title: G1890_rep3

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
20110929_G1890
Gene expression after 3hr exposure to 1uM alpha-factor

hyb_protocol: Agilent protocol.

scan_protocol: Agilent protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Agilent One-Color Microarray-Based Gene Expression Analysis kit (Agilent) according to the manufacturer's protocol.

extract_protocol: RNA was prepared using Qiagen RNeasy kit following manufacturer's protocol.

treatment_protocol: Yeast cells after 3hr exposure to 1 uM alpha-factor.

tag: strain

value: G1890 (derived from BY4741)


title: M-14-225

status: Public on Sep 01 2012

type: RNA

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

country: USA

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.

label: biotin

molecule: total RNA

organism: Homo sapiens

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

tag: gender

value: male

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: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: M-07-194

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: yes (speech delay)


title: M-12-148

description: Blood gene expression data from ASD

value: Caucasian

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder


title: G1890_rep2

description:
20110928_G1890
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, 121F pre flu 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 pre vs. active H1N1 (flu) 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 121F pre flu 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 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

tag: protocol

value: stimulated with 121F pre flu plasma


title: UPN727 cells, 121G active flu plasma

source_name: UPN727 cells stimulated with 121G active flu plasma

value: stimulated with 121G active flu plasma


title: UPN727 cells, 1223B active flu plasma

source_name: UPN727 cells stimulated with 1223B active flu plasma

value: stimulated with 1223B active flu plasma


title: M-13-157

description: Blood gene expression data from ASD

value: Black

value: Non-Hispanic

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: UPN727 cells, 033S pre flu plasma

source_name: UPN727 cells stimulated with 033S pre flu plasma

value: stimulated with 033S pre flu plasma


title: R620009 (miRNA)

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 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

value: female

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: 46 (miRNA)


title: M-06-217

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

value: Asian

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, autologous plasma, flu, biological replicate 2

source_name: UPN727 cells stimulated with autologous plasma

tag: responder cell line

tag: protocol

value: stimulated with autologous plasma


title: 610700 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: tissue

tag: disease state


title: UPN727 cells, 1223A pre flu plasma

source_name: UPN727 cells stimulated with 1223A pre flu plasma

value: stimulated with 1223A pre flu plasma


title: UPN727 cells, 033T active flu plasma

source_name: UPN727 cells stimulated with 033T active flu plasma

value: stimulated with 033T active flu plasma


title: 9B

description:
20110927_9B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 98A

description:
20110927_98A
Gene expression after 3hr exposure to 1uM alpha-factor


title: G1890_rep1

value: G1890 (derived from BY4741)


title: AC02-1336-05

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: tylenol, motrin


title: UPN727 cells, 1090A pre flu plasma

source_name: UPN727 cells stimulated with 1090A pre flu plasma

tag: responder cell line

tag: protocol

value: stimulated with 1090A pre flu plasma


title: UPN727 cells, autologous plasma, flu, biological replicate 1


title: M-04-240

description: Blood gene expression data from ASD

tag: ethnicity

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 49 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: RNM06 (miRNA)


title: 48 (miRNA)


title: M-04-201

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Other

value: Hispanic

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: R50 (miRNA)

tag: Sex

value: female


title: 8A

description:
20110929_8A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: M-03-255

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: neurological disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: UPN727 cells, healthy control 1837 plasma

description: Gene expression data from cell lines stimulated with healthy control plasma

source_name: UPN727 cells stimulated with HCy1837 plasma

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of autologous, healthy control (HC), or cystic fibrosis (CF) 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

value: stimulated with HCy1837 plasma


title: M-03-230

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: 88A

description:
20110928_88A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 27 (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 233 plasma

source_name: UPN727 cells stimulated with HCy233 plasma

tag: responder cell line

value: stimulated with HCy233 plasma


title: 89B

description:
20111101_89B
Gene expression after 3hr exposure to 1uM alpha-factor


title: UPN727 cells, healthy control 284 plasma

source_name: UPN727 cells stimulated with HCy284 plasma

tag: protocol

value: stimulated with HCy284 plasma


title: 95B

description:
20110928_95B
Gene expression after 3hr exposure to 1uM alpha-factor


title: UPN727 cells, healthy control 393 plasma

source_name: UPN727 cells stimulated with HCy393 plasma

value: stimulated with HCy393 plasma


title: M-03-203

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: male

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

tag: neurological disorder

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: R58 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

value: case


title: NM03 (miRNA)

tag: sample type


title: 85B

description:
20110927_85B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: M-03-175

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: R8 (miRNA)

tag: Sex


title: 75B

description:
20110929_75B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 71B

description:
20111005_71B
Gene expression after 3hr exposure to 1uM alpha-factor


title: M-02-147

description: Blood gene expression data from ASD

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: F-16-149

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)


title: UPN727 cells, healthy control 1006 plasma

source_name: UPN727 cells stimulated with HCy1006 plasma

tag: responder cell line

tag: protocol

value: stimulated with HCy1006 plasma


title: 81B

description:
20110929_81B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 633322 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: UPN727 cells, healthy control 385 plasma

source_name: UPN727 cells stimulated with HCy385 plasma

value: stimulated with HCy385 plasma


title: F-16-115

description: Blood gene expression data from ASD

value: Black

value: Non-Hispanic

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: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy


title: UPN727 cells, healthy control 295 plasma

source_name: UPN727 cells stimulated with HCy295 plasma

tag: responder cell line

tag: protocol

value: stimulated with HCy295 plasma


title: 6A

description:
20110928_6A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, healthy control 2301 plasma

source_name: UPN727 cells stimulated with HCy2301 plasma

value: stimulated with HCy2301 plasma


title: UPN727 cells, healthy control 390 plasma

source_name: UPN727 cells stimulated with HCy390 plasma

value: stimulated with HCy390 plasma


title: UPN727 cells, healthy control 294 plasma

source_name: UPN727 cells stimulated with HCy294 plasma

value: stimulated with HCy294 plasma


title: UPN727 cells, healthy control 252 plasma

source_name: UPN727 cells stimulated with HCy252 plasma

value: stimulated with HCy252 plasma


title: 656578 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: F-13-101

description: Blood gene expression data from ASD

source_name: Blood

tag: diagnosis

value: CONTROL

tag: gender

tag: age at blood drawing (months)

tag: race

value: Other (West Indian)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (insect bites)

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: seizure

tag: other diseases


title: F-15-059

description: Blood gene expression data from ASD

value: Other (Puerto Rican)

value: Hispanic

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy


title: 653809 (miRNA)

source_name: cardiac tissue, HCM

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type

value: case


title: R342632 (miRNA)


title: 653513 (miRNA)

value: male


title: F-13-112

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Black

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder


title: 632093 (miRNA)


title: UPN727 cells, healthy control 226 plasma

source_name: UPN727 cells stimulated with HCy226 plasma

tag: responder cell line

tag: protocol

value: stimulated with HCy226 plasma


title: 70B

description:
20110929_70B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 69A

description:
20111005_69A
Gene expression after 3hr exposure to 1uM alpha-factor


title: R655639 (miRNA)

tag: Sex

tag: age (yrs)


title: 60C

description:
20110928_60C
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-12-241

description: Blood gene expression data from ASD

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: 68B

description:
20110929_68B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 65A

description:
20110928_65A
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-12-174

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Mixed (Black, Filipino)

