title: BBC_36hE_n3

description: Gene expression in zebrafish eye treated with 0.3 uM BBC for 36 h

value: 84 hpf

value: 0.3 uM BBC for 36 h


title: MBZ_12hE_n2

status: Public on Mar 24 2016

type: RNA

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

country: Japan

institute: Mie University Graduate School of Medicine

description: Gene expression in zebrafish eye treated with 0.3 uM MBZ for 12 h

hyb_protocol: 1500 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacture's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction 100 uL was hybridized to an Agilent Zebrafish DNA Oligo Microarray (GPL6457) for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using Agi4x44PreProcess package in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.

molecule: total RNA

organism: Danio rerio

source_name: eye

label_protocol: Three hundred nanograms of total RNA from each eye depot were converted into labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

growth_protocol: Zebrafish were raised at 28.5 ± 0.5°C with a 14 h/10 h light/dark cycle.

extract_protocol: Zebrafish was stored in RNA-later (Applied Biosystems, Foster City, CA, USA).  The eyes of zebrafish were collected by surgical extraction under a microscope. Total RNA was then extracted using an RNeasy Plus Micro Kit (Qiagen, Valencia, CA, USA), qualified by an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and quantified using a spectrophotometer (NanoDrop ND-100, Wilmington, DE, USA).

treatment_protocol: Zebrafish (AB line) at 48 hpf were treated with 0.3 uM of MBZ or BBC for 12, 24 or 36 hours.

tag: tissue

value: eye

tag: age

value: 60 hpf

tag: treatment

value: 0.3 uM MBZ for 12 h


title: BBC_36hE_n2


title: VEE strain 213391

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

country: USA

institute: Lawrence Livermore National Laboratory

hyb_protocol: DNA samples were prepared for hybridization using the NimbleGen Hybridization Kit LS (Roche). Three µg of labeled DNA was hybridized to each array, incubating for 40-45 hours at 42°C. Arrays were washed using the NimbleGen Wash Buffer Kit (Roche).

scan_protocol: The fluorescent signal on the array was scanned using a 2 µm Roche MS200 fluorescent scanner.

data_processing: Array feature intensities were generated using the NimbleScan software available from Roche NimbleGen. We used custom analysis software to call alleles at each locus. The software fits a linear model of strand and allele effects to the logs of the raw intensity values from all probes for the locus, and calls the allele as the one with the largest coefficient in the fitted model.

organism: Venezuelan equine encephalitis virus

source_name: VEE strain 213391

label_protocol: Fluorescent labeling of samples was performed using the NimbleGen One-Color DNA Labeling Kit (Roche). One µg VEEV cDNA was added to Cy-3 labeled random primers, followed by isothermal amplification at 37°C using Klenow polymerase.  Labeled DNA was purified via isopropanol precipitation and resuspended in water for microarray hybridization.

extract_protocol: Viral genomic RNA was extracted and purified using the Direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. cDNA was synthesized from extracted RNA via reverse transcription using SuperScript III. Random hexamers and oligo dT primers were used for priming.

tag: strain

value: VEE strain 213391


title: BBC_36hE_n4


title: Angel_muscle_baseline

city: Davis

first: Heather

last: Knych

state: California

address: 620 W.  Health Sciencse Drive

department: CAHFS

institute: University of California Davis

description: Gene expression data from horse muscle before administration of low dose of clenbuterol (0.8 µg/kg orally twice a day for 30 days); baseline1 time point

hyb_protocol: Following fragmentation 10ug of cRNA were hypridized for 16 hr at 45C on Equus caballus Gene 1.0 ST Array [transcript (gene) version] represents the equine gene 1.ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console.  Data visualization and filtering was performed in Transcriptome Analysis console version 3.0

label: biotin

organism: Equus caballus

source_name: Horse before receiving low dose of clenbuterol

label_protocol: Biotinylated cRNA were prepared according the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual 2001, Affymetrix)

extract_protocol: Muscle biopsy samples were placed in 600 µl of lysis buffer, contaning 2-β- mercaptoethanol (Qiagen Inc, Valencia, CA).  The tissue sample was then transferred to MagNa Green Beads tubes (Roche Diagnostics, Mannhein, Germany).  Homogenization was performed using a MagNaLyse (Roche Diagnostics, Mannhein, Germany) at 6000 rpm for 30 sec followed by a 1.0 min cool down period.  Homogenization intervals were continued until pieces of muscle were no longer visible (≤3 times).  Total RNA was purified using an miRNeasy Mini kit (RNeasy Mini, Qiagen Inc, Valencia, CA) and following the manufacturer’s instructions. Total RNA integrity was assessed using the Experion Automated Electrophoresis System (Bio-rad, Hercules, CA).  Only RNA samples with RIN ≥ 8 and 260/280 ratios between 1.7 and 2.1 were used (Denisov et al 2008) (Fleige et al 2006)

treatment_protocol: Five of the horses received 0.8 µg/kg clenbuterol PO BID for 30 days and an additional 4 horses received 0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days

tag: breed

value: Thoroughbred horse

tag: treated with

tag: time point

value: baseline before receiving low dose of clenbuterol drug

value: muscle


title: BBC_24hE_n4

description: Gene expression in zebrafish eye treated with 0.3 uM BBC for 24 h

value: 72 hpf

value: 0.3 uM BBC for 24 h


title: PHH from Donor 1 (D1), treated with DMSO

city: Stuttgart

first: Ulrich

middle: M.

last: Zanger

address: Auerbachstr. 112

country: Germany

institute: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology

description: Gene expression data from PHH treated with DMSO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 1.0ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® scanner 7G (Affymetrix).

data_processing: After visual inspection of the obtained GeneChip images, the Affymetrix Expression Console (Affymetrix) was used for quality control of microarrays and pre-processing of expression data  via robust multi-array average (RMA; Gene Level - Default).

organism: Homo sapiens

source_name: primary human hepatocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After the treatment for 24h with the indicated agonists the cells were lysed.

extract_protocol: Total RNA was isolated using Rneasy kit from Qiagen according to the manufacture´s conditions. All (24) used RNA samples had an RNA integrity number (RIN) > 9 (determined with the Bioanalyzer 2100 from Agilent Technologies) to ensure high quality of RNA.

treatment_protocol: Hepatocytes were isolated and seeded at a density of 4x105 viable cells/well onto BioCoat Collagen I Cellware 12-well culture plates in William’s E Medium, supplemented with 10% FBS, 100 U/ml Pen/Strep, 2 mM L-glutamine,32 mU/ml human insulin, 1 mM sodium pyruvate, 1 x nonessential amino acids, 15 mM HEPES, and 0.8 µg/ml hydrocortisone. After 24 h fully attached cells were adapted for another 12 h to William’s E Medium, supplemented with 10% FBS, 100 U/ml Pen/Strep, 2 mM L-glutamine,32 mU/ml human insulin, 0.1  µM dexamethasone and 0.1% DMSO. Cells were treated  for 24 hours in fresh medium with  1µM CITCO, 10 µM rifampicin, 50 µM WY14,643 or vehicle  (0.1% dimethylsulfoxide (DMSO).

tag: gender

value: male


title: VEE strain 2177B

source_name: VEE strain 2177B

value: VEE strain 2177B


title: VEE strain 212857

source_name: VEE strain 212857

value: VEE strain 212857


title: VEE strain 125567

source_name: VEE strain 125567

value: VEE strain 125567


title: BBC_36hE_n1


title: BBC_24hE_n3


title: MBZ_24hE_n3

description: Gene expression in zebrafish eye treated with 0.3 uM MBZ for 24 h

value: 0.3 uM MBZ for 24 h


title: BBC_12hE_n3

description: Gene expression in zebrafish eye treated with 0.3 uM BBC for 12 h

value: 0.3 uM BBC for 12 h


title: BBC_24hE_n1


title: BBC_12hE_n4


title: VEE strain 242959

source_name: VEE strain 242959

value: VEE strain 242959


title: VEE strain 12.563

source_name: VEE strain 12.563

value: VEE strain 12.563


title: VEE strain 23647

source_name: VEE strain 23647

value: VEE strain 23647


title: VEE strain 204381

source_name: VEE strain 204381

value: VEE strain 204381


title: VEE strain 12.399

source_name: VEE strain 12.399

value: VEE strain 12.399


title: VEE strain 111/73

source_name: VEE strain 111/73

value: VEE strain 111/73


title: VEE strain 02-2720-98


title: BBC_12hE_n1

value: eye

value: 60 hpf


title: VEE strain 00SMH290

source_name: VEE strain 00SMH290

value: VEE strain 00SMH290


title: Chicken DCs stimulated with IBDV

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

country: China

institute: nanjing agricultural university

description:
IBDV-stimulated group.
Total RNA was extracted from cultured DCs stimulated with IBDV.

hyb_protocol: Pre-hybridization:  1) Assembled  CustomArray™ microarray with Hybridization Cap and Clips.  2) Fill the hybridization chambers with nuclease-free water. Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation.  3) Incubate at 65°C for 10min.  4) Remove the microarray from the incubator and bring to room temperature. Remove the adhesive tape and aspirate the water out of the hybridization chambers.  5 ) Fill the hybridization chambers with Pre-hybridization Solution. Mix gently by pipetting. A small air bubble can be introduced to improve the mixing process if the arrays are rotated. Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape.  6) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation. Hybridization:  1) Prepare the hybridization solution with labeled mRNA target .  2) Denature the hybridization solution at 95°C for 3 minutes, and then cool for 20 seconds on ice. Remove the hybridization solution from ice and keep it at room temperature.  3) Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.  4) Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.  5) Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting. A small air bubble will form, and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.  6) Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue, and cover the solution portals with adhesive tape.  7) Load the microarray onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation. Hybridization washing:  1) Remove the microarray from the hybridization oven. Remove the adhesive tape and pipet the hybridization solution out of the chambers.  2) Using the Wash solution 1, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 1 from the hybridization chambers.  3) Using the Wash solution 2, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 2 from the hybridization chambers.  4) Using the Wash solution 3, rinse the hybridization chambers, fill the chambers, and incubate the array for 3 minutes at room temperature. Remove the Wash solution 3 from the hybridization chambers.  5) Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix 4000B (Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then, cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip, cover it, taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method. Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensities between test sample and control sample were calculated. The p-values are calculated with ANOVA Method (O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than the threshold, it means no differential expression was observed.

