title: GT_L5_67

city: King of Prussia

first: Guanghui

last: Hu

state: PA

address: 709 Swedeland Road

institute: GlaxoSmithKline

hyb_protocol: Hybridization cocktails were prepared in accordance with NuGEN protocols. Cocktails were then hybridized to mouse 430_2 whole genome Gene Chips in two batches, in accordance with Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The raw signal intensities (.cel files) for each scan were imported into the gene expression analysis software, Resolver version 4.0 (Rosetta Biosoftware, Seattle, USA). Signal extraction was performed within Resolver and the normalised data (Weng et al., 2006), was then exported for further analysis.

source_name: 12 Week Smoke 12 Week RA

label_protocol: For each sample, 50ng of total RNA was converted to amplified antisense sscDNA using the NuGEN Ovation RNA Amplification System V2, following manufacturer's instructions. cDNAs were purified using the Agencourt AMPure Magnetic Bead Purification System. The amplified cDNA concentrations were determined by measurement on a Thermo Electron Varioskan spectral scanning multimode reader and quality was assessed by nano chips on an Agilent 2100 bioanalyser. 4.4ug of amplified cDNA was fragmented and biotin-labelled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies).

growth_protocol: Female C57BL/6 mice were purchased from Jackson Laboratory (Bar Harbor, ME)

extract_protocol: Mouse gastrocnemius muscle tissue was collected, rinsed in ice-cold PBS, drained, and cut into sections < 5mm in thickness.  Muscle sections were placed immediately into > 10 volumes of RNALater Stabilization Reagent (Applied Biosystems/Ambion, Austin, TX), incubated overnight at 2-8°C, and then stored at -80°C. From 6 randomly selected mice per treatment group, total RNA was extracted from muscle tissue using a Polytron type homogeniser (YellowLine DI 25 Basic ) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1ml of TriZol to 20mg of tissue. RNA was further purified using RNeasy 96 universal tissue version 1.0 protocol on a Qiagen Biorobot 8000, including on-column DNAse-1 step and elution in water. The quantity of extracted RNA was determined using a Thermo Electron Varioskan spectral scanning multimode reader and quality was assessed using nano and pico chips on an Agilent 2100 bioanalyser (South Plainfield, NJ, USA). RNA yields were in the range of   550ng-5ug (average of 1.8ug) All samples were of good quality as ascertained on the bioanalyser.

treatment_protocol: Mice received nose-only exposure of 4% mainstream cigarette smoke or air (sham exposure) for 2 hours/day, 5 days/week for 2, 12 or 24 weeks.  Mice undergoing smoke cessation received cigarette smoke exposure for 12 weeks, and then sham exposure for 12 weeks.

value: gastrocnemius muscle


title: GT_L27_124

status: Public on Sep 01 2012

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: primary tumor 3.67 months survival

city: São Paulo

first: Fatima

middle: Solange

last: Pasini

state: São Paulo

address: Av. Dr. Arnaldo, 455 sala 4115

department: Departamento de Radiologia e Oncologia

country: Brazil

institute: Faculdade de Medicina da USP

description: Gene expression data from gastric cancer of patient undergoing gastrectomy as a primary treatment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data normalization and probe summarization were performed by  Robust Multichip Analysis (RMA) using R Bioconductor software.

organism: Homo sapiens

source_name: primary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Trizol extraction of total RNA and Clean-up (Quiagen) werw performed according to the manufacturers' instructions .

tag: age (y)

tag: gender

value: male

tag: histological type

value: Diffuse

tag: tumor stage (ajcc)

value: IIIa

tag: time (months) overall survival

tag: status

value: death

value: gastric cancer tumor


title: 670152 (mRNA)

city: Rochester

first: Virginia

middle: Bartleson

last: Hebl

state: MN

address: 200 1st St. SW

institute: Mayo Clinic

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina BeadArray Reader and the standard Illumina scanning protocol.

data_processing: Illumina BeadStudio processed without background correction or normalization for non-normalized data. Fastlo (PMID 15166021) normalized and log2 transformed for normalized data.

label: Biotin

source_name: cardiac tissue, HCM

label_protocol: Standard Illumina labeling protocol.

extract_protocol: RNA was extracted using the QIAGEN MicroRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

tag: Sex

value: female

tag: age (yrs)

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: primary tumor 12.93 months survival

value: Intestinal

value: III


title: 634021 (mRNA)


title: GT_L28_90


title: GT_L30_101


title: primary tumor 13.6 months survival


title: R35 (mRNA)


title: GT_L9_76


title: Nod2-UN3,experimental replicate 3

city: Boston

first: Nikolaos

last: Mavrogiorgos

state: MA

address: 650 Albany street, EBRC building, room 610

institute: Boston University

description: uninfected

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw affinity data was normalized using a Robust Multichip Analysis (RMA) method at probe level

source_name: BMDM, Nod2 KO, uninfected

label_protocol: Whole Transcript (WT) Sense Target Labeling (Affymetrix)

growth_protocol: Murine BMDM were prepared from C57BL/6 mice or NOD2 deficient mice on C57BL/6 background. Mature BMDM were plated in 6 well plates at 1x10^6 cells/well

extract_protocol: Cells lysates were made and RNA was isolated  using Rneasy Mini Kit, Qiagen

tag: cell type

value: BMDM

tag: genotype

tag: infection status

value: uninfected


title: Nod2-UN1,experimental replicate 1

description: uninfected


title: primary tumor 24.5 months survival


title: WT-GC3,experimental replicate 3

description: infected with Neisseria gonorrrhoeae, strain MS11, MOI 10:1 for 3 hrs

source_name: BMDM, WT, infected with GC

value: wild-type


title: 637810 (mRNA)


title: R671993 (mRNA)


title: GT_K7_53

source_name: 12 Week Smoke 12 Week FA


title: Nod2-UN2,experimental replicate 2

description: uninfected


title: primary tumor 33.57 months survival

value: IIIb


title: WT-GC2,experimental replicate 2

value: infected with Neisseria gonorrrhoeae, strain MS11, MOI 10:1 for 3 hrs


title: GT_L11_112

value: gastrocnemius muscle


title: 647527 (mRNA)

value: male


title: primary tumor 22.4 months survival


title: Lung T0 C3H-1

city: Irvine

first: William

last: Gordon

state: CA

address: 839 Health sciences way

department: Medicine

institute: University of CA Irvine

description: Gene expression data from NNK exposure before mature tumor formation

hyb_protocol: Affymetrix standard protcol performed UCI HTGC

data_processing: PLIER algorithm using Expression console software (Affymetrix)

source_name: Mouse Lung

growth_protocol: Mice were maintained under normal ligh dark conditions and with access to food and water in the UCI animal facility

extract_protocol: Trizol was used to extract total RNA followed by cleanup over Invitrogen RNA columns

treatment_protocol: NNK was injected at 100mg/kg once a week for four weeks

value: lung

tag: time after exposure

value: 0 weeks

tag: treatment


title: GT_K29_160

tag: strain


title: 47 (mRNA)

tag: tissue


title: WT-GC1,experimental replicate 1


title: WT-UN3,experimental replicate 3

description: uninfected

source_name: BMDM, WT, uninfected


title: primary tumor 64.83 months survival

tag: age (y)

value: Mixed

value: IIIa

value: alive


title: GT_K26_115


title: WT-UN2,experimental replicate 2

description: uninfected


title: primary tumor 58.23 months survival

tag: gender

value: Diffuse

value: gastric cancer tumor


title: primary tumor 53.1 months survival

value: female

tag: histological type


title: primary tumor 58.77 months survival

value: Intestinal

tag: tumor stage (ajcc)


title: GT_K25_51


title: WT-UN1,experimental replicate 1

description: uninfected


title: 631131 (mRNA)

value: cardiac

value: hypertrophic cardiomyopathy (HCM)

value: case


title: Nod2-GC1, experimental replicate 1

source_name: BMDM, Nod2 KO, infected with GC

value: BMDM


title: RNM04 (mRNA)


title: 645586 (mRNA)


title: 653448 (mRNA)


title: GT_J5_133

source_name: 24 Week Smoke


title: GT_K11_39


title: Nod2-GC2,experimental replicate 2


title: primary tumor 51.17 months survival

tag: time (months) overall survival


title: GT_K12_69


title: GT_J8_55


title: 661552 (mRNA)


title: Nod2-GC3, experimental replicate 3


title: 638751 (mRNA)


title: GT_J6_169


title: UPN727 cells, recent onset 1579 plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN727 cells stimulated with recent onset (RO) Type 1 Diabetic plasma

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log ratios.  Each sample was independently analyzed.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Paired 2 sample ttest as a statistic analysis method in Partek GS.

source_name: UPN727 cells stimulated with RO1579 plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of autologous, longitudinal, longstanding (LS), healthy control (HC), or recent onset (RO) T1D plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: protocol

value: stimulated with RO1579 plasma

tag: responder cell line


title: GT_J29_157


title: 673367 (mRNA)

tag: Sex

tag: age (yrs)


title: 100-01#16 iPSC

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, all arrays were hybridized at 45C for 16 hr.