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder


title: 680701 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: UPN727 cells, healthy control 1730 plasma

source_name: UPN727 cells stimulated with HC1730 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC1730 plasma


title: UPN727 cells, healthy control 217 plasma

source_name: UPN727 cells stimulated with HCy217 plasma

value: stimulated with HCy217 plasma


title: 45 (miRNA)


title: 41 (miRNA)


title: UPN727 cells, healthy control 1534 plasma

source_name: UPN727 cells stimulated with HC1534 plasma

value: stimulated with HC1534 plasma


title: F-11-192

description: Blood gene expression data from ASD

tag: diagnosis

value: female

value: Mixed (Chinese, Spanish)

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: F-11-093

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

value: yes (pollen & dust)

tag: developmental/speech disorder

tag: neurological disorder


title: UPN727 cells, healthy control 1369 plasma

source_name: UPN727 cells stimulated with HC1369 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC1369 plasma


title: 57B

description:
20111005_57B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 649284 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: 5A

description:
20110927_5A
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-09-071

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

value: Unknown

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: F-12-037

description: Blood gene expression data from ASD

tag: age at blood drawing (months)

tag: race

value: Mixed (Arabic, White)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (seasonal allergies)

tag: developmental/speech disorder

tag: neurological disorder


title: R32 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type

value: case


title: 59C_rep1

description:
20110928_59C
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, healthy control 381 plasma

description: Gene expression data from cell lines stimulated with healthy control plasma

source_name: UPN727 cells stimulated with HC381 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC381 plasma


title: 59C_rep2


title: RNM08 (miRNA)


title: 55A

description:
20111005_55A
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-11-214

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: Caucasian

value: Non-Hispanic

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, healthy control 2300 plasma

source_name: UPN727 cells stimulated with HC2300 plasma

value: stimulated with HC2300 plasma


title: UPN727 cells, healthy control 1259 plasma

source_name: UPN727 cells stimulated with HC1259 plasma

value: stimulated with HC1259 plasma


title: 54D_rep3

description:
20111101_54D
Gene expression after 3hr exposure to 1uM alpha-factor


title: UPN727 cells, healthy control 1265 plasma

source_name: UPN727 cells stimulated with HC1265 plasma

value: stimulated with HC1265 plasma


title: 54D_rep2

description:
20110928_54D
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-05-239

description: Blood gene expression data from ASD

value: female

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder


title: RNM05 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: UPN727 cells, healthy control 1249 plasma

source_name: UPN727 cells stimulated with HC1249 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC1249 plasma


title: F-05-188

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: Other (Puerto Rican)

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: F-04-202

description: Blood gene expression data from ASD

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: other diseases


title: F-06-098

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: Other (Spanish)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder


title: UPN727 cells, healthy control 1301 plasma

source_name: UPN727 cells stimulated with HC1301 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC1301 plasma


title: 587005 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: 54D_rep1

description:
20110927_54D
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 36 (miRNA)


title: 44 (miRNA)


title: F-04-172

description: Blood gene expression data from ASD

value: CONTROL

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: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: UPN727 cells, healthy control 1365 plasma

source_name: UPN727 cells stimulated with HC1365 plasma

tag: responder cell line

tag: protocol

value: stimulated with HC1365 plasma


title: R619278 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type

value: case


title: 49A_rep1

description:
20110929_49A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 4B

description:
20110928_4B
Gene expression after 3hr exposure to 1uM alpha-factor


title: F-03-066

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

value: yes (dogs)

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: other diseases


title: RNM02 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue


title: F-04-081

description: Blood gene expression data from ASD

tag: allergies

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: F-04-207

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Mixed (Caucasian, Black)

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: developmental/speech disorder


title: F-04-162

description: Blood gene expression data from ASD

value: Mixed (Puerto Rican, Black)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: other diseases


title: 48A

description:
20110927_48A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: F-03-046

description: Blood gene expression data from ASD

value: female

tag: allergies

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: UPN727 cells, cystic fibrosis patient CF4305 plasma

description: Gene expression data from cell lines stimulated with cystic fibrosis patient plasma

source_name: UPN727 cells stimulated with CF4305 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4305 plasma


title: AC05-1013-04

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: ethnicity

tag: hours (minutes since last caloric intake)

value: yes (speech delay)

value: yes (suspected anxiety disorder)

value: ProAir Inhaler, Nyquil, Cingulair, Vitamin C, Exstenderal, Multivitamin

tag: cerebral palsy

tag: seizure


title: 47A

description:
20111005_47A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, healthy control 1271 plasma

source_name: UPN727 cells stimulated with HC1271 plasma

value: stimulated with HC1271 plasma


title: UPN727 cells, cystic fibrosis patient CF4304 plasma

source_name: UPN727 cells stimulated with CF4304 plasma

value: stimulated with CF4304 plasma


title: UPN727 cells, cystic fibrosis patient CF4285 plasma

source_name: UPN727 cells stimulated with CF4285 plasma

value: stimulated with CF4285 plasma


title: R607466 (miRNA)

source_name: cardiac tissue, HCM

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: UPN727 cells, cystic fibrosis patient CF4271 plasma

source_name: UPN727 cells stimulated with CF4271 plasma

value: stimulated with CF4271 plasma


title: R59 (miRNA)

value: case


title: 49A_rep2

description:
20111005_49A
Gene expression after 3hr exposure to 1uM alpha-factor


title: 50B

description:
20110929_50B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 656880 (miRNA)


title: 647526 (miRNA)

value: male


title: 24 (miRNA)


title: 46B

description:
20110929_46B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 41A

description:
20110928_41A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC05-1013-01

description: Blood gene expression data from ASD

source_name: Blood

value: PDD-NOS

value: Non-Hispanic

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (suspected ADD)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Antibiotics, Adderall, Extdreeyl, Vitamin C, Multivitamin

tag: other diseases


title: 43A

description:
20110928_43A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 17 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue


title: 45B

description:
20110929_45B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 9 (miRNA)

value: female

tag: disease state

tag: sample type


title: 669841 (miRNA)


title: 3A

description:
20110927_3A
Gene expression after 3hr exposure to 1uM alpha-factor


title: UPN727 cells, cystic fibrosis patient CF4265 plasma

source_name: UPN727 cells stimulated with CF4265 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4265 plasma


title: AC05-1003-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

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

tag: neurological disorder

tag: psychiatric disorder

value: tylenol

tag: cerebral palsy

tag: seizure


title: UPN727 cells, cystic fibrosis patient CF4297 plasma

source_name: UPN727 cells stimulated with CF4297 plasma

value: stimulated with CF4297 plasma


title: 39A_rep2

description:
20111101_39A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, cystic fibrosis patient CF4138 plasma

source_name: UPN727 cells stimulated with CF4138 plasma

value: stimulated with CF4138 plasma


title: UPN727 cells, cystic fibrosis patient CF4256 plasma

source_name: UPN727 cells stimulated with CF4256 plasma

value: stimulated with CF4256 plasma


title: AC05-1009-01

description: Blood gene expression data from ASD

value: AUTISM

value: yes (excessively clumsy, uncoordinated)

value: yes (suspected OCD, ADD)

tag: gastrointestinal disorder

value: yes

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: singulair, actos, vitamins, methyl B-12 shots, allergy shots

tag: other diseases


title: AC05-1001-01

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)

value: yes (speech delay, learning disability)

value: yes (GERD)


title: 39A_rep1

description:
20111005_39A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC05-0071-01