organism: Gallus gallus

source_name: BMDCs, stimulated with IBDV

label_protocol: Samples were labeled with ULS-Cy5. The labeling efficiency can be calculated by the concentration of CyDye and RNA measured by spectrophotometer. For good microarray result, the recommended labeling efficiency is 1.0~3.6.

growth_protocol: Chicken BMDCs were generated and expanded in vitro by culturing bone marrow precursors with 50 ng/ml recombinant chicken GM-CSF (Abcam, USA) and 50 ng/ml IL-4 (Kingfisher, USA) and in the RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), penicillin (100 U/ml), and streptomycin (100 μg/ml) under a humidified atmosphere containing 5% CO2 maintained at 37 ˚C.

extract_protocol: Total RNA was separately isolated using the RNeasy total RNA isolation kit (QIAGEN).

treatment_protocol: At day 6, the non-adherent, relatively immature DCs were harvested and plated in fresh medium (1x1^06 cells/ml). Then, cultured chicken BMDCs were randomly divided into control group and IBDV-stimulated group. Each group consisted of three wells of BMDCs from three chickens.

tag: cell type

value: bone marrow-derived dendritic cells (BMDCs)

value: infectious bursal disease virus (IBDV)


title: Chicken control DCs

description:
Control group.
Total RNA was extracted from cultured DCs for control.

source_name: BMDCs, control

value: control


title: VEE strain 00SMH264

source_name: VEE strain 00SMH264

value: VEE strain 00SMH264


title: BBC_12hE_n2

source_name: eye


title: VEE strain 243938

source_name: VEE strain 243938

value: VEE strain 243938


title: VEE strain 00SMH515-11C

source_name: VEE strain 00SMH515-11C

value: VEE strain 00SMH515-11C


title: 71_blood

status: Public on Mar 23 2016

type: genomic

city: Seattle

first: Chu

last: Chen

state: Washington

address: 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800

department: PHS

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The arrays were scanned using the Gene Chip 3000 scanner.

data_processing:
Affymetrix software tool and Genotyping Console 3.0.2 were used to determine signal intensities and whether samples passed the Affymetrix QC threshold of Contrast QC > 0.4 and a QC Call Rate > 86%. Genotype calls were made using Birdseed v2. We used R package AROMA to normalize raw allele intensity and used R package pscn to determine CNA segment.
The sample data table contains genotyping data. Genotypes are reported as 0, 1, 2 and -1 (0 = AA, 1 = AB, 2 = BB, -1 = no signal).
The processed_CNV_probe_level.txt contains estimated DNA copy number for each probe in each sample.

molecule: genomic DNA

source_name: HPV-neg OSCC_white blood cell

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from tumor cells was extracted using the Qiagen DNA Micro Kit. DNA from the white blood cells was isolated by salt precipitation

tag: subject status

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

tag: patient id

tag: age (yrs)

tag: Sex

value: M

tag: tumor site

value: Oral Cavity

tag: smoking

value: Current

tag: ajcc stage

value: II

tag: vital status

value: Alive

tag: follow up time (year)

value: white blood cell


title: 73_tumor

source_name: HPV-neg OSCC_tumor

value: F

value: Former

value: I

value: tumor


title: 72_blood

value: IV


title: 69_blood

value: Dead-oral ca


title: 74_blood


title: 70_blood


title: 66_tumor


title: 67_tumor


title: 67_blood


title: 75_blood


title: 68_tumor

value: Never

value: Dead -unk cause


title: 70_tumor


title: 73_blood


title: 65_tumor


title: 75_tumor


title: 63_blood


title: 71_tumor


title: 74_tumor


title: 64_tumor

value: Oropharynx


title: 66_blood


title: 62_tumor


title: 63_tumor


title: 68_blood


title: 64_blood


title: 65_blood


title: 72_tumor


title: 62_blood


title: 69_tumor


title: 61_tumor


title: 58_tumor


title: 59_blood


title: 60_blood


title: 61_blood


title: 58_blood


title: 55_tumor

value: III

value: Dead-non OC


title: 56_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: M


title: 57_tumor

value: Oral Cavity


title: 54_tumor


title: 54_blood


title: 53_blood


title: 49_tumor


title: 52_blood


title: 48_blood

value: Current


title: 53_tumor

value: Alive


title: 51_tumor


title: 56_blood

value: white blood cell


title: 50_tumor

value: II


title: 49_blood

value: F

value: Former


title: 50_blood


title: 55_blood


title: 52_tumor

value: tumor


title: 48_tumor

value: IV


title: 47_tumor

value: I


title: 51_blood

value: Dead-oral ca


title: 47_blood


title: 60_tumor


title: 57_blood


title: 59_tumor

value: Never


title: 46_tumor


title: 43_blood


title: 45_tumor


title: 46_blood


title: 41_tumor


title: 45_blood


title: 38_blood


title: 44_tumor


title: 37_tumor


title: 41_blood


title: 42_tumor


title: 43_tumor


title: 35_tumor


title: 37_blood


title: 44_blood


title: 39_tumor


title: 40_blood


title: 40_tumor


title: 42_blood


title: 36_tumor


title: 34_tumor


title: 38_tumor


title: 34_blood


title: 39_blood


title: MGH_NCI-H1703_mutant KRAS_rep3

city: Boston

first: Meng

last: Wang

state: MA

address: CNY149-4406 13th st Charlestown

department: Radiation Oncology

institute: Mass. General Hospital

description: This sample is of KRASmutant NSCLC NCI-H1703 cells. It is the first of three wild-type biological replicates used in this experiment, each from separate

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: We performed raw data quality control by principle component analysis and subsequent clustering by visualizing the distribution of expression levels to identify experimental outliers. After outlier removal, raw data files for each sample were normalized, background-corrected and saved to logarithmic scale using a Robust Multi-Array Analysis. Normalized data were analyzed and presented using R project. The normalized data from the experiments were fit into linear models using the Bioconductor package limma. Pair-wise comparisons of interest were performed using moderated t-statistics to test for significant differential expression. False discovery rate (FDR) at the .05 level for each probe was computed. Probes with p<0.05 and showing a fold change > 1 were considered differentially expressed. All probes were annotated with gene names.   To better visualize the effect of differentially expressed genes, pathway analysis was performed on those transcripts that had a significance of P < 0.05. Enriched networks, pathways, cellular processes etc were generated through the use of IPA (Ingenuity® Systems) in all three contrasts. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to annotate genes with chromosomal location in order to cluster highly repressed genes in mutant samples.

source_name: NSCLC NCI-H1703 mutant KRAS

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: NCI-H1703 cells were grown in RPMI media with 10% BGS at 37°C.

extract_protocol: Total RNA was extracted and purified using the miRNeasy kit (Qiagen Inc., Valencia, CA, USA) following the manufacturer's instructions including treatment with DNAase.

treatment_protocol: NCI-H1703 clones maintained at 1 mg/mL puromycin.

tag: genotype

value: mut p53, mut p16, wild type KRAS

tag: derivation

value: stage 1 lung squamous cell carcinoma of a 54-year-old Caucasian male smoker.

tag: cell line


title: 33_blood


title: MGH_NCI-H1703_mutant KRAS_rep2

description: This sample is of KRAS mutant NSCLC NCI-H1703 cells. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 33_tumor


title: 32_tumor


title: 36_blood


title: 31_blood


title: MGH_NCI-H1703_mutant KRAS_rep1

description: This sample is of KRASmutant NSCLC NCI-H1703 cells. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MGH_NCI-H1703_vector_rep3

description: This sample is of KRAS wild type NSCLC NCI-H1703 cells. It is the first of three wild-type biological replicates used in this experiment, each from separate

source_name: NSCLC NCI-H1703 empty vector control


title: MGH_NCI-H1703_vector_rep1

description: This sample is of KRAS wild type NSCLC NCI-H1703 cells. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 35_blood


title: MGH_NCI-H1703_vector_rep2

description: This sample is of KRAS wild type NSCLC NCI-H1703 cells. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: N1638 2

city: Amsterdam

first: Erdogan

last: Taskesen

state: North Holland

address: Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research (CNCR)

country: Netherlands

institute: VU University Amsterdam

hyb_protocol: The labeled material was hybridized to Affymetrix mouse 430 2.0 3' IVT GeneChips using the Affymetrix hybridization wash and stain kit according to manufacturer's instructions.

scan_protocol: The GeneChips were scanned in an AffymetrixGeneChip Scanner 3000 7G.

data_processing: RAW probe intensity values was measured in two batches. Raw data is normalized per batch with Robust Multi-array Average (RMA), and batch correction is applied using Combat. Probe intensity values are subsequently mean centered per probe set. Gene symbols are mapped using MM9. As a result of the normalization, intensities higher than 0 are relatively up-regulated, and intensities lower than 0 are relatively down-regulated.

organism: Mus musculus

source_name: LSK cells

label_protocol: RNA was amplified using the Nugen Ovation V2 system, according to manufacturer's instructions and the resulting product was biotin labeled using the Nugen Encore Biotin system.

growth_protocol: Stemspan, mFlt3L, mTpo and mSCF

extract_protocol: C57BL6 mice carrying the Apc 15lox allele were crossed with mice carrying the hypomorphic Apc 1638N or Apc 1572T allele, which resulted in a series of Apc genotypes: wt/wt (WT), 15lox/15lox (KO), 15lox/1572T (T1572) and 15lox/1638N (N1638). Bone marrow was extracted and LSK cells were sorted. LSK cells were transduced with MSCV-Cre-IRES-GFP virus. GFP+ cells were sorted, RNA of more than 10,000 cells was extracted using Qiagen RNEasy micro columns.

