title: Wt threonine24h x alcAypkA threonine24h Replicate 1

city: Ribeirão Preto

first: Ana

middle: Cristina

last: Colabardini

state: São Paulo

address: Av do Café s/n Cidade Universitária

department: Ciências Farmacêuticas

country: Brazil

institute: FCFRP-USP

description: Biological replicate 1 of 2.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: total RNA from Wt grown on glycerol 2% threonine 100mM, labeled with Cyanine-3

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40°C.

growth_protocol: A. nidulans strains (Wt and alcAypkA) were grown on minimal medium with glucose 4% or glycerol 2% threonine 100mM during 16 or 24 hours at 37°C.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

tag: genotype/variation

value: Wt

tag: protocol

value: glycerol 2% threonine 100mM during 24h

source_name: total RNA from alcAypkA grown on glycerol 2% threonine 100mM, labeled with Cyanine-5

value: alcAypkA


title: Wt threonine24h x alcAypkA threonine24h Replicate 2

status: Public on Oct 10 2012

type: RNA

description: Biological replicate 2 of 2.

molecule: total RNA


title: Wt threonine16h x alcAypkA threonine16h Replicate 1

description: Biological replicate 1 of 2.

value: glycerol 2% threonine 100mM during 16h


title: Wt glucose 16h x alcAypkA glucose 16h Replicate 2

description: Biological replicate 2 of 2.

source_name: total RNA from Wt grown on glucose 4%, labeled with Cyanine-3

value: glucose 4% during 16h

source_name: total RNA from alcAypkA grown on glucose 4%, labeled with Cyanine-5


title: Wt threonine16h x alcAypkA threonine16h Replicate 2

description: Biological replicate 2 of 2.


title: Wt glucose 16h x alcAypkA glucose 16h Replicate 1

description: Biological replicate 1 of 2.


title: Wt glucose 24h x alcAypkA glucose 24h Replicate 2

description: Biological replicate 2 of 2.

value: glucose 4% during 24h


title: HNSCC_primary_9004464

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls. Lowess-normalization.

organism: Homo sapiens

label_protocol: Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]  Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.

tag: gender

value: male

tag: tissue

value: head-neck

tag: tumor type

value: HNSCC

tag: age

tag: location

value: oral cavity

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

source_name: UHR

tag: sample type

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004458

hyb_protocol: Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0  Last Updated: 2/2006 Number of Pages: 70

value: female


title: HNSCC_primary_9004453


title: HNSCC_primary_9004457


title: HNSCC_primary_9004450


title: HNSCC_primary_9004448


title: HNSCC_primary_9004452


title: Genistein diet, biological rep5

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

description: Genistein 7

hyb_protocol: GeneChip® Hybridization Oven 640 (Affymetrix)

scan_protocol: GeneChip® Scanner 3000  (Affymetrix）

data_processing: The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model [details on PMID 18764774, 18958174, 22784577]. The log values are log10 (rawdata - gamma): z-score = (log10 (rawdata- gamma) - mu)/sigma.

label: biotin

organism: Rattus norvegicus

source_name: Genistein diet

label_protocol: One-Cycle Target Labeling and Control Reagents (Affymetrix)

growth_protocol: Male Sprague Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 weeks of age. The animals were housed individually in a room with controlled temperature and humidity and a 12 h light dark cycle.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Three groups of rats were fed an experimental diet containing 2 g/kg of either genistein or daidzein, or a control diet free of isoflavone for 14 days.  The basal composition of the experimental diet was (in g/kg): casein, 200; palm oil, 100; corn starch, 150; cellulose, 20; mineral mixture (AIN-93G), 35; vitamin mixture (AIN-93), 10; L-cystine, 3.0; choline bitartrate, 2.0 and sucrose to 1 kg.

tag: strain

value: Sprague-Dawley

value: liver

value: Experiment was started at 4 wks of age, rats were adapted to the condition for 5 days and fed the diet indicated for 14 days.

tag: diet

value: containing 2 g/kg of Genistein


title: Wt glucose 24h x alcAypkA glucose 24h Replicate 1

description: Biological replicate 1 of 2.


title: Genistein diet, biological rep1

description: Genistein 2


title: HNSCC_primary_9004451


title: HNSCC_primary_9004447


title: Genistein diet, biological rep4

description: Genistein 6


title: Genistein diet, biological rep3

description: Genistein 3-re


title: HNSCC_primary_9004449


title: Genistein diet, biological rep2

description: Genistein 4


title: Daidzein diet, biological rep5

description: Daidzein 7

source_name: Daidzein diet

value: containing 2 g/kg of Daidzein


title: HNSCC_primary_9004446


title: Daidzein diet, biological rep3

description: Daidzein 3


title: Daidzein diet, biological rep2

description: Daidzein 2


title: Non-isoflavone diet, biological rep4

description: Control 6

source_name: Non-isoflavone diet (control)

value: control (Non-isoflavone)


title: Daidzein diet, biological rep1

description: Daidzein 1


title: Non-isoflavone diet, biological rep3

description: Control 5


title: HNSCC_primary_9004437


title: Daidzein diet, biological rep4

description: Daidzein 4


title: Non-isoflavone diet, biological rep5

description: Control 8


title: HNSCC_primary_9004436


title: Non-isoflavone diet, biological rep2

description: Control 3


title: HNSCC_primary_9004434


title: HNSCC_primary_9004439


title: Non-isoflavone diet, biological rep1

description: Control 1


title: HNSCC_primary_9004430


title: HNSCC_primary_9004425

value: oropharynx


title: HNSCC_primary_9004427


title: HNSCC_primary_9004433


title: HNSCC_primary_9004431


title: HNSCC_primary_9004423


title: HNSCC_primary_9004418


title: HNSCC_primary_9004420


title: HNSCC_primary_9004411


title: HNSCC_primary_9004415


title: HNSCC_primary_9004414


title: normal melanocyte HEMa-LP, microRNA biological rep 2

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

country: USA

institute: University of Louisville

description: miRNA expression data from HEMa-LP cells.

hyb_protocol: Labeled miRNA was hybridized for 16 hr at 45C on Affymetrix miRNA 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Fluidics Protocol FS450-0003.

scan_protocol: GeneChips were scanned using Affymetrix' GeneChip Scanner GCS3000 7G and Command Console Version 1.0

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using RMA default analysis settings as normalization method and a 2-Way ANOVA was set-up to determine differentially expressed miRNAs.

