitrogen and stored at -80 °C until use. 10-20 mg frozen tissue was placed in a pre-chilled mortar and ground to a fine powder. Quick-RNA Miniprep Kit (Zymo Research) was used to extract RNA according to manufacturer«s instructions.
Whole transcriptome sequencing was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent) and Qubit (ThermoFisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Backman Coulter). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent). Concentration of each library was determined using either the QPCR Quantification Kit for Illumina (Agilent) or the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)

value: fruiting body, stipe


title: CC_FB_S_R2


title: HCC70 JQ1_3

city: Cleveland

first: Gurkan

last: Bebek

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Univ.

description: Gene expression data from HCC70 cells treated with BET inhibitor, JQ1, for 72 hours.

hyb_protocol: Hybridized arrays were automatically stained and scanned with the Affymetrix standard stain and scan protocol.

data_processing: The Affymetrix Human Gene 2.0. St Microarray were processed with RMA (robust multichip average algorithm) as implemented in Bioconductor package oligo [CITE_A], where background subtraction, quantile normalization and summarization (via median-polish) was accomplished. The top differentially expressed genes were identified using empirical Bayesian procedure of limma package. FDR method was selected to adjust the p-values for multiple testing.

label: biotin

label_protocol: For each sample, 150 ng RNA was used to synthesize and label cDNA with biotin for hybridization to Human Gene 2.0 ST expression microarrays using the GeneChip WT Plus labeling kit and protocol.

extract_protocol: Cells were harvested and RNA was extracted with Trizol reagent (Ambion, 15596018) and treated with DNase I (Ambion, AM1906).

tag: agent


title: Chinese horse breeds_Series 12: NQ12


title: 34733T: Prostate adenocarcinoma sampel 2

description:
Prostate adenocarcinoma samples 1 and 2
raw_data_file: 33787T_34733T_raw.txt


title: HCC70 Control_3

description: Gene expression data from HCC70 cells treated with vehicle.

scan_protocol: Hybridized arrays were automatically stained and scanned with the Affymetrix standard stain and scan protocol.

source_name: HCC70 cells treated with vehicle

value: control


title: 33787T: Prostate adenocarcinoma sampel 1


title: EXP20N: Control prostate benign epithelium sample 13

description:
Control prostate benign epithelium samples 13 and 14
raw_data_file: EXP20N_EXP25N_raw.txt

source_name: Prostate benign epithelium

value: Prostate benign epithelium


title: EXP25N: Control prostate benign epithelium sample 14


title: HCC70 JQ1_2

source_name: HCC70 cells treated with BET inhibitor, JQ1, for 72 hours


title: HCC70 JQ1_1


title: CC_FB_S_R1

source_name: fruiting body, stipe


title: Chinese horse breeds_Series 10: NQ10


title: CC_FB_CL_R3

source_name: fruiting body, cap+lamellae

value: fruiting body, cap+lamellae


title: HCC70 Control_2


title: MDA-MB-231 Control_3

description: Gene expression data from MDA-MB-231 cells treated with vehicle.

source_name: MDA-MB-231 cells treated with vehicle


title: Chinese horse breeds_Series 11: NQ11


title: MDA-MB-231 JQ1_3

description: Gene expression data from MDA-MB-231 cells treated with BET inhibitor, JQ1, for 72 hours.


title: EXP11N: Control prostate benign epithelium sample 10

description:
Control prostate benign epithelium samples 9 and 10
raw_data_file: EXP10N_EXP11N_raw.txt


title: EXP15N: Control prostate benign epithelium sample 12

description:
Control prostate benign epithelium samples 11 and 12
raw_data_file: EXP14N_EXP15N_raw.txt


title: EXP14N: Control prostate benign epithelium sample 11


title: CC_FB_CL_R1


title: MDA-MB-231 Control_2


title: Chinese horse breeds_Series 8: NQ8

description: Genomic DNA extracted from blood was genotyped with the Illumina Equine SNP70 Bead Array


title: C75_2

city: shanghai

first: cuilan

last: hou

address: luding road

institute: shanghai jiaotong university

data_processing:
Sequencing-received raw data were subsequently filtered for Perl scripts to ensure data quality. All clean data were obtained by removing all adaptor-polluted reads, low quality tags, empty reads, and reads which had slumber of N bases accounting for more than 5% from raw sequences. Finally, statistics analyses were performed on the clean qualitative and quantitative data obtained.
Read counts of every sample was analyzed using HTSeq v6.0. RPKM (Reads Per Kilo base Millon Mapped Reads) and computed to estimate gene expression levels.
Differential expression analysis of two conditions was performed using the DEGseq R package (1.28.0). Pvalue <0.05 and |FoldChange|>1.5 were set as the threshold for significantly differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Counts, RPKMs

organism: Mus musculus

source_name: lung tissue

growth_protocol: Twenty-one C57BL/6 mice (eight weeks) were purchased from the Shanghai Laboratory Animal Center (Chinese Academy of Sciences, China), and raised under controlled conditions (45-55% relative humidity, 22±2℃ and 12 hour dark-light cycles), with unrestricted access to food and water.