description: Blood gene expression data from ASD

value: male

value: Non-Hispanic

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: Tylenol Cold, Prozac, Mutelax, Centrum Kids Vitamins

tag: cerebral palsy


title: AC05-1005-04

description: Blood gene expression data from ASD

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: claritin

tag: seizure


title: R53 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: AC05-0070-01

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)

value: yes (speech delay)

tag: ct

tag: mri

tag: medications/vitamin names

value: Tylenol Cold & Flu, Fish oil, Singulair

tag: other diseases


title: UPN727 cells, cystic fibrosis patient CF4184 plasma

source_name: UPN727 cells stimulated with CF4184 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4184 plasma


title: 38C

description:
20111005_38C
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC05-0078-01

description: Blood gene expression data from ASD

value: AUTISM

value: Asian

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: cerebral palsy

tag: seizure


title: R16 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: UPN727 cells, cystic fibrosis patient CF4133 plasma

source_name: UPN727 cells stimulated with CF4133 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4133 plasma


title: UPN727 cells, cystic fibrosis patient CF4107 plasma

source_name: UPN727 cells stimulated with CF4107 plasma

value: stimulated with CF4107 plasma


title: UPN727 cells, cystic fibrosis patient CF4088 plasma

source_name: UPN727 cells stimulated with CF4088 plasma

value: stimulated with CF4088 plasma


title: 37B

description:
20111101_37B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: UPN727 cells, cystic fibrosis patient CF4157 plasma

source_name: UPN727 cells stimulated with CF4157 plasma

value: stimulated with CF4157 plasma


title: R1 (miRNA)


title: AC05-0007-01

description: Blood gene expression data from ASD

tag: diagnosis

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: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: ct

tag: mri

tag: medications/vitamin names

value: antibiotic (name unknown), singular, prevacid, carnitor, coenzyme Q-10, vitamin E, thiamin, riboflavin, vitamin C, A-lipoeic acid, pepcid, nasonex

tag: other diseases

value: mitochondrial disorder


title: 36A

description:
20110928_36A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC05-0002-04

description: Blood gene expression data from ASD

value: yes (MR), delayed speech

tag: neurological disorder

tag: psychiatric disorder

value: yes (seizures)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Adderall

tag: cerebral palsy

tag: seizure

value: Landau-Kleffner Syndrome, childhood disintegration disorder


title: RR632698 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: UPN727 cells, cystic fibrosis patient CF4047 plasma

source_name: UPN727 cells stimulated with CF4047 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4047 plasma


title: UPN727 cells, cystic fibrosis patient CF4087 plasma

source_name: UPN727 cells stimulated with CF4087 plasma

value: stimulated with CF4087 plasma


title: 35B

description:
20110928_35B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 350A

description:
20111005_350A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC05-0002-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

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

tag: ct

tag: mri

tag: medications/vitamin names

value: Deficeve, Lamitreal, Seroquel, Calonidre, Colanibire, Carnitur (not sure how to spell these)

tag: other diseases

value: Landau-Kleffner Syndrome, abnormal EEG, childhood disintegration disorder


title: 29 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: 22 (miRNA)


title: UPN727 cells, cystic fibrosis patient CF4045 plasma

source_name: UPN727 cells stimulated with CF4045 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4045 plasma


title: 34B

description:
20110929_34B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 33C

description:
20110928_33C
Gene expression after 3hr exposure to 1uM alpha-factor


title: UPN727 cells, cystic fibrosis patient CF4091 plasma

description: Gene expression data from cell lines stimulated with cystic fibrosis patient plasma

source_name: UPN727 cells stimulated with CF4091 plasma

value: stimulated with CF4091 plasma


title: AC05-0018-01

description: Blood gene expression data from ASD

tag: diagnosis

value: ASPERGER'S DISORDER

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

value: yes

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: cerebral palsy

tag: seizure


title: AC03-1009-01

description: Blood gene expression data from ASD

value: male

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: yes (suspected anxiety disorder)

tag: ct

tag: mri

tag: medications/vitamin names

value: omega 369

tag: other diseases


title: UPN727 cells, cystic fibrosis patient CF4026 plasma

source_name: UPN727 cells stimulated with CF4026 plasma

tag: responder cell line

tag: protocol

value: stimulated with CF4026 plasma


title: UPN727 cells, cystic fibrosis patient CF4024 plasma

source_name: UPN727 cells stimulated with CF4024 plasma

value: stimulated with CF4024 plasma


title: 18 (miRNA)

source_name: cardiac tissue, HCM

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: AC03-1003-01

description: Blood gene expression data from ASD

source_name: Blood

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Robutussin, Privacet, daily vitamins

tag: cerebral palsy


title: 25 (miRNA)

tag: Sex


title: 639124 (miRNA)

value: female

tag: age (yrs)


title: AC04-0015-01

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

tag: allergies

tag: developmental/speech disorder

value: yes (suspected tics)

value: yes (GERD)

value: yes (3p duplication, maternally inherited)

tag: ct

tag: mri

tag: medications/vitamin names

value: Tylenol cold/ congestion, Claritin

tag: seizure

tag: other diseases

value: metabolic abnormalities


title: 33 (miRNA)

value: male

tag: tissue

tag: disease state

tag: sample type


title: 676073 (miRNA)


title: 32A

description:
20110929_32A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 313C

description:
20110928_313C
Gene expression after 3hr exposure to 1uM alpha-factor


title: 301A

description:
20110929_301A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC03-1002-01

description: Blood gene expression data from ASD

tag: diagnosis

value: ASPERGER'S DISORDER

tag: gender

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: Non-Hispanic

tag: chronic diseases

value: yes (MR), delayed speech

tag: neurological disorder

tag: psychiatric disorder

value: yes (ADD)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: ritalin, risperdal, lithium


title: AC03-1001-01

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

tag: allergies

tag: developmental/speech disorder

value: yes (OCD)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Amoxicillin

tag: cerebral palsy

tag: seizure

value: abnormal MRI and EEG


title: UPN727 cells, autologous plasma, biological replicate 4

description: Gene expression data from cell lines stimulated with autologous plasma

source_name: UPN727 cells stimuated with AutoB3W1 plasma

tag: responder cell line

tag: protocol

value: stimuated with AutoB3W1 plasma


title: AC04-0020-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

tag: ethnicity

value: Hispanic

tag: chronic diseases

value: yes (suspected anxiety disorder)

value: Seroquel; Tylenol; multivitamin; melatonin

tag: other diseases

value: abnormal Eeg, congenital heart defect


title: UPN727 cells, autologous plasma, biological replicate 5

source_name: UPN727 cells stimuated with AutoB3W1+2 plasma

value: stimuated with AutoB3W1+2 plasma


title: UPN727 cells, cystic fibrosis patient CF4017 plasma

source_name: UPN727 cells stimulated with CF4017 plasma

value: stimulated with CF4017 plasma


title: UPN727 cells, autologous plasma, biological replicate 3

source_name: UPN727 cells stimuated with AutoB1S3 plasma

value: stimuated with AutoB1S3 plasma


title: RRNM09 (miRNA)

tag: Sex

value: female

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: 300B

description:
20110928_300B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC02-1278-04

description: Blood gene expression data from ASD

value: CONTROL

value: male

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

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: ct

tag: mri

tag: medications/vitamin names

value: Robitussin

tag: cerebral palsy


title: UPN727 cells, autologous plasma, biological replicate 1

source_name: UPN727 cells stimuated with AutoB1S1 plasma

tag: responder cell line

tag: protocol

value: stimuated with AutoB1S1 plasma


title: 56 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: UPN727 cells, autologous plasma, biological replicate 2

