title: 0562-01-A


title: 121-01-C

status: Public on Oct 09 2011

type: RNA

city: Philadelphia

first: mark

last: alter

state: PA

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

country: USA

institute: University of Pennsylvania

hyb_protocol: Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640.

scan_protocol: Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array.

data_processing: RMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: lymphocytes

label_protocol: Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.

extract_protocol: Qiagen Qiaquick kit (Germantown, MD).

tag: scan batch

value: Batch 1

tag: group

value: control

tag: subject age

tag: paternal age

tag: maternal age


title: SARRC-0146-01-C


title: 0199-01-C

value: autism


title: 0993-01-C


title: 0711-04-A


title: 0991-01-C


title: 0986-01-C

value: Batch 2


title: SARRC-0994-01-C


title: 0301-01-A


title: 0989-01-C


title: 0998-01-C


title: 0983-01-C


title: 0978-01-C


title: 1118-01-C


title: 0977-01-C


title: 0979-01-C


title: 0990-01-C


title: 0992-01-c


title: 0975-01-C


title: 0972-01-C


title: 0974-01-C


title: 0968-01-C


title: 0982-01-c


title: 0967-01-C


title: 0966-01-C


title: 0514-01-C


title: 0653-01-C


title: 0702-01-C-b


title: 0537-01-C


title: 0970-01-C


title: 0510-01-C


title: 0523-01-C


title: 0651-01-C


title: 0198-01-c


title: 0511-01-c


title: 0516-01-C


title: 0652-01-C


title: 0205-01-C


title: 0515-01-C


title: 0466-01-C


title: 0193-01-C


title: 0196-01-C


title: 0536-01-C


title: 0195-01-C


title: 0671-01-C


title: 0201-01-C-RR


title: 0192-01-C


title: 0178-01-C


title: 0175-01-C


title: 0184-01-1


title: 0191-01-C


title: 0167-01-C


title: 0156-01-C


title: 0164-01-c


title: 0159-01-C


title: 0147-01-C


title: 0165-01-C


title: 0152-01-C


title: 0153-01-C


title: 0170-01-C


title: 0137-01-C


title: 0148-01-C


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_10

status: Public on Oct 08 2011

city: Cambridge

last: Hao

state: MA

address: 52 Oxford St. Rm.442

department: FAS Center for Systems Biology

institute: Harvard University

hyb_protocol: 300 ng Cy3-labeled and 300 ng Cy5-labeled cDNA was competitively hybridized to Agilent 8×15K S. cerevisiae two-color expression microarrays (G2509F) in Agilent hybridization buffer for 17 hours at 60 °C.

scan_protocol: Microarrays were washed and scanned immediately using an Axon 4000B scanner

data_processing: The average intensity of the Cy3 and Cy5 fluorescence at each spot was then extracted using GenePix 5.1 software.  Lowess and quantile normalization were performed using the MATLAB bioinformatics toolbox before further analysis.

organism: Saccharomyces cerevisiae

label_protocol: Purified cDNA samples were then labeled with NHS-ester Cy3 or Cy5 (GE Biosciences).

growth_protocol: Yeast strains were grown using the regular synthetic medium at 30 °C with shaking and cell samples were collected at early/mid-logarithmic phase (OD600 0.2 ~ 0.3).

extract_protocol: Cell cultures were added directly into cold methanol (~ -50 °C) with volume ratio of 2:3, and incubated in an ethanol-dry ice bath for at least 20 minutes.  Cells were collected by centrifugation and quickly washed with ice-cold water to remove alcohol, and resuspended in RNAlater solution (Ambion).  For each sample, 5×107 cells were used to isolate total RNA with the RNase Mini kit (Qiangen), and RNA integrity was analyzed on an agarose gel or with an Agilent bioanalyzer.  cDNA was synthesized from 10 μg total RNA with 1:1 ratio of random 10-mers and oligo-dT primers (Operon), and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma), using the Superscript III reverse transcription system (Invitrogen).  cDNA was purified with a PCR purification kit (Qiagen) after hydrolyzing RNA.

treatment_protocol: To inhibit PKA activity, yeast cells at early/mid-logarithmic phase were treated with indicated concentrations of PKA inhibitor 1-NM-PP1 for indicated times. To remove 1-NM-PP1, cells were harvested by filtering and then washed and resuspended in pre-warmed with synthetic medium without 1-NM-PP1.

tag: strain background

tag: treatment

value: 40 min:No 1-NM-PP1

source_name: Reference

tag: strain

tag: sample type

value: Mixture of  the '750 nM 1-NM-PP1 oscillatory treatment 5 min x 3' samples (9-16) by equal volume


title: 0155-01-c


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_3

value: 10 min:No 1-NM-PP1

value: Mixture of  the '750 nM 1-NM-PP1 oscillatory treatment 5 min x 3' samples (1-8) by equal volume


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_4

value: 15 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_16

value: 70 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_9

value: 30 min_chip_2:No 1-NM-PP1


title: 0180-01-C


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_7

value: 30 min_chip_1:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_8

value: 35 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_5

value: 20 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_15

value: 65 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_14

value: 60 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_12

value: 50 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_6


title: 0120-01-C

value: Batch 1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_13

value: 55 min:No 1-NM-PP1


title: 0118-01-C

value: control


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_11


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_1

value: 0 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 3_2

value: 5 min:750 nM 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_16

value: Mixture of  the '750 nM 1-NM-PP1 oscillatory treatment 5 min x 6' samples (9-16) by equal volume


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_15


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_11


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_13


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_10

value: 40 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_12


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_6

value: Mixture of  the '750 nM 1-NM-PP1 oscillatory treatment 5 min x 6' samples (1-8) by equal volume


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_7

value: 30 min:No 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_9

value: 35 min_chip 2:750 nM 1-NM-PP1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_8

value: 35 min_chip_1:750 nM 1-NM-PP1


title: Human embryonic artificial trisomy8 cell clone3 sample3

city: osaka

first: Hisakatsu

last: Nawata

department: Medicine

country: Japan

institute: Kyoto University

description: Gene expression in human embryonic artificial trisomy 8 cells

hyb_protocol: 500ng of Cy3 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (One-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (One-Color Microarray-Based Gene Expression Analysis, Agilent)

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565CA) using the default settings for 4x44k format one-color arrays.

data_processing: Data was analyzed with Agilent Feature Extraction and GeneSpring GX v11.5 softwares.

source_name: Human embryonic artificial trisomy 8 cell clone3 sample3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human embryonic diploid cells were cultured in Eagle’s Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum at 37℃ with 5% CO2 in a humidified environment.Human embryonic artificial trisomy 8 cells were cultured in Eagle’s Minimum Essential Medium (MEM) plus 800 ug/ml G418 (nakarai, kyoto, Japan) supplemented with 10% fetal bovine serum at 37℃ with 5% CO2 in a humidified environment.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Cells were not treated prior to RNA extraction.

tag: cell type

value: embryonic fibroblast cells

tag: gender

value: male

tag: chromosomal variation

value: trisomy 8

tag: clone


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_4


title: Human embryonic artificial trisomy8 cell clone2 sample3

source_name: Human embryonic artificial trisomy 8 cell clone2 sample3


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_14


title: Human embryonic artificial trisomy8 cell clone3 sample2

source_name: Human embryonic artificial trisomy 8 cell clone3 sample2


title: Human embryonic artificial trisomy8 cell clone1 sample3

source_name: Human embryonic artificial trisomy 8 cell clone1 sample3


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_2


title: Human embryonic artificial trisomy8 cell clone2 sample2

source_name: Human embryonic artificial trisomy 8 cell clone2 sample2


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_1


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_5

value: 20 min:No 1-NM-PP1


title: Human embryonic diploid cell clone2 sample3

description: Gene expression in human embryonic diploid cells

source_name: Human embryonic diploid cell, clone2, sample3

value: euploid


title: Human embryonic diploid cell clone4 sample3

source_name: Human embryonic diploid cell, clone4, sample3


title: Human embryonic artificial trisomy8 cell clone1 sample2

source_name: Human embryonic artificial trisomy 8 cell clone1 sample2


title: 750 nM 1-NM-PP1 oscillatory treatment 5 min x 6_3

value: 10 min:No 1-NM-PP1


title: Human embryonic artificial trisomy8 cell clone3 sample1

source_name: Human embryonic artificial trisomy 8 cell clone3 sample1


title: Human embryonic diploid cell clone2 sample2

source_name: Human embryonic diploid cell, clone2, sample2


title: Human embryonic diploid cell clone4 sample2

source_name: Human embryonic diploid cell, clone4, sample2


title: 120 nM 1-NM-PP1 treatment for 20 min_7

value: 60 min:No 1-NM-PP1

value: Mixture of all the '120 nM 1-NM-PP1 treatment for 20 min' samples (1-8) by equal volume


title: Human embryonic artificial trisomy8 cell clone2 sample1

source_name: Human embryonic artificial trisomy 8 cell clone2 sample1


title: Human embryonic artificial trisomy8 cell clone1 sample1

source_name: Human embryonic artificial trisomy 8 cell clone1 sample1


title: 120 nM 1-NM-PP1 treatment for 20 min_8

value: 70 min:No 1-NM-PP1


title: Human embryonic diploid cell clone4 sample1

source_name: Human embryonic diploid cell, clone4, sample1


title: 120 nM 1-NM-PP1 treatment for 20 min_6

value: 50 min:No 1-NM-PP1


title: Human embryonic diploid cell clone2 sample1

source_name: Human embryonic diploid cell, clone2, sample1


title: Human embryonic diploid cell clone1 sample3

source_name: Human embryonic diploid cell, clone1, sample3


title: 120 nM 1-NM-PP1 treatment for 20 min_5

source_name: Reference


title: 3 µM 1-NM-PP1 treatment for 20 min_6

value: Mixture of all the '3 µM 1-NM-PP1 treatment for 20 min' samples (1-8) by equal volume


title: 120 nM 1-NM-PP1 treatment for 20 min_2


title: 3 µM 1-NM-PP1 treatment for 20 min_7


title: 120 nM 1-NM-PP1 treatment for 20 min_4


title: 3 µM 1-NM-PP1 treatment for 20 min_8


title: 120 nM 1-NM-PP1 treatment for 20 min_1

value: 0 min:No 1-NM-PP1


title: Human embryonic diploid cell clone1 sample2

source_name: Human embryonic diploid cell, clone1, sample2


title: Pool placentas Wild-type #2

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

institute: INSERM

hyb_protocol: Classical hybridation protocol at the Genom'IC Cochin Institute Plateform on 4 quadrant slide according to nimblegen protocol.