source_name: HEMa-LP cell

label_protocol: Biotinylated miRNA were prepared according to the standard protocol for Genisphere FlashTag kit from 500 ng total RNA.

growth_protocol: normal melanocytes HEMa-LP cells were cultured in Medium 254 supplemented with Human Melanocyte Growth Supplement-2 (HMGS-2) in a 5% CO2 incubator at 37C. Malignant melanoma A375 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% exosome-depleted fetal bovine serum (FBS). FBS was depleted of exosomes by ultracentrifugation at 100,000 x g for 16h at 4C.

extract_protocol: Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines.

treatment_protocol: Cells were trypsinized and harvested for RNA isolation. Exosomes were purified from cell culture supernatants by a combination of ultrafiltration and ultracentrifugation.

value: cell

tag: cancer status

value: Normal Melanocytes

tag: cell line

value: HEMa-LP


title: normal melanocyte HEMa-LP, microRNA exosome

description: miRNA expression data from HEMa-LP exosomes.

source_name: HEMa-LP exosome

value: exosome


title: HNSCC_primary_9004416

value: male


title: HNSCC_primary_9004412

value: head-neck


title: HNSCC_primary_9004405

value: HNSCC


title: HNSCC_primary_9004407

value: oral cavity


title: normal melanocyte HEMa-LP, microRNA biological rep 1


title: melanoma exosome A375, microRNA biological rep 1

description: miRNA expression data from A375 exosomes.

source_name: A375 exosome

value: Melanoma


title: melanoma cell A375, microRNA biological rep2

description: miRNA expression data from A375 cells.

source_name: A375 cell


title: melanoma cell A375, microRNA biological rep 1

description: miRNA expression data from A375 cells.


title: melanoma exosome A375, microRNA biological rep 2


title: HNSCC_primary_9004401

value: Stratagene Universal human reference cell line (UHR)


title: HNSCC_primary_9004400


title: HNSCC_primary_9004421


title: HNSCC_primary_9004402


title: HNSCC_primary_9004404


title: HNSCC_primary_9004399


title: HNSCC_primary_9004398


title: HNSCC_primary_9004397

value: female


title: HNSCC_primary_9004393


title: HNSCC_primary_9004396


title: HNSCC_primary_9004382


title: HNSCC_primary_9004380


title: HNSCC_primary_9004381


title: HNSCC_primary_9004378


title: HNSCC_primary_9004388


title: HCmel3_ReTx_rep5

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

description:
excised_tumour_skin
8294816100_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Variance stabilization and normalisation using vsn2 package from bioconductor in R without background correction.

organism: Mus musculus

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase.

extract_protocol: Total RNA was isolated using TRI Reagent and purified using Rneasy columns (Quiagen).  RNA quality was assayed using Agilent Bioanalyzer.

tag: adoptive cell therapies (act)

tag: recipient strain

tag: hcmel3 strain

tag: material


title: HNSCC_primary_9004385

tag: gender

tag: tissue

tag: tumor type

tag: age


title: HNSCC_primary_9004391

tag: location

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt


title: HNSCC_primary_9004392

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

tag: sample type


title: HCmel3_Tnfa_rep1

description:
melanoma_culture
8294816119_D


title: HCmel3_untreated_rep2

description:
melanoma_culture
8294816119_B


title: HCmel3R_rep2

description:
melanoma_culture
8294816119_F


title: HCmel3_ReTx_rep4

description:
excised_tumour_skin
8294816100_C


title: HCmel3_Tnfa_rep2

description:
melanoma_culture
8294816119_E


title: HCmel3R_rep1

description:
melanoma_culture
8294816101_F


title: HCmel3_ReTx_rep3

description:
excised_tumour_skin
8294816101_E


title: Brain Non-infected bio rep1 tech rep2

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

country: China

institute: Institute of Military Veterinary Academy of Military Medical Sciences

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C1_H014

hyb_protocol: Hybridization was performed by Phalanx Biotech Group, Hsinchu, Taiwan, following their standard operating protocol. See http://www.phalanx.com.tw/.

scan_protocol: Scanning was performed by Phalanx Biotech Group, Hsinchu, Taiwan, following their standard operating protocol. See http://www.phalanx.com.tw/.

data_processing: For raw dataset, the Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, CA, USA). Finally the expression data were normalized using a variance stabilizing method VSN ( Huber et al. Bioinformatics 18 Suppl 1: S96-104) in Bioconductor (http://www.bioconductor.org).

source_name: Brain non-infected

label_protocol: Labeling was performed by Phalanx Biotech Group, Hsinchu, Taiwan. The sample preparation reagent used for this service is Ambion MessageAmp aRNA kit (Cat. No. 1753) or Ambion amino allyl cDNA kit (Cat. No. 1705). Optical density was measured by NanoDrop ND-1000.  The ratio of absorbance at 260 nm and 280 nm  provides a estimate of RNA purity. Ratios between 1.8 and 2.2 indicate a pure sample. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP  was used to conjugate the purified aRNA/cDNA with the NHS-CyDye.  Labeling efficiency can be calculated by the concentration of CyDye and aRNA/cDNA measured by NanoDrop ND-1000. For the sake of good microarray result, labeling efficiency  should be above 10. See http://www.phalanx.com.tw/.

extract_protocol: RNA was extracted with mirVana™ miRNA Isolation Kit (Cat. No. 1561, Ambion, USA).We performed  proceducer FⅠin the Total RNA Isolation Procedure. Optical density was measured by NanoDrop ND-1000. The ratio of absorbance at 260 nm and 280 nm  provides a estimate of RNA purityRIN score was given by Agilent RNA 6000 Nano Assay.  RNA Integrity Number (RIN) algorithm assigns a 1 to 10 RIN score, where level 10 RNA is completely intact.  For the sake of good microarray result, RIN score should be above 7.

tag: strain

value: BALB/c

value: 6 weeks

value: Brain

tag: infection

value: Sham-infected with DMEM,  Dulbecco's modiﬁed Eagle's medium


title: Brain infected ERA bio rep3 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates. Raw data was at GA_Phalanx_expression_raw_data. xls
B3_H012

source_name: Brain infected ERA

value: Infected with laboratory-adapted rabies virus, ERA


title: Brain Non-infected bio rep3 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C3_H018


title: Brain Non-infected bio rep3 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C3_H017


title: Brain Non-infected bio rep1 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C1_H013


title: Brain Non-infected bio rep2 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C2_H016


title: Brain infected ERA bio rep3 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
B3_H011


title: HCmel3_ReTx_rep1

description:
excised_tumour_skin
8294816101_A

tag: adoptive cell therapies (act)

tag: recipient strain


title: HCmel3_untreated_rep1

description:
melanoma_culture
8294816119_A

tag: hcmel3 strain

tag: material


title: HCmel3_ReTx_rep2

description:
excised_tumour_skin
8294816101_B


title: melanoma cell A375, mRNA biological rep2

description: Gene expression data from A375 cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome HG-U133Plus2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using Fluidics Protocol FS450-0001.