source_name: UPN727 cells stimuated with AutoB1S2 plasma

value: stimuated with AutoB1S2 plasma


title: 30B

description:
20111005_30B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 27A

description:
20110927_27A
Gene expression after 3hr exposure to 1uM alpha-factor


title: 635265 (miRNA)


title: AC02-1278-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

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

tag: neurological disorder

tag: psychiatric disorder

value: CMA varient of unknown significance, deletion 11p11.12

value: zofran, Clonidine, Benadryl, Priloces

tag: seizure

tag: other diseases


title: 2B

description:
20110929_2B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 635263 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue


title: 20 (miRNA)

tag: disease state

tag: sample type


title: RNM07 (miRNA)


title: AC02-1247-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

value: yes (learning disability)

value: yes (excessively clumsy, uncoordinated)

value: yes (bipolar, ADD)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Depakote, Risperdal, advil

tag: cerebral palsy


title: AC02-1274-04

description: Blood gene expression data from ASD

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: Adderal

tag: seizure


title: AC02-1274-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: gastrointestinal disorder

tag: autoimmune disorder

value: amoxicillin, adderall

tag: other diseases


title: 26B

description:
20110928_26B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC02-1225-01

description: Blood gene expression data from ASD

tag: genetic testing

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: multivitamin

tag: cerebral palsy


title: U251 miR-31 overexpression

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

country: China

institute: ZheJiang University

description: U251 cells transfected with has-miR-31

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133_plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned with the affymetrix genechip 7G plus, and AGCC is used for the image processing.

data_processing: Genespring 10.0, is used for automatically normalizing the chip data and analyzing the fold change.

label_protocol: Start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, GeneChip 3 IVT Express Kit (Lot no. 901228) is used in the experiment.

growth_protocol: Cells were cultured in DMEM cell culture media with 10%FBS

extract_protocol: Total RNA was extracted with trizol according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: glioma

tag: mir-31 transfection


title: U251 control

description: U251 cells transfected with control

value: control


title: 588103 (miRNA)

tag: Sex

value: male

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: RNM01 (miRNA)


title: R57 (miRNA)

value: female


title: 261A_rep2

description:
20111101_261A
Gene expression after 3hr exposure to 1uM alpha-factor


title: 25B

description:
20110927_25B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 263B

description:
20110927_263B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 261A_rep1

description:
20110927_261A
Gene expression after 3hr exposure to 1uM alpha-factor


title: 54 (miRNA)


title: AC02-1217-04

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: gender

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

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

value: ear drops, imipramine, DDAVP

tag: seizure


title: AC02-1226-01

description: Blood gene expression data from ASD

value: AUTISM

value: Asian

tag: genetic testing

tag: birth defects

value: yes (kidney defect from birth)

tag: ct

tag: mri

tag: medications/vitamin names

value: Tylenol

tag: cerebral palsy

tag: other diseases


title: M-15-080

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Unknown

tag: ethnicity

value: :unknown


title: M-16-018

description: Blood gene expression data from ASD

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (ADD)

value: concerta, Amitrypilene


title: 24B

description:
20110929_24B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC02-1224-01

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

value: male

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: benefiber, multivitamin

tag: seizure


title: 256A

description:
20110929_256A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1217-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

value: female

tag: ct

tag: mri

tag: medications/vitamin names

value: Focalin

tag: cerebral palsy

tag: other diseases


title: M-15-030

description: Blood gene expression data from ASD

value: CONTROL

tag: gender

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

value: yes (ADHD)


title: M-13-116

description: Blood gene expression data from ASD

value: Black

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder


title: R40 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: M-15-023

description: Blood gene expression data from ASD

tag: diagnosis

value: :unknown

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: AC02-1215-01

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: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

value: Clariton, multivitamin

value: deletion 15g 13.2g-13.3g


title: M-14-021

description: Blood gene expression data from ASD

tag: diagnosis

value: male

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: M-13-087

description: Blood gene expression data from ASD

value: Hispanic

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: 37 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

tag: disease state

tag: sample type


title: 22C

description:
20110928_22C
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 213C_rep2

description:
20110929_213C
Gene expression after 3hr exposure to 1uM alpha-factor


title: 666295 (miRNA)


title: 215B

description:
20110929_215B
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1206-01

description: Blood gene expression data from ASD

value: PDD-NOS

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: yes (anxiety disorder, OCD, ADD)

value: zithromax, Zoloft, Strattera, Benadryl

tag: other diseases


title: 213C_rep1

description:
20110928_213C
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1201-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

value: Mixed (Black, Caucasian)

value: yes (excessively clumsy, uncoordinated)

value: yes (anxiety 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: M-13-032

description: Blood gene expression data from ASD

value: CONTROL

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 (asthma)

value: albuterol, flovent


title: 644621 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: M-13-012

description: Blood gene expression data from ASD

tag: diagnosis

value: male

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (ADHD)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: Adderall

tag: other diseases


title: M-12-152

description: Blood gene expression data from ASD

tag: gender

tag: age at blood drawing (months)

tag: race

value: Asian

tag: ethnicity

value: :unknown

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: M-13-005

description: Blood gene expression data from ASD

tag: diagnosis

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder


title: AC02-1198-01

description: Blood gene expression data from ASD

value: AUTISM

value: female

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

value: cough medicine, melatonin


title: 20A_rep1

description:
20110928_20A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC02-1189-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: gender

tag: age at blood drawing (months)

tag: race

value: Mixed (Black, Caucasian)

tag: ethnicity

value: yes (delayed speech)

tag: birth defects

tag: other diseases


title: M-12-102

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: Other

value: Non-Hispanic

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: R26 (miRNA)

tag: Sex

tag: age (yrs)

tag: tissue

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

tag: sample type


title: 7 (miRNA)

value: male

value: case


title: NM10 (miRNA)


title: 670934 (miRNA)


title: AC02-1168-01

description: Blood gene expression data from ASD

tag: gender

value: Caucasian

value: Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (mood disorder, Pica)

tag: gastrointestinal disorder

tag: autoimmune disorder

value: yes (asthma)

tag: genetic testing

value: oral steroids, asthma medications, Flovent, albuterol


title: 20A_rep2

description:
20111101_20A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 19B

description:
20110928_19B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 1B

description:
20111005_1B
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1168-05

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

tag: ethnicity

value: yes (speech delay)

value: yes (abnormal EEG, meningitis)