tag: background strain

tag: genotype/variation


title: N1638 3


title: 30_tumor

value: III


title: 30_blood

value: HPV-negative oral squamous cell carcinoma (OSCC) patient


title: N1638 1


title: 32_blood


title: 29_blood

value: M


title: T1572 2


title: 28_blood

value: Oral Cavity


title: T1572 3


title: 29_tumor


title: 25_blood

value: Current

value: Dead -unk cause


title: 27_blood

value: white blood cell


title: 25_tumor

value: II


title: KO 3


title: 27_tumor


title: T1572 1


title: 23_blood

value: F

value: Unk

value: Dead-non OC


title: KO 2


title: KO 1


title: 28_tumor

value: IV

value: Alive

value: tumor


title: 24_blood


title: 26_blood

value: Former

value: I


title: 22_blood

value: Dead-oral ca


title: 24_tumor

value: III


title: 21_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: Oropharynx


title: WT 5

value: wt/wt


title: 20_tumor

value: Never


title: 23_tumor

value: Oral Cavity


title: WT 6


title: 31_tumor

value: Current


title: 22_tumor

value: M


title: 19_blood

value: F

value: white blood cell


title: WT 4


title: WT 3


title: 21_blood

value: Dead-non OC


title: 18_tumor

value: IV


title: 20_blood

value: Alive


title: 17_blood


title: WT 2


title: 17_tumor

value: tumor


title: 19_tumor

value: Former


title: 18_blood


title: WT 1


title: WT eye cup at P13

city: Singapore

first: Bernice

middle: H

last: Wong

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School, Singapore

description:
P13_WT
RNA from eye cups, pooled from 6 wild-type animals.

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix GeneChip® Mouse Genome 430 2.0 Array for 16hrs at 45oC. GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: .CEL files were processed with Partek Genomics Suite 6.6 according to the gene expression workflow using RMA import settings.

source_name: WT eye cups at P13

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® 3' IVT PLUS Reagent Kit User Manual, Affymetrix).

extract_protocol: Eye cups were ground with a cell pellet homogenizer (VWR) on ice in Trizol (Roche). Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Eyes were enucleated from P13 mice. Cornea, lens and optic nerve were removed, leaving behind eye cups. Excess PBS was drained with Kimwipes, and tissues were flash-frozen immediately in liquid nitrogen.

value: wild-type

tag: age

value: postnatal day 13 (P13)

tag: tissue

value: eye cups


title: 15_blood

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: I

tag: cell type


title: 13_blood

tag: subject status


title: 14_tumor

tag: patient id

value: II

value: Dead -unk cause


title: Log ND/Diff 0.5% LW (TG6)

city: Nice

first: Thierry

last: Girolle

address: parc valrose

country: France

institute: INSERM CNRS UNSA iBV

description: Log ND/Diff 0.5% LW (TG6)

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: undifferentiated TG6

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: GSC cells were kept in an undifferentiated, self-renewing state by using defined medium (DMEM, Hamm's F12, G5, B27, N2 (invitrogen).  Cell differentiation has been carried out usin serum medium (DMEM, 0.5% FCS). When indicated the cells were treated with TWS119 (inhibitor of GSK3beta, during the differentiation process).

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: human glioma stem cells (GSC) primary culture

tag: culture status

value: undifferentiated

tag: treated with

value: none (untreated)

source_name: differentiated TG6

value: differentiated

value: TWS119 (LW)


title: 14_blood

tag: age (yrs)

tag: Sex

value: M

tag: tumor site

value: Oral Cavity

value: white blood cell


title: 16_blood

value: Oropharynx

tag: smoking

value: Current

tag: ajcc stage

value: III

tag: vital status

value: Dead-oral ca


title: 12_blood

value: F

tag: follow up time (year)


title: Log Diff 0.5% LW/ND (TG1)

description: Log Diff 0.5% LW/ND (TG1)

source_name: differentiated TG1

source_name: undifferentiated TG1


title: 11_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: IV

value: Dead-non OC

value: tumor


title: 12_tumor


title: 11_blood


title: KO eye cup at P13

description:
P13_KO
RNA from eye cups, pooled from 6 Mfsd2a KO animals.

source_name: Mfsd2a KO eye cups at P13

value: Mfsd2a KO

value: postnatal day 13 (P13)

value: eye cups


title: Log Diff 0.5%/ND (TG1)

description: Log Diff 0.5%/ND (TG1)

value: human glioma stem cells (GSC) primary culture

value: differentiated

value: none (untreated)

value: undifferentiated


title: 13_tumor

value: M

value: Oral Cavity

value: Never

value: Alive


title: 6_blood

value: Current

value: white blood cell


title: 9_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: F

value: Former

value: II


title: 10_tumor

value: IV

value: Dead-non OC

value: tumor


title: Log ND/Diff 0,5% (TG6)

description: Log ND/Diff 0,5% (TG6)

value: human glioma stem cells (GSC) primary culture


title: 7_blood

value: Dead-oral ca


title: C380 Saccharin 1 hr

city: Edinburgh

first: Ian

last: Simpson

address: 10 Crichton Street

department: Institute for Adaptive and Neural Computation

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Following fragmentation and labeling, samples (3760 ng of sscDNA) were hybridized for 20 hr at 48C on Rat Genome Array Chips (Rat1.1ST). Microarray chips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: Microarray chips were scanned using the Affymetrix GeneAtlas Imaging station.

data_processing: R/Bioconductor, quantile normalised

label: Biotin

organism: Rattus norvegicus

source_name: Gustatory cortex of adult rats after drinking of novel 0.1% saccharin

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

growth_protocol: Rats were kept at water restricted protocol for 3 days prior to last exposure to novel taste or control water before decapitation and gustatory cortex extraction

extract_protocol: RNA was extracted with Rneasy lipid tissue kit

treatment_protocol: Total RNA was extracted from insular cortex or occipital cortex specimens using RNeasy lipid tissue kit (QIAGEN) (Venlo, Netherlands) according to the manufacturer's instructions. Total RNA was reverse-transcribed using high capacity cDNA reverse transcription kit

tag: treatment

value: drinking of novel 0.1% saccharin

tag: gender

value: male

value: 2 months old

value: gustatory cortex

tag: time point

value: 1 hr


title: 10_blood

value: Oral Cavity


title: 8_tumor

value: M

value: Never

value: Alive


title: C378 Water 1 hr

source_name: Gustatory cortex of adult rats after drinking of water

value: drinking of water

tag: age


title: C379 Saccharin 1 hr

tag: tissue


title: 15_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: Current

value: I

tag: cell type


title: 6_tumor

tag: subject status

value: IV

value: Dead-non OC


title: C377 Saccharin 1 hr


title: C376 Water 1 hr


title: 16_tumor

tag: patient id

value: Oropharynx

value: III

value: tumor


title: 9_blood

value: F

value: Former

value: II

value: white blood cell


title: C375 Saccharin 1 hr

value: drinking of novel 0.1% saccharin

value: male

value: 2 months old

value: gustatory cortex

value: 1 hr


title: 7_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: Oral Cavity

value: Dead-oral ca


title: 8_blood

value: M

value: Never

value: IV

value: Alive


title: C372 Saccharin 3 hr

value: 3 hr


title: C373 Water 1 hr

value: drinking of water


title: C374 Water 1 hr


title: 3_tumor

value: Current

value: Dead -unk cause

value: tumor


title: C371 Water 3 hr


title: C368 Saccharin 3 hr

value: drinking of novel 0.1% saccharin


title: C369 Water 3 hr

value: male


title: C370 Saccharin 3 hr

value: 2 months old


title: 2_blood

value: white blood cell


title: 5_blood

value: I

value: Dead-non OC


title: C367 Water 3 hr

value: gustatory cortex


title: SAL 25 RS

city: Montreal

first: Anne Marie

middle: Lucie

last: Downey

state: Quebec

address: 3655 Promenade Sir William Osler, Room 115

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

hyb_protocol: 600ng of Cy3 labelled cRNA was prepared for hybridization using the Gene Expression Hybridization Kit (Agilent Technologies) following manufacturer's instructions. Samples were hybridized for 17 hours at 65°C. Slides were washed according to manufacturer's instructions.

scan_protocol: Slides were scanned with Agilent SureScan G2600D DNA microarray scanner

data_processing: Probe intensities were processed using Feature Extraction ver. 11.5.1.1 (Agilent Technologies) software with protocol GE1_1100_Jul11 and grid 028279_D_F_20110601.

source_name: round spermatids from control rat #25

label_protocol: Cyanine-3 (Cy3) labelled RNA was prepared from 100ng total RNA using the One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) following manufacturer's instructions, followed by clean up using Rneasy mini kit colums. Quantity and yield of cRNA was determined using NanoDrop spectrophotometer

extract_protocol:
germ cells were isolated by unit gravity sedimentation using the STA-PUT method and frozen at -80°C
Total RNA was extracted using TRIzol reagent and cleaned up using RNeasy mini kit columns

treatment_protocol: Male rats were gavaged with 6 mg/Kg cyclophosphamide or saline 6 days/week for 4 weeks

value: saline

value: round spermatid


title: 3_blood

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: M

value: Oral Cavity


title: C366 Saccharin 3 hr

value: 3 hr


title: 4_blood

value: F

value: Never

value: IV

value: Dead-oral ca


title: SAL 16 RS

source_name: round spermatids from control rat #16


title: 26_tumor

value: Former

value: Alive

value: tumor


title: SAL 15 RS

source_name: round spermatids from control rat #15

value: male


title: C365 Water 3 hr

value: drinking of water

value: 2 months old


title: SAL 17 RS

source_name: round spermatids from control rat #17


title: 1_blood

source_name: HPV-neg OSCC_white blood cell

value: II

value: white blood cell


title: 4_tumor

source_name: HPV-neg OSCC_tumor


title: 5_tumor

value: Current

value: I

value: Dead-non OC


title: SAL 29 RS

source_name: round spermatids from control rat #29

value: saline

value: round spermatid


title: CPA 15 RS

source_name: round spermatids from CPA treated rat #15

value: cyclophosphamide


title: CPA 26 RS

source_name: round spermatids from CPA treated rat #26


title: CPA 14 RS

source_name: round spermatids from CPA treated rat #14


title: SAL 28 RS

source_name: round spermatids from control rat #28


title: 1_tumor

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

value: M

value: Oral Cavity

value: Never


title: CPA 16 2012 P

source_name: pachytene spermatocytes from CPA treated rat #16 2012

value: pachytene spermatocyte


title: CPA 16 2011 P

source_name: pachytene spermatocytes from CPA treated rat #16 2011


title: SAL 16 P

source_name: pachytene spermatocytes from control rat #16


title: CPA 25 RS

source_name: round spermatids from CPA treated rat #25


title: EGFP-overexpressed Huh-7 cells, biological rep2

city: shanghai

last: Liang

state: shanghai

address: 320 Yue-Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeViewTM Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek Genomics Suite 6.6.

source_name: Huh-7 cells with EGFP overexpreesion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip® 3’IVT Express Kit, Affymetrix).