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using RMA default analysis settings as normalization method and a 2-Way ANOVA was set-up to determine differentially expressed genes.

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix' IVT Express kit from 100 ng total RNA.

tag: cancer status

tag: cell line


title: Brain infected ERA bio rep2 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
B2_H010

tag: age

tag: tissue


title: Brain infected ERA bio rep1 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
B1_H007


title: Brain Non-infected bio rep2 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
C2_H015


title: Brain infected ERA bio rep1 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
B1_H008


title: Brain infected FJDRV bio rep1 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
A1_H002

source_name: Brain infected FJDRV

value: Infected with street rabies virus, FJDRV, isolated from brain of rabid dog in Fujian provice of China


title: Brain infected FJDRV bio rep1 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates. Raw data was at GA_Phalanx_expression_raw_data. xls
A1_H001


title: Brain infected FJDRV bio rep3 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
A3_H006


title: Brain infected FJDRV bio rep3 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
A3_H005


title: Brain infected FJDRV bio rep2 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
A2_H003


title: Harlan mice, control, biological rep 2

city: Saint Louis

first: Audrey

last: Watson

state: Missouri

address: 1100 South Grand

institute: Saint Louis University

description: Gene expression data from control pancreas of C57BL6/NHsd mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The prelimainary data analysis was performed R/Bioconductor using gcRMA normalization method (which outputs log2-transformed expression values) and statistical analysiswas performed with Partek Genomics Suite software.

source_name: Pancreas, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3_ivt_express_kit_manual, 2008, Affymetrix).

extract_protocol: RNA was extracted with Trizol reagent according to manufacturer's instructions and further purified by Rneasy Kit (Qiagen)

value: Pancreas

tag: gender

value: 8 week

tag: disease state

value: control


title: Harlan mice, control, biological rep 3


title: Jackson mice,  cerulein treated, biological rep 3

description: Gene expression data from pancreas of C57BL6/J mice with cerulein induced chronic pancreatitis

source_name: Pancreas, chronic pancreatitis

value: cerulein induced chronic pancreatitis


title: Jackson mice, control, biological rep 3

description: Gene expression data from control pancreas of C57BL6/J mice


title: Brain infected FJDRV bio rep2 tech rep2

description:
It is the first of the three biological replicates and the first of two technical replicates. Raw data was at GA_Phalanx_expression_raw_data. xls
A2_H004


title: Harlan mice, control, biological rep1


title: Jackson mice, cerulein treated, biological rep 2


title: Jackson mice, controls, biological rep1


title: Jackson mice, control, biological rep 2


title: TC01 bile_3

city: Paterna

first: Manuel

last: Zúñiga

state: Valencia

address: Avda. Profesor Agustín Escardino 7

department: Biotecnología

country: Spain

institute: Instituto de Agroquímica y Tecnología de Alimentos

hyb_protocol: SDS based hybridization solution, during 24 hours

scan_protocol: FUJIFILM FLA-3000

data_processing:
The software for image analysis is ArrayVision 7.0 (Imaging Research Inc.). This software yields raw and background substracted data.
The Background Substracted Signals are raw individual data. After considering the three replicates performed in the experiment and after median normalization, first between replicates and after between conditions, we obtain the ratio values for each gene/ORF (see supplementary file on Series record).

organism: Lacticaseibacillus casei

source_name: Cultured cells

label_protocol: First-strand cDNA was synthesized from 45 µg RNA using the Transcriptor first strand cdna synthesis kit (Roche) with random hexamer primers as recommended by the manufacturer. Labelled cDNA was purified with illustra MicroSpin G-50 Columns (GE Healthcare) as recommended by the manufacturer.

growth_protocol: Cells were stored at -80C in MRS medium supplemented with 15% glycerol (stock culture). For the assay, cells from the stock culture were inoculated in MRS agar plates. A single colony was used to inoculate 5 ml of MRS medium and the culture was incubated overnight at 37C. This culture was used to inoculate MRS medium at 0.05 O.D. 595 nm. for the treatment or control assays.

extract_protocol: Total RNA was isolated from L. casei by using TRIZOL reagent (Invitrogen). Cells were collected by centrifugation, washed with cold 50 mM EDTA (pH 8.0), resuspended in 1 ml of TRIZOL reagent, and then mechanically disrupted with glass beads in a cell disrupter (Savant Instruments, Holbrook, N.Y.). Additional steps were performed according to the instructions of the TRIZOL manufacturer. RNA samples purified as described above were treated with the Ambion Turbo DNA-free kit (Applied Biosystems) using the routine DNase I treatment outlined by the supplier in order to remove contaminating DNA. The quality and concentration of the RNA samples were subsequently evaluated by using the Experion automated electrophoresis system (Bio-Rad). Samples with 23S/16S ratios lower than 0.85 were discarded.

treatment_protocol: Cells were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The culture was then two fold diluted with prewarmed MRS medium supplemented with 0.2% bovine bile (Sigma) and incubation continued for 45 min.

tag: agent

value: bile

value: TC01. L. casei BL23 with a complete deletion of gene LCABL_02080.


title: TC01 bile_1


title: TC01 MRS_1

treatment_protocol: Cells were grown in MRS medium at 37C without shaking until O.D. 595 nm. reached 0.5. The culture was then two fold diluted with prewarmed MRS medium and incubation continued for 45 min.


title: TC01 MRS_2


title: TC01 MRS_3


title: Harlan mice, cerulein treated, biological rep 2

description: Gene expression data from pancreas of C57BL6/NHsd mice with cerulein induced chronic pancreatitis


title: Wild type heart at 3.5 weeks old 3

city: Goettingen

first: belal

middle: Awd

last: Mohamed

state: Lower Saxony

address: Heinrich Dueker Weg 12

department: Institute of Human Genetics

institute: Medical university, Goettingen

description: Gene expression data of 3.5-week-old wild type heart

hyb_protocol: Hybridization was performed for 18 hours at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640 followed by washing and staining in Gene Chip® Fluidics Station 450 (Affymetrix),

scan_protocol: the arrays were scanned using the GeneChip® scanner 3000 7G (Affymetrix).

data_processing: Data were analyzed using R (Version 2.13.0) and Bioconductor using the rma-function of package Affy (affy_1.30.0) and the CDF-package mogene10stv1mmentrezgcdf_14.1.0 from Brainarray (http://brainarray.mbni.med.umich.edu)

label: Biotin

source_name: Wild type mouse heart 3.5weeks old

label_protocol: Using the WT Target Labeling Kit (Affymetrix), cDNA was synthesized according to the manufacture´s recommendations. Global gene expression analysis was applied using the Gene-Chip® Mouse Gene 1.0 ST arrays (Affymetrix).

growth_protocol: Total RNA was extracted from heart ventricles of 3.5-week-old Hspa4+/+ and Hspa4-/- males (n = 3 mice for each genotype).