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: The gene expression raw data were extracted using the Affymetrix Gene Chip Operation System. Quality control was performed on the basis of Affymetrix quality control metrics.

source_name: undifferentiated 100-01#16 iPSC

label_protocol: Approximately 150 ng of RNA from each sample was labeled using GeneChip 3’IVT Express (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: iPSC were cultured in hES medium containing bFGF.

extract_protocol: Total RNA samples were isolated using RNeasy kit.

treatment_protocol: Cells were washed with PBS and Rneasy kit was used to isolate total RNA.

value: iPSC cell line

tag: cell line

tag: origin

value: established by retroviral transduction of primary human fibroblasts from centenarians


title: 663118 (mRNA)

value: male

tag: disease state

tag: sample type


title: UPN727 cells, recent onset 159 plasma

source_name: UPN727 cells stimulated with RO159 plasma

value: stimulated with RO159 plasma


title: 683304 (mRNA)


title: GT_J12_130

value: gastrocnemius muscle


title: UPN727 cells, recent onset 1225 plasma

source_name: UPN727 cells stimulated with RO1225 plasma

value: stimulated with RO1225 plasma


title: UPN727 cells, unrelated healthy control 1678 plasma

description: Gene expression data from UPN727 cells stimulated with unrelated healthy control plasma

source_name: UPN727 cells stimulated with HC1678 plasma

value: stimulated with HC1678 plasma


title: GT_I5_32

source_name: 24 Week FA


title: C2C12_Wild type terminally differentiated cells

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

description: Myotube (differentiated)

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit, P/N 900720

scan_protocol: gene chip scanner 3000 7G

data_processing: The data were pre-processed with AGCC  (Affymetrix) and Expression Console 1.1 using RMA

source_name: C2C12cells, wild type terminally differentiated cells

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents, P/N 900652

growth_protocol: C2C12 at p27 were grown in DMEM 10%FBS at 60-80% confluence

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

treatment_protocol: microRNA mimics (Qiagen) were transfected using Hiperfect reagent (Qiagen) at 50nM concentration. After 36hrs total RNA was collected. The experiment was repeated three times

value: Myotube (differentiated)


title: C2C12_Let-7b over-expression, replica 3

source_name: C2C12 cells, microRNA overexpression

value: Let-7b over-expression


title: UPN727 cells, unrelated healthy control 382 plasma

source_name: UPN727 cells stimulated with HC382 plasma

value: stimulated with HC382 plasma


title: 653447 (mRNA)

source_name: cardiac tissue, HCM


title: C2C12_Wild type proliferant cells, 70% confluence

description: Myoblast (proliferant)

source_name: C2C12 cells, wild type proliferant cells, 70% confluence

value: Myoblast (proliferant)


title: C2C12_Let-7b over-expression, replica 1


title: UPN727 cells, longstanding T1D 1110 plasma

description: Gene expression data from UPN727 cells stimulated with longstanding Type 1 Diabetic plasma

source_name: UPN727 cells stimulated with LS1110 plasma

value: stimulated with LS1110 plasma


title: GT_I4_70


title: GT_J10_1


title: 687046 (mRNA)

value: cardiac


title: C2C12_miR-1 over-expression, replica 3

value: miR-1 over-expression


title: UPN727 cells, longstanding T1D 599 plasma

source_name: UPN727 cells stimulated with LS599 plasma

value: stimulated with LS599 plasma


title: C2C12_Let-7b over-expression, replica 2


title: 663702 (mRNA)

value: female

value: hypertrophic cardiomyopathy (HCM)

value: case


title: UPN727 cells, longstanding T1D 1053 plasma

source_name: UPN727 cells stimulated with LS1053 plasma

value: stimulated with LS1053 plasma


title: 46 (mRNA)


title: UPN727 cells, longstanding T1D 66 plasma

source_name: UPN727 cells stimulated with LS66 plasma

value: stimulated with LS66 plasma


title: R656518 (mRNA)

value: male


title: C2C12_miR-145 over-expression, replica 3

value: miR-145 over-expression


title: GT_I30_3

value: gastrocnemius muscle


title: C2C12_miR-1 over-expression, replica 1


title: R620009 (mRNA)


title: 370118 (mRNA)


title: C2C12_miR-145 over-expression, replica 2


title: GT_I29_161


title: GT_I11_38


title: UPN727 cells, longstanding T1D 96 plasma

source_name: UPN727 cells stimulated with LS96 plasma

value: stimulated with LS96 plasma


title: UPN727 cells, longstanding T1D 1296 plasma

source_name: UPN727 cells stimulated with LS1296 plasma

value: stimulated with LS1296 plasma


title: 49 (mRNA)


title: 610700 (mRNA)


title: C2C12_miR-145 over-expression, replica 1


title: GT_I1_10


title: UPN727 cells, longstanding T1D 311 plasma

source_name: UPN727 cells stimulated with LS311 plasma

value: stimulated with LS311 plasma


title: C2C12_miR-1 over-expression, replica 2


title: C2C12_miR-29a over-expression, replica 3

value: miR-29a over-expression


title: 48 (mRNA)


title: GT_G5_58

source_name: 12 Week Smoke


title: GT_g8_162


title: UPN727 cells, longstanding T1D 38 plasma

source_name: UPN727 cells stimulated with LS38 plasma

value: stimulated with LS38 plasma


title: UPN727 cells, longstanding T1D 35 plasma

source_name: UPN727 cells stimulated with LS35 plasma

value: stimulated with LS35 plasma


title: RNM06 (mRNA)

value: cardiac


title: UPN727 cells, longstanding T1D 264 plasma

source_name: UPN727 cells stimulated with LS264 plasma

value: stimulated with LS264 plasma


title: R50 (mRNA)


title: UPN727 cells, longstanding T1D 59 plasma

source_name: UPN727 cells stimulated with LS59 plasma

value: stimulated with LS59 plasma


title: C2C12_miR-29a over-expression, replica 2


title: C2C12_miR-365 over-expression, replica 2

value: miR-365 over-expression


title: C2C12_miR-365 over-expression, replica 3


title: C2C12_miR-29a over-expression, replica 1


title: GT_G8_170


title: 27 (mRNA)

value: hypertrophic cardiomyopathy (HCM)


title: GT_G4_145


title: C2C12_miR-365 over-expression, replica 1


title: GT_G12_100


title: UPN727 cells, longitudinal A plasma, timepoint 6

description: Gene expression data from UPN727 cells stimulated with longitudinal Type 1 Diabetic plasma

source_name: UPN727 cells stimulated with LO2132 (timepoint 6) plasma


title: GT_G2_94


title: R58 (mRNA)

value: case


title: UPN727 cells, longitudinal A plasma, timepoint 4

source_name: UPN727 cells stimulated with LO1377 (timepoint 4) plasma


title: NM03 (mRNA)

value: female


title: UPN727 cells, longitudinal A plasma, timepoint 5

source_name: UPN727 cells stimulated with LO1910 (timepoint 5) plasma


title: R8 (mRNA)

source_name: cardiac tissue, HCM


title: GT_G1_56


title: GT_G11_8


title: C2C12_miR-22 over-expression, replica 3

source_name: C2C12 cells, microRNA overexpression

value: miR-22 over-expression


title: C2C12_miR-22 over-expression, replica 2


title: 633322 (mRNA)


title: UPN727 cells, longitudinal A plasma, timepoint 3

source_name: UPN727 cells stimulated with LO1063 (timepoint 3) plasma


title: GT_F9_140

source_name: 12 Week FA


title: UPN727 cells, longitudinal A plasma, timepoint 2

source_name: UPN727 cells stimulated with LO350 (timepoint 2) plasma


title: C2C12_miR-34a over-expression, replica 2

value: miR-34a over-expression


title: GT_F5_159


title: 656578 (mRNA)


title: GT_F8_97


title: GT_F4_96


title: 653809 (mRNA)