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: asthma meds, flovent, albuterol

tag: cerebral palsy

tag: seizure

tag: other diseases

value: meningitis


title: HMSC-SK 4756083018_R006_C008

type: genomic

city: Nashville

first: Scott

last: Borinstein

address: 2200 Pierce Ave

institute: Vanderbilt University

description:
4756083018_R006_C008
Bisulfite Treated DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

source_name: hMSC Primary Culture

label_protocol: Standard Illumina Protocol

growth_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit, then bisulfite treated with EZ DNA Methyation-Gold kit according to standard instructions

extract_protocol: Standard Illumina Protocol

tag: sample group

value: HMSC-SK

tag: cell type

value: mesenchymal stem cell


title: 196A

description:
20110928_196A
Gene expression after 3hr exposure to 1uM alpha-factor


title: HMSC-DP 4756083018_R005_C008

description:
4756083018_R005_C008
Bisulfite Treated DNA

value: HMSC-DP


title: AC02-1181-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: gender

value: female

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

value: yes (anxiety disorder, OCD)

tag: gastrointestinal disorder


title: M-12-060

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: male

tag: age at blood drawing (months)

tag: race

value: Other

tag: ethnicity

value: :unknown

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: AC02-1153-01

description: Blood gene expression data from ASD

value: AUTISM

value: Caucasian

value: yes (psoriasis)

tag: ct

tag: mri

tag: medications/vitamin names

value: Advil

tag: cerebral palsy

tag: seizure

tag: other diseases


title: M-12-070

description: Blood gene expression data from ASD

tag: gender

value: Black

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder


title: AC02-1115-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: multivitamin


title: M-11-155

description: Blood gene expression data from ASD

tag: race

tag: ethnicity

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: HMSC-P 4756083018_R004_C008

description:
4756083018_R004_C008
Bisulfite Treated DNA

tag: sample group

value: HMSC-P

tag: cell type

value: mesenchymal stem cell


title: 193A

description:
20110929_193A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: M-11-003

description: Blood gene expression data from ASD

tag: gender

tag: hours (minutes since last caloric intake)

value: yes (delay due to prematurity - born at 27 weeks)

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 189C

description:
20110929_189C
Gene expression after 3hr exposure to 1uM alpha-factor


title: 192A

description:
20110928_192A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1007-04

description: Blood gene expression data from ASD

tag: diagnosis

value: ASPERGER'S DISORDER

tag: age at blood drawing (months)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (abnormal CT Scan and Febrile Seizures)

tag: psychiatric disorder

tag: gastrointestinal disorder


title: M-12-052

description: Blood gene expression data from ASD

tag: race

tag: ethnicity

value: Non-Hispanic

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: AC02-1008-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: gender

tag: hours (minutes since last caloric intake)

value: yes (eating disorder)

tag: ct

tag: mri

tag: medications/vitamin names


title: Ewing sarcoma E35 4756083018_R008_C002

description:
4756083018_R008_C002
Bisulfite Treated DNA

source_name: Primary Tumor Sample

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: HMSC-S57 4756083018_R003_C008

description:
4756083018_R003_C008
Bisulfite Treated DNA

tag: cell type


title: M-09-090

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: male

tag: age at blood drawing (months)

value: :unknown

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: AC01-0076-01

description: Blood gene expression data from ASD

value: AUTISM

tag: race

value: Unknown

tag: ethnicity

value: Hispanic

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: Tylenol cold, Vitamins, Benedryl

value: positive lead test, congenital heart defect


title: Ewing sarcoma E27 4756083018_R008_C001

description:
4756083018_R008_C001
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: M-06-103

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: hours (minutes since last caloric intake)

tag: ct

tag: mri

tag: medications/vitamin names


title: AC01-0061-01

description: Blood gene expression data from ASD

value: female

tag: race

value: Caucasian

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

value: antibiotics, steriod, ibuterol w/ nebulizer, antiseizure kepra, neurontin risperdal, ritalin, antibiotic, benadryl, women's multi-vitamin

tag: cerebral palsy

tag: seizure

tag: other diseases


title: AC01-0037-01

description: Blood gene expression data from ASD

tag: ethnicity

value: yes (speech delay)

tag: neurological disorder

tag: psychiatric disorder

value: yes (ADD)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects

value: mulivitamin


title: 17A

description:
20110927_17A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: M-04-065

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: ct

tag: mri


title: 178B

description:
20110929_178B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 171A_rep2

description:
20111101_171A
Gene expression after 3hr exposure to 1uM alpha-factor


title: Ewing sarcoma E67 4756083018_R008_C006

description:
4756083018_R008_C006
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: 171A_rep1

description:
20111005_171A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC01-0004-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: race

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: medications/vitamin names

value: fluoride

tag: cerebral palsy

tag: seizure

tag: other diseases


title: 15A

description:
20111005_15A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: Ewing sarcoma E74 4756083018_R005_C012

description:
4756083018_R005_C012
Bisulfite Treated DNA

value: primary Ewing sarcoma tumor


title: M-04-048

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

value: male

tag: ethnicity

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: Ewing sarcoma E74 4756083018_R007_C007

description:
4756083018_R007_C007
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: 182B

description:
20111005_182B
Gene expression after 3hr exposure to 1uM alpha-factor


title: 154A_rep2

description:
20111101_154A
Gene expression after 3hr exposure to 1uM alpha-factor


title: Ewing sarcoma E66 4756083018_R006_C011

description:
4756083018_R006_C011
Bisulfite Treated DNA


title: A-0125-A1

description: Blood gene expression data from ASD

tag: gender

tag: age at blood drawing (months)

tag: race

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes

tag: allergies

tag: ct

tag: mri

value: multivitamin, fluoride


title: M-06-019

description: Blood gene expression data from ASD

tag: diagnosis

tag: ethnicity

tag: developmental/speech disorder

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: Ewing sarcoma E43 4756083018_R008_C003

description:
4756083018_R008_C003
Bisulfite Treated DNA

tag: sample group


title: 14C

description:
20111005_14C
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: A-0119-A2

description: Blood gene expression data from ASD

value: AUTISM

tag: gender

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: birth defects


title: Ewing sarcoma E67 4756083018_R007_C011

description:
4756083018_R007_C011
Bisulfite Treated DNA

tag: tissue


title: Ewing sarcoma E43 4756083018_R007_C009

description:
4756083018_R007_C009
Bisulfite Treated DNA


title: M-04-047

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Unknown

value: Hispanic

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

tag: allergies

tag: ct

tag: mri


title: A-0125-A2

description: Blood gene expression data from ASD

value: Caucasian

tag: ethnicity

tag: developmental/speech disorder

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure

tag: other diseases


title: A-0103-P1

description: Blood gene expression data from ASD

tag: gender

value: yes (motor coordination disorder)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing


title: Ewing sarcoma E66 4756083018_R007_C006

description:
4756083018_R007_C006
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: M-03-169

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

value: Mixed

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: birth defects


title: M-04-035

description: Blood gene expression data from ASD

tag: ethnicity

tag: developmental/speech disorder

tag: ct

tag: mri

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: M-04-022

description: Blood gene expression data from ASD

tag: gender

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: other diseases


title: 149A

description:
20110929_149A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: M-03-168

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: race

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies


title: 154A_rep1

description:
20110927_154A
Gene expression after 3hr exposure to 1uM alpha-factor


title: M-04-006

description: Blood gene expression data from ASD

tag: ethnicity

tag: developmental/speech disorder

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names


title: A-0119-A1

description: Blood gene expression data from ASD

tag: gender

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: cerebral palsy

tag: seizure


title: M-03-075

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: autoimmune disorder

tag: genetic testing

tag: other diseases


title: A-0114-P2

description: Blood gene expression data from ASD

value: female

tag: race

value: Mixed (Black, Caucasian)