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

tag: background strain

value: male

tag: genotype/variation


title: TUP1 KO rep2

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Probe value were extracted from .CEL files by the RMA package, differential analysis carried out based on the Limma package.

organism: Saccharomyces cerevisiae

label_protocol: standard Affymetrix protocol

growth_protocol: grown to a final OD600nm of 0.8 in 200 mL of YEP containing 2% Glucose.

extract_protocol: standard Affymetrix protocol

tag: genetic background

value: TUP1 knock out


title: Brain infected ERA bio rep2 tech rep1

description:
It is the first of the three biological replicates and the first of two technical replicates.  Raw data was at GA_Phalanx_expression_raw_data. xls
B2_H009


title: Jackson mice, cerulein treated, biological rep1


title: Mutant heart at 3.5 weeks old 1

description: Gene expression data of 3.5-week-old mutant heart

source_name: Mutant mouse heart 3.5weeks old


title: Harlan mice, cerulein treated, biological rep 3


title: Mutant heart at 3.5 weeks old 3


title: wild type rep2

source_name: wt

value: wild type


title: wild type rep1


title: HNSCC_primary_4361181

data_processing: Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls

extract_protocol:
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample_reference_protocol:  A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.

value: head-neck

tag: tumor type

value: HNSCC

tag: location

value: oropharynx

tag: ct

tag: cn (clinical n-status = lymph node metastasis status)

tag: pt

tag: pn (pathological n-status = lymph node metastasis status)

tag: grade

tag: hpv

source_name: UHR

tag: sample type

value: Stratagene Universal human reference cell line (UHR)


title: TC01 bile_2

tag: strain


title: Wild type heart at 3.5 weeks old 2


title: SSN6 KO rep1

value: Ssn6 knockout


title: COLO-357_PD-0332991 treated 72 h_rep3

city: Indianapolis

first: Fang

last: Liu

state: IN

address: Walnut street

department: Endocrinology

institute: Indiana University

hyb_protocol: biotin-labeled cRNA samples were hybridized to Illumina HumanHT-12 BeadChips (Version 4.00), using protocol provided by the manufacturer

scan_protocol: BeadChips were imaged using the Illumina BeadArray Reader

data_processing: Array data analysis was performed using BRB-Array Tools (Version 3.8.1) and the Database for Annotation, Visualization and Integrated Discovery (DAVID, version 6.7)

label_protocol: Illumina TotalPrep Kit

growth_protocol: AsPC-1 cells were grown in RPMI 1640, COLO-357 cells were grown in DMEM, supplemented with 5% FBS, 100 units/ml penicillin, and 100 µg/ml streptomycin

extract_protocol: QIAGEN Rneasy purification kit

treatment_protocol: AsPC-1 and COLO-357 cells were treated with vehicle control or 5 µM PD-0332991 for 24 h or 72 h

tag: cell line

tag: cell type

value: human pancreatic ductal adenocarcinoma (PDAC)


title: COLO-357_PD-0332991 treated 72 h_rep1


title: COLO-357_vehicle control 72 h_rep2

source_name: COLO-357_vehicle control 72 h


title: Wild type heart at 3.5 weeks old 1

tag: gender


title: Harlan mice, cerulein treated, biological rep1

tag: tissue

tag: age

tag: disease state


title: SSN6 KO rep2

tag: genetic background

tag: genotype/variation


title: COLO-357_PD-0332991 treated 72 h_rep2


title: TUP1 KO rep1


title: Mutant heart at 3.5 weeks old 2

tag: background strain


title: COLO-357_vehicle control 72 h_rep3


title: COLO-357_PD-0332991 treated 24 h_rep3


title: COLO-357_vehicle control 72 h_rep1


title: COLO-357_PD-0332991 treated 24 h_rep2


title: COLO-357_PD-0332991 treated 24 h_rep1


title: Brain Non-infected rep3

description:
It is the third of the three biological replicates. Raw data and chip image was at C3_Raw_Data. xls and C3_Chip. tif respectively.
C3

hyb_protocol: Hybridization was performed by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

scan_protocol: Scanning was performed  by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

data_processing: For raw dataset, Hybridization images were collected using a  laser scanner (GenePix 4000B, Molecular Device) and digitized  using Array-Pro image analysis software (Media Cybernetics).  Finally the expression data were normalized using a variance stabilizing method VSN ( Huber et al. Bioinformatics 18 Suppl 1: S96-104) in Bioconductor (http://www.bioconductor.org).

label_protocol: Labeling was performed by LC Sciences, Texas, USA, following their standard operating protocol. See http://www.LCsciences.com.

extract_protocol: RNA was extracted with mirVana™ miRNA Isolation Kit (Cat. No. 1561, Ambion, USA).We performed  proceducer FⅠin the Total RNA Isolation Procedure. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, CA).

value: BALB/c

value: 6 weeks

value: Brain

tag: infection

value: Sham-infected with DMEM,  Dulbecco's modiﬁed Eagle's medium


title: Brain Non-infected rep2

description:
It is the second of the three biological replicates.  Raw data and chip image was at C2_Raw_Data. xls and C2_Chip. tif respectively.
C2


title: Brain infected ERA rep3

description:
It is the third of the three biological replicates.  Raw data and chip image was at B3_Raw_Data. xls and B3_Chip. tif respectively.
B3

value: Infected with laboratory-adapted rabies virus, ERA


title: PCC6803_Wt+empty_plasmid_24h_copper depletion_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA.

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays.