extract_protocol:
RNA was harvested using Trizol reagent.
Ribosomal RNA was removed from 3 μg RNA (including mRNAs and lncRNAs) using an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA). Afterwards, sequencing libraries were obtained according to the manufacturer’s instruction. Next, PCR products were purified (AMPure XP system) and the library qualification was assessed, using the Agilent TapeStation 2200 system (Agilent Technologies,USA).

treatment_protocol: The weight and health status of the mice were monitored regularly, and mice were randomly assigned to three groups: the model group, which mice were received a single MCT (60 mg/kg, subcutaneous injection, Sigma, Germany) for 5 weeks to induce PAH; The treatment group, where randomly selected MCT-injected mice received C75 (2 mg/kg, subcutaneous injection, dissolved in 0.5% DMSO) once a week for 5 weeks, and the control group, which received an equivalent injuection of saline each week.

value: intraperitoneal injection 0.1 mL MCT and 0.1 mL C75 once a week for 5 weeks

value: lung


title: Chinese horse breeds_Series 9: NQ9


title: HCC70 Control_1


title: MDA-MB-231 JQ1_2

source_name: MDA-MB-231 cells treated with BET inhibitor, JQ1, for 72 hours


title: Chinese horse breeds_Series 6: NQ6


title: C75_1


title: CC_YFB_S_R2

source_name: young fruiting body, stipe

value: young fruiting body, stipe


title: MCT_2

value: intraperitoneal injection 0.1 mL saline and 0.1 mL MCT once a week for 5 weeks


title: EXP10N: Control prostate benign epithelium sample 9


title: CC_FB_CL_R2


title: CC_YFB_S_R3


title: CC_YFB_L_R3

source_name: young fruiting body, lamellae

value: young fruiting body, lamellae


title: EXP23N: Control prostate benign epithelium sample 8

description:
Control prostate benign epithelium samples 7 and 8
raw_data_file: EXP13N_EXP23N_raw.txt


title: CC_YFB_S_R1


title: PC_FB_R3

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v. 10.0.1). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package v. 2.15 of CLC Genomics Workbench Tool (v. 10.0.1) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Phanerodontia chrysosporium

source_name: fruiting body

growth_protocol: Phanerochaete chrysosporium RP-78 was fruited on YMPG media (10 g glucose, 10 g malt extract, 2 g peptone, 2 g yeast extract, 1 g asparagine, 2 g KH2PO4, 1 g MgSO4 x 7 H2O, 20 g agar for 1L with 1 mg thiamine added after cooling) covered with cellophane for 7 days at 37 °C in the dark, then placed in a moist growth chamber at 25 °C in an area with dimmed ambient light conditions, following the recommendations of Jill Gaskell (US Forest Products Laboratory, Washington, D. C., USA). Vegetative mycelium, young fruiting body and fruiting body stages were harvested for RNA extraction. Young fruiting body stage was defined as fruiting body initials that forms a compact mat well-delimited from the surrounding vegetative mycelium, while the fruiting bodies were harvested just after they started releasing spores (visible on the lids of Petri dishes).

extract_protocol:
After harvesting, samples were immediately placed on liquid nitrogen and stored at -80 °C until use.  10-20 mg frozen tissue was placed in a pre-chilled mortar and ground to a fine powder. Quick-RNA Miniprep Kit (Zymo Research) was used according to manufacturer«s instructions.
Whole transcriptome sequencing was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent) and Qubit (ThermoFisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Backman Coulter). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent). Concentration of each library was determined using either the QPCR Quantification Kit for Illumina (Agilent) or the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)

value: fruiting body


title: MDA-MB-231 Control_1


title: PC_FB_R2

value: CALKCANXX


title: EXP13N: Control prostate benign epithelium sample 7


title: Control_2

value: intraperitoneal injection 0.2 mL saline once a week for 5 weeks


title: 34931N: Control prostate benign epithelium sample 4

description:
Control prostate benign epithelium samples 3 and 4
raw_data_file: 34902N_34931N_raw.txt