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum and 1× penicillin-streptomycin . Cells were cultured at 37°C in a 5% CO2 humidified incubator.

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

treatment_protocol: Cells were transfected with recombinant lentivirus, which contained the complete SNORD126 expression cassette or empty cassette

value: hepatocellular carcinoma cell line

tag: cell line


title: SNORD126-overexpressed Huh-7 cells, biological rep3

source_name: Huh-7 cells with SNORD126 overexpreesion


title: CPA 16 RS

source_name: round spermatids from CPA treated rat #16

value: male


title: SAL 26 P

source_name: pachytene spermatocytes from control rat #26


title: SAL 28 P

source_name: pachytene spermatocytes from control rat #28


title: CPA 29 P

source_name: pachytene spermatocytes from CPA treated rat #29


title: Patient 44 C394_AC-10K-3

city: Naples

first: Amelia

last: Cimmino

address: via pietro Castellino 111

department: IGB

country: Italy

institute: CNR

description: Tissues were defined as bladder cancer

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 4.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. MicroRNA oligos are represented as duplicate, quadruplicate, or sextuplet spots.  Duplicate and sextuplet spots were averaged while quadruplicate spots, represented by quadruplicate spots as two distant pairs of two adjacent spots, may have been flagged according to the following.  If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged.

source_name: Bladder cancer

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

value: Patient 44

value: Male

tag: race

value: Caucasian

tag: Stage

tag: grade

tag: surgery type

value: Cystectomy

tag: patient status

value: Alive

value: Bladder cancer


title: SAL 13 P

source_name: pachytene spermatocytes from control rat #13

tag: Sex


title: EGFP-overexpressed Huh-7 cells, biological rep1


title: SNORD126-overexpressed Huh-7 cells, biological rep2


title: PC12_NGFU0_12h_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R beadarray package.

source_name: PC12, NGFU0, 12h, rep1

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: PC12 cells were obtained from the ATCC (American Type Culture Collection, UK) and were cultured at 37C  at 5% CO2 in RPMI 1640, supplemented with 5% Fetal Bovine Serum, 10% Horse Serum, 1% penicillin and streptomycin (PAN Biotech, Germany) and 1% glutamine (PAN Biotech, Germany).

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For cell stimulation, 500.000 cells/well were seeded on collagen coated 6 well plates (Corning, NY, USA). The following day, cells were stimulated with 50ng/ml rat Nerve Growth Factor (NGF; Promega, Madison, WI, USA) or 75 ng/ml of recombinant human (E.coli-derived) Epidermal Growth Factor (R&D Systems, Wiesbaden, Germany)  for the corresponding times. To inhibit MAPKK MEK PC12 cells were treated with the MEK inhibitor U0126 (Promega, Madison, WI, USA) at a concentration of 10 mM. The inhibitor was applied to PC12 cells 30 min before stimulation with NGF, respectively. Stock solutions of 10 mM of U0126 were prepared by resolving 1 mg of U0126 in 234 ml DMSO (Sigma-Aldrich, St. Louis, USA). Stocks were stored at -20°C but for no longer than one week.

value: adrenal medulla

value: cell line from a pheochromocytoma of the adrenal medulla

tag: stimulus

value: NGF

tag: inhibitor


title: PC12_NGFU0_24h_rep1

source_name: PC12, NGFU0, 24h, rep1


title: PC12_NGFU0_48h_rep1

source_name: PC12, NGFU0, 48h, rep1


title: MM.281-MM96db

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 1.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Log2-transformed expression values were extracted from CEL files raw data and normalized using RMA procedure in the affy package for Bioconductor and the Transcript Cluster Annotations included in the cdf definition files version 18 available at the Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html

source_name: Newly-diagnosed MM patient 281

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100 nanograms of purified total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: translocation

tag: disease state

value: multiple myeloma primary tumor


title: CPA 7 P

source_name: pachytene spermatocytes from CPA treated rat #7

tag: treatment

value: cyclophosphamide


title: SNORD126-overexpressed Huh-7 cells, biological rep1

tag: age


title: CPA 15 P

source_name: pachytene spermatocytes from CPA treated rat #15


title: EGFP-overexpressed Huh-7 cells, biological rep3

tag: tissue


title: Patient 44 C393_AC-10K-2

description: Tissues were defined as bladder cancer


title: Patient 44 C392_AC-10K-1

description: Tissues were defined as bladder cancer


title: CPA 27 RS

source_name: round spermatids from CPA treated rat #27

tag: cell type

value: round spermatid


title: PC12_U0_48h_rep1


title: Patient 43 C390_AC-2K-2

description: Tissues were defined as bladder cancer

value: Patient 43


title: Patient 42 C388_17K-3

description: Tissues were defined as bladder cancer

value: Patient 42

value: Transurethral Resection


title: PC12_U0_24h_rep1


title: Patient 43 C389_AC-2K-1

description: Tissues were defined as bladder cancer


title: PC12_U0_2h_rep1


title: Patient 42 C387_17K-2

description: Tissues were defined as bladder cancer


title: Patient 42 C386_17K-1

description: Tissues were defined as bladder cancer


title: Patient 43 C391_AC-2K-3

description: Tissues were defined as bladder cancer


title: Patient 44 C385_16N-3

description: Tissues were defined as pericancerous bladder tissue

source_name: pericancerous bladder tissue

value: pericancerous bladder tissue


title: PC12_NGF_48h_rep1

source_name: PC12, NGF,48h, rep1


title: Patient 43 C384_16N-2


title: Patient 39 P3679_U16

description: Tissues were defined as normal bladder epithelium

source_name: Normal bladder epithelium

value: Patient 39

value: Retropubic prostatectomy

value: Normal bladder epithelium


title: PC12_NGFU0_4h_rep1

source_name: PC12, NGFU0, 4h, rep1


title: PC12_NGF_12h_rep2

source_name: PC12, NGF,12h, rep2


title: PC12_NGF_12h_rep3

source_name: PC12, NGF,12h, rep3


title: PC12_NGFU0_8h_rep1

source_name: PC12, NGU0F, 8h, rep1


title: PC12_U0_12h_rep1


title: PC12_Ctl_6h_rep2

source_name: PC12, Control,6h, rep2


title: Patient 38 P3678_U15

value: Patient 38

value: Male

value: Caucasian

value: Dead


title: Patient 37 P3677_NU8-3

value: Patient 37

value: Alive


title: PC12_NGFU0_2h_rep1

source_name: PC12, NGFU0, 2h, rep1

value: adrenal medulla

value: cell line from a pheochromocytoma of the adrenal medulla

value: NGF


title: Patient 42 C383_16N-1


title: Patient 40 P3680_U17

value: Patient 40


title: PC12_NGFU0_1h_rep1

source_name: PC12, NGFU0, 1h, rep1


title: PC12_Ctl_48h_rep1

source_name: PC12, Control,48h, rep1


title: PC12_NGFU0_6h_rep1

source_name: PC12, NGFU0, 6h, rep1


title: PC12_U0_8h_rep1


title: Patient 41 P3681_U18

value: Patient 41


title: Patient 36 P3676_NU23

value: Patient 36


title: 2_tumor

source_name: HPV-neg OSCC_tumor

tag: subject status

value: HPV-negative oral squamous cell carcinoma (OSCC) patient

tag: age (yrs)

value: M

tag: tumor site

value: Oral Cavity

tag: smoking

value: Current

tag: ajcc stage

value: IV

tag: vital status

tag: follow up time (year)

value: tumor


title: PC12_U0_4h_rep1

tag: cell line


title: Patient 34 P3674_MNK

tag: patient id

value: Patient 34

tag: Sex

value: Male

tag: race

tag: Stage

tag: grade

tag: surgery type

value: Retropubic prostatectomy

tag: patient status

value: Normal bladder epithelium


title: PC12_NGF_24h_rep1

source_name: PC12, NGF,24h, rep1

tag: tissue

tag: stimulus

tag: inhibitor


title: JQ1 500 nM 24h 3

city: Salamanca

first: Javier

last: Pérez Peña

address: C/Richard Ford Nº39, 2ºB

department: Centro Regional de Investigaciones Biomédicas

country: Spain

institute: Universidad de Castilla La Mancha

description: Gene expression data from MDA-MB-231 cells after 24h treatement with JQ1 500 nM

hyb_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix) and then hybridized to Human Gene 2.0 ST Array (Affymetrix).

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The data were analysed with Transcriptome Analysis Console (TAC) Software.