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The Synechocystis 6803 WT strain used in this study was provided by S. Shestakov (Moscow State University, Russia) and was propagated on BG11 (Rippka et al., 1979) containing 0.75% (w/v) agar (Bacto agar, Difco) plates. Liquid cultures of WT and mutant strains were grown in BG11 medium containing 10 mM TES buffer (pH 8.0) under continuous illumination with white light of 40 µmol photons•m–2•s–1 at 30°C or at 120 µmol photons•m–2•s–1 for high light treatment. Media for mutant strains were supplemented with 40 µg mL–1 kanamycin (Km), 20 µg mL–1 spectinomycin (Spec), or a combination of 40 µg mL–1 kanamycin and 20 µg mL–1 spectinomycin.

extract_protocol: Synechocystis 6803 liquid cultures were collected by quenching on ice and immediate centrifugation at 4 °C.  RNA was extracted following the protocol by Pinto et al., 2009 (Pinto, Thapper et al. 2009) with an additional phenol/chloroform/Isoamyl alcohol (25:24:1 v/v) extraction preceding the RNA precipitation.

treatment_protocol: For induction of the PpetJ promoter CuSO4 was omitted from the medium, cells were first washed for two times, and then resuspended in copper-free medium. Cultures were incubated in copper-free medium for the indicated time. Repression was achieved by adding 2.5-5 µM CuSO4 to the medium.

tag: genotype

value: WT


title: wild type rep3


title: COLO-357_vehicle control 24 h_rep2

source_name: COLO-357_vehicle control 24 h


title: Brain Non-infected rep1

description:
It is the first of the three biological replicates.  Raw data and chip image was at C1_Raw_Data. xls and C1_Chip. tif respectively.
C1


title: AsPC-1_PD-0332991 treated 72 h_rep3

source_name: AsPC-1_PD-0332991 treated 72 h


title: PCC6803_PsrR1+_24h_copper depletion_2

source_name: PCC6803_PsrR1+_24h_copper depletion_2


title: PCC6803_Wt+empty_plasmid_24h_copper depletion_2


title: Brain infected ERA rep2

description:
It is the second of the three biological replicates.  Raw data and chip image was at B2_Raw_Data. xls and B2_Chip. tif respectively.
B2


title: Brain infected ERA rep1

description:
It is the first of the three biological replicates.  Raw data and chip image was at B1_Raw_Data. xls and B1_Chip. tif respectively.
B1


title: PCC6803_Wt+empty_plasmid_24h_copper depletion_3


title: PCC6803_Wt+empty_plasmid_0h_copper depletion_2


title: PCC6803_Wt+empty_plasmid_0h_copper depletion_1


title: PCC6803_PsrR1+_0h_copper depletion_2

source_name: PCC6803_PsrR1+_0h_copper depletion_2


title: AsPC-1_vehicle control 72 h_rep2

source_name: AsPC-1_vehicle control 72 h


title: COLO-357_vehicle control 24 h_rep3


title: COLO-357_vehicle control 24 h_rep1


title: PCC6803_PsrR1+_0h_copper depletion_1

source_name: PCC6803_PsrR1+_0h_copper depletion_1


title: PCC6803_PsrR1+_24h_copper depletion_1

source_name: PCC6803_PsrR1+_24h_copper depletion_1


title: AsPC-1_vehicle control 72 h_rep1


title: AsPC-1_PD-0332991 treated 24 h_rep2

source_name: AsPC-1_PD-0332991 treated 24 h


title: AsPC-1_PD-0332991 treated 24 h_rep1


title: AsPC-1_PD-0332991 treated 72 h_rep1


title: AsPC-1_vehicle control 72 h_rep3


title: AsPC-1_PD-0332991 treated 24 h_rep3


title: Brain infected FJDRV rep3

description:
It is the third of the three biological replicates.  Raw data and chip image was at A3_Raw_Data. xls and A3_Chip. tif respectively.
A3

source_name: Brain infected FJDRV

value: Infected with street rabies virus, FJDRV, isolated from brain of rabid dog in Fujian provice of China


title: Brain infected FJDRV rep2

description:
It is the second of the three biological replicates.  Raw data and chip image was at A2_Raw_Data. xls and A2_Chip. tif respectively.
A2


title: Brain infected FJDRV rep1

description:
It is the first of the three biological replicates.  Raw data and chip image was at A1_Raw_Data. xls and A1_Chip. tif respectively.
A1


title: PCC6803_PsrR1+_24h_copper depletion_3

source_name: PCC6803_PsrR1+_24h_copper depletion_3


title: AsPC-1_vehicle control 24 h_rep3

source_name: AsPC-1_vehicle control 24 h


title: AsPC-1_vehicle control 24 h_rep2


title: LU85

status: Public on Oct 09 2012

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: BAC aCGH microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, or (3) background corrected intensity value <0 signal units. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.

molecule: genomic DNA

source_name: Lung tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).

extract_protocol: Total DNA from fresh frozen lung tumor tissue was extracted as described PMID:17334996.

tag: osbin

tag: os

tag: Sex

value: F

tag: histology

value: AC

tag: smoking

tag: Stage

value: IA-IIIA

source_name: promega male reference

value: reference


title: LU821

value: IA

tag: sample type


title: LU70

value: M

value: IB


title: LU740

value: IIIA


title: LU998

value: LCNEC


title: LU635


title: LU80

value: IIB


title: AsPC-1_PD-0332991 treated 72 h_rep2

tag: cell line

tag: cell type

value: human pancreatic ductal adenocarcinoma (PDAC)


title: LU87


title: LU804


title: LU628


title: LU79


title: LU486

value: SqCC


title: LU887


title: LU510


title: LU473


title: LU583

value: IIA


title: LU66


title: LU464


title: AsPC-1_vehicle control 24 h_rep1


title: LU485


title: LU48


title: LU460


title: LU454


title: LU468


title: LU500


title: LU444


title: LU436


title: LU434


title: LU418


title: LU409


title: LU376


title: LU411


title: LU350

value: SCLC


title: LU352


title: LU38


title: LU400


title: LU402


title: LU329090


title: LU372


title: LU375


title: LU370


title: LU324492


title: LU302


title: LU332


title: LU449


title: LU415


title: LU295


title: LU320


title: LU330


title: LU427


title: LU398


title: LU382


title: LU348


title: LU318


title: LU277


title: LU292


title: LU324


title: LU276


title: LU219


title: LU257


title: LU17689


title: LU164


title: LU272


title: LU262


title: LU170290


title: LU271


title: 7293

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on Agilent's Whole Rat Genome 4x44K arrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.1.1.1). Intensities were base 2 log-transformed. Control probes were removed.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Qiagen RNA isolation micro kit