title: MDA-MB-231 JQ1_1


title: PC_FB_R1


title: Chinese horse breeds_Series 7: NQ7

source_name: Naqu horse

value: unknown

value: blood

value: 3 years


title: Control_1


title: MCT_1


title: CC_YFB_C_R3

source_name: young fruting body, cap

value: young fruting body, cap


title: CC_YFB_L_R2


title: PC_YFB_R1

source_name: young fruiting body

value: young fruiting body


title: PC_YFB_R2


title: CC_YFB_C_R2


title: 34902N: Control prostate benign epithelium sample 3

value: Mock


title: CTCF_ChIPSeq

city: New York

first: Ping

last: Chi

state: NY

address: 1275 York Ave

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

description: CTCF ChIP-seq in human melanoma A375 cell line

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with default configurations
bowtie --wrapper basic-0 -v 3 -q -p 10 -a -m 1 -k 1 --best --strata -S
Genome_build: hg19

source_name: melanoma cell line

growth_protocol: A375 cell line was cultured in DMEM supplemented with L-glutamine (2mmol/L), penicillin (100U/ml), streptomycin (100ug/ml) and 10% heat-inactivated FBS. Cell line was cultured at 37°C with 5% CO2 and has been tested negative for mycoplasma (MycoAlert PLUS Mycoplasma Detection kit; Lonza).

extract_protocol:
Chromatin was sheared to around 150bp to 600bp using Covaris E220 machine and incubated with 6ul CTCF antibody (Cell Signaling Technology; #3418) overnight at 4°C with rotation.
ChIP library was constructed using KAPA HTP library prep kit

treatment_protocol: no treatment

value: skin

value: melanoma cells

tag: antibody


title: EXP5N: Control prostate benign epithelium sample 6

description:
Control prostate benign epithelium samples 5 and 6
raw_data_file: 34939N_EXP5N_raw.txt

value: Prostate benign epithelium


title: 34939N: Control prostate benign epithelium sample 5


title: 8 WT mice combined [PF9-12]

city: Boston

first: Bernardo

last: Sabatini

address: 200 Longwood Avenue

institute: Harvard Medical School

data_processing:
Base-calling, filtering, trimming, read assignment to cell, alignment, UMI processing of reads to counts: Previously published pipeline (Klein et al., 2015) run with default parameters against custom transciptome also built with same pipeline (Ensembl GRCm38 genome and GRCm38.84 annotation, filtering the annotation gtf file gencode.v17.annotation.gtf for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN").
Removal of low quality cells: First, cells with fewer than 500 UMI counts were excluded. Next, Cells with fewer than 400 or greater than 5500 unique genes were excluded. Cells with greater than 15% of UMIs devoted to mitochondrial genes were also excluded. Finally a doublet detection algorithm (Wolock et al., bioRxiv, 2018) was used to remove putative cell doublets. This resulted in a final dataset of 10471 cells
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: For processed data there are 4 txt files. MandelbaumProcessedData1: list of genes whose expression was mapped to thalamus, but outside of PF. MandelbaumProcessedData2: list of genes whose expression was mapped ventral and dorsal to PF and also to medial PF. MandelbaumProcessedData3: List of genes whose expression was mapped to PF.  MandelbaumProcessedData4:  List of genes whose expression was found to be correlated or anti-correlated with the gene ProDynorphin which can be mapped to medial PF. For more information see Mandelbaum et al, Neuron 2019. 10.1016/j.neuron.2019.02.035.  pf1_MATRIX.csv: Gene Expression Matrix of count data per cell; PF[SAMPLE_ID].counts.tsv.gz: Raw cell/counts tables by sample;

source_name: grouped samples of PF its surronding tissue in the Thalamus

extract_protocol:
RNA was isolated within droplets according to the inDrops protocol (Klein et al Cell 2015)(Zilionis et al Nature Protocols 2017).
inDrops library preparation was performed as previously described (Klein et al., 2015)(Zilionis et al., 2017) Libraries were sequenced on the Illumina NextSeq system.
custom inDrops single-cell RNA-Seq; The inDrops scRNA-seq is version "v3": R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail.