title: C2C12_miR-22 over-expression, replica 1


title: UPN727 cells, autologous plasma, biological replicate 7

description: Gene expression data from UPN727 cells stimulated with autologous plasma

source_name: UPN727 cells stimulated with Auto250S15 plasma

value: stimulated with Auto250S15 plasma


title: C2C12_miR-34a over-expression, replica 3


title: C2C12_miR-34a over-expression, replica 1


title: UPN727 cells, unrelated healthy control 1365 plasma

source_name: UPN727 cells stimulated with HC1365 plasma

value: stimulated with HC1365 plasma


title: R342632 (mRNA)


title: 653513 (mRNA)

value: male


title: GT_F2_57

value: gastrocnemius muscle


title: UPN727 cells, longitudinal A plasma, timepoint 1

source_name: UPN727 cells stimulated with LO3 (timepoint 1) plasma


title: UPN727 cells, unrelated healthy control 1730 plasma

source_name: UPN727 cells stimulated with HC1730 plasma

value: stimulated with HC1730 plasma


title: UPN727 cells, unrelated healthy control 1369 plasma

source_name: UPN727 cells stimulated with HC1369 plasma

value: stimulated with HC1369 plasma


title: GT_F1_48


title: C2C12_Control (AllStar negative control, Qiagen), technical replica 2

source_name: C2C12 cells, control microRNA

value: control (AllStar negative control)


title: 632093 (mRNA)


title: GT_D6_95

source_name: 2 Week Smoke


title: GT_D5_16


title: C2C12_Control (AllStar negative control, Qiagen), replica 2


title: R655639 (mRNA)


title: 680701 (mRNA)


title: C2C12_Control (AllStar negative control, Qiagen), replica 3


title: GT_D4_172


title: UPN727 cells, unrelated healthy control 1601 plasma

source_name: UPN727 cells stimulated with HC1601 plasma

value: stimulated with HC1601 plasma


title: GT_D2_49


title: C2C12_Control (AllStar negative control, Qiagen), technical replica 3


title: 41 (mRNA)

value: cardiac


title: 45 (mRNA)


title: 649284 (mRNA)


title: C2C12_Control (AllStar negative control, Qiagen), technical replica 1


title: UPN727 cells, unrelated healthy control 1543 plasma

source_name: UPN727 cells stimulated with HC1543 plasma

value: stimulated with HC1543 plasma


title: UPN727 cells, unrelated healthy control 304 plasma

source_name: UPN727 cells stimulated with HC304 plasma

value: stimulated with HC304 plasma


title: UPN727 cells, unrelated healthy control 307 plasma

source_name: UPN727 cells stimulated with HC307 plasma

value: stimulated with HC307 plasma


title: UPN727 cells, unrelated healthy control 305 plasma

source_name: UPN727 cells stimulated with HC305 plasma

value: stimulated with HC305 plasma


title: GT_D12_14


title: R32 (mRNA)

source_name: cardiac tissue, HCM

value: hypertrophic cardiomyopathy (HCM)

value: case


title: C2C12_Control (AllStar negative control, Qiagen), replica 1


title: UPN727 cells, unrelated healthy control 308 plasma

source_name: UPN727 cells stimulated with HC308 plasma

value: stimulated with HC308 plasma


title: RNM08 (mRNA)


title: GT_C6_60

source_name: 2 Week FA


title: RNM05 (mRNA)

value: female


title: GT_C5_143


title: UPN727 cells, recent onset 3139 plasma

source_name: UPN727 cells stimulated with RO3139 plasma

value: stimulated with RO3139 plasma


title: UPN727 cells, recent onset 3045 plasma

source_name: UPN727 cells stimulated with RO3045 plasma

value: stimulated with RO3045 plasma


title: UPN727 cells, recent onset 3153 plasma

source_name: UPN727 cells stimulated with RO3153 plasma

value: stimulated with RO3153 plasma


title: GT_C8_98

value: gastrocnemius muscle


title: 44 (mRNA)


title: GT_C4_131


title: RNM02 (mRNA)

value: male


title: GT_D10_66


title: UPN727 cells, recent onset 3040 plasma

source_name: UPN727 cells stimulated with RO3040 plasma

value: stimulated with RO3040 plasma


title: GT_C3_92


title: UPN727 cells, recent onset 3052 plasma

source_name: UPN727 cells stimulated with RO3052 plasma

value: stimulated with RO3052 plasma


title: 36 (mRNA)


title: UPN727 cells, recent onset 3087 plasma

source_name: UPN727 cells stimulated with RO3087 plasma

value: stimulated with RO3087 plasma


title: R619278 (mRNA)

value: cardiac


title: GT_C10_23


title: R607466 (mRNA)


title: GT_A8_13

source_name: Untreated Week 0


title: 587005 (mRNA)


title: UPN727 cells, autologous plasma, biological replicate 6

source_name: UPN727 cells stimulated with Auto250S14 plasma

value: stimulated with Auto250S14 plasma


title: GT_A9_152


title: R59 (mRNA)


title: UPN727 cells, unrelated healthy control 2369 plasma

source_name: UPN727 cells stimulated with HC2369 plasma

value: stimulated with HC2369 plasma


title: GT_A3_36


title: 656880 (mRNA)


title: Hp+_ULCUS_CagA+:B231 sample

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v.2.4) Lumi R-package

source_name: Endoscopic human antral tissue

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Ambion) as per the manufacturer’s protocol.

value: Male

tag: age

value: yes

tag: caga presence


title: Hp-:B241 sample

description: Hp-

value: Female

value: no


title: UPN727 cells, unrelated healthy control 1265 plasma

source_name: UPN727 cells stimulated with HC1265 plasma

value: stimulated with HC1265 plasma


title: GT_A5_136

tag: strain


title: UPN727 cells, unrelated healthy control 388 plasma

source_name: UPN727 cells stimulated with HC388 plasma

value: stimulated with HC388 plasma


title: Hp+_ULCUS_CagA+:B211 sample


title: UPN727 cells, unrelated healthy control 1089 plasma

source_name: UPN727 cells stimulated with HC1089 plasma

value: stimulated with HC1089 plasma


title: UPN727 cells, unrelated healthy control 1142 plasma

source_name: UPN727 cells stimulated with HC1142 plasma

value: stimulated with HC1142 plasma


title: 17 (mRNA)

source_name: cardiac tissue, HCM

tag: tissue

value: hypertrophic cardiomyopathy (HCM)

value: case


title: 647526 (mRNA)

value: male


title: UPN727 cells, unrelated healthy control 1249 plasma

source_name: UPN727 cells stimulated with HC1249 plasma

value: stimulated with HC1249 plasma


title: 24 (mRNA)


title: Hp+_ULCUS_CagA-:B238 sample


title: GT_A7_111

value: gastrocnemius muscle


title: 9 (mRNA)

value: female


title: GT_A11_52


title: UPN727 cells, unrelated healthy control 394 plasma

source_name: UPN727 cells stimulated with HC394 plasma

value: stimulated with HC394 plasma


title: Hp+_Normal_CagA+:B210 sample


title: UPN727 cells, unrelated healthy control 1777 plasma

source_name: UPN727 cells stimulated with HC1777 plasma

value: stimulated with HC1777 plasma


title: 669841 (mRNA)

value: cardiac


title: R16 (mRNA)


title: UPN727 cells, unrelated healthy control 384 plasma

source_name: UPN727 cells stimulated with HC384 plasma

value: stimulated with HC384 plasma


title: Hp+_Normal_CagA+:B195 sample

value: Male

value: yes


title: Hp-:B203 sample

description: Hp-

value: Female

value: no


title: R53 (mRNA)


title: 29 (mRNA)


title: UPN727 cells, unrelated healthy control 381 plasma

source_name: UPN727 cells stimulated with HC381 plasma

value: stimulated with HC381 plasma


title: R1 (mRNA)


title: UPN727 cells, unrelated healthy control 379 plasma

source_name: UPN727 cells stimulated with HC379 plasma

value: stimulated with HC379 plasma


title: UPN727 cells, unrelated healthy control 227 plasma

source_name: UPN727 cells stimulated with HC227 plasma

value: stimulated with HC227 plasma


title: Hp-:B193 sample

description: Hp-


title: Hp+_ULCUS_CagA-:B166 sample


title: Hp-:B172 sample

description: Hp-


title: Hp+_ULCUS_CagA+:B187 sample


title: Hp+_ULCUS_CagA+:B186a sample


title: Hp+_ULCUS_CagA+:B186c sample


title: Hp+_ULCUS_CagA+:B137 sample


title: UPN727 cells, unrelated healthy control 2614 plasma

source_name: UPN727 cells stimulated with HC2614 plasma

value: stimulated with HC2614 plasma


title: Hp+_ULCUS_CagA+:B186b sample


title: UPN727 cells, unrelated healthy control 322 plasma

source_name: UPN727 cells stimulated with HC322 plasma

value: stimulated with HC322 plasma


title: UPN727 cells, unrelated healthy control 390 plasma

source_name: UPN727 cells stimulated with HC390 plasma

value: stimulated with HC390 plasma


title: 639124 (mRNA)