tag: strain

value: Fischer

tag: gender

value: Female

tag: source

value: Bone marrow

value: rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC)

tag: clone name

tag: treatment

value: Cells were treated with TGF-ß and PDGF-bb containing basal rMAPC media for period of 6 days

tag: time point

value: Day 4

tag: replicate


title: 7287

tag: age

value: Day 0


title: 7294

value: Day 6


title: LU145

tag: osbin

value: F

value: AC

value: reference


title: 7291


title: 7288

value: Day 2


title: LU147

tag: os


title: 7285


title: 7290


title: 7307

extract_protocol: commercially obtained from Tebu Bio

tag: control

value: commercially obtained from Tebu Bio (Rat Aortic RNA)


title: 7309


title: LU190

tag: Sex

tag: histology

value: LCNEC

value: IA


title: LU143

value: M

tag: smoking

tag: Stage

value: IIB


title: LU2

value: IB

tag: sample type


title: 7292

value: Fischer

value: Female

tag: cell type


title: LU14


title: LU16


title: 7284

tag: strain

value: Bone marrow

value: rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC)


title: 7286

tag: gender

value: Cells were treated with TGF-ß and PDGF-bb containing basal rMAPC media for period of 6 days


title: 7289

tag: source

value: Day 4


title: LU215


title: LU137


title: LU123


title: 7280

value: 3 week

tag: clone name


title: V. campbellii, dark, biological rep5

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: Gene expression data from wild type V. campbellii (STR) grown for 24 hours in the dark

hyb_protocol: The cocktail was hybridized onto the custom designed Vharveyi520694 microarray (Affymetrix). Hybridization was carried out for 16 h at 49°C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000. GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: CEL files were processed using the Bioconductor affy package.

organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

source_name: ATCC BAA-1116 dark

label_protocol: Target preparation and hybridization to arrays: 600 ng of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures. The labeling reaction was carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol. Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX). The fragmentation from the reaction was carried out in a volume of 33 uL containing 1X fragmentation buffer (Ambion), labeled mRNA, and incubated at 70°C for 15 minutes. After incubation, the reaction was stopped by adding 1 uL of stop solution.

growth_protocol: Ten total cultures (five biological replicates of the wild type (STR) V. campbellii BAA-1116 grown under continuous dark for 24 hours and five biological replicates of the wild type (STR) V. campbellii BAA-1116 grown under a 12 hour dark:12 hour light cycle [white light illumination at 54 µmol photons s-1 m-2]) were seeded with 5.0E+5 bacteria/mL in 25 mL M9 minimal salts medium plus glucose in 125 mL baffled Erlenmeyer flasksand. Cultures were incubated at 30°C and 200 rpm for 24 hours and then harvested for total RNA extraction.

extract_protocol: Total RNA were extracted using RiboPure Bacteria Kit (Ambion Inc., Austin, TX) according to the manufacturer's instructions. The quality and quantity of RNA samples were determined using the RNA 6000 Nano kit with 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) and NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer. The RNA samples were accepted for mRNA enrichment if the A260/A280 ratios were between 1.9-2.1, the ratio of intensities of the 23S and 16S rRNA were 1.5-2.5: 1 and the RNA integrity no. was between 7 and 10. mRNA enrichment was performed with 10 ug total RNA using using the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. The quantity of mRNA samples were determined by NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.

treatment_protocol: Bacterial cultures were exposed to 24 hours of continuous dark or a 12 hour dark:12 hour light cycle.

tag: treatment

value: dark


title: 7283

tag: time point

value: Day 0


title: LU111

value: AC

value: IIIA

value: reference


title: 7279

tag: replicate


title: 7_control (for SCC)

status: Public on Oct 08 2012

city: Bochum

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

hyb_protocol: Labeled miRNA samples  were  hybridized  at  55°C  for  20  hrs  on  separate  Human  miRNA  Microarrays Release 16.0 (8x60K format, (Agilent Technologies, Santa Clara, USA). Afterwards, microarrays  were  washed  with  increasing  stringency  using  Gene  Expression Wash Buffers  (Agilent Technologies, Santa Clara, USA) followed by drying with acetonitrile  (Sigma-Aldich, St.Louis, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies, Santa Clara, USA) on the Agilent DNA Microarray Scanner.

data_processing: Fluorescent signal intensities were extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies, Santa Clara, USA). All the steps described were carried out according to the manufacturer´s instructions.

source_name: skin biopsy

label_protocol: For assessment of labeling and hybridization efficiencies total RNA samples were spiked with in-vitro synthesized oligonucleotides by using the MicroRNA Spike-In Kit (Agilent Technologies, Santa Clara, USA). A total of 100 ng total RNA per sample were introduced into a labeling reaction. The  spiked  total  RNA  was  treated  with  alkaline  calf  intestine  phosphatase  (CIP).  The dephosphorylated RNA was labeled with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions using T4 RNA ligase, incorporating Cyanine 3-Cytidine biphosphate (pCp). The Cyanine-3-labeled miRNA samples were prepared for One-Color based hybridization with Complete miRNA Labeling and Hyb Kit (Agilent Technologies, Santa Clara, USA) according to the manufacturer´s instructions.

extract_protocol: totalRNA was isolated using the miRNeasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA concentration and purity was determined by NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). RNA integrity control (RIN) was determined by means of capillary electrophoresis with the 2100 Bioanalyzer and the RNA 6000 NanoLabCHip Kits (both Agilent Technologies, Santa Clara, USA).

treatment_protocol: All cutaneous specimens were harvested in the operating room, immediately stored in RNAlater (Quiagen, Hilden, Germany) and kept at - 80 °C until RNA isolation.