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies


title: 141B

description:
20110928_141B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: Ewing sarcoma E34 4756083018_R007_C002

description:
4756083018_R007_C002
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: Ewing sarcoma E58 4756083018_R007_C005

description:
4756083018_R007_C005
Bisulfite Treated DNA


title: Ewing sarcoma E34 4756083018_R003_C009

description:
4756083018_R003_C009
Bisulfite Treated DNA


title: 138C

description:
20110929_138C
Gene expression after 3hr exposure to 1uM alpha-factor


title: 136A

description:
20110928_136A
Gene expression after 3hr exposure to 1uM alpha-factor


title: A-0098-P1

description: Blood gene expression data from ASD

tag: gender

value: Non-Hispanic

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: birth defects

tag: ct

tag: mri

tag: medications/vitamin names

value: Adderall, Tenex, Risperdal


title: A-0082-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: age at blood drawing (months)

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: genetic testing

tag: cerebral palsy

tag: seizure

tag: other diseases


title: M-03-040

description: Blood gene expression data from ASD

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies


title: 11B

description:
20110927_11B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: A-0079-P2

description: Blood gene expression data from ASD

tag: gender

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

value: yes (ADHD)

tag: birth defects

tag: ct


title: M-03-058

description: Blood gene expression data from ASD

tag: diagnosis

value: CONTROL

tag: age at blood drawing (months)

value: Other

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: mri

tag: medications/vitamin names


title: Ewing sarcoma E75 4756083018_R008_C007

description:
4756083018_R008_C007
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: 120A

description:
20111005_120A
Gene expression after 3hr exposure to 1uM alpha-factor


title: Ewing sarcoma E75 4756083018_R006_C012

description:
4756083018_R006_C012
Bisulfite Treated DNA


title: Ewing sarcoma E26 4756083018_R007_C001

description:
4756083018_R007_C001
Bisulfite Treated DNA


title: 117C

description:
20110928_117C
Gene expression after 3hr exposure to 1uM alpha-factor


title: M-02-141

description: Blood gene expression data from ASD

value: male

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (speech delay)

value: yes (behaviorial issues)

tag: genetic testing

tag: cerebral palsy

tag: seizure

tag: other diseases


title: A-0077-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: gender

tag: allergies

value: yes

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: birth defects

tag: ct


title: Ewing sarcoma E56 4756083018_R005_C005

description:
4756083018_R005_C005
Bisulfite Treated DNA

tag: sample group


title: AC02-1211-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: Caucasian

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: mri

tag: medications/vitamin names


title: Ewing sarcoma E56 4756083018_R006_C010

description:
4756083018_R006_C010
Bisulfite Treated DNA

tag: tissue


title: 114B

description:
20110929_114B
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 111B

description:
20110928_111B
Gene expression after 3hr exposure to 1uM alpha-factor


title: A-0081-P1

description: Blood gene expression data from ASD

value: AUTISM

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: genetic testing

value: Zoloft

tag: cerebral palsy

tag: seizure

tag: other diseases


title: M-03-049

description: Blood gene expression data from ASD

tag: gender

value: Unknown

value: Hispanic

value: :unknown

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: psychiatric disorder

tag: birth defects

tag: ct


title: A-0076-A1

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: Non-Hispanic

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: mri

value: abnormal

tag: medications/vitamin names

value: multivitamin, Allegra


title: AC02-1189-01

description: Blood gene expression data from ASD

value: PDD-NOS

tag: race

value: Black

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: genetic testing


title: Ewing sarcoma E58 4756083018_R008_C010

description:
4756083018_R008_C010
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: A-0085-P2

description: Blood gene expression data from ASD

tag: gender

value: female

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: cerebral palsy

tag: seizure

tag: other diseases


title: A-0075-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: male

tag: age at blood drawing (months)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: birth defects

tag: ct


title: Ewing sarcoma E42 4756083018_R007_C003

description:
4756083018_R007_C003
Bisulfite Treated DNA


title: 104A

description:
20110927_104A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: 10A

description:
20110927_10A
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1183-01

description: Blood gene expression data from ASD

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: genetic testing

tag: mri

tag: medications/vitamin names


title: A-0071-P1

description: Blood gene expression data from ASD

tag: gender

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: multivitamin

tag: cerebral palsy

tag: seizure


title: Ewing sarcoma E42 4756083018_R006_C009

description:
4756083018_R006_C009
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: 12C

description:
20110928_12C
Gene expression after 3hr exposure to 1uM alpha-factor


title: AC02-1197-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: birth defects

tag: ct

tag: other diseases


title: AC02-1336-04

description: Blood gene expression data from ASD

value: CONTROL

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: genetic testing

tag: mri

tag: medications/vitamin names


title: AC02-1172-01

description: Blood gene expression data from ASD

tag: gender

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: cerebral palsy

tag: seizure


title: AC02-1318-04

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder


title: Ewing sarcoma E73 4756083018_R004_C012

description:
4756083018_R004_C012
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: A-0074-P2

description: Blood gene expression data from ASD

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: birth defects

tag: ct

tag: other diseases


title: Ewing sarcoma E73 4756083018_R006_C007

description:
4756083018_R006_C007
Bisulfite Treated DNA


title: 103A

description:
20110928_103A
Gene expression after 3hr exposure to 1uM alpha-factor

tag: strain


title: AC02-1293-01

description: Blood gene expression data from ASD

tag: gender

tag: allergies

tag: developmental/speech disorder

value: yes (speech delay)

tag: neurological disorder

tag: genetic testing

tag: mri

tag: medications/vitamin names

value: motrin

tag: cerebral palsy


title: AC02-1178-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: Caucasian

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: seizure


title: AC02-1141-01

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (ADHD)

tag: birth defects

tag: ct

value: Clonidine, trozedone, and fluvoxamine (Luvox)


title: Ewing sarcoma E65 4756083018_R006_C006

description:
4756083018_R006_C006
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: AC02-1354-01

description: Blood gene expression data from ASD

tag: gender

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: genetic testing

tag: mri

tag: other diseases

value: positive lead test


title: AC02-1113-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: Non-Hispanic

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: autoimmune disorder

tag: medications/vitamin names

tag: cerebral palsy


title: Ewing sarcoma E57 4756083018_R007_C010

description:
4756083018_R007_C010
Bisulfite Treated DNA


title: ICEclc_10mM3CBA_stationary_inrR-/-_replicate1

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description:
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
ICEclcB13 in Pseudomonas knackmussii strain B13

hyb_protocol: 60 ng of labeled cDNA was then loaded onto each microarray, hybridized for 17 hours at 65ºC, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60ºC for 30 minutes) was omitted.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR: Hi:100% and XDR Lo:10%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocols GE1-v5_95_Feb07 or GE1_105_Dec08 and Grid: 020923_D_F_20080708) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were then transported to GeneSpring GX v11.0, Generic Single Color experiment, thresholding 1.0, Quantile normalization, no baseline transformation performed. Data were grouped according to genotypes (wt, inrR-/-, rpoS), filtered on expression value (20-100th percentile), analysed for significance (Oneway ANOVA unequal variance, corrected p-value cut-off 0.05, assymptotic p-value  computation, Benjamini-Hochberg multiple testing correction).