scan_protocol: Standard nimblegen protocol.

data_processing: RMA from the .pair files (Nimblescan v4.0).

organism: Mus musculus

source_name: Placenta

label_protocol: Classical CY3 labeling at the Genom'IC Cochin Institute Plateform.

growth_protocol: Mice were pregnant, at 16.5 days post fectundation, the placenta were dissected free of fœtal membranes.

extract_protocol: TriZol total RNA extraction.

value: FVB/N

tag: genotype/variation

value: Wild-type


title: Pool placentas STOX1 #2


title: Human embryonic diploid cell clone1 sample1

source_name: Human embryonic diploid cell, clone1, sample1


title: 3 µM 1-NM-PP1 treatment for 20 min_4

value: 30 min:No 1-NM-PP1


title: 3 µM 1-NM-PP1 treatment for 20 min_5

value: 40 min:No 1-NM-PP1


title: 3 µM 1-NM-PP1 treatment for 20 min_3

value: 20 min:3 µM 1-NM-PP1


title: 3 µM 1-NM-PP1 treatment for 20 min_2

value: 10 min:3 µM 1-NM-PP1


title: 3 µM 1-NM-PP1 treatment for 40 min_7

value: Mixture of all the '3 µM 1-NM-PP1 treatment for 40 min' samples (1-8) by equal volume


title: 3 µM 1-NM-PP1 treatment for 40 min_8


title: 3 µM 1-NM-PP1 treatment for 20 min_1


title: 3 µM 1-NM-PP1 treatment for 40 min_5

value: 40 min:3 µM 1-NM-PP1


title: 3 µM 1-NM-PP1 treatment for 40 min_6


title: 3 µM 1-NM-PP1 treatment for 40 min_4

value: 30 min:3 µM 1-NM-PP1


title: Pool placentas Wild-type #1


title: 3 µM 1-NM-PP1 treatment for 40 min_3


title: 3 µM 1-NM-PP1 treatment for 40 min_2


title: 3 µM 1-NM-PP1 treatment for 40 min_1


title: Thoroughbred reference vs Twilight Reference DNA

type: genomic

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

description: Thoroughbred

hyb_protocol: Cy5 and Cy3 labeled samples combined with hyb buffers were hybridized to array, washed, and scanned

scan_protocol: Scanned on an Agilent C2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Equus caballus

source_name: Thoroughbred

label_protocol: 4ug DNA labeled with Biorime Plus Kit (Invitrogen)

extract_protocol: genomic DNA isolated using standard PCI extraction

tag: tissue

value: White Blood Cells

source_name: Twilight Reference DNA


title: Thoroughbred reference vs Thoroughbred reference

description: Thoroughbred 2


title: Breed vs Thoroughbred reference 14

description: Welsh Arabian Pony

source_name: Welsh Arabian Pony

source_name: Thoroughbred Reference


title: Breed vs Thoroughbred reference 15

description: Donkey

source_name: Donkey


title: liver_control_replicate9

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.24.1) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 9

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Twelve week-old male C57Bl/6 mice (Charles River, L'Arbresle Cedex, France) were housed 2 per cage in a light-and-temperature controlled facility (lights on 6:30 to 18:30, 21°C) and acclimated for 3 weeks.

extract_protocol: At the end of treatment, mice were fasted from 7:00 to 13:00 with drinking water available and were subsequently sacrificed by cervical dislocation under isoflurane anesthesia. Livers were dissected, directly frozen in liquid nitrogen and stored at −80°C until further analysis. Total RNA was prepared from mouse livers using Trizol reagent (Invitrogen, Breda,The Netherlands), treated with DNase and purified on columns using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following the supplier’s protocol. RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: Mice were randomized by weight-matching into three groups (n = 10 in control group, n = 12 in fenofibrate, and n=11 fish oil intervention group), and fed a research diet (No. D10012M, Research Diets, NJ supplemented with sunflower oil (containing 81.3% oleic acid, 7% energy intake) in control group, sunflower oil (7% energy intake) and fenofibrate (0.03% w/w) in fenofibrate group, and fish oil (Marinol C-38 fish oil: 23.1% EPA and 21.1% DHA, 7% energy intake) in fish oil group for 2 weeks.

value: male

tag: agent

value: control

value: liver

tag: age

value: 17 weeks


title: non-malignant pancreas sample 6 (miRNA)

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: miRNA expression of human non-malignant pancreas

hyb_protocol: As manufacturer recommended standard protocols

scan_protocol: GenePix Personal 4100A Scanner was used for scanning.

data_processing: Data was normalized by variance stabilization normalization using vsn package (R/Bioconductor) which returned the data in log2 scale.  For a probe with multiple spots, the mean was used for representing the probe signal.

source_name: non-malignant pancreas

extract_protocol: miRNA was isolated by miRNeasy mini kit according to manufacturer’s instructions

value: pancreas

tag: disease status

value: non-malignant pancreas

tag: ajcc stage

tag: grade

tag: tumor content


title: non-malignant pancreas sample 5 (miRNA)

label_protocol: As manufacturer recommended standard protocols


title: non-malignant pancreas sample 7 (miRNA)


title: liver_fishoil_replicate11

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 11

value: fish oil


title: Breed vs Thoroughbred reference 11

description: Quarter Horse 1

source_name: Quarter Horse 1


title: 120 nM 1-NM-PP1 treatment for 20 min_3

value: Mixture of all the '120 nM 1-NM-PP1 treatment for 20 min' samples (1-8) by equal volume


title: Breed vs Thoroughbred reference 12

description: Shagya Arabian

source_name: Shagya Arabian


title: non-malignant pancreas sample 4 (miRNA)


title: Breed vs Thoroughbred reference 9

description: Paso Fino

source_name: Paso Fino


title: non-malignant pancreas sample 5 (mRNA)

description: gene expression of human non-malignant pancreas

hyb_protocol: As recommended by manufacturer

scan_protocol: GeneChip Scanner 3000 7G was used for scanning.  Affymetrix GeneChip Command Console software (AGCC 3.2) was used for image processing

data_processing: Data was normalized by GCRMA (R/Bioconductor).  The presence/abscence calls was then determined by using “Presence-Absence calls with Negative Probesets” (panp) package (Bioconductor) with default parameters

label_protocol: As recommended by manufacturer

extract_protocol: Roche's MagNA Pure Compact Nucleic Acid Purification System was used for automated RNA isolation.


title: non-malignant pancreas sample 7 (mRNA)


title: liver_control_replicate10

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 10


title: Pool placentas STOX1 #1

value: FVB/N


title: non-malignant pancreas sample 3 (miRNA)


title: Breed vs Thoroughbred reference 13

description: Shire

source_name: Shire


title: Breed vs Thoroughbred reference 5

description: Hanoverian

source_name: Hanoverian


title: non-malignant pancreas sample 6 (mRNA)


title: liver_fishoil_replicate10

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 10


title: Breed vs Thoroughbred reference 7

description: Lusitano

source_name: Lusitano


title: liver_fenofibrate_replicate11

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 11

value: fenofibrate


title: liver_fenofibrate_replicate12

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 12


title: Breed vs Thoroughbred reference 1

description: Andalusion

source_name: Andalusion


title: non-malignant pancreas sample 4 (mRNA)


title: Breed vs Thoroughbred reference 8

description: Miniature

source_name: Miniature


title: human PDAC 25 (miRNA)

description: miRNA expression of human PDAC

source_name: human pancreatic tumor

value: pancreatic cancer


title: non-malignant pancreas sample 2 (miRNA)


title: non-malignant pancreas sample 1 (miRNA)


title: Breed vs Thoroughbred reference 6

description: Hungarian

source_name: Hungarian

source_name: Thoroughbred Reference


title: Breed vs Thoroughbred reference 3

description: Curly

source_name: Curly


title: Breed vs Thoroughbred reference 10

description: Peruvian

source_name: Peruvian


title: liver_fishoil_replicate9

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 9


title: human PDAC 24 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate10

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 10


title: non-malignant pancreas sample 3 (mRNA)

source_name: non-malignant pancreas


title: Breed vs Thoroughbred reference 2

description: Arabian

source_name: Arabian


title: Breed vs Thoroughbred reference 4

description: Gypsy Vanner

source_name: Gypsy Vanner


title: non-malignant pancreas sample 2 (mRNA)


title: human PDAC 25 (mRNA)

description: gene expression of human PDAC


title: Breed vs Twilight Reference DNA

description: Quarter Horse 2

source_name: Quarter Horse 2

source_name: Twilight Reference DNA


title: liver_control_replicate7

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 7


title: liver_control_replicate8

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 8


title: non-malignant pancreas sample 1 (mRNA)


title: human PDAC 21 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 22 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 23 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 24 (mRNA)

description: gene expression of human PDAC


title: human PDAC 19 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate9

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate9


title: liver_fishoil_replicate8

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate8


title: liver_fishoil_replicate7

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 7


title: human PDAC 20 (miRNA)

description: miRNA expression of human PDAC

source_name: human pancreatic tumor


title: human PDAC 23 (mRNA)

description: gene expression of human PDAC


title: human PDAC 22 (mRNA)

description: gene expression of human PDAC


title: human PDAC 20 (mRNA)

description: gene expression of human PDAC


title: human PDAC 21 (mRNA)

description: gene expression of human PDAC


title: human PDAC 18 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 17 (miRNA)

description: miRNA expression of human PDAC


title: liver_control_replicate6

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 6


title: liver_control_replicate5


title: human PDAC 15 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 19 (mRNA)

description: gene expression of human PDAC


title: liver_fishoil_replicate5

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate5


title: liver_control_replicate3

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 3


title: human PDAC 18 (mRNA)

description: gene expression of human PDAC


title: liver_control_replicate4

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 4


title: human PDAC 16 (mRNA)

description: gene expression of human PDAC


title: human PDAC 17 (mRNA)

description: gene expression of human PDAC


title: human PDAC 14 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 13 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate8