tag: genotype

value: wild type

value: post natal day 56

value: Parafascicular nuclues and its surronding tissue in the Thalamus


title: PC_VM_R3

source_name: vegetative mycelium

value: vegetative mycelium


title: 8 WT mice combined [PF1-4]


title: 8 WT mice combined [PF5-8]


title: SC_FB_R3

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package v 2.1 of CLC Genomics Workbench Tool (v 9.5.2) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Schizophyllum commune H4-8 v3.0 (Schco3), JGI project ID: 16355
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Schizophyllum commune

growth_protocol: Schizophyllum commune the H4-8a and H4-8b monokaryons were grown on MM medium. After dikaryon formation an agar plug (5 mm) was placed on the center of fresh MM medium at 30 °C for five days in the dark, then it was placed at 25 °C for 10 days in a 12/12 hrs light/dark cycle (cool white F18w/840), upside down. Dikaryotic vegetative mycelium, stage 1 and 2 primordia, young fruiting body and fruiting body stages were harvested for RNA-seq. We defined stage 1 primordia as up to 2 mm fruiting body initials, stage 2 primordia as 3-4 mm tall initials with an apical pit on the top, the young fruiting body as a 5-7 mm tall cup-like structure with visible pseudolamellae inside, while fully expanded ones were considered fruiting body.


title: PC_VM_R2


title: 34733N: Control prostate benign epithelium sample 2

description:
Control prostate benign epithelium samples 1 and 2
raw_data_file: 33787N_34733N_raw.txt


title: CB12 control

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

country: Germany

institute: University Hospital Tuebingen

data_processing:
Paired-end reads were aligned with STAR (V2.5.4b) against the Ensembl H.sapiens genome v91 allowing gapped alignments to account for splicing.
Read counts for all genes were determined using GenomicAlignments (V1.14.2) and DESeq2 (V1.18.1).
Genome_build: Ensembl v91 H.sapiens
Supplementary_files_format_and_content: CSV file with raw read counts per gene identified by Ensembl gene ID

source_name: CD34+ HSPCs from cord blood

growth_protocol: Cells were cultured in StemSpan II media (StemCell Technologies) including 10% fetal bovine serum (FBS, Biochrom) and 100 IU/ml penicillin-streptomycin (Lonza) supplemented with cytokines: stem cell factor (SCF), thrombopoietin (TPO), FLT3-L, interleukin-6 (IL-6), interleukin-3 (IL-3) (100 ng/mL each, PeproTech) and StemRegenin1 (SR1; 0.75 mM) and UM729 (both StemCell Technologies). Cells were maintained at a cell density of 7.5-20x105/ml and at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated with Macherey Nagel NucleoSpin RNA Kit.
Libraries were generated with NEBNext Ultra II Directional RNA + polyA.
Poly(A)-selected sequencing libraries were generated according to manufacturer instructions and sequenced on a NextSeq 500 at 75bp paired-end resolution at a depth of ~30 million reads.

tag: donor id

tag: genetic aberration

value: control

tag: cell type

value: CD34+ HSPCs from cord blood


title: PC_VM_R1

value: CALKCANXX


title: CC_YFB_L_R1

value: young fruiting body, lamellae


title: SC_FB_R1

value: fruiting body


title: SC_FB_R2


title: CB11 control


title: NN_liver_3

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

institute: South China Agricultural University

description: liver RNA_repeat 3

data_processing:
BGI SOAPnuke software used for trimming and filtering.
Sequenced reads were mapped to gga5 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene expression analysis step 1: sequenced reads were then mapped to gga5 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression analysis step 2: Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using RSEM v1.2.12.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: liver of broiler fed with normal diet

extract_protocol:
Livers and abdominal fats were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