value: hypertrophic cardiomyopathy (HCM)

value: case


title: 676073 (mRNA)

value: male


title: 22 (mRNA)

value: female


title: UPN727 cells, unrelated healthy control 2301 plasma

source_name: UPN727 cells stimulated with HC2301 plasma

value: stimulated with HC2301 plasma


title: Hp+_Normal_CagA+:B136 sample

source_name: Endoscopic human antral tissue


title: 18 (mRNA)

value: cardiac


title: 33 (mRNA)


title: RR632698 (mRNA)


title: 25 (mRNA)


title: UPN727 cells, unrelated healthy control 1006 plasma

source_name: UPN727 cells stimulated with HC1006 plasma

value: stimulated with HC1006 plasma


title: UPN727 cells, unrelated healthy control 272 plasma

source_name: UPN727 cells stimulated with HC272 plasma

value: stimulated with HC272 plasma


title: UPN727 cells, unrelated healthy control 375 plasma

source_name: UPN727 cells stimulated with HC375 plasma

value: stimulated with HC375 plasma


title: Hp+_ULCUS_CagA-:B134 sample

value: Male

value: yes


title: 635263 (mRNA)


title: MCF10A_HER2HER3_2

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: 2 ug of fragmented and labeled ssDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 16h according to the manufacturers instructions. Washing prior to scanning was done with the Affymetrix Fluidic Station protocol FS450_0007.

scan_protocol: Arrays were scanning using an Affymetrix GeneChip Scanner 3000 and Affymetrix AGCC software.

data_processing: Raw data was normalized and probeset-level values calculated using the rma() function of the R/bioconductor (R version version 2.8) package affy using the Bioconductor annotation packages.

source_name: MCF10A cells

label_protocol: 200 ng total RNA were amplified using the GeneChipWT cDNA Synthesis Kit (Affymetrix) and 5.5ug of the resulting single-stranded cDNA (ssDNA) were fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MCF10A cells expressing empty vector, HER2, HER3 or HER2/HER3 were grown in three-dimensional cultures for 15 days in the presence of heregulin.

extract_protocol: Total RNA was isolated from the three-dimensional structures with a standard TRIZOL extraction method.

treatment_protocol: Cells were grown in three-dimensional cultures in DMEM/F12 medium supplemented with heregulin, horse serum, epidermal growth factor, hydrocortisone, cholera toxin, insulin, penicillin and streptomycin.

tag: transduction


title: Hp+_ULCUS_CagA-:B114 sample

tag: gender

value: no


title: Hp+_ULCUS_CagA+:B109 sample


title: RRNM09 (mRNA)

source_name: cardiac tissue, HCM


title: UPN727 cells, recent onset 2359 plasma

source_name: UPN727 cells stimulated with RO2359 plasma

value: stimulated with RO2359 plasma


title: Hp+_Normal_CagA-:B094 sample


title: Hp+_Normal_CagA-:B108 sample

value: Female


title: 56 (mRNA)


title: UPN727 cells, recent onset 1997 plasma

source_name: UPN727 cells stimulated with RO1997 plasma

value: stimulated with RO1997 plasma


title: Hp+_ULCUS_CagA-:B092 sample


title: UPN727 cells, recent onset 2751 plasma

source_name: UPN727 cells stimulated with RO2751 plasma

value: stimulated with RO2751 plasma


title: UPN727 cells, recent onset 2936 plasma

source_name: UPN727 cells stimulated with RO2936 plasma

value: stimulated with RO2936 plasma


title: Hp+_Normal_CagA+:B091 sample


title: RNM01 (mRNA)

value: hypertrophic cardiomyopathy (HCM)


title: MCF10A_HER3_2


title: 635265 (mRNA)

value: case


title: R57 (mRNA)


title: MCF10A_HER2_2


title: MCF10A_HER3_1


title: MCF10A_HER2HER3_1


title: 20 (mRNA)


title: UPN727 cells, recent onset 972 plasma

source_name: UPN727 cells stimulated with RO972 plasma

value: stimulated with RO972 plasma


title: UPN727 cells, recent onset 2559 plasma

source_name: UPN727 cells stimulated with RO2559 plasma

value: stimulated with RO2559 plasma


title: RNM07 (mRNA)

value: male


title: UPN727 cells, recent onset 2503 plasma

source_name: UPN727 cells stimulated with RO2503 plasma

value: stimulated with RO2503 plasma


title: MCF10A_Empty vector_2

value: Empty vector


title: 588103 (mRNA)

value: cardiac


title: Hp+_ULCUS_CagA-:B088 sample


title: 54 (mRNA)


title: MCF10A_Empty vector_1


title: UPN727 cells, recent onset 2903 plasma

source_name: UPN727 cells stimulated with RO2903 plasma

value: stimulated with RO2903 plasma


title: UPN727 cells, recent onset 2991 plasma

source_name: UPN727 cells stimulated with RO2991 plasma

value: stimulated with RO2991 plasma


title: R40 (mRNA)

value: female


title: MCF10A_HER2_1


title: Hp+_ULCUS_CagA-:B083 sample

value: Male

value: yes

value: no


title: Hp-:B082 sample

description: Hp-


title: UPN727 cells, recent onset 1057 plasma

source_name: UPN727 cells stimulated with RO1057 plasma

value: stimulated with RO1057 plasma


title: Hp-:B084 sample

description: Hp-

value: Female


title: 37 (mRNA)


title: UPN727 cells, recent onset 189 plasma

source_name: UPN727 cells stimulated with RO189 plasma

value: stimulated with RO189 plasma


title: 6-shogaol, rep1

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

description: Gene expression of MCF-7 cells treated with 10uM of 6-shogaol for 48h

hyb_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.

source_name: MCF-7 cells treated with 10uM 6-shogaol for 48h

growth_protocol: MCF-7 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37°C, 5% CO2.

extract_protocol: Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm.

treatment_protocol: Cells were treated with vehicle control (DMSO) or 10uM of 6-shogaol for 48h

tag: cell type

value: Breast cancer cell


title: 6-shogaol, rep2

label_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.


title: Control, rep 1

description: Gene expression of MCF-7 cells treated with vehicle control (DMSO) for 48h


title: 644621 (mRNA)

value: hypertrophic cardiomyopathy (HCM)

value: case


title: UPN727 cells, recent onset 930 plasma

source_name: UPN727 cells stimulated with RO930 plasma

value: stimulated with RO930 plasma


title: UPN727 cells, recent onset 62 plasma

source_name: UPN727 cells stimulated with RO62 plasma

value: stimulated with RO62 plasma


title: 666295 (mRNA)


title: 670934 (mRNA)


title: UPN727 cells, recent onset 201 plasma

source_name: UPN727 cells stimulated with RO201 plasma

value: stimulated with RO201 plasma


title: Hp+_ULCUS_CagA-:B046 sample

source_name: Endoscopic human antral tissue


title: NM10 (mRNA)

source_name: cardiac tissue, HCM

value: male


title: Control, rep 2

source_name: MCF-7 cells treated with vehicle control (DMSO) for 48h


title: Hp+_ULCUS_CagA-:B074 sample


title: Hp-:B062 sample

description: Hp-


title: Hp+_Normal_CagA-:B068 sample


title: Hp+_Normal_CagA-:B044 sample


title: polysome unbound fraction (polysome free) in human embryonic stem cells

city: Rehovot

first: Natali

last: Molotski

address: Rehovot

department: Biological Chemistry

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data was analyzed using Partek Genomics Suite 6.5. Initial normalization of probe intensity across arrays was performed using the RMA (robust multichip analysis) algorithm. The value of each gene was then further normalized by the average probe intensity values of the spiked-in controls.

label: Affymetrix standard protocol

source_name: polysome extract human embryonic stem cells

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA from polysome pools was isolated from each pool using PureLink RNA mini kit (Invitrogen)

value: H9 human embryonic stem cells

value: polysome unbound RNA fraction


title: R26 (mRNA)

value: cardiac


title: 7 (mRNA)


title: gene expression in human embryonic stem cells

data_processing: Data was analyzed using Partek Genomics Suite 6.5. Normalization of probe intensity across arrays was performed using the RMA (robust multichip analysis) algorithm.