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 cells were grown in DMEM with 10% of FBS and added to a final concentration of 500.000 cells/plate

extract_protocol: Total RNA was extracted from purified cell populations using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 500 nM JQ1 for 12h and 24h.

value: Breast

tag: agent

value: JQ1 500 nM

tag: time point


title: PC12_U0_1h_rep1

value: adrenal medulla

tag: cell type

value: cell line from a pheochromocytoma of the adrenal medulla


title: PC12_NGF_12h_rep1

source_name: PC12, NGF,12h, rep1

value: NGF


title: JQ1 500 nM 24h 2

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix) and then hybridized to Human Gene 2.0 ST Array (Affymetrix).


title: Patient 33 P3673_NU204

value: Patient 33

tag: age

value: Caucasian

value: Dead


title: Patient 35 P3675_NU22

value: Patient 35

value: Alive


title: JQ1 500 nM 24h 1


title: Patient 32 P3672_U14

value: Patient 32


title: Patient 31 P3671_U13

value: Patient 31


title: Patient 30 P3670_U10

value: Patient 30


title: PC12_Ctl_24h_rep2

source_name: PC12, Control,24h, rep2


title: PC12_Ctl_12h_rep2

source_name: PC12, Control,12h, rep2


title: PC12_EGF_24h_rep1

source_name: PC12, EGF, 24h, rep1

value: EGF


title: Patient 28 P3668_U6

source_name: Normal bladder epithelium

value: Patient 28

value: Male


title: JQ1 500 nM 12h 3

description: Gene expression data from MDA-MB-231 cells after 12h treatement with JQ1 500 nM


title: Patient 29 P3669_U9

value: Patient 29

value: Retropubic prostatectomy

value: Normal bladder epithelium


title: JQ1 500 nM 12h 2

value: Breast

value: JQ1 500 nM


title: Control 3

description: Gene expression data from MDA-MB-231 cells under standard conditions


title: Control 2


title: PC12_EGF_6h_rep1

source_name: PC12, EGF, 6h, rep1

value: adrenal medulla

value: cell line from a pheochromocytoma of the adrenal medulla


title: PC12_EGF_4h_rep1

source_name: PC12, EGF, 4h, rep1


title: JQ1 500 nM 12h 1


title: PC12_EGF_12h_rep1

source_name: PC12, EGF, 12h, rep1


title: PC12_EGF_8h_rep1

source_name: PC12, EGF, 8h, rep1


title: Patient 27 P3667_U3

value: Patient 27

value: Caucasian


title: Patient 26 P3666_U2

value: Patient 26


title: Control 1


title: Patient 23 P3663_H11

description: Tissues were defined as bladder cancer

source_name: Bladder cancer

value: Patient 23

value: Female

value: Cystectomy

value: Alive

value: Bladder cancer


title: Patient 24 P3664_H12

description: Tissues were defined as bladder cancer

value: Patient 24


title: PC12_EGF_3h_rep1

source_name: PC12, EGF, 3h, rep1

value: EGF


title: Patient 25 P3665_U1

value: Patient 25

value: Male


title: PC12_EGF_1h_rep1

source_name: PC12, EGF, 1h, rep1


title: Patient 21 P3661_H9

description: Tissues were defined as bladder cancer

value: Patient 21


title: Patient 22 P3662_H10

description: Tissues were defined as bladder cancer

value: Patient 22

value: Dead


title: PC12_Ctl_24h_rep1

source_name: PC12, Control,24h, rep1

value: adrenal medulla


title: PC12_Ctl_12h_rep1

source_name: PC12, Control,12h, rep1

value: cell line from a pheochromocytoma of the adrenal medulla


title: Patient 20 P3660_L12

description: Tissues were defined as bladder cancer

value: Patient 20

value: Ta

value: Transurethral Resection


title: PC12_Ctl_6h_rep1

source_name: PC12, Control,6h, rep1


title: Patient 19 P3659_L11

description: Tissues were defined as bladder cancer

value: Patient 19

value: Caucasian


title: PC12_NGF_6h_rep1

source_name: PC12, NGF, 6h, rep1

value: NGF


title: PC12_EGF_2h_rep1

source_name: PC12, EGF, 2h, rep1


title: PC12_NGF_8h_rep1

source_name: PC12, NGF, 8h, rep1


title: Patient 17 P3657_L9

description: Tissues were defined as bladder cancer

value: Patient 17

value: Alive


title: Patient 14 P3654_L6

description: Tissues were defined as bladder cancer

value: Patient 14

value: Bladder cancer


title: PC12_NGF_3h_rep1

source_name: PC12, NGF, 3h, rep1


title: Patient 13 P3653_L5

description: Tissues were defined as bladder cancer

value: Patient 13


title: Patient 18 P3658_L10

description: Tissues were defined as bladder cancer

value: Patient 18

value: Male


title: SAL 25 P

source_name: pachytene spermatocytes from control rat #25

tag: treatment

value: saline

value: male

value: pachytene spermatocyte


title: Patient 16 P3656_L8

description: Tissues were defined as bladder cancer

value: Patient 16


title: 172mM SCFA replicate 1

city: Toronto

first: Debora

middle: Eleanor

last: Barnett Foster

state: Ontario

address: 350 Victoria Street

department: Chemistry and Biology

institute: Ryerson University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B-C scanner.

data_processing: Images were quantified and normalized using extraction protocol GE2_107_Sept09 and Agilent Feature Extraction Software (version 10.7.3.1).

organism: Escherichia coli

source_name: enterohemorrhagic E. coli_172mM short chain fatty acid mix

label_protocol: 175 ng of each sample was used to generate 300 ng of cRNA with labelling protocol version GE2 v6.5

growth_protocol: overnight bacterial culture in Luria Broth at 37C with shaking

extract_protocol: total RNA extracted using Trizol Extraction Protocol

treatment_protocol: overnight culture subcultured in either of the SCFA mixes (or the sodium chloride controls) at 37C, static with 5%CO2 to OD600 of 1

tag: e. coli subset

value: enterohemorrhagic E.coli

tag: treated with

value: 172mM short chain fatty acid mix

value: 172mM NaCl


title: PC12_NGF_5h_rep1

source_name: PC12, NGF, 5h, rep1

tag: cell line

value: adrenal medulla

value: cell line from a pheochromocytoma of the adrenal medulla


title: 172mM SCFA replicate 2


title: PC12_Ctl_0h_rep2

source_name: PC12, Control,0h, rep2


title: PC12_NGF_4h_rep1

source_name: PC12, NGF, 4h, rep1

value: NGF


title: Patient 12 P3652_L4

description: Tissues were defined as bladder cancer

tag: patient id

value: Patient 12

tag: Sex

value: Female

value: Caucasian

value: Ta

value: Transurethral Resection


title: PC12_NGF_1h_rep1

source_name: PC12, NGF, 1h, rep1


title: PC12_NGF_2h_rep1

source_name: PC12, NGF, 2h, rep1


title: Patient 15 P3655_L7

description: Tissues were defined as bladder cancer

source_name: Bladder cancer

value: Patient 15

tag: race

tag: Stage

value: Alive

value: Bladder cancer


title: Patient 11 P3651_L3

description: Tissues were defined as bladder cancer

value: Patient 11

value: Male

tag: grade

tag: surgery type

value: Dead


title: PC12_Ctl_8h_rep1

source_name: PC12, Control,8h, rep1

tag: tissue


title: 30mM SCFA replicate 2

source_name: enterohemorrhagic E. coli_30mM short chain fatty acid mix

value: enterohemorrhagic E.coli

value: 30mM short chain fatty acid mix

value: 30mM NaCl


title: Patient 9 P3649_L1

description: Tissues were defined as bladder cancer

value: Patient 9

tag: patient status


title: Patient 10 P3650_L2

description: Tissues were defined as bladder cancer

value: Patient 10


title: Patient 8 P3648_H8

description: Tissues were defined as bladder cancer

value: Patient 8

value: Cystectomy


title: 30mM SCFA replicate 4


title: 30mM SCFA replicate 1


title: 30mM SCFA replicate 3


title: PC12_Ctl_2h_rep1

source_name: PC12, Control,2h, rep1

value: adrenal medulla

value: cell line from a pheochromocytoma of the adrenal medulla

tag: stimulus

tag: inhibitor


title: PC12_NGF_0.5h_rep1

source_name: PC12, NGF, 0.5h, rep1

value: NGF


title: Patient 6 P3646_H6

description: Tissues were defined as bladder cancer

value: Patient 6

value: Caucasian


title: B. racemosa Leaf-treated HepG2, biological rep2

city: Onna-son, Kunigami-gun

first: Nurhanani

last: Razali

state: Okinawa

address: 1919-1 Tancha

department: Membranology

institute: Okinawa Institute of Science and Technology Graduate University (OIST)

description: Gene expression profiles in HepG2 cells treated with the water leaf extract of B. racemosa

hyb_protocol: Following fragmentation, 1 µg of cRNA were hybridized for 16 h at 45 °C on Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 under standard condition.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: CEL. files for each array were generated using the Affymetrix GeneChip Operating Software (GCOS) and were further analysed using Partek Genomics Suite software. Gene expression profiling was performed using arrays of HuGene-1_0-st-v1. A custom CDF (HuGene-1_0-st-v1.r3.cdf) with Entrez based gene definitions was used to annotate the arrays. The raw fluorenscence intensity values were normalized applying quantile normalization, while background correction was performed with Robust Multiarray Average (RMA). Probe set summarization was performed with Median Polish.

source_name: Leaf-treated HepG2 cells for 24h

label_protocol: Biotinylated cRNA (antisense RNA) were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix)

growth_protocol: HepG2 cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% foetal bovine serum, 1% penicillin and 1% streptomycin. Cells were maintained in humifified air with 5% CO2 at 37°C

extract_protocol: Extraction of tcRNA was performed using RNeasy Mini Kit (Qiagen) and DNase I treatement was done on the extracted tcRNA using RNase-free DNase set (Qiagen) according to manufacturer's protocols.