value: Xinghua

tag: diet

value: normal diet

value: liver


title: CC_P2_R3

source_name: stage 2 primordium

tag: tissue

value: stage 2 primordium


title: CC_P2_R4


title: CC_P2_R2


title: 33787N: Control prostate benign epithelium sample 1

source_name: Prostate benign epithelium

tag: treatment

value: Mock


title: SC_YFB_R3

value: young fruiting body


title: NN_liver_1

description: liver RNA_repeat 1

tag: age


title: SC_YFB_R2


title: CC_P2_R1


title: SC_YFB_R1


title: CC_P1_R4

source_name: stage 1 primordium

value: stage 1 primordium


title: HN_liver_3

description: liver RNA_repeat 3

source_name: liver of broiler fed with high-fat diet

value: high-fat diet


title: CC_P1_R3


title: CC_P1_R2


title: HN_liver_2

description: liver RNA_repeat 2


title: SC_P2_R3


title: CC_P1_R1


title: SC_P2_R2


title: HN_liver_1

description: liver RNA_repeat 1


title: CB12 MLL-AF4


title: NN_fat_3

description: abdominal fat RNA_repeat 3

source_name: abdominal fat of broiler fed with normal diet

value: abdominal fat


title: CC_H_R4

source_name: secondary hyphal knot

value: secondary hyphal knot


title: SC_P1_R2


title: NN_fat_2

description: abdominal fat RNA_repeat 2


title: CC_YFB_C_R1

value: young fruting body, cap


title: SC_P1_R3


title: CC_H_R2


title: CC_H_R3


title: NN_fat_1

description: abdominal fat RNA_repeat 1


title: SC_P1_R1


title: NN_liver_2

description: liver RNA_repeat 2


title: CB11 MLL-AF4


title: SC_VM_R3

value: vegetative mycelium


title: SC_VM_R2


title: HN_fat_2

description: abdominal fat RNA_repeat 2

source_name: abdominal fat of broiler fed with high-fat diet


title: SC_VM_R1


title: HN_fat_1

description: abdominal fat RNA_repeat 1


title: CC_VM_R3


title: CC_VM_R2


title: CC_VM_R1


title: HN_fat_3

description: abdominal fat RNA_repeat 3


title: 2T P 8

status: Public on Mar 15 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 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: pancreatic cancer organoids passage 8

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

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

tag: tissue/cell type

value: pancreatic cancer organoids passage 8


title: heart of CKD mice, rep 2

city: Chongqing

first: Yinghui

last: Huang

address: Shapingba

institute: Army medical university

description: Expression data from the heart of CKD mice

hyb_protocol: Following labeling, cDNA was hybridized on a Affymetrix Clariom S mouse.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

source_name: heart of CKD mice

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: Mice were housed in a specific pathogen-free animal facility in plastic cages with a 12 hours light/dark cycle.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: Mice were inflicted with 2/3 electrocoagulation of the right renal cortex and received left total nephrectomy 2 weeks later to construct CKD model. Mice underwent laparotomy without kidney operation served as sham group.

value: heart

value: Balb/c

value: CKD


title: 28N1

source_name: non-cancer organoids

value: non-cancer organoids


title: 45L

source_name: non-cancer liver organoids

value: non-cancer liver organoids


title: 39N


title: heart of sham mice, rep 2

description: Expression data from the heart of sham mice

source_name: heart of sham mice

value: sham


title: heart of CKD mice, rep 1


title: 2T P 72

source_name: pancreatic cancer organoids passage 72

value: pancreatic cancer organoids passage 72


title: 30T

source_name: organoids established using cancer tissue but failed in long culture


title: 39T

value: organoids established using cancer tissue but failed in long culture


title: 44T

source_name: neuroendocrine carcinoma organoids

value: neuroendocrine carcinoma organoids


title: 41N


title: 314 P 58

source_name: cholangiocarcinoma organoids passage 58

value: cholangiocarcinoma organoids passage 58


title: 34L-1


title: 27T


title: 28N2


title: heart of sham mice, rep 1


title: 24T


title: 40N1


title: CCO-P32

source_name: cholangiocarcinoma organoids passage 32

value: cholangiocarcinoma organoids passage 32


title: 36N


title: 9T

source_name: cholangiocarcinoma organoids

value: cholangiocarcinoma organoids


title: 2T

source_name: pancreatic cancer organoids

value: pancreatic cancer organoids


title: 42L


title: 9T-TI

source_name: cholangiocarcinoma tissue

value: cholangiocarcinoma tissue


title: 314 P 177

source_name: cholangiocarcinoma organoids passage 117


title: 26T


title: 21T

source_name: gallbladder cancer organoids

value: gallbladder cancer organoids


title: 36T


title: NCC-CC1

source_name: cholangiocarcinoma cell line

value: cholangiocarcinoma cell line


title: Pt-ptc + Pt-dpp double pRNAi embryo_2

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

description: There were no biological replicates.  This sample represents the same RNA used in GSM3070092.

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

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

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

organism: Parasteatoda tepidariorum

source_name: pd-RNAi

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

growth_protocol: Embryos were incubated at 25˚C.