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 8


title: non-malignant pancreas sample 7 (SNP)

description: genomic DNA of human non-malignant pancreas

data_processing:
CEL files were processed by Affymetrix GTC 3.0.1  which uses the BRLMM-P-Plus algorithm and regional GC correction configuration for Copy Number/LOH analysis.  Normalization was performed using the reference HapMap270.
log2 ratio of SNP and CN markers in common with the reference HapMap270 file.

extract_protocol: Roche's MagNA Pure Compact Nucleic Acid Purification System was used for automated DNA isolation


title: human PDAC 14 (mRNA)

description: gene expression of human PDAC


title: human PDAC 12 (miRNA)

description: miRNA expression of human PDAC


title: liver_fishoil_replicate6

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 18


title: human PDAC 16 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate6

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 6


title: human PDAC 13 (mRNA)

description: gene expression of human PDAC


title: non-malignant pancreas sample 5 (SNP)

source_name: non-malignant pancreas


title: human PDAC 11 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 12 (mRNA)

description: gene expression of human PDAC


title: human PDAC 15 (mRNA)

description: gene expression of human PDAC


title: non-malignant pancreas sample 4 (SNP)


title: liver_fenofibrate_replicate5

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 5


title: non-malignant pancreas sample 6 (SNP)


title: human PDAC 11 (mRNA)

description: gene expression of human PDAC


title: human PDAC 9 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 10 (mRNA)

description: gene expression of human PDAC


title: liver_fenofibrate_replicate3

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 3


title: human PDAC 8 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate2

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 2


title: human PDAC 10 (miRNA)

description: miRNA expression of human PDAC


title: non-malignant pancreas sample 1 (SNP)


title: non-malignant pancreas sample 2 (SNP)


title: human PDAC 9 (mRNA)

description: gene expression of human PDAC


title: human PDAC 7 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 25 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 21 (SNP)

description: genomic DNA of human PDAC


title: liver_fenofibrate_replicate1

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 1


title: human PDAC 6 (miRNA)

description: miRNA expression of human PDAC


title: liver_fishoil_replicate4

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 4


title: liver_fenofibrate_replicate4

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 4


title: human PDAC 24 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 8 (mRNA)

description: gene expression of human PDAC


title: human PDAC 5 (miRNA)

description: miRNA expression of human PDAC


title: liver_fenofibrate_replicate7

source_name: liver from C57Bl/6J mouse  fed the fenofibrate diet for 2 weeks, replicate 7


title: human PDAC 22 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 19 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 7 (mRNA)

description: gene expression of human PDAC


title: human PDAC 6 (mRNA)

description: gene expression of human PDAC


title: liver_fishoil_replicate3

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 3


title: human PDAC 17 (SNP)

description: genomic DNA of human PDAC

source_name: human pancreatic tumor


title: non-malignant pancreas sample 3 (SNP)


title: human PDAC 4 (miRNA)

description: miRNA expression of human PDAC


title: liver_control_replicate2

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate 2


title: human PDAC 3 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 5 (mRNA)

description: gene expression of human PDAC


title: human PDAC 2 (miRNA)

description: miRNA expression of human PDAC


title: liver_control_replicate1

source_name: liver from C57Bl/6J mouse  fed the control diet for 2 weeks, replicate


title: human PDAC 1 (miRNA)

description: miRNA expression of human PDAC


title: human PDAC 16 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 3 (mRNA)

description: gene expression of human PDAC


title: human PDAC 4 (mRNA)

description: gene expression of human PDAC


title: liver_fishoil_replicate2

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 2


title: human PDAC 15 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 13 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 14 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 2 (mRNA)

description: gene expression of human PDAC


title: liver_fishoil_replicate1

source_name: liver from C57Bl/6J mouse  fed the fish oil diet for 2 weeks, replicate 1


title: human PDAC 18 (SNP)

description: genomic DNA of human PDAC


title: human PDAC 1 (mRNA)

description: gene expression of human PDAC


title: human PDAC 12 (SNP)

description: genomic DNA of human PDAC


title: ControlLacW8 LAC1

status: Public on Oct 07 2011

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

hyb_protocol: standard Affymetrix protcol

scan_protocol: HTAPS scanner was used

data_processing: data was normalized using the gcrma using R package

source_name: Lacrimal gland

label_protocol: NuGEN Ovation

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

treatment_protocol: Mice were treated either with mLTBD-mIgG1 or MOPC21

value: Lacrimal gland

value: NOD

tag: time

value: Week 8


title: ControlLacW14 LAC1

value: Week 14


title: MOPCLacW16 LAC4

value: Week 16


title: ControlLacW16 LAC3


title: ControlSubW16 SUB2

source_name: Salivary gland

value: Salivary gland


title: ControlSubW14 SUB2


title: LTBRLacW16 LAC3


title: LTBRLacW12 LAC1

value: Week 12


title: MOPCSubW12 SUB3


title: ControlSubW16 SUB4


title: human PDAC 20 (SNP)

description: genomic DNA of human PDAC


title: MOPCLacW12 LAC4


title: human PDAC 23 (SNP)

description: genomic DNA of human PDAC


title: ControlSubW8 SUB4


title: ControlSubW12 SUB2


title: ControlSubW8 SUB3


title: ControlLacW14 LAC4


title: ControlSubW8 SUB2


title: ControlLacW8 LAC4


title: ControlLacW8 LAC2


title: ControlSubW14 SUB3


title: ControlSubW14 SUB4


title: MOPCSubW16 SUB2


title: human PDAC 10 (SNP)

description: genomic DNA of human PDAC


title: ControlLacW8 LAC3


title: ControlLacW14 LAC3


title: human PDAC 9 (SNP)

description: genomic DNA of human PDAC


title: MOPCSubW16 SUB1


title: MOPCSubW16 SUB4


title: MOPCSubW16 SUB3


title: human PDAC 11 (SNP)

description: genomic DNA of human PDAC


title: ControlLacW14 LAC2


title: MOPCLacW16 LAC2


title: LTBRSubW16 SUB4


title: MOPCLacW16 LAC3


title: MOPCLacW16 LAC1


title: MOPCLacW12 LAC2


title: LTBRLacW16 LAC4


title: LTBRSubW16 SUB2


title: LTBRSubW16 SUB3


title: LTBRSubW16 SUB1


title: MOPCSubW12 SUB4


title: LTBRLacW16 LAC2


title: ControlLacW16 LAC4


title: LTBRLacW16 LAC1


title: MOPCSubW12 SUB2


title: ControlSubW16 SUB3


title: ControlLacW16 LAC1


title: MOPCLacW12 LAC3


title: ControlSubW8 SUB1


title: MOPCSubW12 SUB1


title: human PDAC 6 (SNP)

description: genomic DNA of human PDAC


title: ControlSubW14 SUB1


title: MOPCLacW12 LAC1


title: 100% MWWE exposure liver replicate 4

city: Waterloo

first: Jennifer

last: Ings

state: Ontario

address: 200 University Ave West

department: Biology

country: Canada

institute: University of Waterloo

description: Biological replicate 4 of 4.

hyb_protocol: Before hybridization, the Cy3- and Cy5-labeled samples were combined and dried using Na-acetate, glycogen, and 95% ethanol precipitation. To the dried sample, 26 µl of hybridization buffer and 2 µl each of calf thymus DNA (10 mg/ml) and yeast tRNA (10 mg/ml) were added. The samples were denatured for 2 min at 95°C, snap cooled on ice for 1 min, and centrifuged for 1 min at maximum speed. The solution was pipetted onto a microarray slide underneath a silanized coverslip by capillary action. The slide was sealed into a hybridization chamber and hybridization was performed overnight at 37°C in a waterbath.

scan_protocol: Image analysis was carried out using VersArray ChipReader software version 3.1 (Bio-Rad) Spot finding and quantification were carried out with ImaGene 3.0 microarray image analysis software (BioDiscovery, Los Angeles, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal, or processed Green signal/processed red signal, depending on the reference sample.

organism: Oncorhynchus mykiss

source_name: Whole tissue

label_protocol: cDNA was synthesized using a commercial kit (Invitrogen, Carlsbad, CA, USA) by incorporating aminoallyl dUTP (AA-dUTP) at 42°C for 3 h. RNA was hydrolyzed with 10 µl of 1 M NaOH and 10 µl of 0.5 M EDTA for 15 min at 70°C and neutralized by adding 10 µl of 1 M HCl. To remove unincorporated AA-dUTP and free amines, the reactions were purified with Qiagen columns using phosphate wash buffer and phosphate elution buffer.The purified sample was precipitated with Na-acetate, glycogen and 95% ethanol at -20⁰C for 1h. Tubes were centrifuged at max speed for 30 min (4⁰C) to collect the AA-cDNA pellet and placed in the fumehood for 15 min to dry. AA-cDNA was resuspended in 0.1 M sodium bicarbonate buffer.  The AA-cDNA was coupled to either red fluorescent dye ester Cy5 or green fluorescent dye ester Cy3 (reference pool and sample were swapped for each array). The coupling reaction was performed for 90 min in the dark at room temperature. The removal of uncoupled dye was performed using the Qiagen PCR purification kit.

extract_protocol: Total RNA extracted using Qiagen Rneasy spin columns, following manufacturer's instructions. 30 ug total RNA was used for each sample.

tag: developmental stage

value: juvenile

source_name: Total RNA pooled from every experimental sample

value: Liver

value: 100% MWWE exposure


title: 100% MWWE exposure liver replicate 2

description: Biological replicate 2 of 4.