source_name: pluripotent human embryonic stem cells

extract_protocol: Total RNA from human embryonic stem cells using RNeasy Plus mini kit (Qiagen).

value: total RNA


title: UPN727 cells, recent onset 946 plasma

source_name: UPN727 cells stimulated with RO946 plasma

value: stimulated with RO946 plasma


title: polysome bound fraction in human embryonic stem cells

value: polysome bound RNA fraction


title: UPN727 cells, recent onset 1442 plasma

source_name: UPN727 cells stimulated with RO1442 plasma

value: stimulated with RO1442 plasma


title: Hp+_Normal_CagA-:B027 sample

value: yes

value: no


title: Hp+_Normal_CagA+:B025 sample

value: Female


title: UPN727 cells, autologous plasma, biological replicate 5 [T1D]

source_name: UPN727 cells stimulated with Auto250S12 plasma

value: stimulated with Auto250S12 plasma


title: Hp+_Normal_CagA-:B010 sample


title: Cyclopamin, 12h, rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: The effect of Cyclopamine on expression of Hedgehog, angiogenesis and axon guidance marker genes was analyzed by seeding a coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of HG133 Plus2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: Coculture of 92% hMSCs and 8% huvEC, treated with cyclopamin, after 12 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Co-culture of hMSC (92%) and hUVEC (8%) were obtained by resuspending a total of 150,000 cell per spherical aggregate in 2 ml of differentiation medium and then seeded in a well of a Deepwell 96 well-plate (Nunc).

extract_protocol: RNA was isolated by using an RNeasy mini kit (Qiagen)

treatment_protocol: coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days. Medium was changed every third day by transferring the spherical aggregate to a new plate.

value: co-culture of hMSC (92%) and hUVEC (8%)

tag: treatment

value: Cyclopamine


title: Control, 12h, rep1

source_name: Coculture of 92% hMSCs and 8% huvEC, no treatment, after 12 hours

value: control


title: Cyclopamin, 12h, rep1


title: Hp+_Normal_CagA+:B002 sample

value: Male


title: UPN727 cells, recent onset 1012 plasma

source_name: UPN727 cells stimulated with RO1012 plasma

value: stimulated with RO1012 plasma


title: M-03-357

first: Sek Won

last: Kong

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Blood gene expression data from ASD

hyb_protocol: The cRNA was quantified (using A260) and fragmented. Fragmented cRNA was hybridized on the GeneChips according to the manufacturer's standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 at 2.5 μm resolution.

data_processing: The data were analyzed with Probe Logarithmic Intensity Error (PLIER) estimation method using Affymetrix Power Tools version 1.10.

source_name: Blood

label_protocol: A total of 1 ug RNA was processed using established Affymetrix protocols for the generation of biotin-labeled cRNA.

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

tag: diagnosis

value: CONTROL

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (amoxicillin)

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, recent onset 246 plasma

source_name: UPN727 cells stimulated with RO246 plasma

tag: protocol

value: stimulated with RO246 plasma

tag: responder cell line


title: M-04-374

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Other (Puerto Rican)

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases


title: M-04-360

description: Blood gene expression data from ASD

value: Other (Dominican)

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing


title: Cyclopamin, 12h, rep3

tag: cell type

tag: treatment


title: M-11-139

description: Blood gene expression data from ASD

value: Black

value: yes (pollen)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, recent onset 2185 plasma

source_name: UPN727 cells stimulated with RO2185 plasma

tag: protocol

value: stimulated with RO2185 plasma

tag: responder cell line


title: UPN727 cells, recent onset 1707 plasma

source_name: UPN727 cells stimulated with RO1707 plasma

value: stimulated with RO1707 plasma


title: Hp+_Normal_CagA-:B024 sample

tag: gender

tag: age

value: yes

tag: caga presence

value: no


title: Hp+_Normal_CagA+:B325 sample

value: Female


title: Control, 12h, rep4

value: co-culture of hMSC (92%) and hUVEC (8%)

value: control


title: Hp+_Normal_CagA-:B317 sample


title: M-04-356

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: male

tag: age at blood drawing (months)

tag: race

value: Unknown

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder


title: Control, 12h, rep3

tag: cell type

tag: treatment


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP990

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

description:
VP990_PolyA
Amplified cDNA.

hyb_protocol: Microarrays were hybridized overnight according to the manufacturer's protocol (Agilent Technologies) using the Agilent Gene Expression Hybridization kit.

scan_protocol: Microarrays were scanned at 3 um resolution on an Agilent DNA Microarray Scanner.

data_processing:
We selected the 4,672 viral probes in common between the MV and V3/V4 ViroChip designs. The raw Agilent background-subtracted intensities corresponding to these probes were then sum-normalized using an in-house developed program, setting all background negative values to zero [PMID 16609730].
Microarray hybridization patterns were interpreted using hierarchical cluster analysis as previously described [PMIDs 16609730, 9843981]. Specifically, out of the 4,672 normalized viral probes, we selected all retroviral probes (n = 486) and used these 486 probes to cluster microarrays and probes using Cluster 3.0 software (Eisen lab, Stanford University, http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm). Microarray clusters were visualized using Java Treeview (http:// http://sourceforge.net/projects/jtreeview/). The sub-cluster of 96 gammaretrovirus probes out of the 486 displayed in Fig. 2 of the 2012 Lee et al. PloS ONE paper is the same cluster as previously observed in the 2006 study by Urisman et al. [PMID 16609730].

The background-subtracted output intensities from Agilent's Feature Extraction Software corresponding to the 4,672 viral probes common to the MV and V3/V4 ViroChip designs are available in 'GSE39684_raw_matrix.txt', which is linked to the Series record as a supplementary file.
The sum-normalized intensities of the 4,672 probes are in the Sample data tables.
The 486 probes corresponding to the retroviruses and used to generate the figure for the paper (2012 Lee et al. PloS ONE) are available in 'GSE39684_retrovirus_probes.txt', which is linked to the Series record as a supplementary file.

source_name: Prostate biopsy, polyA

label_protocol: Randomly amplified cDNA was labelled using a Cy3 fluorescent dye via aa-dNTP incorporation (Wang  et al., 2002; Chiu et al., 2006; Chiu et al., 2008).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen). Prospectively collected samples were polyA purified using Oligotex kits (Qiagen).

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP991

description:
VP991_PolyA
Amplified cDNA.


title: UPN727 cells, recent onset 2676 plasma

source_name: UPN727 cells stimulated with RO2676 plasma

tag: protocol

value: stimulated with RO2676 plasma

tag: responder cell line


title: UPN727 cells, unrelated healthy control 295 plasma

source_name: UPN727 cells stimulated with HC295 plasma

value: stimulated with HC295 plasma


title: Hp+_Normal_CagA+:B303 sample

source_name: Endoscopic human antral tissue

tag: gender

tag: age

tag: caga presence


title: UPN727 cells, recent onset 2808 plasma

source_name: UPN727 cells stimulated with RO2808 plasma

value: stimulated with RO2808 plasma


title: M-04-299

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, unrelated healthy control 385 plasma

source_name: UPN727 cells stimulated with HC385 plasma

tag: protocol

value: stimulated with HC385 plasma

tag: responder cell line


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP988

description:
VP988_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment


title: Hp+_Normal_CagA+:B290 sample

tag: gender

value: Male

tag: age

tag: caga presence


title: Hp+_ULCUS_CagA+:B297 sample


title: M-04-312

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder


title: M-02-326

description: Blood gene expression data from ASD

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Hp+_ULCUS_CagA+:B286 sample

tag: gender

tag: age

tag: caga presence


title: M-02-340

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Other (Spanish)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP986

description:
VP986_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment

value: yes


title: Hp+_Normal_CagA+:B284 sample


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP985

description:
VP985_PolyA
Amplified cDNA.


title: UPN727 cells, unrelated healthy control 2790 plasma

source_name: UPN727 cells stimulated with HC2790 plasma

tag: protocol

value: stimulated with HC2790 plasma

tag: responder cell line


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP982

description:
VP982_PolyA
Amplified cDNA.


title: M-07-305

description: Blood gene expression data from ASD

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: UPN727 cells, unrelated healthy control 217 plasma

source_name: UPN727 cells stimulated with HC217 plasma

value: stimulated with HC217 plasma


title: Hp+_Normal_CagA+:B274 sample

tag: gender

tag: age

tag: caga presence


title: M-11-292

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Other (Puerto Rican)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: other diseases


title: M-14-190

description: Blood gene expression data from ASD

value: Black

value: Non-Hispanic

value: :unknown

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: M-04-285

description: Blood gene expression data from ASD

value: CONTROL

tag: gender

value: male

value: Other (Trinidadian)

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: UPN727 cells, autologous plasma, biological replicate 4 [T1D]

source_name: UPN727 cells stimulated with Auto250S10 plasma

tag: protocol

value: stimulated with Auto250S10 plasma

tag: responder cell line


title: Hp+_Normal_CagA-:B267 sample

value: Female

tag: age

tag: caga presence

value: no


title: UPN727 cells, recent onset 2953 plasma

source_name: UPN727 cells stimulated with RO2953 plasma

value: stimulated with RO2953 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP979

description:
VP979_PolyA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP977

description:
VP977_PolyA
Amplified cDNA.