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

value: whole embryo

tag: developmental stage

value: late stage 5

value: Pt-dpp + Pt-ptc double pRNAi

tag: treatment protocol

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

source_name: normal

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


title: CCO-P7

source_name: cholangiocarcinoma organoids passage 7

value: cholangiocarcinoma organoids passage 7


title: Fayoumi biological replicate2 individual injected with avian influenza virus [FI2_A]

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

description:
FI2_A
MethylC-seq

data_processing:
Sequenced reads were aligned to the galGal4 genome assembly using Bismark version 0.13.0 with the following configurations: -N 1 -L 20 --bowtie2 --bam -1 -2 -p -o.
Extracted CG methylation rates were generated by Bismark_methylation_extractor subprogram.
Single site methylation rate was used to identify the differential methylation sites and differential methylation regions, and then false discovery rate (FDR) was used to correct it (p = 0.01).
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: *_bismark_bt2_pe.bismark.zero.cov: Tab-delimited text files include chromosome, position of methylcytosines which were identified for each chicken line (LI represents Leghorn chicken injected with AIV; FI represents Fayoumi chicken injected with AIV). The files contain <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>.

source_name: Lung

extract_protocol:
DNA from lung tissue was isolated by phenol-chloroform extraction.
Libraries were prepared as below. Five μg DNA was sonicated to produce 200-400 bp fragments, followed by end repair with a nucleotide triphosphate mix free of dCTP. Cytosine methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA according to the manufacturer’s instructions for genomic DNA library construction. Adapter-ligated DNA with the length of 320-500 bp was isolated by 2% agarose gel electrophoresis, and sodium bisulfite conversion was performed on it using the MethylEasy Xceed kit (Human Genetic Signatures, NSW, Australia) was used according to the manufacturer’s instructions. The 300 ng of bisulfite-converted, adapter-ligated DNA molecules were enriched by 14 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive Pfu TurboCx Hotstart DNA polymerase (Stratagene), 5 μL of 10× Pfu Turbo reaction buffer, 25 μM dNTPs, 1 μL of Primer 1.1, and 1 μL of Primer 2.1 (50 μL final). The thermocycling parameters were as follows: 98°C for 2 min, followed by 4 cycles of 98°C for 15 s, 60°C for 30 s, and 72°C for 1 min, ending with incubation at 72°C for 10 min. The reaction products were purified using the MinElute PCR purification kit (Qiagen, Valencia, CA) and then separated by 2% agarose gel electrophoresis and purified by the MinElute gel purification kit (Qiagen, Valencia, CA). DNA library prepared above was sequenced using the Illumina Genome Analyzer II (GA II) according to the manufacturer’s instructions. Each sample had two technical replicates.

treatment_protocol: Two Leghorn and two Fayoumi birds were euthanized at 3 weeks and injected with avian influenza virus, and lungs were harvested. The animal experiment was performed according to the guidelines approved by the Institutional Animal Care and Use Committee, Texas A&M University.

tag: breed

value: Fayoumi M43

value: 3 weeks

value: Lung

value: Avian influenza virus infection

tag: chicken identifier


title: Leghorn biological replicate2 individual injected with avian influenza virus [LI2-A]

description:
LI2-A
MethylC-seq

value: Leghorn GB2


title: RNA-Seq - NeuN positive/TDP-43 positive S7

city: Philadelphia

first: Edward

middle: B

last: Lee

state: Pennsylvania

address: 422 Curie Blvd

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were aligned against GRCh38 (GENCODE release 22) using STAR (Version 2.2.4) with option --outFilterIntronMotifs RemoveNonCanonical
Reads mapping to rRNA, the mitochondrial genome and non-uniquely were removed.
Differentially expressed genes were obtained by running DESeq2 1.10.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file with raw counts for each sample

source_name: Nuclei

extract_protocol:
Nuclei were extracted from frozen post-mortem frontal cortex and neuronal nuclei populations were obtained by FACS. Total RNA was extracted with the Qiagen AllPrep DNA/RNA/miRNA Universal Kit.
Illumina sequencing libraries were created with the Ovation SoLo RNA-seq kit from NuGEN Technologies according to the manufacturer's instructions.

value: Frontal cortex

tag: gender

value: Male

tag: diagnosis

value: FTD-ALS

tag: genotype/variation

value: TDP-43 positive

value: NeuN positive


title: Fayoumi biological replicate1 individual injected with avian inluenza virus [FI1_A]

description:
FI1_A
MethylC-seq


title: Fayoumi biological replicate1 individual injected with avian influenza virus [FI1_B]

description:
FI1_B
MethylC-seq


title: Leghorn biological replicate2 individual injected with avian influenza virus [LI2-B]

description:
LI2-B
MethylC-seq


title: 16481: Small RNAs from ovaries of KG09351 transgenic strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the raw counts of clipped read occurrences in each library.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries

tag: strain


title: KG10047.SuHwvF: Small RNAs from ovaries of KG10047 transgenic strain, carrying the Su(Hw) mutation