value: liver

tag: treatment


title: 100% MWWE exposure liver replicate 3

description: Biological replicate 3 of 4.


title: LTBRSubW12 SUB3

tag: strain


title: LTBRLacW12 LAC4


title: human PDAC 3 (SNP)

description: genomic DNA of human PDAC

value: pancreas


title: 100% MWWE exposure liver replicate 1

description: Biological replicate 1 of 4.


title: 50% MWWE exposure liver replicate 4

description: Biological replicate 4 of 4.

value: 50% MWWE exposure


title: human PDAC 4 (SNP)

description: genomic DNA of human PDAC


title: LTBRSubW12 SUB4


title: LTBRLacW12 LAC2


title: ControlSubW16 SUB1


title: 50% MWWE exposure liver replicate 3

description: Biological replicate 3 of 4.


title: human PDAC 5 (SNP)

description: genomic DNA of human PDAC


title: ControlLacW16 LAC2


title: LTBRLacW12 LAC3


title: ControlSubW12 SUB3


title: 4241Dvs4241A

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Performed at 50°C for 18 hours using the MAUI hybridization system (BioMicro Systems, Inc, Salt Lake City Utah, USA), then washed with 0.2X SSC/ 0.2% SDS at 65°C for one min, followed by half min each in non-stringent wash buffer (6X SSPE, 0.01% Tween-20), then in 0.2x SSC, in 0.05X SSC and in milliQ water at room temperature.

scan_protocol: Slides were dried by centrifugation at 500rpm for 5mins and scanned on an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA)

data_processing: NimbleScan RMA function

organism: Burkholderia pseudomallei

source_name: Test

label_protocol: Kreatech BAC array labelling kit (Kreatech, BV, Netherlands) with 2µg of DNA per strain, per array

extract_protocol: Bacterial cultures were grown in LB media and genomic DNA was extracted using the Qiagen Genomic DNA kit (Qiagen, Hilden, Germany)

tag: test

value: Variant

source_name: Control

tag: reference

value: Initial


title: 50% MWWE exposure liver replicate 2

description: Biological replicate 2 of 4.


title: 699Dvs699C


title: human PDAC 2 (SNP)

description: genomic DNA of human PDAC


title: ControlLacW12 LAC4


title: 50% MWWE exposure liver replicate 1

description: Biological replicate 1 of 4.


title: 10% MWWE exposure liver replicate 4

description: Biological replicate 4 of 4.

value: 10% MWWE exposure


title: 3351Evs3351C


title: ControlSubW12 SUB4


title: 4236Dvs4236A


title: 1142Bvs1142A


title: ControlSubW12 SUB1


title: human PDAC 1 (SNP)

description: genomic DNA of human PDAC

value: pancreatic cancer


title: 10% MWWE exposure liver replicate 3

description: Biological replicate 3 of 4.


title: human PDAC 7 (SNP)

description: genomic DNA of human PDAC


title: 10% MWWE exposure liver replicate 2

description: Biological replicate 2 of 4.


title: 10% MWWE exposure liver replicate 1

description: Biological replicate 1 of 4.


title: ControlLacW12 LAC3

value: Lacrimal gland


title: Control liver replicate 4

description: Biological replicate 4 of 4.

value: Control


title: y_tr_72_Rep1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

description:
Gene expression in root tips of soybean.
KS39

hyb_protocol: Hybridization of the GeneChips was carried out  following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridization was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: ArrayAssist Enterprise (Agilent, CA).

organism: Glycine max

source_name: One centimeter long tap root tip of soybean genotype Young, Al, 72hr

label_protocol: The labeling of the RNA was done as per the manufacturer's instructions (Affymetrix, Santa Clara, CA).  Briefly, two microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Plants were grown in hydroponic conditions in growth chamber at 28oC /16 hours light and 20oC/8 hours dark cycle.

extract_protocol: Total RNA was extracted using Qiagen plant RNeasy extraction kit according to manufacturer's protocol.

treatment_protocol: 10 µM Al  (treated) or 0 µM Al (control).

tag: genotype

value: Young

value: root

tag: aluminum sensitivity

value: sensitive

value: aluminum

tag: treatment time


title: Control liver replicate 3

description: Biological replicate 3 of 4.


title: Control liver replicate 2

description: Biological replicate 2 of 4.


title: y_tr_72_Rep2

description:
Gene expression in root tips of soybean.
KS40


title: y_tr_48_Rep2

description:
Gene expression in root tips of soybean.
KS21

source_name: One centimeter long tap root tip of soybean genotype Young, Al, 48hr


title: Surgical sample OPE162

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

institute: National Cancer Center Reseach Institute

description:
OPE162
Gene expression data from surgical sample of esophageal cancer.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ﾟC on the GeneChip Human Genome Array U95Av2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.

source_name: Esophagus, cancerous portion, surgical

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by the two-cycle cDNA synthesis system. The procedure was according to the standard Affymetrix protocol (Section 2: Eukaryotic sample and array processing).

growth_protocol: All esophageal cancer tissues and non-cancerous tissues were provided by the Central Hospital or East Hospital at the National Cancer Center after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

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

treatment_protocol: All surgical samples were obtained from esophageal cancer patients without neoadjuvant therapy, and all biopsy samples were obtained before treatment. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. Surgical and biopsy samples were immediately frozen at -80ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenized before total RNA extraction.

tag: disease state

value: esophageal cancer

value: cancerous portion of esophagus

tag: sample type

value: surgical

tag: patient identifier


title: Control liver replicate 1

description: Biological replicate 1 of 4.

tag: tissue

value: juvenile

value: Liver

tag: age


title: y_tr_12_Rep1

description:
Gene expression in root tips of soybean.
KS8

source_name: One centimeter long tap root tip of soybean genotype Young, Al, 12hr


title: y_tr_12_Rep3

description:
Gene expression in root tips of soybean.
KS35


title: y_tr_48_Rep1

description:
Gene expression in root tips of soybean.
KS9


title: Surgical sample OPE145

description:
OPE145
Gene expression data from surgical sample of esophageal cancer.


title: ControlLacW12 LAC2

value: NOD

value: Week 12


title: y_tr_12_Rep2

description:
Gene expression in root tips of soybean.
KS20


title: Surgical sample OPE143

description:
OPE143
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE136

description:
OPE136
Gene expression data from surgical sample of esophageal cancer.


title: y_tr_2_Rep2

description:
Gene expression in root tips of soybean.
KS19

source_name: One centimeter long tap root tip of soybean genotype Young, Al, 2hr


title: 415Evs415A

value: Variant


title: Surgical sample OPE131

description:
OPE131
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE148

description:
OPE148
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE129

description:
OPE129
Gene expression data from surgical sample of esophageal cancer.


title: human PDAC 8 (SNP)

description: genomic DNA of human PDAC

value: pancreas

tag: disease status

tag: ajcc stage


title: y_con_72_Rep3

description:
Gene expression in root tips of soybean.
KS44

source_name: One centimeter long tap root tip of soybean genotype Young, untreated, 72hr

value: untreated


title: INS1 control, bioological rep2

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on 230 2.0 rat Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using  the affymetrix 3000 genescanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 150

organism: Rattus norvegicus

source_name: Insulinoma 832/13 INS-1 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting from 1 ug total RNA (Expression Analysis Technical Manual, 701025 Rev5, Affymetrix).

growth_protocol: The rat insulinoma 832/13 INS-1 cell line was used between passages 7 and 25. Cells were cultured at 5% CO2–95% air at 37°C in RPMI 640 medium  containing 11 mM D-glucose supplemented with 10% (v/v) heat-inactivated fetal bovine serum,  100 U/ml penicillin-streptomycin, 10 mM HEPES, 1 mM sodium pyruvate (Invitrogen), and 50 μM  β-mercaptoethanol (Invitrogen) (INS-1 medium).

extract_protocol: Total RNA was extracted and purified from cultured cells using the RNA-Plus reagent according to the manufacturer’s instructions (Q-BIOgene).

treatment_protocol: COUP-TFII depletion experiments in the 832/13 INS-1 cell line were performed as described previously (Perilhou A, Tourrel-Cuzin C, Kharroubi I, Henique C, Fauveau V, Kitamura T, Magnan C, Postic C, Prip-Buus C, Vasseur-Cognet M (2008). The transcription factor COUP-TFII is negatively regulated by insulin and glucose via FoxO1 and ChREBP controlled pathways. . Mol Cell Biol 28: 6568-6579). Briefly, cells were transfected with COUP-TFII siRNA or a scrambled siRNA using a Amaxa device following manufacturer instructions.

tag: passage

value: between passages 7 and 25

tag: cell line

value: Insulinoma 832/13 INS-1 cell line

value: scrambled


title: y_con_72_Rep2

description:
Gene expression in root tips of soybean.
KS43

value: Young


title: INS1 control, biological rep3


title: y_tr_72_Rep3

description:
Gene expression in root tips of soybean.
KS41

value: root


title: INS1 control, biological rep1


title: siRNA treated, biological rep3

value: COUP-TFII knockdown


title: siRNA treated, biological rep1


title: y_con_48_Rep3

description:
Gene expression in root tips of soybean.
KS38

source_name: One centimeter long tap root tip of soybean genotype Young, untreated, 48hr

value: sensitive


title: siRNA treated, biological rep2


title: Surgical sample OPE128

description:
OPE128
Gene expression data from surgical sample of esophageal cancer.

value: esophageal cancer


title: y_con_48_Rep2

description:
Gene expression in root tips of soybean.
KS24


title: Surgical sample OPE124

description:
OPE124
Gene expression data from surgical sample of esophageal cancer.

value: cancerous portion of esophagus


title: y_con_72_Rep1

description:
Gene expression in root tips of soybean.
KS42


title: Surgical sample OPE113

description:
OPE113
Gene expression data from surgical sample of esophageal cancer.

value: surgical


title: Surgical sample OPE120

description:
OPE120
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE067

description:
OPE067
Gene expression data from surgical sample of esophageal cancer.