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP981

description:
VP981_PolyA
Amplified cDNA.


title: UPN727 cells, unrelated healthy control 226 plasma

source_name: UPN727 cells stimulated with HC226 plasma

value: stimulated with HC226 plasma


title: UPN727 cells, recent onset 2944 plasma

source_name: UPN727 cells stimulated with RO2944 plasma

value: stimulated with RO2944 plasma


title: Hp-:B261 sample

description: Hp-

value: Male


title: UPN727 cells, recent onset 1037 plasma

source_name: UPN727 cells stimulated with RO1037 plasma

value: stimulated with RO1037 plasma


title: Hp-:B252 sample

description: Hp-


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP975

description:
VP975_PolyA
Amplified cDNA.

value: yes


title: A809126 (miRNA)

source_name: cardiac tissue, control

label_protocol: Standard Illumina labeling protocol for microRNA arrays.

extract_protocol: RNA was extracted using the QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

tag: Sex

tag: age (yrs)

value: cardiac

tag: sample type

value: control


title: A702013 (miRNA)


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP974

description:
VP974_PolyA
Amplified cDNA.


title: UPN727 cells, recent onset 2024 plasma

source_name: UPN727 cells stimulated with RO2024 plasma

value: stimulated with RO2024 plasma


title: M-09-268

description: Blood gene expression data from ASD

source_name: Blood

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Other

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: other diseases


title: F-03-067

description: Blood gene expression data from ASD

value: CONTROL

tag: gender

value: female

value: Other (Portuguese, Spanish)

value: Non-Hispanic

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: F-04-076

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Unknown

tag: ethnicity

tag: hours (minutes since last caloric intake)


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP965

description:
VP965_PolyA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment


title: F-03-167

description: Blood gene expression data from ASD

value: Asian

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing


title: UPN727 cells, recent onset 1437 plasma

source_name: UPN727 cells stimulated with RO1437 plasma

tag: protocol

value: stimulated with RO1437 plasma

tag: responder cell line


title: 4062 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: sample type


title: A505654 (miRNA)


title: UPN727 cells, recent onset 253 plasma

source_name: UPN727 cells stimulated with RO253 plasma

value: stimulated with RO253 plasma


title: F-02-218

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Mixed (Black, American Indian)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 5603 (miRNA)

tag: tissue

value: cardiac


title: F-02-117

description: Blood gene expression data from ASD

value: Caucasian

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing


title: UPN727 cells, unrelated healthy control 224 plasma

source_name: UPN727 cells stimulated with HC224 plasma

tag: protocol

value: stimulated with HC224 plasma

tag: responder cell line


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP960

description:
VP960_PolyA
Amplified cDNA.

source_name: Prostate biopsy, polyA

tag: cohort

tag: polya enrichment

value: yes


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP962

description:
VP962_PolyA
Amplified cDNA.


title: F-02-083

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

value: unknown

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP963

description:
VP963_PolyA
Amplified cDNA.

tag: tissue


title: UPN727 cells, unrelated healthy control 233 plasma

source_name: UPN727 cells stimulated with HC233 plasma

value: stimulated with HC233 plasma


title: 1403 (miRNA)

tag: Sex

tag: age (yrs)

tag: sample type

value: control


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP955

description:
VP955_PolyA
Amplified cDNA.


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP957

description:
VP957_PolyA
Amplified cDNA.


title: AC05-1032-01

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

value: yes (depression)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: Wellbutrin, Rispiradol, Fish Oil, Multivitamin

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 4049 (miRNA)

value: female


title: UPN727 cells, unrelated healthy control 294 plasma

source_name: UPN727 cells stimulated with HC294 plasma

tag: protocol

value: stimulated with HC294 plasma

tag: responder cell line


title: UPN727 cells, unrelated healthy control 285 plasma

source_name: UPN727 cells stimulated with HC285 plasma

value: stimulated with HC285 plasma


title: AC05-1024-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: advil, motrin, cough suppressant, sudafed, benedryl, multi-vitamin, fish oil (omega-3)


title: UPN727 cells, autologous plasma, biological replicate 3 [T1D]

source_name: UPN727 cells stimulated with Auto250S9 plasma

value: stimulated with Auto250S9 plasma


title: 12799 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: sample type


title: 191002 (miRNA)


title: 91099 (miRNA)


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP949

description:
VP949_PolyA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: AC05-1032-05

description: Blood gene expression data from ASD

value: CONTROL

value: Caucasian

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: tylenol, multivitamin

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP945

description:
VP945_PolyA
Amplified cDNA.


title: 171102 (miRNA)

tag: Sex

value: control


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP946

description:
VP946_PolyA
Amplified cDNA.


title: UPN727 cells, recent onset 2109 plasma

source_name: UPN727 cells stimulated with RO2109 plasma

tag: protocol

value: stimulated with RO2109 plasma

tag: responder cell line


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP947

description:
VP947_PolyA
Amplified cDNA.

tag: tissue


title: UPN727 cells, recent onset 1939 plasma

source_name: UPN727 cells stimulated with RO1939 plasma

value: stimulated with RO1939 plasma


title: UPN727 cells, unrelated healthy control 223 plasma

source_name: UPN727 cells stimulated with HC223 plasma

value: stimulated with HC223 plasma


title: 5140 (miRNA)

value: female

tag: age (yrs)

tag: sample type


title: 22100 (miRNA)


title: UPN727 cells, unrelated healthy control 2146 plasma

source_name: UPN727 cells stimulated with HC2146 plasma

value: stimulated with HC2146 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP935

description:
VP935_PolyA
Amplified cDNA.

tag: cohort

tag: polya enrichment


title: AC05-1015-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

value: yes (suspected anxiety disorder, suspected OCD, pica)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: medidale, celexa, tenex, cingulair, melatonin, tylenol


title: AC05-1001-04

description: Blood gene expression data from ASD

value: male

value: Non-Hispanic

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: cerebral palsy

tag: seizure

tag: other diseases


title: R5126 (miRNA)

tag: Sex

tag: tissue

value: cardiac

tag: sample type


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP934

description:
VP934_PolyA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: AC05-1016-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (anxiety disorder, ADD)

tag: birth defects

value: Antibiotics, Robitussin, Tylenol, Antibiotics, Melatonin, Robitussin, Tylenol


title: R300305 (miRNA)

tag: age (yrs)

value: control


title: AC05-0023-04

description: Blood gene expression data from ASD

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: ct

tag: mri

tag: medications/vitamin names

value: Tylenol, Tylenol, Multivitamins, Omega 3

tag: cerebral palsy

tag: seizure

tag: other diseases


title: R26309 (miRNA)

tag: Sex

value: female

tag: tissue

tag: sample type


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP898

description:
VP898_PolyA
Amplified cDNA.

tag: cohort

tag: polya enrichment


title: UPN727 cells, autologous plasma, biological replicate 2 [T1D]

source_name: UPN727 cells stimulated with Auto250S8 plasma

tag: protocol

value: stimulated with Auto250S8 plasma

tag: responder cell line


title: UPN727 cells, recent onset 2598 plasma

source_name: UPN727 cells stimulated with RO2598 plasma

value: stimulated with RO2598 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP897

description:
VP897_PolyA
Amplified cDNA.


title: UPN727 cells, recent onset 2366 plasma

source_name: UPN727 cells stimulated with RO2366 plasma

value: stimulated with RO2366 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP891

description:
VP891_PolyA
Amplified cDNA.


title: AC03-1009-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: birth defects


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP90

description:
VP90_PolyA
Amplified cDNA.