value: female

tag: age

tag: tissue source

value: skin

tag: tissue

value: adjacent healthy tissue near the tumor border (intraindividual control)


title: LU1054

tag: osbin

tag: os

value: F

value: SCLC


title: 7275

value: Fischer


title: V. campbellii, dark, biological rep1


title: V. campbellii, light, biological rep5

description: Gene expression data from wild type V. campbellii (STR) grown under a 12 hour dark:12 hour light cycle

source_name: ATCC BAA-1116 light

value: light


title: V. campbellii, dark, biological rep3


title: 7282

value: Female

value: Bone marrow

value: Day 6


title: V. campbellii, light, biological rep4


title: 7278

value: rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC)

value: Cells were treated with TGF-ß and PDGF-bb containing basal rMAPC media for period of 6 days


title: V. campbellii, dark, biological rep2

value: dark


title: LU136

tag: Sex

tag: histology

value: IIB


title: 7273

value: 3 week

value: Day 4


title: 7277


title: 7274


title: 7272

value: Day 2


title: V. campbellii, light, biological rep3


title: 7281


title: 7276


title: V. campbellii, light, biological rep2


title: 7271

value: Day 0


title: 6_control (for SCC)

value: female

value: skin


title: 5_control (for SCC)

value: male

value: adjacent healthy tissue near the tumor border (intraindividual control)


title: V. campbellii, dark, biological rep4


title: V. campbellii, light, biological rep1


title: 3_control (for SCC)


title: 4_control (for SCC)


title: 6_SCC

source_name: SCC biopsy

value: cutaneous squamous cell carcinoma (cSCC)


title: 1_SCC


title: 2_SCC


title: 2_control (for SCC)


title: 4_SCC


title: 1_control (for SCC)


title: 3_SCC


title: 5_SCC


title: 7_SCC


title: HSG IFNgamma 24hr rep3

city: Baltimore

first: John

last: Hall

address: 5200 Eastern Ave, MFL Center Twr STE 5300

department: Medicine

institute: Johns Hopkins School of Medicine

description: 24 hours - IFNg [50ng/ml]

hyb_protocol: cRNA was hybridized to Illumina Human HT-12 v3 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

scan_protocol: All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing:
A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no
background correction.  The expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed.
For the data matrices, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.
Detection Pvalues near 0 indicate Present  (above background).
In our analysis we considered expression values with a Detection Pvalue below 0.01 to be Present.

source_name: Human submandibular gland cell line

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

growth_protocol: HSGs were maintained in MEM supplemented with 10% vol/vol FBS and 2mM L-glutamine.

extract_protocol:
Total RNA was extracted from cultured cells using the Trizol reagent method (Invitrogen, Carlsbad, California).
Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA).  The quality of total RNA samples was
assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: At time zero, IFNa [1000U/ml] or IFNg [50ng/ml] was added to cells.  RNA was extracted from untreated, IFNa-treated and IFNg-treated cells at 4, 12, 24, or 48 hours after the addition of IFN.

tag: cell line

value: HSG

tag: time

value: 24 hours

value: IFNg [50ng/ml]


title: HSG untreated 48hr rep3

description: 48 hours - untreated

value: 48 hours

value: untreated


title: HSG IFNgamma 48hr rep1

description: 48 hours - IFNg [50ng/ml]


title: HSG untreated 48hr rep2

description: 48 hours - untreated


title: HSG IFNalpha 48hr rep3

description: 48 hours - IFNa [1000U/ml]

value: IFNa [1000U/ml]


title: HSG IFNalpha 48hr rep2

description: 48 hours - IFNa [1000U/ml]


title: HSG untreated 48hr rep1

description: 48 hours - untreated


title: HSG IFNalpha 24hr rep1

description: 24 hours - IFNa [1000U/ml]


title: HSG untreated 24hr rep1

description: 24 hours - untreated


title: HSG IFNgamma 24hr rep2

description: 24 hours - IFNg [50ng/ml]


title: Hydra MyD88 D3 control germfree4

city: Kiel

first: Sören

last: Franzenburg

address: Am Botanischen Garten 1-9

department: cell- and developmental biology

institute: zoological institute Kiel

description: MyD88-Hairpin in LigAF1 D5

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent High-Resolution Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction 10.7 Image Analysis Software (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 019161_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Hydra vulgaris

source_name: Hydra Myd88 Knockdown empty sterile4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Agilent one-color Quick Amp Labeling Kit protocol according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hydra vulgaris (AEP) was cultivated in S-Medium at 18°C in 50 ml beakers. Animals were fed 3 times a week with Artemia salina. Medium was exchanged after a minimum of 6 hours of digestion. Animals were starved over the weekend. Total RNA was extracted on Monday

extract_protocol: Polyps were homogenized in TRIZOL (Invitrogen) by vortexing. Total RNA was isolated using TRIZOL plus protocol from Invitrogen and the quality and the yield was determined by NanoDrop ND-1000 spectrophotometer (Thermo scientific). In addition quality was checked by agarose gelelectrophoresis.

treatment_protocol: Polyps were fed on Monday, Wednesday and Friday morning with Artemia salina. Medium was exchanged after a minimum of 6 hours of digestion. Animals were starved over the weekend. Total RNA was extracted on Monday. Therefore 15 polyps without visible sexual differentiation and without buds were put into a tube and stored on Ice. Sterile Animals were achived by a 7 days treatment with 50 µg/ml Ampicillin, Neomycin, Streptomycin and Rifampicin. After that, polyps were transferred into sterile-filtered S-Medium and fed 3 times with Artemia salina sterilized with the same complex antibiotic mixture.

tag: developmental stage

value: adult polyps

value: whole polyps

value: not sexually differentiated

tag: number of individulas per sample

tag: date of rna-extraction [ymd]

tag: knockdown

value: control

tag: phenotype

value: sterile, no marker gene GFP-Signal

value: AEP


title: Hydra MyD88 D3 control germfree2

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra Myd88 Knockdown empty sterile2

tag: gender

tag: strain


title: Hydra MyD88 D3 knockdown4

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown endoderm and ectoderm3

value: marker gene GFP-Signal endodermal and ectodermal cells


title: HSG IFNalpha 24hr rep2

description: 24 hours - IFNa [1000U/ml]

tag: treatment


title: HSG untreated 24hr rep3

description: 24 hours - untreated


title: Control, biological rep. 2

city: Oslo

first: Nina

last: Iversen

address: Kirkeveien 166

department: Dept. of Medical Genetics

country: Norway

institute: Oslo University Hospital

hyb_protocol: Biotinylated and fragmented single stranded cDNAs were hybridized to the GeneChips. The arrays were washed and stained using FS-450 fluidics station.