title: y_con_12_Rep3

description:
Gene expression in root tips of soybean.
KS36

source_name: One centimeter long tap root tip of soybean genotype Young, untreated, 12hr


title: y_con_12_Rep2

description:
Gene expression in root tips of soybean.
KS23


title: y_con_12_Rep1

description:
Gene expression in root tips of soybean.
KS11


title: Surgical sample OPE127

description:
OPE127
Gene expression data from surgical sample of esophageal cancer.


title: Biopsy sample BPY6118N

description:
BPY6118N
Gene expression data from biopsy sample of the non-cancerous portion in esophageal cancer.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

source_name: Esophagus, non-cancerous portion, biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: non-cancerous portion of esophagus

value: biopsy


title: Surgical sample OPE094

description:
OPE094
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE078

description:
OPE078
Gene expression data from surgical sample of esophageal cancer.


title: y_con_48_Rep1

description:
Gene expression in root tips of soybean.
KS12


title: y_tr_48_Rep3

description:
Gene expression in root tips of soybean.
KS37

value: aluminum


title: Biopsy sample BPY6416N

description:
BPY6416N
Gene expression data from biopsy sample of the non-cancerous portion in esophageal cancer.


title: Biopsy sample BPY5978N

description:
BPY5978N
Gene expression data from biopsy sample of the non-cancerous portion in esophageal cancer.


title: Biopsy sample BPY6007N

description:
BPY6007N
Gene expression data from biopsy sample of the non-cancerous portion in esophageal cancer.


title: Biopsy sample BPY4272N

description:
BPY4272N
Gene expression data from biopsy sample of the non-cancerous portion in esophageal cancer.


title: y_con_2_Rep2

description:
Gene expression in root tips of soybean.
KS22

source_name: One centimeter long tap root tip of soybean genotype Young, untreated, 2hr


title: y_con_2_Rep1

description:
Gene expression in root tips of soybean.
KS10


title: Surgical sample OPE453N

description:
OPE453N
Gene expression data from surgical sample of the non-cancerous portion in esophageal cancer.

source_name: Esophagus, non-cancerous portion, surgical


title: p_tr_72_Rep2b

description:
Gene expression in root tips of soybean.
KS30

source_name: One centimeter long tap root tip of soybean genotype PI 416937, Al, 72hr

value: tolerant


title: Surgical sample OPE063

description:
OPE063
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE041

description:
OPE041
Gene expression data from surgical sample of esophageal cancer.


title: p_tr_48_Rep2b

description:
Gene expression in root tips of soybean.
KS15

source_name: One centimeter long tap root tip of soybean genotype PI 416937, Al, 48hr


title: Surgical sample OPE438N

description:
OPE438N
Gene expression data from surgical sample of the non-cancerous portion in esophageal cancer.


title: p_tr_72_Rep1b

description:
Gene expression in root tips of soybean.
KS29


title: Surgical sample OPE030

description:
OPE030
Gene expression data from surgical sample of esophageal cancer.


title: p_tr_72_Rep3b

description:
Gene expression in root tips of soybean.
KS31


title: Surgical sample OPE015

description:
OPE015
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE049

description:
OPE049
Gene expression data from surgical sample of esophageal cancer.


title: Surgical sample OPE233N

description:
OPE233N
Gene expression data from surgical sample of the non-cancerous portion in esophageal cancer.


title: p_tr_48_Rep1b

description:
Gene expression in root tips of soybean.
KS3


title: p_tr_12_Rep3b

description:
Gene expression in root tips of soybean.
KS25

source_name: One centimeter long tap root tip of soybean genotype PI 416937, Al, 12hr


title: Biopsy sample BPY136

description:
BPY136
Gene expression data from biopsy sample of esophageal cancer.

source_name: Esophagus, cancerous portion, biopsy


title: p_tr_12_Rep2b

description:
Gene expression in root tips of soybean.
KS14


title: p_tr_48_Rep3b

description:
Gene expression in root tips of soybean.
KS27


title: Surgical sample OPE231N

description:
OPE231N
Gene expression data from surgical sample of the non-cancerous portion in esophageal cancer.


title: p_tr_12_Rep1b

description:
Gene expression in root tips of soybean.
KS2


title: Biopsy sample BPY143

description:
BPY143
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY145

description:
BPY145
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY129

description:
BPY129
Gene expression data from biopsy sample of esophageal cancer.


title: p_tr_2_Rep1b

description:
Gene expression in root tips of soybean.
KS1

source_name: One centimeter long tap root tip of soybean genotype PI 416937, Al, 2hr


title: Biopsy sample BPY162

description:
BPY162
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY067

description:
BPY067
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY131

description:
BPY131
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY148

description:
BPY148
Gene expression data from biopsy sample of esophageal cancer.


title: p_tr_2_Rep2b

description:
Gene expression in root tips of soybean.
KS13


title: p_con_48_Rep1b

description:
Gene expression in root tips of soybean.
KS6

source_name: One centimeter long tap root tip of soybean genotype PI 416937, untreated, 48hr


title: Biopsy sample BPY078

description:
BPY078
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY063

description:
BPY063
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY127

description:
BPY127
Gene expression data from biopsy sample of esophageal cancer.


title: p_con_72_Rep3b

description:
Gene expression in root tips of soybean.
KS34

source_name: One centimeter long tap root tip of soybean genotype PI 416937, untreated, 72hr


title: Biopsy sample BPY128

description:
BPY128
Gene expression data from biopsy sample of esophageal cancer.


title: p_con_72_Rep1b

description:
Gene expression in root tips of soybean.
KS32


title: p_con_48_Rep3b

description:
Gene expression in root tips of soybean.
KS28


title: Biopsy sample BPY094

description:
BPY094
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY113

description:
BPY113
Gene expression data from biopsy sample of esophageal cancer.


title: Biopsy sample BPY124

description:
BPY124
Gene expression data from biopsy sample of esophageal cancer.


title: p_con_72_Rep2b

description:
Gene expression in root tips of soybean.
KS33


title: Biopsy sample BPY120

description:
BPY120
Gene expression data from biopsy sample of esophageal cancer.


title: p_con_48_Rep2b

description:
Gene expression in root tips of soybean.
KS18


title: p_con_12_Rep3b

description:
Gene expression in root tips of soybean.
KS26

source_name: One centimeter long tap root tip of soybean genotype PI 416937, untreated, 12hr


title: p_con_2_Rep2b

description:
Gene expression in root tips of soybean.
KS16

source_name: One centimeter long tap root tip of soybean genotype PI 416937, untreated, 2hr


title: p_con_12_Rep2b

description:
Gene expression in root tips of soybean.
KS17


title: Biopsy sample BPY041

description:
BPY041
Gene expression data from biopsy sample of esophageal cancer.


title: moPB_CD34_BMP4 treated biological rep 3

city: Boston

first: Teresa

middle: Venezia

last: Bowman

address: One Blackfan Circle, 7th floor

institute: Children's Hospital Boston

description: Gene expression data from CD34 cells in erythroid differentiation medium for 2 hrs with 25ng/ul rhBMP4

hyb_protocol: Following fragmentation, approximately 10 ug of cRNA were hybridized for 18 hr on Affymetrix 3' Expression GeneChip U133plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Raw expression data was preprocessed by MAS5 and then log10 transformed. Biological replicates across arrays were then quantile normalized.

label_protocol: RNA amplification and labeling was performed using GeneChip HT 3' IVT Express Kit.

growth_protocol: CD34+ cells were expanded in Stemspan SFEM medium supplemented with 1XCC100 cytokine mix + 2% pen/strep. On day 6 of expansion, cells were transferred to erythroid differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM β-estradiol) for 2 hours.

extract_protocol: Rneasy Micro Kit from Qiagen was used for total RNA extraction and DNA removal.

treatment_protocol: To activate the Wnt or BMP pathways, the cells were exposed to 0.5uM BIO or 25ng/ul rhBMP4, respectively, during the two hours in differentiation conditions.

tag: cell type

value: moPB CD34+ selected cells

value: healthy normal volunteer


title: moPB_CD34_BMP4 treated biological rep 2

source_name: CD34 cells in erythroid differentiation medium for 2 hrs with 25ng/ul rhBMP4


title: p_con_12_Rep1b

description:
Gene expression in root tips of soybean.
KS5

tag: treatment

value: untreated


title: Biopsy sample BPY049

description:
BPY049
Gene expression data from biopsy sample of esophageal cancer.


title: moPB_CD34_BMP4 treated biological rep 1


title: Biopsy sample BPY030

description:
BPY030
Gene expression data from biopsy sample of esophageal cancer.


title: moPB_CD34_BIO treated biological rep 1

description: Gene expression data from CD34 cells in erythroid differentiation medium for 2 hrs with 0.5uM BIO


title: p_con_2_Rep1b

description:
Gene expression in root tips of soybean.
KS4


title: moPB_CD34_BIO treated biological rep 2

source_name: CD34 cells in erythroid differentiation medium for 2 hrs with 0.5uM BIO


title: Arciga-Reyes_3-3_smg7b-1-1_Rep1_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Individual seeds were sown in 5 inch diameter pots and stratified before they were transfered to a growth chamber. Seedlings were grown under continuous light at 22 C for 17 days after germination.  22 °C average, 22 °C day, 22 °C night 65 % average, 65 % day, 65 % night  Constant light

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

extract_protocol: Qiagen RNAeasy kit protocol

value: whole plant

tag: stock code

tag: ecotype

value: Col-0 (Columbia, N60000)

tag: genotype/variation

value: T-DNA insertion


title: Arciga-Reyes_3-4_smg7b-1-2_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Id3 Lo OT-I, replicate 2

city: San Diego

first: John

middle: Adam

last: Best

address: 9500 Gilman Dr

institute: UCSD

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: RMA, Genepattern, The Sample data table contains raw expression data post RMA, excluding unlabeled probes or duplicate probes (that showed identical value).