organism: Pseudomonas knackmussii

label_protocol: cDNA was synthesized from total RNA and directly labeled with cyanine-3-dCTP using a modification of a protocol described elsewhere (Charbonnier et al. 2005). Briefly, each 50-µL reaction contained 10 µg of total RNA, 1.25 µg of random hexanucleotide primers (Promega), 100 µM each of unlabeled dATP, dGTP, and dTTP (Invitrogen), 25 µM of unlabeled dCTP (Invitrogen), 25 µM of cyanine-3-labeled dCTP (Perkin-Elmer), 25 U SUPERase•In (Ambion), and 400 U Superscript II reverse transcriptase (Invitrogen). Reactions were performed by heating at 42ºC for 2 hours followed by 70ºC for 10 min. RNA was then removed by adding 100 mM NaOH, heating to 65ºC for 20 min, and neutralizing with 100 mM HCl and 300 mM sodium acetate (pH 5.2). Labeled cDNA products were purified using the MinElute PCR purification kit (Qiagen) and the quantity and incorporation frequency of cyanine-3-labeled dCTP were calculated using the MICROARRAY function on a NanoDrop Spectrophotometer.

growth_protocol: P. knackmussii B13, the original host of ICEclc, was cultivated in minimal medium (MM) based on the type 21C medium (Gerhardt et al. 1981). This MM was complemented with 10mM 3CBA and the bacteria were grown at 30°C. Bacterial growth was assessed from culture turbidity at 600 nm (OD600). Cells were recovered 48 h after the beginning of the stationary phase. For RNA isolation, 100 ml of culture was immediately harvested by centrifugation (at 15,000 × g for 1 min at 4°C) and the supernatant was decanted. Cell pellets were resuspended in 4 ml RNAprotect Bacteria Reagent (QIAGEN GmbH). After 5 min incubation, the suspensions were centrifuged again (at 5,000 × g for 5 min at room temperature); the supernatant was discarded and pellets were stored at -80°C.

extract_protocol: Prior to RNA extraction, pellets were slowly thawed, then resuspended in 0.5 ml TES buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 mM NaCl], followed by addition of and mixing with 0.25 ml lysis solution [20 mM sodium acetate (pH 5.5), 1 mM EDTA, 0.5% SDS]. After that, the total RNA was further purified by the hot acid-phenol method as described previously [Baumann et al. 1996]. RNA samples were purified from contaminating DNA by treatment with 50 U of DNase I (RNase free; Roche) during 1 h at 37°C. Finally, the RNA was dissolved in 50 µl diethylpyrocarbonate (DEPC)-treated water and quantified by absorbance at 260 and 280 nm on a NanoDrop spectrophotometer (Witec AG). The integrity of RNA was determined by agarose gel electrophoresis and the absence of DNA was verified by PCR.

tag: strain

tag: genotype

value: deletion in inrR


title: ICEclc_10mM3CBA_stationary_inrR-/-_replicate3


title: ICEclc_10mM3CBA_stationary_inrR-/-_replicate2


title: Ewing sarcoma E41 4756083018_R006_C003

description:
4756083018_R006_C003
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: 102A

description:
20110928_102A
Gene expression after 3hr exposure to 1uM alpha-factor


title: ICEclc_10mM3CBA_stationary_rpoS_replicate3

value: deletion in rpoS


title: Ewing sarcoma E57 4756083018_R006_C005

description:
4756083018_R006_C005
Bisulfite Treated DNA


title: AC02-1009-01

description: Blood gene expression data from ASD

tag: gender

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (adhd)

tag: birth defects

tag: ct

tag: seizure


title: AC02-1351-01

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: age at blood drawing (months)

tag: developmental/speech disorder

value: yes (MR)

tag: neurological disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes

tag: genetic testing

tag: mri

tag: other diseases


title: ICEclc_10mM3CBA_stationary_rpoS_replicate2

tag: strain

tag: genotype


title: ICEclc_10mM3CBA_stationary_rpoS_replicate1


title: AC02-1140-01

description: Blood gene expression data from ASD

tag: gender

value: male

tag: race

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: autoimmune disorder

tag: medications/vitamin names

value: immodium, concerta

tag: cerebral palsy


title: Ewing sarcoma E33 4756083018_R006_C002

description:
4756083018_R006_C002
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: AC02-1006-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: birth defects

tag: ct

tag: seizure


title: Ewing sarcoma E25 4756083018_R006_C001

description:
4756083018_R006_C001
Bisulfite Treated DNA


title: AC02-1344-01

description: Blood gene expression data from ASD

tag: gender

tag: race

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing

tag: mri

value: Benedryl, Zyrtec

tag: other diseases

value: suspected diagnosis of Stickler syndrome


title: Ewing sarcoma E53 4756083018_R002_C005

description:
4756083018_R002_C005
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: AC02-1333-01

description: Blood gene expression data from ASD

tag: diagnosis

value: female

tag: age at blood drawing (months)

value: Caucasian

tag: ethnicity

tag: hours (minutes since last caloric intake)

value: yes (speech delay)

value: yes (anxiety disorder)

tag: autoimmune disorder

tag: medications/vitamin names

value: Abilify, Inderal, Multivitamin, Omega-3

tag: cerebral palsy


title: AC02-1004-01

description: Blood gene expression data from ASD

value: Non-Hispanic

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

tag: birth defects

tag: ct

tag: seizure


title: AC02-1324-04

description: Blood gene expression data from ASD

value: CONTROL

tag: gender

tag: race

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing

tag: mri

value: motrin

tag: other diseases


title: ICEclc_10mM3CBA_stationary_WT_replicate5

tag: strain

tag: genotype

value: wild type


title: AC02-1317-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: age at blood drawing (months)

tag: ethnicity

tag: hours (minutes since last caloric intake)

value: yes (seizures)

value: yes (depression, ADD)

value: yes (GERD)

tag: autoimmune disorder

tag: medications/vitamin names

value: Risperdal, Adderall, melatonin, multivitamin, calcium

tag: cerebral palsy


title: AC02-1003-01

description: Blood gene expression data from ASD

value: AUTISM

value: male

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (Abnormal EEG diagnosed at 3 years, Febrile Seizures (with fever), Other Seizures (Grand mal or generalized tonic clinic) every 2 weeks since age 7 months, and Intractability (high frequency and/or resistance to any medications).)

tag: birth defects

tag: ct

value: Keppra (Antiepileptics or anti-seizure medication)

tag: seizure

value: yes


title: A-0134-P1

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: gender

tag: race

value: Mixed (Caucasian, Asian)

value: yes (Tourette's or Tics diagnosed at 9 years)

tag: psychiatric disorder

value: yes (adhd/add)

tag: gastrointestinal disorder

tag: genetic testing

tag: mri

value: Adderoll, Abilify, Clonidine, Mood Stabilizers or anti-psychotics, melatonin, lactaid

tag: other diseases


title: AC02-1007-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: age at blood drawing (months)