title: 16481.SuHwvF: Small RNAs from ovaries of KG09351 transgenic strain, carrying the Su(Hw) mutation


title: RNA-Seq - NeuN positive/TDP-43 negative S6

value: TDP-43 negative


title: Leghorn biological replicate1 individual injected with avian influenza virus [LI1-B]

description:
LI1-B
MethylC-seq


title: RNA-Seq - NeuN positive/TDP-43 negative S5

value: FTD


title: Fayoumi biological replicate2 individual injected with avian influenza virus [FI2_C]

description:
FI2_C
MethylC-seq


title: 314 TISSUE

source_name: cholangiocarcinoma xenograft tissue

value: cholangiocarcinoma xenograft tissue


title: KG10047_2: Small RNAs from ovaries of KG10047 transgenic strain


title: RNA-Seq - NeuN positive/TDP-43 positive S6


title: RNA-Seq - NeuN positive/TDP-43 negative S7


title: RNA-Seq - NeuN positive/TDP-43 negative S4

value: Female


title: RNA-Seq - Unsorted S4

value: unsorted


title: Leghorn biological replicate1 individual injected with avian influenza virus [LI1-C]

description:
LI1-C
MethylC-seq


title: RNA-Seq - NeuN positive/TDP-43 positive S4


title: RNA-Seq - NeuN positive/TDP-43 negative S3


title: RNA-Seq - NeuN positive/TDP-43 positive S2


title: RNA-Seq - NeuN positive/TDP-43 positive S3


title: RNA-Seq - NeuN positive/TDP-43 negative S1


title: RNA-Seq - NeuN positive/TDP-43 negative S2


title: RNA-Seq - NeuN positive/TDP-43 positive S1


title: RNA-Seq - NeuN positive/TDP-43 positive S5


title: ATAC-Seq - NeuN positive/TDP-43 positive S6

description:
tagmented genomic DNA
S6_TP

data_processing:
Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against GRCh38 (GENCODE release 22) using STAR (Version 2.2.4) with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
Autosome genomic sequences were devided into 1000 base pair bins and ATAC-seq counts within each bin were determined.
Differentially accessible regions were identified with edgeR (Version 3.12.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited file with raw counts for each sample

extract_protocol:
Nuclei were extracted from frozen post-mortem frontal cortex and neuronal nuclei populations were obtained by FACS.
ATAC-seq libraries were created as described in Buenrostro et al. 2015. Briefly, cells were lysed and treated with Tn5 Transposase from the Nextera Library Prep kit from Illumina for 30 min at 37°C. DNA was purified with Qiagen MinElute PCR purification kit and libraries were generated by PCR amplification using Nextera Index Primers from Illumina.


title: ATAC-Seq - NeuN positive/TDP-43 positive S7

description:
tagmented genomic DNA
S7_TP


title: ATAC-Seq - NeuN positive/TDP-43 negative S4

description:
tagmented genomic DNA
S4_TN


title: ATAC-Seq - NeuN positive/TDP-43 negative S7

description:
tagmented genomic DNA
S7_TN


title: ATAC-Seq - NeuN positive/TDP-43 negative S6

description:
tagmented genomic DNA
S6_TN


title: ATAC-Seq - NeuN positive/TDP-43 positive S1

description:
tagmented genomic DNA
S1_TP


title: ATAC-Seq - NeuN positive/TDP-43 positive S4

description:
tagmented genomic DNA
S4_TP


title: ATAC-Seq - NeuN positive/TDP-43 negative S5

description:
tagmented genomic DNA
S5_TN


title: ATAC-Seq - NeuN positive/TDP-43 positive S3

description:
tagmented genomic DNA
S3_TP


title: ATAC-Seq - NeuN positive/TDP-43 negative S3

description:
tagmented genomic DNA
S3_TN


title: ATAC-Seq - NeuN positive/TDP-43 positive S2

description:
tagmented genomic DNA
S2_TP


title: ATAC-Seq - NeuN positive/TDP-43 negative S2

description:
tagmented genomic DNA
S2_TN


title: ATAC-Seq - NeuN positive/TDP-43 negative S1

description:
tagmented genomic DNA
S1_TN


title: ATAC-Seq - NeuN positive/TDP-43 positive S5

description:
tagmented genomic DNA
S5_TP


title: Participant ID and visit (v) # phchp365v1 Independent Test Cohorts (n=201) (505 visits)