treatment_protocol: The cells were seeded and treated with the 50 µg/ml of the water leaf extract of B. racemosa for 24 h. Following this, cells were trypsinized and precipitated by centrifugation at 16200 x g for 5 min. Cells were washed with PBS before tcRNA was extracted from the cells.

value: B. racemosa leaf-treated


title: B. racemosa Leaf-treated HepG2, biological rep3


title: Patient 5 P3645_H5

description: Tissues were defined as bladder cancer

value: Patient 5

value: Alive

value: Bladder cancer


title: B. racemosa Leaf-treated HepG2, biological rep1


title: Untreated HepG2, biological rep1

description: Gene expression profiles in HepG2 cells untreated

source_name: Untreated HepG2 cells

value: Untreated


title: Patient 3 P3643_H3

description: Tissues were defined as bladder cancer

value: Patient 3

value: Male

value: Dead


title: Untreated HepG2, biological rep3


title: PC12_Ctl_4h_rep1

source_name: PC12, Control,4h, rep1


title: Patient 2 P3642_H2

description: Tissues were defined as bladder cancer

value: Patient 2


title: Untreated HepG2, biological rep2


title: Patient 4 P3644_H4

description: Tissues were defined as bladder cancer

value: Patient 4


title: PC12_Ctl_0h_rep1

source_name: PC12, Control,0h, rep1


title: 3T3 tun10h - rep3

status: Public on Mar 22 2016

city: Charleston

first: John

middle: Alan

last: Diehl

state: SC

address: 86 Jonathan Lucas Street

institute: Medical University of South Carolina

hyb_protocol: Add hybridation master mix (GeneChip® Eukaryotic Hybridization kit) into Biotin labled RNA.  Incubate at 99°C for 5 minutes, then 45°C for 5 minutes.inject it into an array. Place the array into hybridization oven trays.Load the trays into the hybridization oven.Incubate the arrays at 48°C and 60 rpm for 16 to 18 hours.

scan_protocol: Wash, stain, and scan were following the Genechip® Expression User Guide for Cartridge Arrays (PN 702731).  Scanning arrays was following the instructions in Affymetrix® Command Console® User Guide (P/N 702569).

data_processing:
Results were analyzed using GENESPRING software.  probe intensities were imported, normalized and summarized to the miRNA level using the RMA algorithm. RMA includes a background-subtracted probe-level quantile normalization prior to the median polish summarization to the miRNA log2-transformed intensities.
ANOVA and T-tests were used to calculate fold change and p-values. 1-way anova was performed. Low p-values identified genes that were not equal across all of the time points.  3 pairwise comparisons were performed, time points 2, 5 and 10 hours each vs the 0 hr. These comparison each gave a p-value and a fold change. All p-values were then corrected for multiple testing. Spotfire (Somerville, MA) software was used to generate heat maps.

label: FlashTag™ Biotin

source_name: NIH3T3 cells treated with 2ug/ml tunicamycin for 10 hours

label_protocol: microRNA was labeled by FlashTag™ Biotin HSR RNA labeling kit (Affymetrix,CA). PolyA tailling buffer, ATP, PAP enzyme were mixed and incubated with RNA at 37°C for 15 min for 3' tailling. Then add the biotin ligation mix, T4 DNA ligase into tailed RNA, incubate them at 25°C for 30 min. Then stop the reaction by adding HSR stop solutions (Affymetrix, CA).

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum.

extract_protocol: Total RNA was purified using miRNeasy Mini Kit (QIAGEN)

treatment_protocol: Asynchronously proliferating cells were challenged 2ug/ml tunicamycin for 2, 5 or 10 hrs.

value: fibroblast


title: 3T3 tun10h - rep2

description: cells treated with 2ug/ml tunicamycin for 10 hours


title: Primary PDGF-driven Glioma Tumor 1 (II)

first: Gilbert

middle: Joseph

last: Rahme

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: SAMPLE 4

data_processing: variance stabilizing transformation followed by robust spline normalization, computed by R through the lumi package

source_name: CNS Tumor tissue

label_protocol: Biotinylated cRNA were prepared using the Ambion MessageAmp kit for Illumina arrays

growth_protocol: GSCs were grown in DMEM/F12 without L-Glutamine supplemented with 1% Penicillin/Streptomycin and 1X B27 without vitamin A at 37 ͦC in a humidified incubator supplemented with 5%CO2. Tumor tissues were collected from mice exhibiting neurological symptoms (paralysis, head tilt) or that were moribund.

extract_protocol: RNA was extracted using the Trizol method.

treatment_protocol: 1*10^6 GSCs were plated on 10cm plastic petri dishes and cultured for 48 hours in 10mls of media and then collected for analysis. Tumor tissues were washed twice in PBS (without calcium and magnesium) and then frozen at -80  ͦC.

tag: strain

value: mixed background (C57BL/6-129S4/SvJae)

value: Primary PDGF-driven Glioma tumor


title: Patient 1 P3641_H1

description: Tissues were defined as bladder cancer

value: Patient 1

value: Female

value: Cystectomy


title: GSC3 +Dox (I)

description: SAMPLE 6

source_name: CNS tumor spheroid culture, Dox treated

growth_protocol: GSCs were grown in DMEM/F12 without L-Glutamine supplemented with 1% Penicillin/Streptomycin and 1X B27 without vitamin A at 37 ͦC in a humidified incubator supplemented with 5%CO2.

treatment_protocol: 1*10^6 GSCs were plated on 10cm plastic petri dishes and cultured for 48 hours in 10mls of media and then collected for analysis. Cells were either untreated (-Dox) or treated with 100ng/ml Doxycyline dissolved in deionized water. Treatment duration laster for 48 hours before collection.

tag: cell type

value: PDGF-driven glioma spheroid cells (PDGF-GSC)

value: Dox


title: 3T3 tun10h - rep1


title: GSC2 (II)

description: SAMPLE 2

source_name: CNS tumor spheroid culture


title: GSC3 (II)

description: SAMPLE 3


title: GSC1 (II)

description: SAMPLE 1


title: GSC2 +Dox (I)

description: SAMPLE 5


title: Primary PDGF-driven Glioma Tumor 2 (II)

description: SAMPLE 5


title: Primary PDGF-driven Glioma Tumor 3 (II)

description: SAMPLE 6


title: GSC2 (I)

description: SAMPLE 2

source_name: CNS tumor spheroid culture, untreated

value: untreated


title: 3T3 tun5h - rep3

source_name: NIH3T3 cells treated with 2ug/ml tunicamycin for 5 hours


title: GSC1 (I)

description: SAMPLE 1


title: GSC3 (I)

description: SAMPLE 3


title: 3T3 tun5h - rep2

description: cells treated with 2ug/ml tunicamycin for 5 hours


title: 3T3 tun2h - rep3

source_name: NIH3T3 cells treated with 2ug/ml tunicamycin for 2 hours


title: 3T3 tun5h - rep1


title: 3T3 0h - rep2

description: cells without treatment

source_name: NIH3T3 cells without treatment


title: 3T3 tun2h - rep1

description: cells treated with 2ug/ml tunicamycin for 2 hours


title: 3T3 0h - rep3

description: cells without treatment


title: 3T3 tun2h - rep2


title: 3T3 0h - rep1

description: cells without treatment


title: GSC1 +Dox (I)

description: SAMPLE 4


title: delhupAB_stat_CL_2

city: Bangalore

first: Avantika

last: Lal

address: GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

description:
delhupAB.stat.2.txt
crosslinked fraction

hyb_protocol: The crosslinked and non-crosslinked DNA was hybridized separately to high resolution tiling microarrays. Labeled DNA fragments (3ug) were hybridized for 16 hours (60 rpms) at 45°C to tiling array chips (Ecoli_Tab520346F, GPL8585) purchased from Affymetrix

scan_protocol: Hybridized, washed and stained microarrays were scanned using a Genechip Scanner 3000 (Affymetrix) according to manufacturer's instructions.

data_processing:
Probe intensities were corrected for background by subtracting the median intensities of control (non-E. coli) probes having the same G+C content. This was followed by quantile normalization of signals from all arrays and log2 transformation. For each probe, log-transformed signals from the non-crosslinked DNA samples were subtracted from those of the corresponding crosslinked DNA samples. The resultant values of log2(crosslinked signal/non-crosslinked signal) were taken as a measure of psoralen binding to each sequence. These were smoothed using a moving average with a sliding window of size 1100 bp.
txt files with 3 columns. Column 1: probe sequence. Column 2: start position of the probe on the E. coli genome. Column 3:  log2(crosslinked signal/non-crosslinked signal)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial cells

label_protocol: Fragmented DNA was 3’ termini biotin labeled using the GeneChip®  DNA Labeling Reagent (Affymetrix 900542) and 60U of Terminal Deoxynucleotidyl Transferase (Promega M1875) at 37°C for 60 minutes. The labeling reaction was stopped by the addition of 0.5M EDTA.

growth_protocol: Cells were grown in LB medium at 37 C with aeration, until mid-exponential phase (OD600=0.95) or stationary phase (OD600=2.4).

extract_protocol: Cells were lysed by adding EDTA (final 0.1 M) and 2% SDS and incubating at 37 C for 1 hour followed by addition of 100 μl proteinase K and overnight incubation at the same temperature. After cell lysis, genomic DNA was isolated by the phenol-chloroform method, treated overnight with DNase free Rnase and purified by the phenol-chloroform method. DNA was resuspended in tris buffer (pH 8) and sheared by sonication to a median length of 300 bp. Sheared DNA was electrophoresced in an agarose gel, eluted, concentrated by ethanol precipitation and dissolved in 25 mm sodium phosphate buffer (pH 7). The DNA was heated at 95 oC for 2 minutes followed by quick addition of DMSO (final 50%) and glyoxal  (final 6-8 % by volume) and reheating at 60 oC for two hours. Glyoxal treated DNA fragments were separated on a 3.5 % agarose gel in phosphate buffer. The gel was incubated with denaturing solution (0.5 M NaOH, 1.5 M NaCl) at 65 oC for 3 hours to reverse psoralen crosslinks. Crosslinked and non-crosslinked DNA fragments were excised separately from the gel, eluted, and concentrated by ethanol precipitation.