tag: tissue


title: R5144 (miRNA)

source_name: cardiac tissue, control

tag: Sex

tag: sample type


title: AC05-1004-04

description: Blood gene expression data from ASD

source_name: Blood

tag: chronic diseases

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: ct

tag: mri

tag: medications/vitamin names

value: multivitamin

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 0431840 (miRNA)

tag: age (yrs)


title: UPN727 cells, recent onset 2348 plasma

source_name: UPN727 cells stimulated with RO2348 plasma

tag: protocol

value: stimulated with RO2348 plasma

tag: responder cell line


title: AC05-0003-04

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: birth defects

value: Multivitamins


title: AC02-1249-01

description: Blood gene expression data from ASD

value: male

tag: chronic diseases

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: ct

tag: mri

tag: medications/vitamin names

value: cold medicine, flouride, iron

tag: cerebral palsy


title: AC02-1240-04

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

value: Hispanic

value: motrin, Metadate

tag: seizure

tag: other diseases


title: AC02-1248-05

description: Blood gene expression data from ASD

value: PDD-NOS

tag: race

value: Caucasian

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: allergies

tag: developmental/speech disorder


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP889

description:
VP889_PolyA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: UPN727 cells, recent onset 2312 plasma

source_name: UPN727 cells stimulated with RO2312 plasma

tag: protocol

value: stimulated with RO2312 plasma

tag: responder cell line


title: UPN727 cells, recent onset 1964 plasma

source_name: UPN727 cells stimulated with RO1964 plasma

value: stimulated with RO1964 plasma


title: AC02-1238-04

description: Blood gene expression data from ASD

tag: chronic diseases

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

value: yes (asthma)

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Xopenex


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP887

description:
VP887_PolyA
Amplified cDNA.

source_name: Prostate biopsy, polyA


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP890

description:
VP890_PolyA
Amplified cDNA.


title: UPN727 cells, recent onset 1973 plasma

source_name: UPN727 cells stimulated with RO1973 plasma

value: stimulated with RO1973 plasma


title: AC02-1223-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

value: female

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: allergies

value: advair, singulair, flonex, albuterol, motrin, tylenol, vitamin C

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, recent onset 2130 plasma

source_name: UPN727 cells stimulated with RO2130 plasma

tag: protocol

value: stimulated with RO2130 plasma

tag: responder cell line


title: UPN727 cells, unrelated healthy control 2593 plasma

source_name: UPN727 cells stimulated with HC2593 plasma

value: stimulated with HC2593 plasma


title: 5059 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: sample type

value: control


title: 5089 (miRNA)


title: 676236 (miRNA)

source_name: cardiac tissue, HCM

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

value: case


title: R34  (miRNA)

value: male


title: AC02-1211-04

description: Blood gene expression data from ASD

tag: diagnosis

value: Caucasian

value: Non-Hispanic

tag: chronic diseases

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: multivitamin


title: 627047 (miRNA)

tag: Sex


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP880

description:
VP880_PolyA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP875

description:
VP875_PolyA
Amplified cDNA.

tag: tissue


title: 639123 (miRNA)

tag: age (yrs)

tag: disease state

tag: sample type


title: 655638 (miRNA)


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP873

description:
VP873_PolyA
Amplified cDNA.


title: R643724 (miRNA)


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP88

description:
VP88_PolyA
Amplified cDNA.


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP878

description:
VP878_PolyA
Amplified cDNA.


title: AC02-1197-04

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, unrelated healthy control 2302 plasma

source_name: UPN727 cells stimulated with HC2302 plasma

tag: protocol

value: stimulated with HC2302 plasma

tag: responder cell line


title: AC02-1184-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: neurological disorder

tag: psychiatric disorder

value: yes (suspected OCD)

tag: gastrointestinal disorder

value: yes (GERD)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: motrin, prozac, multivitamin


title: UPN727 cells, autologous plasma, biological replicate 1 [T1D]

source_name: UPN727 cells stimulated with Auto250S7 plasma

value: stimulated with Auto250S7 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP847

description:
VP847_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment


title: R634935 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: disease state

tag: sample type


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP818

description:
VP818_PolyA
Amplified cDNA.


title: UPN727 cells, unrelated healthy control 2074 plasma

source_name: UPN727 cells stimulated with HC2074 plasma

tag: protocol

value: stimulated with HC2074 plasma

tag: responder cell line


title: AC02-1181-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: zythromax, antibiotics, albuterol, zythromax, antibiotics, albuterol, pulmocort, clariton

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP817

description:
VP817_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment


title: 673482 (miRNA)

tag: Sex

tag: age (yrs)

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: UPN727 cells, gram-positive pneumonia patient 1287 plasma

description: Gene expression data from UPN727 cells stimulated with bacterial pneumonia plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1287 plasma

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of healthy control or bacterial pneumonia plasma.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cell line

tag: protocol


title: AC02-1005-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Unknown

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

value: yes (petit mal or absence seizures)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: 629740 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP800

description:
VP800_PolyA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: UPN727 cells, gram-positive pneumonia patient 1344 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1344 plasma

tag: responder cell line

tag: protocol


title: AC02-1173-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP79

description:
VP79_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment


title: AC02-1010-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: AC01-0030-04

description: Blood gene expression data from ASD

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: multivitamin, fiber supplement


title: UPN727 cells, gram-positive pneumonia patient 1275 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1275 plasma

tag: responder cell line

tag: protocol


title: AC01-0069-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

value: female

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: Depacote, Kepra, Risperdal

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 43 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP784

description:
VP784_PolyA
Amplified cDNA.

tag: cohort

tag: polya enrichment


title: UPN727 cells, gram-positive pneumonia patient 1412 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1412 plasma


title: UPN727 cells, gram-positive pneumonia patient 1224 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1224 plasma


title: 671852 (miRNA)


title: UPN727 cells, gram-positive pneumonia patient 1325 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1325 plasma


title: Prostate Biopsy from 2012 Cohort, Trizol Extracted, PolyA purified, VP742

description:
VP742_PolyA
Amplified cDNA.


title: UPN727 cells, gram-positive pneumonia patient 1410 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1410 plasma


title: 673368 (miRNA)


title: A-0097-P2

description: Blood gene expression data from ASD

source_name: Blood

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: A-0104-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, gram-positive pneumonia patient 1403 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1403 plasma

tag: responder cell line

tag: protocol


title: 28 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP51

description:
VP51_PolyA
Amplified cDNA.

source_name: Prostate biopsy, polyA

tag: cohort

tag: polya enrichment


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP50

description:
VP50_Total_RNA
Amplified cDNA.

source_name: Prostate biopsy, total RNA

value: no


title: 639649 (miRNA)

value: cardiac


title: 39 (miRNA)

value: hypertrophic cardiomyopathy (HCM)


title: AC02-1387-04

description: Blood gene expression data from ASD

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: motrin


title: R633573 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type

value: case


title: AC02-1392-04

description: Blood gene expression data from ASD

tag: diagnosis

value: ASPERGER'S DISORDER

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: Zoloft, Nasonex, Melatonin, Vyvanse

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, gram-positive pneumonia patient 1382 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1382 plasma

tag: responder cell line

tag: protocol


title: A-0087-P2

description: Blood gene expression data from ASD

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP62

description:
VP62_2012
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: yes


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP50

description:
VP50_PolyA
Amplified cDNA.


title: AC02-1387-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Non-Hispanic

value: yes (speech delay)

tag: neurological disorder

value: yes (Suspected of being extra clumsy, uncoordinated; suspected unusual gait)

tag: psychiatric disorder

tag: gastrointestinal disorder

value: advil

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, healthy control 233 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC233 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC233 plasma


title: UPN727 cells, gram-positive pneumonia patient 1353 plasma

source_name: UPN727 cells stimuated with gram-positive pneumonia patient 1353 plasma


title: UPN727 cells, healthy control 272 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC272 plasma

value: stimuated with HC272 plasma


title: AC02-1187-04

description: Blood gene expression data from ASD

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: prilosec, advil


title: UPN727 cells, healthy control 285 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC285 plasma

value: stimuated with HC285 plasma


title: UPN727 cells, healthy control 1006 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC1006 plasma

value: stimuated with HC1006 plasma


title: 631132 (miRNA)

source_name: cardiac tissue, HCM

tag: Sex

value: male

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: AC02-1382-01

description: Blood gene expression data from ASD

tag: diagnosis

value: ASPERGER'S DISORDER

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: neurological disorder

value: yes  (positive lead screen)

tag: psychiatric disorder

value: yes (anxiety disorder, ADD)

tag: gastrointestinal disorder

tag: medications/vitamin names

value: melatonin, multivitamins

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 30 (miRNA)

value: female

value: case


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP49

description:
VP49_Total_RNA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: no


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP49

description:
VP49_PolyA
Amplified cDNA.

value: yes


title: AC02-1380-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

value: yes (abnormal MRI)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: abnormal MRI

value: antibiotics, flonase, multivitamin


title: 670152 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: UPN727 cells, healthy control 390 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC390 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC390 plasma


title: AC02-1378-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes (GERD)

value: yes (asthma)

tag: medications/vitamin names

value: none, miralax, singulair, multivitamin, glycolax

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, healthy control 393 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC393 plasma

value: stimuated with HC393 plasma


title: 3 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: tissue

value: case


title: R35 (miRNA)

tag: disease state

tag: sample type


title: 634021 (miRNA)


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP42

description:
VP42_Total_RNA
Amplified cDNA.