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: autoimmune disorder

value: Prozac


title: Ewing sarcoma E53 4756083018_R005_C010

description:
4756083018_R005_C010
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: ICEclc_10mM3CBA_stationary_WT_replicate4

tag: strain

tag: genotype

value: wild type


title: AC02-1302-04

description: Blood gene expression data from ASD

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes (ADD)

value: yes (GERD)

tag: birth defects

tag: ct

tag: medications/vitamin names

value: Tamiflu, Concerta

tag: cerebral palsy

tag: seizure

value: positive lead test


title: AC02-1302-01

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

value: male

tag: age at blood drawing (months)

tag: race

value: yes (speech delay)

tag: psychiatric disorder

tag: gastrointestinal disorder

value: yes (asthma)

tag: genetic testing

tag: mri

value: none, singulair, inhaler

tag: other diseases


title: AC02-1297-01

description: Blood gene expression data from ASD

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (mood disorder)

tag: autoimmune disorder

value: Tylenol, Tylenol


title: ICEclc_10mM3CBA_stationary_WT_replicate3

tag: strain

tag: genotype


title: AC02-1310-01

description: Blood gene expression data from ASD

value: Hispanic

tag: developmental/speech disorder

tag: neurological disorder

tag: birth defects

tag: ct

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: A-0133-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: AUTISM

tag: gender

tag: age at blood drawing (months)

tag: race

value: Caucasian

value: yes (mild hyperlexia)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing


title: ICEclc_10mM3CBA_stationary_WT_replicate2


title: Ewing sarcoma E72 4756083018_R005_C007

description:
4756083018_R005_C007
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: ICEclc_10mM3CBA_stationary_WT_replicate1

tag: strain

tag: genotype

value: wild type


title: AC02-1289-01

description: Blood gene expression data from ASD

tag: ethnicity

value: Non-Hispanic

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

tag: developmental/speech disorder

tag: neurological disorder

value: yes

tag: autoimmune disorder

tag: mri

value: pediapops, multivitamin, flouride

tag: other diseases


title: Ewing sarcoma E64 4756083018_R005_C011

description:
4756083018_R005_C011
Bisulfite Treated DNA


title: Ewing sarcoma E64 4756083018_R005_C006

description:
4756083018_R005_C006
Bisulfite Treated DNA


title: Ewing sarcoma E72 4756083018_R003_C012

description:
4756083018_R003_C012
Bisulfite Treated DNA


title: Ewing sarcoma E48 4756083018_R001_C010

description:
4756083018_R001_C010
Bisulfite Treated DNA


title: Ewing sarcoma E48 4756083018_R005_C004

description:
4756083018_R005_C004
Bisulfite Treated DNA


title: A-0132-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

tag: age at blood drawing (months)

tag: race

value: Unknown

value: unknown

tag: birth defects

tag: ct

tag: medications/vitamin names

tag: cerebral palsy

tag: seizure


title: Ewing sarcoma E40 4756083018_R005_C003

description:
4756083018_R005_C003
Bisulfite Treated DNA

tag: sample group

tag: tissue


title: A-0131-P1

description: Blood gene expression data from ASD

value: male

tag: ethnicity

tag: hours (minutes since last caloric intake)

value: :unknown

tag: chronic diseases

tag: allergies

value: yes (global)

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing


title: Ewing sarcoma E32 4756083018_R005_C002

description:
4756083018_R005_C002
Bisulfite Treated DNA


title: A-0128-P1

description: Blood gene expression data from ASD

tag: diagnosis

value: PDD-NOS

tag: gender

tag: developmental/speech disorder

tag: neurological disorder

value: yes (chronic GERD)

tag: autoimmune disorder

tag: mri

value: prilosec

tag: other diseases


title: A-0127-P1

description: Blood gene expression data from ASD

tag: age at blood drawing (months)

tag: race

tag: birth defects

tag: ct

tag: medications/vitamin names

value: GlycoLax

tag: cerebral palsy

tag: seizure


title: AC02-1262-01

description: Blood gene expression data from ASD

value: AUTISM

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: allergies

value: yes (speech delay)

value: yes (seizures, Landau-Kleffner Syndrome, abnomral EEG)

tag: psychiatric disorder

value: yes (anxiety disorder)

value: Biaxin, Singulair, Lexapro, Biaxin, tylenol, echinacea


title: AC02-1288-01

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: Caucasian

value: Non-Hispanic

tag: developmental/speech disorder

tag: gastrointestinal disorder

tag: genetic testing

value: OTC cold medications, Risperdal, multivitamin


title: WT_Aorta_E2_4hr_rep1,2

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.  The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing:
Raw microarray data was normalized using the GCRMA method (considering all samples with the same name as a group), and differential expression analyzed using Limma with array quality weighting. The relevant references are: Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3, and Ritchie ME, Diyagama D, Neilson J, et al. Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics. 2006;7:261. Three contrasts were performed: DPM_E2-DPM_Veh (estrogen response in DPM), WT_E2-WT_Veh (estrogen response in WT), and (DPM_E2-DPM_Veh)-(WT_E2-WT_Veh) (differential estrogen response between DPM and WT).
Columns 2 through 5 in the log2FC_results table are normalized relative log2 expression level coefficients, calculated by Limma for all replicate samples of the same characteristics. Columns 6 through 11 are the results of Limma contrast fits for the indicated contrasts:  DPM_E2-DPM_Veh (estrogen response in DPM), WT_E2-WT_Veh (estrogen response in WT), and (DPM_E2-DPM_Veh)-(WT_E2-WT_Veh) (differential estrogen response between DPM and WT). The first column in each pair is the log2 fold change in the contrast. For (WT_E2-WT_Veh), for example this would be equal to the column 4 coefficent - the column 5 coefficient. The second column in each pair is the P.value assigned to the contrast (probability that a contrast of that magnitude would arise by chance).

organism: Mus musculus

source_name: WT Aorta +E2 4hr

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Transgenic disrupting peptide mice (DPM) express the Estrogen Receptor (ER) alpha amino acids 176-253 peptide under CMV promoter control. This peptide blocks interactions between ER and striatin, which inhibits rapid non-genomic signaling by ER to cellular kinases. 12-14 week old female WT and DPM mice (4 mice per sample) were overiectomized, and 1 week later aortas were harvested for ex vivo treatment.

extract_protocol: Total RNA from 4 aortas per sample was collected using TRIzol (InVitrogen) and the RNeasy kit (Qiagen).

treatment_protocol: Aortas were treated + 10 nM beta-estradiol (E2) or + EtOH vehicle (Veh) for 4 hrs ex vivo.

tag: background strain

tag: genotype/variation

value: wild type


title: A-0119-P1

description: Blood gene expression data from ASD

tag: age at blood drawing (months)

tag: race

tag: neurological disorder

tag: autoimmune disorder

tag: birth defects

tag: mri

tag: other diseases


title: AC02-1253-01

description: Blood gene expression data from ASD

value: ASPERGER'S DISORDER

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

tag: ct

tag: medications/vitamin names

value: ibuprofen, excedrine, multivitamin

tag: cerebral palsy

tag: seizure


title: A-0126-P1

description: Blood gene expression data from ASD

tag: diagnosis

tag: gender

value: male

tag: allergies

tag: developmental/speech disorder

tag: psychiatric disorder

tag: gastrointestinal disorder

tag: genetic testing


title: A-0120-P1

description: Blood gene expression data from ASD

tag: age at blood drawing (months)

tag: race

value: yes (global)

tag: neurological disorder

value: yes (seizures)

tag: autoimmune disorder

tag: birth defects

value: flouride

value: yes


title: DPM_Aorta_Veh_4hr_rep1-3

source_name: DPM Aorta +Veh (ctrl) 4hr

tag: background strain

tag: genotype/variation

value: DPM


title: A-0116-P1

description: Blood gene expression data from ASD

value: AUTISM

tag: ethnicity

tag: hours (minutes since last caloric intake)

tag: chronic diseases

value: yes (Developmental Coordination Disorder)

tag: ct

tag: mri

tag: medications/vitamin names

tag: other diseases


title: Ewing sarcoma E24 4756083018_R005_C001

description:
4756083018_R005_C001
Bisulfite Treated DNA

tag: sample group

tag: tissue

value: primary Ewing sarcoma tumor


title: Ewing sarcoma E51 4756083018_R008_C004

description:
4756083018_R008_C004
Bisulfite Treated DNA