treatment_protocol: Cells from 25 mL culture were harvested by centrifugation at the given time points and washed with cold phosphate buffer (pH7.2). The cells were resuspended in 10 ml Tris-Cl buffer (pH 8) and incubated at 37oC for 2 minutes. EDTA (final 0.5 mM) was added and cells were incubated at the same temperature for another two minutes. The cells were immediately chilled on ice and MgCl2 (final 1 mM) was added. 100 μl of saturated trimethylpsoralen solution in ethanol (Sigma-Aldrich, cat.no T6137) was added to the chilled cell suspension, mixed by gentle shaking and incubated at 4oC for 10 minutes. The cells were then exposed to UV light of wavelength 365 nM and intensity 1.2 kJ.m-2min-1 for 45 seconds, immediately washed with M69 buffer and finally resuspended in the same buffer.

value: Psoralen + UV

tag: genotype

value: delta hupAB

tag: growth phase

value: Stationary


title: delhupAB_stat_NCL_2

description:
delhupAB.stat.2.txt
Non-crosslinked fraction

tag: treatment


title: exp_CL_2

description:
exp.2.txt
crosslinked fraction

value: Wild-type

value: Mid-Exponential


title: exp_NCL_2

description:
exp.2.txt
Non-crosslinked fraction


title: delhupAB_stat_NCL_1

description:
delhupAB.stat.1.txt
Non-crosslinked fraction


title: delhupAB_stat_CL_1

description:
delhupAB.stat.1.txt
crosslinked fraction


title: exp_CL_1

description:
exp.1.txt
crosslinked fraction


title: WT_WNV_Brain_CD45+ cells 3

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

hyb_protocol: RNA for the microarray was processed using a NuGEN WT-Ovation Pico RNA Amplification System together with a NuGEN WT-Ovation Exon Module. Samples were hybridized and loaded onto Affymetrix Mouse gene 2.0. Arrays

scan_protocol: scanned with a HiScan bead array system, and data were collected using GeneChip Operating Software

data_processing:
Data from Affymetrix Mouse gene 2.0 Expression BeadChip were normalized and median polished using Robust Multichip Average background correction with log2-adjusted values. After obtaining the log2 expression values for genes, significance testing was performed comparing the two groups (CD45+ cells from brains of WT and IPS-1-/- mice). Significance of expression differences was assessed using a false discovery rate (FDR) cutoff of 0.05 and a twofold change. Analysis and visualization of data and pathway analysis were performed using PartekGS software and Ingenuity Pathway Analysis software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: WT_Brain_day 10 post infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Mice were infected with 100 PFU WNV s.c. Brains were harvested at day 10 p.i. CD45+ cells from brains were isolated for microarray analysis.

tag: genotype/variation

value: WT

tag: infected with

value: 100 PFU West Nile Virus (WNV)

tag: time point

value: day 10 p.i

value: Brain

value: CD45+ cells


title: stat_NCL_2

description:
stat.2.txt
Non-crosslinked fraction


title: stat_CL_2

description:
stat.2.txt
crosslinked fraction


title: stat_CL_3

description:
stat.3.txt
crosslinked fraction


title: exp_NCL_1

description:
exp.1.txt
Non-crosslinked fraction


title: stat_NCL_1

description:
stat.1.txt
Non-crosslinked fraction


title: VHL_1

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

institute: Genome Institute of Singapore

description: Gene expression in VHL mutant at 4dpf

hyb_protocol: 1.65 µg of Cy-3-labelled cRNA (specific activity > 9.0 pmol Cy3 per µg cRNA) was fragmented at 60°C for 30 minutes in  reaction volume of 30 µL containing 1 X Agilent fragmentation buffer  and 2X Agilent blocking agent following the manufacturer's instructions. To terminate fragmentation, 30 µL 2x GEx Hybridization Buffer HI-RPM was added to the reaction. The sample was hybridized to custom-designed whole genome  zebrafish oligo microarrays (G2514F) for 17 hours at 65oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37oC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: GenePix 4000B (Axon Instruments)  according to manufacturer’s protocol (One-Colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling), Version 5.7, March 2008). The scanner was set to 4X44K array slides (Scan area 61 x 21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction Software version 10.7.3.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. As we used custom arrays, the output of Feature Extraction was processed using the GIS Unigene & Gene Ontology Annotation Tool (http://123.136.65.67/) to find Genbank Accession and Unigene ID’s using Danio rerio Build (DR Build #126_66).  Limma Version 3.24.10 (Biocondutor). Background correction was applied using the “normexp” function and normalisation was performed using normalise between arrays “quantile” function. To average replicate spots, the “avereps” function was applied. The linear model was applied using “lmfit” and a contrast matrix was applied using eBayes (fit2). From these normalised entity lists, a significance cut off of p≤ 0.01 and fold change cut off of ≥ 2 were  applied.

source_name: Primary tissue_VHL mutant_4dpf_30 embryos

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 400ng RNA using the One-Color Microarray- One-Colour Input Quick Amp Labelling kit version 5.7 (Agilent) according to manufacturer's instructions, followed by  RNeasy mini spin columns (Qiagen).

growth_protocol: Embryos were for 4 days incubated at 28oC in E3 (5mM NaCl, 0.17mM KCl, 0.33mM CaCl2, 0.33mM MgCl2, pH 7.2) medium containing 0.0001 % methylene blue (Sigma-Aldrich).

extract_protocol: Extraction of total RNA from zebrafish embryos was performed using the mIRVANA miRNA isolation kit (Invitrogen) excluding the step for enrichment of miRNA. This kit uses a glass fiber filter (GFF)-based method, to reduce size bias. Extracted RNA was quantified using the Nanodrop ND-1000 spectrophotometer. Quality of RNA was assessed using Agilent Bioanalyser 2100 Nanochip 6000, samples with RNA Integrity Numbers ≥ 7 were accepted.

value: TL/LWT mix

value: von Hippel Lindau mutants

tag: age

value: 4 days post fertilisation

value: Primary tissue from 30 embryos


title: stat_CL_1

description:
stat.1.txt
crosslinked fraction


title: STI KO_WNV_Brain_CD45+ cells 1

source_name: STI KO_Brain_day 10 post infection

value: STI knockout


title: STI KO_WNV_Brain_CD45+ cells 2


title: WT_2

description: Gene expression in wild-type at 4dpf

source_name: Primary tissue_WT_4dpf_30 embryos

value: wild type


title: WT_WNV_Brain_CD45+ cells 4


title: STI KO_WNV_Brain_CD45+ cells 3


title: WT_WNV_Brain_CD45+ cells 2


title: VHL_3

description: Gene expression in VHL mutant at 4dpf


title: WT_4

description: Gene expression in wild-type at 4dpf


title: STI KO_WNV_Brain_CD45+ cells 4


title: stat_transcriptome

hyb_protocol: According to Affymetrix specifications

scan_protocol: Scanned using a Genechip Scanner 3000 (Affymetrix) according to Affymetrix specifications

data_processing:
Probe intensities were corrected for background by subtracting the median intensities of control (non-E. coli) probes having the same G+C content.
.txt files with 3 columns. Column 1: probe sequence. Column 2: start position of probe on E. coli chromosome. Column 3 = log2 background-corrected intensity values for each probe

source_name: bacterial cells

label_protocol: Fragmented cDNAs were then 3’ termini biotin labeled using the GeneChip ® DNA Labeling Reagent (Affymetrix 900542) and 60U of Terminal Deoxynucleotidyl Transferase (Promega M1875) at 37°C for 60 minutes. The labeling reaction was stopped by the addition of 0.5M EDTA. Labeled cDNA fragments (3ug) were then hybridized for 16 hours (60 rpms) at 45°C to tiling array chips (Ecoli_Tab520346F, GPL8585).

extract_protocol: RNA was purified using the RNeasy ® Mini Kit (Qiagen ® 74104) following the manufacturer’s recommendations. Isolated RNAs (10 ug) were used for Random Primer cDNA synthesis using SuperScript IITM Reverse Transcriptase, (Invitrogen Life Technologies 18064-071). RNA was removed by treating the reaction mixture with 1N NaOH followed by neutralizing with 1N HCl. cDNAs were purified using MiniElute ® PCR Purification columns (Qiagen ® 28004) and fragmented to 50-200 bp by 0.6U/ug of DNase I for 10 minutes at 37°C in 1X One-Phor-All buffer (Amersham Biosciences 27-0901-02). DNase I was inactivated by heating at 98°C for 10 minutes.

treatment_protocol: Cells from 12.5 ml culture were harvested by centrifugation


title: WT_WNV_Brain_CD45+ cells 1


title: exp_transcriptome


title: WT_3

description: Gene expression in wild-type at 4dpf


title: VHL_4

description: Gene expression in VHL mutant at 4dpf


title: stat_NCL_3

description:
stat.3.txt
Non-crosslinked fraction


title: Patient 7 P3647_H7

description: Tissues were defined as bladder cancer

source_name: Bladder cancer

tag: patient id

value: Patient 7

tag: Sex

value: Male

tag: race

value: Caucasian

value: Cystectomy

value: Alive

value: Bladder cancer


title: Porcine_kidney_control_(n=2)

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers, 2 rue de la miletrie

institute: Inserm U1313 IRMETIST, Université de Poitiers, CHU de Poitiers-Service Biochimie

description: Control (N=2)

hyb_protocol: The slides (Agilent Porcine V2 ref 026440) were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent)

scan_protocol: The slides were scanned on a Tecan MS200 scanner.