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

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

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

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-MDD

tag: vas stress score (1-100)

value: Independent Test cohort blood gene expression data


title: Participant ID and visit (v) # phchp357v4 Independent Test Cohorts (n=201) (505 visits)

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

value: M-BP


title: Participant ID and visit (v) # phchp367v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp364v1 Independent Test Cohorts (n=201) (505 visits)

value: F-PTSD


title: Participant ID and visit (v) # phchp357v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp366v1 Independent Test Cohorts (n=201) (505 visits)

value: M-SZ


title: Participant ID and visit (v) # phchp357v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp350v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp358v2 Independent Test Cohorts (n=201) (505 visits)

value: M-PTSD


title: Participant ID and visit (v) # phchp367v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp360v3 Independent Test Cohorts (n=201) (505 visits)

value: F-BP


title: Participant ID and visit (v) # phchp358v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp358v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp355v1 Independent Test Cohorts (n=201) (505 visits)

value: F-MDD


title: Participant ID and visit (v) # phchp357v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp356v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp355v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp352v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp349v1 Independent Test Cohorts (n=201) (505 visits)

value: M-PSYCH


title: Participant ID and visit (v) # phchp357v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp350v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp360v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp352v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp350v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp349v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp353v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp349v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp352v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp343v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp344v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp338v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp330v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp332v2 Independent Test Cohorts (n=201) (505 visits)

value: F-SZA


title: Participant ID and visit (v) # phchp336v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp343v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp346v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp331v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp346v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp338v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp348v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp336v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp350v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp343v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp338v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp332v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp338v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp332v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp346v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp335v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp318v3 Independent Test Cohorts (n=201) (505 visits)


title: RNA-Seq - Unsorted S3

value: Frontal cortex


title: Participant ID and visit (v) # phchp315v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp314v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp327v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp318v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp338v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp314v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp312v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp324v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp322v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp314v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp312v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp309v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp312v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp308v4 Independent Test Cohorts (n=201) (505 visits)

value: M-SZA


title: Participant ID and visit (v) # phchp309v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp309v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp308v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp308v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp308v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp298v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp293v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp297v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp298v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp300v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp287v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp298v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp298v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp287v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp294v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp287v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp277v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp297v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp283v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp295v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp290v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp290v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp297v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp277v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp276v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp297v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp277v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp293v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp277v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp276v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp290v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp277v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp318v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp275v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp273v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp276v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp273v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp259v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp254v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp270v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp254v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp259v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp276v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp259v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp265v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp254v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp242v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp253v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp241v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp275v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp247v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp253v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp242v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp275v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp242v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp239v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp240v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp240v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp239v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp239v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp238v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp240v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp238v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp232v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp236v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp236v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp238v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp235v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp236v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp253v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp228v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp232v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp229v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp235v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp224v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp232v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp227v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp227v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp227v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp222v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp225v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp223v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp222v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp221v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp221v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp219v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp219v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp217v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp211v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp212v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp219v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp221v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp211v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp235v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp211v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp210v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp208v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp212v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp208v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp210v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp210v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp203v1 Independent Test Cohorts (n=201) (505 visits)

value: M-MOOD


title: Participant ID and visit (v) # phchp208v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp203v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp207v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp200v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp199v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp200v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp199v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp200v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp199v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp198v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp206v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp197v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp198v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp197v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp197v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp197v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp198v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp195v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp195v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp194v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp191v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp192v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp194v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp194v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp195v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp191v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp190v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp192v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp189v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp192v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp190v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp191v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp188v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp188v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp189v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp190v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp190v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp188v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp187v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp185v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp186v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp187v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp186v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp186v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp186v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp186v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp185v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp185v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp183v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp180v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp183v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp181v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp179v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp181v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp177v1 Independent Test Cohorts (n=201) (505 visits)

value: F-SZ


title: Participant ID and visit (v) # phchp180v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp180v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp179v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp184v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp184v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp181v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp179v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp177v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp175v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp184v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp174v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp178v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp171v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp172v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp169v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp171v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp170v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp168v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp172v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp170v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp161v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp168v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp165v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp170v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp172v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp152v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp165v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp168v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp149v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp165v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp148v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp149v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp144v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp158v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp147v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp161v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp156v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp149v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp147v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp161v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp143v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp143v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp147v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v6 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp143v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v4 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp140v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v5 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp139v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp140v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp142v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp138v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp138v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp138v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp136v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp140v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp136v1 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp129v3 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp131v2 Independent Test Cohorts (n=201) (505 visits)


title: Participant ID and visit (v) # phchp128v2 Independent Test Cohorts (n=201) (505 visits)