source_name: OT-I cells sorted at day 6 of VSV-OVA infection with low expression of Id3-yfp

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Glass slide teasing  Flow sorting

treatment_protocol: 10^5 p.f.u VSV-OVA

tag: strain

tag: gender

value: Male

value: Spleen

tag: phenotypic markers

tag: id3-yfp expression

value: low


title: Arciga-Reyes_3-1_wildtype-1_Rep1_ATH1


title: Arciga-Reyes_3-2_wildtype-2_Rep2_ATH1


title: Id3 Lo OT-I, replicate 1


title: H3396 E2 1h

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

institute: IGBMC

hyb_protocol: The arrays were further washed and stained with streptavidine-phycoerythrin in an Affymetrix GeneChip® Fluidics station 450 using the script protocol F450-0007

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G

data_processing: Expression values were generated with Affymetrix software Expression Console version 1.1

source_name: H3396 breast cancer cells, 1h estrogen treatment

label_protocol: cDNA was prepared by reverse transcription of 2ug total RNA using Superscript II enzyme primed by random hexamers. Genome wide gene expression data for each Superscript II enzyme primed by random hexamers. Genome wide gene expression data for each time point were obtained with Affymetrix GeneChip Gene 1.0 ST Array System for Human in GeneChip WT Terminal using

growth_protocol: H3396 cells were maintained in RPMI 1640 supplemented with 10 mM HEPES, 10% fetal bovine serum (FBS), and antibiotics.

extract_protocol: Total RNA was isolated with GenEluteTM Mammalian Total RNA Miniprep Kit (RTN 350) from Sigma according to the manufacturer’s instructions

treatment_protocol: H3396 cells were cultured in charcoal stripped medium for 72 hours before treatment for 1h, 2h, 6h and 24h with 1.10-8 M estrogen or vehicle control

value: estrogen

tag: time

value: 1 h


title: H3396 E2 2h

source_name: H3396 breast cancer cells, 2h estrogen treatment

value: 2 h


title: Biopsy sample BPY015

description:
BPY015
Gene expression data from biopsy sample of esophageal cancer.

tag: disease state

value: esophageal cancer

value: cancerous portion of esophagus

tag: sample type

tag: patient identifier


title: Arciga-Reyes_2-3_upf2i-1_Rep1_ATH1

description: Seeds were cold treated at 4C for three days Growth chamber Agar 65% 22oC

extract_protocol: Seedlings harvested and snap-frozen in liquid nitrogen and RNA extracted as described in the Qiagen RNAeasy kit.

tag: tissue

value: RNAi gene_knock_out


title: H3396 E2 0h

source_name: H3396 breast cancer cells, 0h estrogen treatment

value: 0 h


title: Arciga-Reyes_2-2_wildtype-2_Rep2_ATH1

value: wild type


title: H3396 E2 24h

source_name: H3396 breast cancer cells, 24h estrogen treatment


title: moPB_CD34_BIO treated biological rep 3

value: moPB CD34+ selected cells

tag: disease status


title: H3396 E2 6h

source_name: H3396 breast cancer cells, 6h estrogen treatment

value: 6 h


title: Arciga-Reyes_2-4_upf2i-2_Rep2_ATH1


title: Id3 Hi OT-I, replicate 2

source_name: OT-I cells sorted at day 6 of VSV-OVA infection with high expression of Id3-yfp

tag: age

value: high


title: Surgical sample OPE411N

description:
OPE411N
Gene expression data from surgical sample of the non-cancerous portion in esophageal cancer.

source_name: Esophagus, non-cancerous portion, surgical

value: non-cancerous portion of esophagus

value: surgical


title: Arciga-Reyes_2-1_wildtype-1_Rep1_ATH1

value: whole plant


title: Arciga-Reyes_2-5_smg5-2-1_Rep1_ATH1

value: mutant


title: moPB_CD34_vehicle control biological rep 3

description: Gene expression data from CD34 cells in erythroid differentiation medium for 2 hrs with vehicle control

value: healthy normal volunteer


title: Somatic donor cell for genome exchange

status: Public on Oct 06 2011

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
SAMPLE 15
Fibroblasts from a normal male adult, approx. p5.

hyb_protocol: Hybridization according to Illumina protocols on Illumina Sentrix Human Expression BeadChip RefSeq 8 v3.0. Arrays were hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with Illumina iScan.  Protocols can be found on the Illumina web page.

data_processing: Data were normalized to average signal, background was subtracted using Illumina GenomeStudio.

source_name: 1-016 skin cells

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit.

growth_protocol: Human activated oocytes, parthenotes and cleavage stages were cultured in Global medium supplemented with 15% plasmanate and cultured in a COOK benchtop incubator at 5% O2, 6% CO2 and 89% N2.

extract_protocol: PicoPure RNA isolation kit (Arcturus).

treatment_protocol: Genome exchange was performed using donated human oocytes. Samples were harvested on d4 to d5 after artificial activation.

value: fibroblast

tag: chip #

tag: array

value: B


title: MII oocytes, rep1

description:
SAMPLE 13
3 mature MII oocytes.

source_name: MII oocytes

tag: cell type

value: oocyte

value: F


title: MII oocytes, rep2

description:
SAMPLE 14
2 mature MII oocytes, biological duplicate.

value: H


title: Amanitin d4

description:
SAMPLE 10
Incubation of zygotes from d1 to d4 in alpha-amanitin to inhibit transcription.

source_name: Amanitin d4

value: blastomere


title: Arciga-Reyes_2-6_smg5-2-2_Rep2_ATH1

tag: stock code


title: Somatic donor cell for genome exchange, rep2

description:
SAMPLE 6
Fibroblasts from a male type 1 diabetes (T1D) patient ID 1-000, biological duplicate.

source_name: 1-000 skin cells


title: moPB_CD34_vehicle control biological rep 1

source_name: CD34 cells in erythroid differentiation medium for 2 hrs with vehicle control


title: Amanitin d3

description:
SAMPLE 9
Incubation fo zygotes from d1 to d3 in alpha-amanitin to inhibit transcription.

source_name: Amanitin d3

value: A


title: Somatic donor cell for genome exchange, rep1

description:
SAMPLE 5
Fibroblasts from a male type 1 diabetes (T1D) patient ID 1-000, approx. p11.

value: G


title: moPB_CD34_vehicle control biological rep 2


title: Parthenotes

description:
SAMPLE 1
4 parthenotes pooled in 1 sample. Parthenotes had 7, 3 and 10 cells.

source_name: Parthenotes April 09


title: Genome exchange, SCNT A and B

description:
SAMPLE 4
4 SCNT cell clusters consisting of 5, 6, 4, 4 blastomeres.

source_name: SCNT A and B

value: D


title: IVF day4 sample, rep2

description:
SAMPLE 8
IVF samples collected on day4 after fertilization, biological duplicate.

source_name: IVF d4


title: Genome exchange, SCNT A1

description:
SAMPLE 3
1 SCNT cell cluster of 12 blastomeres (most advanced SCNT cell cluster of this study).

source_name: SCNT A1

value: C


title: IVF day4 sample, rep1

description:
SAMPLE 7
IVF samples collected on day4 after fertilization.


title: Genome exchange, SCNT C

description:
SAMPLE 2
4 SCNT cell clusters pooled together. Clusters had 7, 7, 5 and 4 blastomeres.

source_name: SCNT C April 09


title: Zebrafish embryo: DMSO100 replicate 4 versus DMF100 replicate 3

city: Liverpool

first: Catherine

last: Turner

state: Merseyside

address: Crown Street

department: Institute of Integrative Biology

institute: University of Liverpool

hyb_protocol: Labelled aRNA (1μg) from each sample to be co-hybridised to the array were mixed and fragmented using an RNA fragmentation kit (Ambion, Applied Biosystems). After fragmentation, samples were combined with pre-warmed (90 µl, 65 ºC)1 x Nexterion Hyb buffer (Schott), denatured and then applied to a pre-prepared microarray slide. Slides were incubated for 16 h at 65 ºC in a pre-heated and humidified hybridisation chamber (Genetix).

scan_protocol: Slides were imaged on a ScanArray Express HT scanner (PerkinElmer, Life Sciences) using ScanArray Express software. The scanned images were quantified using BlueFuse 3.3 Software (BlueGnome).

data_processing: Statistical analysis of microarray data was carried out within the R software environment. Data was normalised, using the marray package (Dudoit and Yang 2002), firstly with a print-tip-group intensity LOESS normalisation and secondly by a between array global scale normalisation using median absolute deviation (MAD) (Yang et al. 2002).

organism: Danio rerio

source_name: Zebrafish embryo, 48 h, DMSO100 exposed

label_protocol: RNA samples were amplified using the SuperScript Indirect RNA Amplification System kit (Invitrogen) and Cy3 or Cy5 dye (GE Healthcare) labelled following the manufacturers protocol for amplification and labelling accompanying the kit.

growth_protocol: Zebrafish embryo were obtained from a breeding fish stock maintained in 10 litre tanks from Aquatic Ecosystems at a stocking level of not more than 10 fish per tank, with 5-7 males per tank, and 3-5 females. Water temprerature was maintained at 28±1 °C. Light regime 14 hours light:10 hours dark. Fish were fed artemia in the mornings and flake food in the evenings.

extract_protocol: Total RNA was extracted from frozen embryo samples by the guanidinium thiocyanate-phenol-chloroform method using in-house made reagent. Extracted total RNA was then purified using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturers instructions.