data_processing: The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The data from all the microarrays were transformed in log2 intensity. Then they were normalized together using the “limma” package function “normalizeQuantiles” and the “quantile” method. Normalization of the data was performed using the Bioconductor packages (http://www.bioconductor.org) and R software v2.15.2.

organism: Sus scrofa

source_name: Control_porcine_non treated_kidney

label_protocol: The labeling was done using the Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: We used 3 months old Large White pigs

extract_protocol: Total RNA from renal cortex was extracted using a commercial kit including a Dnase to remove genomic DNA (Rneasy plus mini, Qiagen, France), following the manufacturer's recommendations.

treatment_protocol: ISCHEMIA samples: Three independent porcine kidney (from different pig) were clamped, removed and maintained clamped 60 min at 37°C, and then flushed with cold (4°C) University of Wisconsin preservation solution (UW) and stored at 4°C for 24h, then kidneys were immediatly sampled and frozen. CONTROL samples: Three independent porcine kidney (from different pig) were removed and then immediatly sampled and frozen.

tag: breed

value: Large White pig

value: 3 months

value: kidney (cortex)

tag: sample group

value: CONTROL


title: Porcine_kidney_control_(n=3)

description: Control (N=3)

tag: tissue


title: Porcine_kidney_control_(n=1)

description: Control (N=1)


title: Porcine_kidney_ischemia_(n=2)

description: ISCHEMIA (N=2)

value: ISCHEMIA


title: Porcine_kidney_ischemia_(n=1)

description: ISCHEMIA (N=1)


title: Mansi47

city: Los Angeles

first: Anton

last: Valouev

address: 1450 Biggy Street, NRT 2509K

institute: University of Southern California

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: Blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed according to standard techniques using proteinase K treatment and phenol–chloroform extraction.

tag: population

value: Mansi


title: Mansi46


title: Mansi45


title: Mansi44


title: Mansi43


title: M, biological rep 2

city: Santander

first: antonio

last: agraz

address: Albert einstein 22

institute: IBBTEC

description: Genome Expression Profile from infants

hyb_protocol: Labeled cDNA was fragmented and hybridized as duplicates/triplicates to HG-U133 plus2.0 GeneChips (Affymetrix) according to the manufacturer's guideline.

scan_protocol: Affymetrix protocol

data_processing: Raw data was normalized by robust mutiarray average (RMA) using affymetrix package and differential expression was statistically evaluated using SAM package and performed in the statistical environment R using bioconductor packages.

source_name: CB-derived CD34+CD33+CD19- myeloid HPCs

label_protocol: To sinthesize biotinylated cDNA was used T7-linked oligo dT primers.

growth_protocol: Cryopreserved bone marrow samples at diagnosis are available from collaborator

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer's guideline.

treatment_protocol: Patient primary cells will be thawed (20-50 x 10⁶  cells per patient), washed and stained with CD19, CD10, CD45 and NG2, and the cells will be FACS-purified using FACS ARIA Fusion sorted.

tag: tissues

value: Cordon Blood cells


title: Porcine_kidney_ischemia_(n=3)

description: ISCHEMIA (N=3)


title: ALL, biological rep 5

description: Genome Expression Profile from infants

source_name: MLL-AF4+ blasts from infant B-ALL

value: blasts


title: preB, biological rep 1

description: Genome Expression Profile from infants

source_name: CB-derived CD34+CD19+CD33- B-cell HPCs


title: HSC, biological rep 2

description: Genome Expression Profile from infants

source_name: CB-derived CD34+CD38-CD19-CD33- HSC


title: M, biological rep 1

description: Genome Expression Profile from infants


title: 0 uM doxorubicin, 2

city: Chicago

first: Paul

middle: W

last: Burridge

address: 320 E Superior St Searle 8-525

department: Pharmacology

institute: Northwestern

description: Control, no doxorubicin

hyb_protocol: Performed by Stanford Functional Genomics Facility

data_processing: Data was processed with AltAnalyze

source_name: H9 hESC

growth_protocol: H9 hESC grown in E8, differentiated with CDM3, grown in CDM3M to d30.

extract_protocol: RNeasy (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Treated for 24 h with doxorubicin

tag: agent


title: 1 uM doxorubicin, 2

description: 1 uM doxorubicin

scan_protocol: Performed by Stanford Functional Genomics Facility

value: 1 uM doxorubicin


title: 0 uM doxorubicin, 1

description: Control, no doxorubicin

label_protocol: Performed by Stanford Functional Genomics Facility


title: preB, biological rep 2

description: Genome Expression Profile from infants


title: ALL, biological rep 6

description: Genome Expression Profile from infants


title: ALL, biological rep 3

description: Genome Expression Profile from infants


title: HSC, biological rep 1

description: Genome Expression Profile from infants


title: Mansi48


title: ALL, biological rep 4

description: Genome Expression Profile from infants


title: ALL, biological rep 1

description: Genome Expression Profile from infants


title: 1 uM doxorubicin, 1

description: 1 uM doxorubicin


title: 10 uM doxorubicin, 1

description: 10 uM doxorubicin

value: 10 uM doxorubicin


title: Mansi41


title: ALL, biological rep 2

description: Genome Expression Profile from infants


title: 10 uM doxorubicin, 2

description: 10 uM doxorubicin


title: Mansi40


title: 0.1 uM doxorubicin, 1

description: 0.1 uM doxorubicin

value: 0.1 uM doxorubicin


title: 0.1 uM doxorubicin, 2

description: 0.1 uM doxorubicin


title: Mansi39


title: Mansi42


title: Mansi38


title: Mansi37


title: Mansi35


title: Mansi36


title: Mansi34


title: Mansi32


title: Mansi33


title: Mansi31


title: Mansi30


title: Mansi29


title: Mansi28


title: Mansi26


title: Mansi25


title: no T cells; + co IgG

city: Vienna

first: Monika

last: Bradl

address: Spitalgasse 4

department: Neuroimmunology

country: Austria

institute: MedUni Vienna, Center for Brain Research

description:
amplified mRNA
gene_US45103052_251487914181_S01_GE1_v5_10_Apr08_1_2_Editor

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

source_name: spinal cord

label_protocol: standard Agilent protocol

extract_protocol: none provided by submitter

tag: strain

value: Lewis

value: spinal cord

value: adult

tag: fixation

value: FFPE


title: Khanty48

value: Khanty


title: no T cells; + NMO IgG

description:
amplified mRNA
gene_US45103052_251487914194_S01_GE1_v5_10_Apr08_1_2_Editor


title: Khanty47


title: MBP T cells + PBS

description:
amplified mRNA
gene_US45103052_251487914181_S01_GE1_v5_10_Apr08_1_4_Editor


title: no T cells; no IgG

description:
amplified mRNA
gene_US45103052_251487914194_S01_GE1_v5_10_Apr08_1_1_Editor


title: Khanty46


title: MBP T cells + co IgG

description:
amplified mRNA
gene_US45103052_251487914194_S01_GE1_v5_10_Apr08_1_3_Editor


title: Khanty45


title: MBP T cells + NMO IgG

description:
amplified mRNA
gene_US45103052_251487914181_S01_GE1_v5_10_Apr08_1_1_Editor


title: treatment: Mixed - genotype: Ofanto - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. CS was imposed withholding water to reach a SWC equal to 12.5% of FC as described for DS, and increasing the temperature up to 40°C as described for HS. (May still include original submitter created erros/discrepancies)

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Triticum turgidum subsp. durum

source_name: Leaf (treatment: Mixed - genotype: Ofanto)

label_protocol: Affy- Whole transcript target preparation

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: germplasm name

value: Ofanto

tag: organism part

value: Leaf

tag: cell type

tag: development stage

value: 3 leaf fully expanded ('PO:0001053')

tag: growth media

value: field soil


title: Khanty44


title: treatment: Mixed - genotype: Ofanto - rep3


title: Khanty43


title: treatment: Heat - genotype: Cappelli - rep1

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. HS was imposed by increasing the temperature for two days at 30°C and 22°C in the 15 hrs light and 9 hrs dark regime, for an initial adaptation phase, then the temperature was increased to 34°C and 26°C light/dark for two days and subsequently to 40°C and 32°C light/dark for an additional day when the flag leaves were collected (May still include original submitter created erros/discrepancies)

source_name: Leaf (treatment: Heat - genotype: Cappelli)

value: Cappelli


title: treatment: Heat - genotype: Cappelli - rep2


title: treatment: Mixed - genotype: Cappelli - rep1

source_name: Leaf (treatment: Mixed - genotype: Cappelli)


title: treatment: Mixed - genotype: Cappelli - rep2


title: treatment: Heat - genotype: Cappelli - rep3


title: Khanty42


title: Khanty41


title: Mansi27


title: treatment: Mixed - genotype: Ofanto - rep1


title: treatment: Heat - genotype: Ofanto - rep3

source_name: Leaf (treatment: Heat - genotype: Ofanto)


title: treatment: Mixed - genotype: Cappelli - rep3


title: Khanty38


title: Khanty39


title: treatment: Heat - genotype: Ofanto - rep2


title: Khanty36


title: Khanty37


title: Khanty40


title: Khanty34


title: Khanty33


title: Khanty32


title: treatment: Drought - genotype: Cappelli - rep2

description: Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. DS was imposed by withholding water and allowing the pots to reach a SWC equal to 12.5% of FC, other growing conditions were as in control plants. To monitor the SWC the pots weight was measured twice per day. The flag leaves detached at mid-point of the light period were collected for transcriptomic analysis three days after the imposition of stress (May still include original submitter created erros/discrepancies)

source_name: Leaf (treatment: Drought - genotype: Cappelli)


title: Khanty29


title: treatment: Drought - genotype: Cappelli - rep1


title: Khanty30


title: treatment: Drought - genotype: Ofanto - rep1

source_name: Leaf (treatment: Drought - genotype: Ofanto)