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: no


title: R671993 (miRNA)


title: 637810 (miRNA)


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP31

description:
VP31_Total_RNA
Amplified cDNA.


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP31

description:
VP31_PolyA
Amplified cDNA.

value: yes


title: AC02-1364-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

value: yes (anxiety disorder, ADD)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri


title: AC02-1364-04

description: Blood gene expression data from ASD

value: CONTROL

tag: race

tag: ethnicity

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: medications/vitamin names

value: advair, singulair, zyrtec, flonase, tylenol

tag: cerebral palsy

tag: seizure

tag: other diseases


title: AC02-1375-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: age at blood drawing (months)

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: multivitamin, miralax


title: UPN727 cells, healthy control 385 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC385 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC385 plasma


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP42

description:
VP42_PolyA
Amplified cDNA.

tag: tissue

tag: cohort

tag: polya enrichment


title: UPN727 cells, healthy control 295 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC295 plasma

value: stimuated with HC295 plasma


title: AC02-1370-01

description: Blood gene expression data from ASD

tag: race

value: Caucasian

tag: ethnicity

value: Hispanic

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (GERD)

tag: autoimmune disorder

value: yes (asthma)

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: none, proair, singulair, albuterol, advair


title: AC02-1361-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: hours (minutes since last caloric intake)

value: yes (speech and motor delay), MR

value: yes (cerebral palsy; unusual gait)

tag: psychiatric disorder

value: yes (anxiety disorder, OCD, ADD)

tag: gastrointestinal disorder

tag: medications/vitamin names

value: Amoxicillin, Zyprexa, Despiramine, Topomax

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, healthy control 2301 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC2301 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC2301 plasma


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP35

description:
VP35_Total_RNA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment

value: no


title: UPN727 cells, healthy control 294 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC294 plasma

value: stimuated with HC294 plasma


title: UPN727 cells, healthy control 217 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC217 plasma

value: stimuated with HC217 plasma


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP30

description:
VP30_PolyA
Amplified cDNA.

value: yes


title: UPN727 cells, healthy control 226 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC226 plasma

value: stimuated with HC226 plasma


title: 647527 (miRNA)

tag: Sex

value: male

tag: age (yrs)

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: AC02-1360-01

description: Blood gene expression data from ASD

source_name: Blood

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (possible abnormal MRI)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: suspected of having abnormal MRI

value: antibiotics, multivitamin


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP30

description:
VP30_Total_RNA
Amplified cDNA.

source_name: Prostate biopsy, total RNA

tag: tissue

tag: cohort

tag: polya enrichment


title: 47 (miRNA)

tag: Sex

tag: age (yrs)

tag: disease state

tag: sample type


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP29

description:
VP29_Total_RNA
Amplified cDNA.


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP29

description:
VP29_PolyA
Amplified cDNA.

source_name: Prostate biopsy, polyA


title: AC02-1356-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: medications/vitamin names

value: antiobiotic, albuterol, Pulmicort

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP27

description:
VP27_Total_RNA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP107

description:
VP107_Total_RNA
Amplified cDNA.

value: no


title: 653448 (miRNA)

tag: Sex

tag: age (yrs)

tag: disease state


title: UPN727 cells, healthy control 1730 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC1730 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC1730 plasma


title: RNM04 (miRNA)

value: female

tag: sample type


title: AC02-1334-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Asian

tag: ethnicity

tag: chronic diseases

tag: allergies

value: yes

tag: developmental/speech disorder

value: yes (speech delay)

tag: neurological disorder

value: yes (Suspected of being extra clumsy, uncoordinated; abnormal EEG)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: Amoxicillin, multivitamin


title: 645586 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

value: case


title: 661552 (miRNA)

value: male

tag: sample type


title: UPN727 cells, healthy control 389 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC389 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC389 plasma


title: AC02-1324-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

value: yes (speech delay, MR)

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes (GERD, severe abdominal p)ain

tag: medications/vitamin names

value: triaminic, probiotics

tag: cerebral palsy

tag: seizure

tag: other diseases


title: AC02-1253-04

description: Blood gene expression data from ASD

value: PDD-NOS

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (depression, bipoloar, anxiety disorder, OCD, ADD)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: clonidine, seroquel, multivitamin


title: AC02-1334-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: multivitamin


title: AC02-1331-01

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

value: yes

value: speech delay

value: yes (unusual gait)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: medications/vitamin names

value: antibiotics, clariton

tag: cerebral palsy


title: UPN727 cells, healthy control 1534 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC1534 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC1534 plasma


title: UPN727 cells, healthy control 1369 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC1369 plasma

value: stimuated with HC1369 plasma


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, PolyA purified, VP10

description:
VP10_PolyA
Amplified cDNA.

tag: tissue

value: prostate biopsy

tag: cohort

tag: polya enrichment


title: Cell Line 22Rv1 Supernatant, Trizol Extracted, 22Rv1

description:
22Rv1_Total_RNA
Amplified cDNA.

source_name: Cell line, total RNA

tag: cell line

value: no


title: UPN727 cells, healthy control 381 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC381 plasma

value: stimuated with HC381 plasma


title: 631131 (miRNA)

source_name: cardiac tissue, HCM

tag: Sex

value: male

tag: age (yrs)

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: AC04-1016-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

value: female

tag: age at blood drawing (months)

tag: race

value: Caucasian

value: Non-Hispanic

value: :unknown

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

tag: neurological disorder

value: yes (abnormal MRI)

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: abnormal

value: Medications/ Vitmatin names (timeline not specified)

tag: seizure

tag: other diseases


title: UPN727 cells, healthy control 1259 plasma [Pneu_S3S24_10Pneu_4HC]

source_name: UPN727 cells stimuated with HC1259 plasma

tag: responder cell line

tag: protocol

value: stimuated with HC1259 plasma


title: AC01-1019-04

description: Blood gene expression data from ASD

value: AUTISM

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: medications/vitamin names

tag: cerebral palsy


title: 638751 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: Cell Line 22Rv1 Supernatant, Trizol Extracted, PolyA purified, 22Rv1

description:
22Rv1_PolyA
Amplified cDNA.

source_name: Cell line, polyA

tag: cell line

tag: polya enrichment

value: yes


title: Prostate Biopsy from 2006 Cohort, Trizol Extracted, VP10

description:
VP10_Total_RNA
Amplified cDNA.

value: prostate biopsy

tag: cohort

value: no


title: UPN727 cells, 1052B active flu plasma

description: Gene expression data from UPN727 cells stimulated with pre vs. active H1N1 (flu) plasma

source_name: UPN727 cells stimulated with 1052B active flu plasma

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of autologous or H1N1 sera.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cell line

value: stimulated with 1052B active flu plasma


title: UPN727 cells, 1052A pre flu plasma

source_name: UPN727 cells stimulated with 1052A pre flu plasma

tag: protocol

value: stimulated with 1052A pre flu plasma


title: AC05-1047-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

value: metadate, melatonin

tag: seizure

tag: other diseases


title: 663118 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: 663702 (miRNA)

value: female


title: 683304 (miRNA)


title: 653447 (miRNA)


title: 687046 (miRNA)


title: R656518 (miRNA)


title: 370118 (miRNA)


title: M-14-129

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

value: Mixed

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: medications/vitamin names

tag: cerebral palsy


title: 673367 (miRNA)


title: UPN727 cells, 1090B active flu plasma

source_name: UPN727 cells stimulated with 1090B active flu plasma

tag: responder cell line

tag: protocol

value: stimulated with 1090B active flu plasma


title: M-12-186

description: Blood gene expression data from ASD

value: Black

tag: ethnicity

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: seizure

tag: other diseases


title: M-16-128

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: psychiatric disorder

value: yes (ADHD)