treatment_protocol: Zebrafish embryo exposures were conducted in accordance with the procedures described in the DIN 38415-6, ISO 7346-1 and the OECD draft test guideline. Embryos were collected approximately 30 min after the assumed time of fertilisation (shortly after lights-on in aquarium) and placed into Petri-dishes (12 cm diameter) containing test solutions before embryos reached the 16-cell stage (1.5 hpf). At 3 to 5 hpf, embryos were plated-out into 24-well polystyrene multi-well plates, untreated, (Nunc, Thermo Fisher Scientific) by assigning a single fertilized egg to each well containing 2 ml of test solution. Each plate contained four plate negative control embryos and twenty exposed embryos. Five replicate plates were run for each solvent concentration and for the negative control. Plating-out of embryos, positioning in the incubator and subsequent microscopical assessment of test plates were undertaken in a randomised order following a block design to reduce bias. Plates were covered by a breathable membrane (Breath-Easy, Sigma-Aldrich) and incubated for 48 h at 26 ± 0.5 °C on a 14:10 h, light:dark photoperiod. After 48 h exposure embryos from each plate (without the four plate control and dead embryos) were pooled together, snap frozen in liquid nitrogen and stored at -80 °C.

value: embryo

tag: developmental stage

value: 48 hpf

tag: toxicant

value: Dimethyl sulfoxide

tag: concentration

source_name: Zebrafish embryo, 48 h, DMF100 exposed

value: Dimethylformamide


title: Zebrafish embryo: DMF100 replicate 3 versus DMSO100 replicate 4


title: Zebrafish embryo: CONTROL replicate 3 versus DMF100 replicate 1

source_name: Zebrafish embryo, 48 h, CONTROL exposed

value: Control


title: Fibroblast skin donor 2, line F

description:
SAMPLE 14
1016 FIBROBLAST

hyb_protocol: Hybridization according to Illumina protocols on Illumina Sentrix Human Expression BeadChip RefSeq 8 v3.0 (GPL6883). Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with Illumina iScan.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal, background was subtracted using Illumina GenomeStudio

source_name: skin cells from skin donor 2, ID 1-016

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit

growth_protocol: human pluripotent stem cells grown HUES medium

extract_protocol: Rneasy Plus Mini kit

treatment_protocol: cell lines grown on a low density mouse embryonic fibroblast feeder layer were collected for RNA isolation

value: adult skin cell


title: Zebrafish embryo: DMF25 replicate 3 versus DMF100 replicate 2

source_name: Zebrafish embryo, 48 h, DMF25 exposed


title: Stolon-SD2 vs SD6

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Stolons collected at 2 days (SD) compared to stolons collected at 6 days (SD)

hyb_protocol: Hybridization and slide processing were performed using the 4 ×44 k POCI array according to Agilent specifications using the Agilent hybridization chamber and oven, including the stabilization and drying wash step.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner, and data were extracted using the feature extraction software package (v9.1.3.1) using a standard protocol. The POCI array design includes 2,256 positive and negative control features that are set up for use with the Agilent’s Two-color spike-in kit (www.chem.agilent.com).

data_processing: The data were imported in Microsoft Excel, and log2 Cy5/Cy3 ratios were calculated after passing quality check and minimal expression levels. logRatios for all 10 hybridizations were exported into Genstat® v9.2 for statistical analysis and calculation of expression estimates and standard errors for each feature during the five developmental stages. Features with a residual variance greater than 2.0 were rejected from the data set.

organism: Solanum tuberosum subsp. andigenum

label_protocol: For microarray hybridizations, first- and second-strand synthesis following the MessageAmp™ II aRNA amplification kit protocol (Ambion) was used following minor modifications. For first-strand synthesis, 2 μg of total RNA was used in the reaction followed by second-strand synthesis with half of the recommended enzyme concentrations. Purified cDNA was used for in vitro transcription using an indirect amino-allyl-labeling method with a 1:1 incorporation ratio of uridine triphosphate (UTP)/5-(3-aminoallyl)-UTP. In vitro transcription was performed at 37°C with a lid temperature of 42°C for a period of 12 h, after which samples were purified according to the manufacturer’s protocol. Purified complementary RNA (cRNA) samples were prepared in 2-μg aliquots and dried using a speed vac and stored at −80°C. For sample labeling, 2 μg of cRNA was resuspended in 5 μl freshly made carbonate buffer (0.1 M Na2CO3) adjusted to pH 9. Equal amounts of either Cy3 or Cy5 dye (GE Healthcare) were added and incubated for 1.5 h at room temperature. Samples were purified using RNeasy MinElute Spin Columns (Qiagen). Dye incorporation was measured using a ND-100 Spectrophotometer v3.3 (Nanodrop Technologies) and 1 μg of both Cy3- and Cy5-labeled cRNA samples was used for each hybridization.

growth_protocol: Andigena plants were grown in the greenhouse under LD standar conditions. Prior to the start of the experiment, plants were randomly chosen from the greenhouse and induced to tuberise in a growth chamber in a SD  16 h:8 h day:night photoperiod.  After 2d, 4d, 6d and 8d of SD treatment, stolon samples were collected in the dark one hour before the beginning of the light period.

extract_protocol: At the end of the treatment, stolon samples were collected, flash frozen in liquid N2, and stored at -80°C until RNA extraction. Stolon samples were ground to a fine powder in liquid N2, and RNA was extracted from approximately 300 mgr of tissue. Total RNA was prepared using the guanidine-HCl method (Logeman et al). DNA contamination was removed by a standard DNase I treatment followed by RNA clean-up with RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol. RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

treatment_protocol: LD (long day) non-inductive conditions (16h light/8h dark) until a 10-leaf stage.

value: Stolons

tag: day of collection

tag: photoperiod

value: SD


title: Stolon-LD vs SD4

description: Stolons collected grown in LD conditions compared to stolons collected at 4 days (SD)

source_name: LD

value: LD


title: Zebrafish embryo: DMF100 replicate 1 versus CONTROL replicate 3


title: Stolon-SD6 vs LD

description: Stolons collected at 6 days (SD) compared to stolons grown in LD conditions


title: Stolon-SD6 vs SD8

description: Stolons collected at 6 days (SD) compared to stolons collected at 8 days (SD)


title: iPS cell oocyte donor 1, line D

description:
SAMPLE 13
1034D

source_name: iPS cell line derived from skin cells of the oocyte donor

value: pluripotent stem cell

tag: stem cell source

value: iPS cells


title: Zebrafish embryo: DMF25 replicate 4 versus DMSO25 replicate 3

source_name: Zebrafish embryo, 48 h, DMSO25 exposed


title: Zebrafish embryo: DMSO25 replicate 1 versus CONTROL replicate 1


title: Fibroblast oocyte donor 1

description:
SAMPLE 11
1034 FIBROBLAST

source_name: skin cells from oocyte donor 1, ID 1-034

value: F


title: Zebrafish embryo: DMSO100 replicate 2 versus DMSO25 replicate 2


title: iPS cell oocyte donor 1, line B

description:
SAMPLE 10
1034B


title: soPS2

description:
SAMPLE 12
A5

source_name: pluripotent stem cell containing a haploid oocyte genome and a diploid somatic cell genome of somatic cell donor 2

value: nuclear transfer


title: iPS cell skin donor 2, line B

description:
SAMPLE 9
1016B

source_name: iPS cell lineB derived from skin cell donor ID 1-016

value: B


title: Stolon-LD vs SD2

description: Stolons grown at LD conditions compared to stolons collected at 2 days (SD)


title: Zebrafish embryo: DMF100 replicate 2 versus DMF25 replicate 3


title: Zebrafish embryo: CONTROL replicate 4 versus DMSO100 replicate 3


title: Zebrafish embryo: DMSO100 replicate 3 versus CONTROL replicate 4


title: Zebrafish embryo: DMF100 replicate 4 versus DMSO25 replicate 4


title: Zebrafish embryo: CONTROL replicate 2 versus DMF25 replicate 1


title: iPS cell skin donor 1 biological duplicate

description:
SAMPLE 8
1000 IPS duplicate

source_name: iPS cell derived from T1D individual with ID 1-000, named H1.5 (Maehr, R. et al., Generation of pluripotent stem cells from patients with type 1 diabetes. Proc Natl Acad Sci U S A (2009))

value: G


title: Stolon-SD4 vs SD8

description: Stolons collected at 4 days (SD) compared to stolons collected at 8 days (SD)


title: Stolon-SD8 vs LD

description: Stolons collected at 8 days (SD) compared to stolons grown LD conditions


title: Stolon-SD4 vs SD6

description: Stolons collected at 4 days (SD) compared to stolons collected at 6 days (SD)


title: Zebrafish embryo: DMSO25 replicate 3 versus DMF25 replicate 4

value: Dimethlyformamide


title: iPS cell skin donor 1

description:
SAMPLE 7
1000 IPS

value: E


title: Stolon-SD2 vs SD4

description: Stolons collected at 2 days (SD) compared to stolons collected at 4 days (SD)


title: IVF day3 sample, rep2

description:
SAMPLE 12
IVF samples collected late on day3 after fertilization, biological duplicate.

source_name: IVF d3

value: blastomere


title: pPS1 biological duplicate

description:
SAMPLE 5
A2 duplicate

source_name: parthenogenetic pluripotent stem cell line derived from oocyte donor 1

value: A

value: oocyte donor (parthenogenetic pluripotent stem cell line)


title: Zebrafish embryo: DMF25 replicate 1 versus CONTROL replicate 2

value: embryo

value: 48 hpf

value: Dimethylformamide


title: Zebrafish embryo: DMF25 replicate 2 versus DMSO100 replicate 1

value: Dimethyl sulfoxide


title: Zebrafish embryo: DMSO25 replicate 4 versus DMF 100 replicate 4


title: Zebrafish embryo: CONTROL replicate 1 versus DMSO25 replicate 1

value: Control


title: Stolon-StSP6A-RNAi vs Stolon-WT-REP2

description: Biological replicate 2 of 2: Transgenic plants with StSP6A silenced by an specific RNAi versus Wild Type

hyb_protocol: Equal amounts of dye of each aRNA labeled with either Cy3 or Cy5, ranging from 200 to 300 pmol, were mixed with 20 ug of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 9 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were then drained with a 2000-rpm spin for 2 min. The slides were stored in darkness until they were scanned.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenPix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

source_name: Stolon-Wild Type

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

growth_protocol: StSP6A over-expressing lines were grown in the greenhouse under non-inductiveLDs and the 2 cm most apical region of the stolons was collected prior to visible swelling in StSP6A over-expressing lines. StSP6A-RNAi lines were grown in the greenhouse under LD non-inductive conditions until a 10-leaf stage. They were subsequently transferred to inductive SD conditions (8 h light/16 h dark), and sampled 6 days after transfer to short days, one hour before the beginning of the light period.

extract_protocol: Total RNA was prepared using the guanidine-HCl method (Logeman et al). DNA contamination was removed by a standard DNase I treatment followed by RNA clean-up with RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol.

value: Stolons

tag: genotype/variation

value: wild type


title: pPS1

description:
SAMPLE 4
A2

value: pluripotent stem cell

value: H


title: Stolon-StSP6A-RNAi vs Stolon-WT-REP1

description: Biological replicate 1 of 2: Transgenic plants with StSP6A silenced by an specific RNAi versus Wild Type


title: Zebrafish embryo: DMSO25 replicate 2 versus DMSO100 replicate 2


title: Stolon-35S-StSP6A vs Stolon-WT-REP2

description: Biological replicate 2 of 2: Transgenic plants inducing StSP6A under the control of the 35S promoter versus Wild Type


title: NYSCF1

description:
SAMPLE 6
A3

source_name: pluripotent stem cell line derived from an IVF blastocyst

value: C

value: IVF blastocysts


title: Stolon-35S-StSP6A vs Stolon-WT-REP1

description: Biological replicate 1 of 2: Transgenic plants inducing StSP6A under the control of the 35S promoter versus Wild Type


title: Stolon-SD8 vs SD2

description: Stolons collected at 8 days (SD) compared to stolons collected at 2 days (SD)

value: SD


title: IVF day3 sample, rep1

description:
SAMPLE 11
IVF samples collected late on day3 after fertilization.

value: D


title: soPS1 biological duplicate

description:
SAMPLE 3
B4 duplicate

source_name: pluripotent stem cell containing a haploid oocyte genome of oocyte donor1 and a diploid somatic cell genome of skin cell donor1

value: F

value: nuclear transfer


title: Zebrafish embryo: DMSO100 replicate 1 versus DMF25 replicate 2

source_name: Zebrafish embryo, 48 h, DMSO100 exposed


title: Id3 Hi OT-I, replicate 1

source_name: OT-I cells sorted at day 6 of VSV-OVA infection with high expression of Id3-yfp

tag: strain

tag: gender

value: Male

value: Spleen

tag: phenotypic markers

tag: id3-yfp expression

value: high


title: soPS1

description:
SAMPLE 2
B4


title: Fibroblast skin donor 1

description:
SAMPLE 1
1000 FIBROBLAST

source_name: T1D male donor skin cells ID 1-000

value: adult skin cell

value: B


title: 24 h after JA treatment_leaf replicate 2

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

description: Biological replicate 2 of 2.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent).

organism: Oryza sativa

source_name: Leaves treated with H2O for 24 h

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice plants were grown under natural daylight in a greenhouse.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Leaf disks (6 mm diameter) were punched from latest leaf of rice seedlings. Leaf disks were floated on JA (500 uM) or H2O and incubated under light at 25C.

tag: tissue origin

value: seedlings

tag: tissue

value: Leaf disks (6 mm diameter)

tag: treatment

value: H2O for 24 h

source_name: Leaves treated with JA for 24 h

value: Jasmonic acid (500uM) for 24 h


title: PIC_G_P2

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

description: Gene expression after 24 of ip injection with Poly (I:C) with thermal gradient

hyb_protocol: Briefly, total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. Each sample (1.65 μg of RNA) was hybridized to Zebrafish array (ID 026437, Agilent) at 65 °C for 17 hours using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Microarrays slides were scanned with Agilent Technologies Scanner model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. One-channel TIFF images were imported into the Gene GeneSpring software GX 11.0.

data_processing: Percentile shift normalization was made to adjust all spot intensities in an array. This normalization takes each column in an experiment independently, and computes the median expression values for this array, across all spots. It then subtracts this value from the expression value of each entity (Bolstad et al, 2003). After Percentile normalization, all data were filtered by comparison of the standard deviation expression among groups (filter by expression). The entities that had values lesser or greater than the standard deviation value were retained. This filter procedure allowed selected genes that have outlier samples, and filter out genes that have a low variation in expression values across all samples.

label_protocol: A loop microarray design approach was taken for the study, all experimental RNA samples were labelled with one dye Cy3 and each stimulated sample was compared to the control sample (pool without stimulation) labelled with the same dye (Cy3). Denatured samples of RNA were reversed transcribed and indirectly labelled with Cy3. RNA labelling, hybridizations, and scanning were performed according to manufacturer’s instructions.

extract_protocol: Total RNA was extracted from brains using 500uL of TriReagent (Molecular Research Center) following the manufacturer’s instructions. RNA concentration was quantified using Nanodrop ND-1000 and RNA integrity and quality was assessed using a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent Technologies). The RNA integrity number (RIN) was calculated for each sample using the Agilent 2100 Expert software, only RNAs with a RIN number > 7 were processed (to reduce experimental biases). Total RNA (2μg) was used to synthesize cDNA with SuperScript III Transcriptase (Invitrogen) and oligo-dT primer (Promega).

treatment_protocol: For microarray screening of fever in zebrafish, RNA extracted of zebrafish brains injected or not with 1mg*Kg-1 of Poly (I:C): zebrafish in thermal gradient (control, n = 9), zebrafish PBS injected in thermal gradient (PBS, n = 9), zebrafish Poly I:C injected without thermal gradient (PIC_sG, n = 9), and zebrafish Poly I:C injected with thermal gradient (PIC_sG, n = 9). Individuals RNAs were grouped into pools from 3 individual for each treatment (3 pools by treatment).

tag: age

value: Adults

value: Whole Brain


title: 12 h after JA treatment_leaf replicate 2

description: Biological replicate 2 of 2.

source_name: Leaves treated with H2O for 12 h

value: H2O for 12 h

source_name: Leaves treated with JA for 12 h

value: Jasmonic acid (500uM) for 12 h


title: PBS_P3

description: Gene expression after 24 of ip injection with PBS with thermal gradient

value: PBS


title: PIC_G_P1


title: 48 h after JA treatment_leaf replicate 1

description: Biological replicate 1 of 2.

source_name: Leaves treated with H2O for 48 h

value: H2O for 48 h

source_name: Leaves treated with JA for 48 h

value: Jasmonic acid (500uM) for 48 h


title: PIC_sG_P3

description: Gene expression after 24 of ip injection with Poly (I:C) without thermal gradient


title: EF59 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep3

city: Columbia

first: Md Shakhawat

last: Hossain

state: Missouri

address: 201 Life Science Center 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri

description: Gene Expression data from Soybean leaves treated with MAMPs

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 45C on Soybean Gene 1.1 ST Array Strip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned with a GeneChip 7G Plus high-resolution scanner

data_processing: The gene level expression values were summarized by RMA by using Expressionist Refiner 6.1 (GeneData). Briefly, the signal intensity cel files from scanner were analyzed by a workflow with GC background subtraction, quantile normalization, and Median-Polish. The gene expression values from different samples were further used for gene differential statistic analysis

source_name: Soybean Leaves Treated with MAMPs

label_protocol: 500 ng of genomic-DNA free total RNA were used to produce fragmented and biotin-labeled cDNA using the Ambion WT Expression Kit (Applied Biosystems) and the Affymetrix WT Terminal Labeling and Hybridization Kit (Affymetrix).

growth_protocol: Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 mmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod).

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

treatment_protocol: Trifoliolate leaves from three-week-old plants were detached and then vacuumed infiltrated with ddiH2O for 2 min. Water-infiltrated trifoliolate leaves from five different plants of each genotype were pooled and cut into approximately 1 cm2 slices. Equal amount of leaf slices (~30 slices) were transferred into two different Petri dishes and then floated overnight on autoclaved ddiH2O. Water was removed from both Petri dishes and was replaced with 5 ml of MAMP solution [1 mM flagellin 22 (flg22) and 50 mg of crab shell chitin (called in this study as chitin)], or 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO). DMSO was included since it was contained in the solution used to dissolve the flg22 peptide]. After a 30 min treatment, mock- and MAMP-treated leaf slices were harvested into different tubes and immediately frozen in liquid nitrogen. Samples were stored at -80 until use. All procedures described above were performed under dark conditions.

value: Leaves Trifoliate

tag: genotype

value: Three weeks-old plants

value: MAMP (flg22+chitin) solution for 30 min


title: EF59 Leaves treated with Mock solution for 30 min Rep1

description: Gene Expression data from Soybean leaves treated with Mock

source_name: Soybean leaves treated with Mock

value: mock solution for 30 min


title: EF59 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep1


title: PIC_sG_P1


title: PBS_P2


title: 24 h after JA treatment_leaf replicate 1

description: Biological replicate 1 of 2.


title: EF59 Leaves treated with Mock solution for 30 min Rep3


title: 12 h after JA treatment_leaf replicate 1

description: Biological replicate 1 of 2.


title: 48 h after JA treatment_leaf replicate 2

description: Biological replicate 2 of 2.


title: EF59 Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep2


title: 6 h after JA treatment_leaf replicate 2

description: Biological replicate 2 of 2.

source_name: Leaves treated with H2O for 6 h

value: H2O for 6 h

source_name: Leaves treated with JA for 6 h

value: Jasmonic acid (500uM) for 6 h


title: PIC_G_P3


title: PIC_sG_P2


title: EF59 Leaves treated with Mock solution for 30 min Rep2


title: Ripley Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep3

value: Ripley


title: Control_P3

description: Gene expression after 24 with thermal gradient

value: control


title: 6 h after JA treatment_leaf replicate 1

description: Biological replicate 1 of 2.

value: seedlings

value: Leaf disks (6 mm diameter)


title: PBS_P1

value: Adults


title: Control_P2

value: Whole Brain


title: Control_P1


title: Ripley Leaves treated with MAMP (flg22+chitin) solution for 30 min Rep1