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G and the scanned images were processed using the AGCC.

data_processing: The RMA algorithm was applied for generation of signal values and normalization using the Partek Genomics Suite software. Probe sets with maximal signal values of less than 5 across all arrays were removed to filter for low and non-expressed genes. For expression comparisons of different groups, profiles were compared using a 1-way ANOVA model.

source_name: SK-BR-3 breast cancer cells stably transfected with empty vector

label_protocol: Extrats were labeled using the GeneChip HT IVT Labeling Kit, following the manufacturer’s protocol.

growth_protocol: SK-BR-3 cells were grown in RPMI1640 containing phenol red and 2 mM L-glutamine, supplemented with 10% heat inactivated FBS. Cells were cultured at 37 °C in an incubator with a humidified atmosphere and 5% CO2.

extract_protocol: Total RNA was isolated using the miRVANA miRNA isolation kit, following the manufacturers descriptions for extraction of total RNA

treatment_protocol: Cells had been stably tranfected with pcDNA3.1/V5/His-pTOPO vectors containing TFPIalpha or TFPIbeta cDNA, or empty vectors, and selected using puromycin (2mg/ul)

value: tumor

tag: origin

value: luminal-like

tag: transfector

value: empty vector


title: Hydra MyD88 D3 control germfree3

description: MyD88-Hairpin in LigAF1 D4

source_name: Hydra Myd88 Knockdown empty sterile3

tag: tissue


title: HSG IFNgamma 12hr rep1

description: 12 hours - IFNg [50ng/ml]

value: 12 hours


title: HSG IFNgamma 24hr rep1

description: 24 hours - IFNg [50ng/ml]

value: HSG


title: HSG IFNgamma 48hr rep3

description: 48 hours - IFNg [50ng/ml]


title: HSG IFNalpha 48hr rep1

description: 48 hours - IFNa [1000U/ml]


title: HSG IFNgamma 48hr rep2

description: 48 hours - IFNg [50ng/ml]


title: HSG IFNgamma 12hr rep3

description: 12 hours - IFNg [50ng/ml]


title: HSG IFNalpha 24hr rep3

description: 24 hours - IFNa [1000U/ml]

value: 24 hours


title: HSG untreated 24hr rep2

description: 24 hours - untreated


title: HSG IFNgamma 12hr rep2

description: 12 hours - IFNg [50ng/ml]

value: IFNg [50ng/ml]


title: Hydra MyD88 D3 control germfree1

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra Myd88 Knockdown empty sterile1


title: HSG IFNalpha 12hr rep1

description: 12 hours - IFNa [1000U/ml]


title: HSG untreated 12hr rep3

description: 12 hours - untreated


title: Overexpress TFPIbeta, biological rep. 3

source_name: SK-BR-3 breast cancer cells stably overexpressing TFPIbeta

value: TFPI beta


title: HSG IFNalpha 12hr rep2

description: 12 hours - IFNa [1000U/ml]


title: Hydra MyD88 D3 knockdown1

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown endoderm and ectoderm1


title: Control, biological rep. 1


title: HSG IFNgamma 4hr rep2

description: 4 hours - IFNg [50ng/ml]

value: 4 hours


title: HSG untreated 12hr rep2

description: 12 hours - untreated

value: untreated


title: HSG IFNalpha 4hr rep1

description: 4 hours - IFNa [1000U/ml]

value: IFNa [1000U/ml]


title: Overexpress TFPIbeta, biological rep. 1


title: Hydra MyD88 D3 knockdown2

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown endoderm and ectoderm2

value: adult polyps

value: whole polyps


title: HSG IFNgamma 4hr rep1

description: 4 hours - IFNg [50ng/ml]


title: HSG untreated 4hr rep3

description: 4 hours - untreated


title: Overexpress TFPIalpha, biological rep. 1

source_name: SK-BR-3 breast cancer cells stably overexpressing TFPIalpha

value: TFPI alpha


title: Overexpress TFPIalpha, biological rep. 2


title: Hydra MyD88 D3 knockdown3

description: MyD88-Hairpin in LigAF1 D3

value: not sexually differentiated


title: HSG untreated 4hr rep2

description: 4 hours - untreated


title: HSG IFNalpha 4hr rep3

description: 4 hours - IFNa [1000U/ml]


title: HSG untreated 12hr rep1

description: 12 hours - untreated


title: Overexpress TFPIbeta, biological rep. 2


title: Hydra MyD88 D3 control3

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown empty3

value: control

value: no marker gene GFP-Signal

value: AEP


title: Hydra MyD88 D3 control2

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown empty2


title: HSG IFNgamma 4hr rep3

description: 4 hours - IFNg [50ng/ml]


title: HSG IFNalpha 4hr rep2

description: 4 hours - IFNa [1000U/ml]


title: Overexpress TFPIalpha, biological rep. 3

value: tumor

value: luminal-like


title: HSG untreated 4hr rep1

description: 4 hours - untreated


title: Hydra MyD88 D3 control1

description: MyD88-Hairpin in LigAF1 D3

source_name: Hydra MyD88 Knockdown empty1


title: Muscle 50 eccentric contractions 12 hours WT Aged 12171

status: Public on Oct 06 2012

city: La Jolla

first: Gretchen

last: Meyer

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Tibialis Anterior Muscle, Wildtype, Aged

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

extract_protocol: Rneasy Kit (Qaigen) extraction of total RNA was performed

tag: genetic background

tag: genotype

value: wild type

value: tibialis anterior

tag: age

value: 50 eccentric contractions 12 hours


title: Muscle 50 eccentric contractions 12 hours KO Aged 1217

source_name: Tibialis Anterior Muscle, Desmin Knockout, Aged


title: Muscle 50 eccentric contractions 12 hours KO Aged 1106


title: Muscle 50 eccentric contractions 12 hours WT Aged 12172


title: Muscle 50 eccentric contractions 12 hours KO Aged 1027


title: irs4 null mutant versus CAI-12 wild-type Replicate1

city: Pittsburgh

first: Hassan

last: Badrane

state: PA

address: 3550 Terrace Street, Scaife Hall, Room S875

institute: University of Pittsburgh

description: Biological replicate 1 of 3. Mutant versus wild-type

hyb_protocol: Two cDNAs labeled with different dyes and from different samples were mixed, denatured in 3.4X SSC, 0.3% SDS, 0.5 µg/µL salmon sperm DNA, and hybridized overnight (14-16 hours) to microarray slides.

scan_protocol: After washing and drying, the slides were scanned in GenePix 4000B (Axon Instruments, Union City, CA). GenePix Pro V3.0 (Axon) was used to extract the spot intensities for both fluorescent dyes, and data were archived in Microsoft Access. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: For individual slides, the threshold intensity for each fluorescent channel was established as the average intensity of spots corresponding to negative control 70mers + 1.5 x the standard deviation. Only intensities higher than threshold were considered. Replicated spots in each slide had to have a coefficient of variation in intensities <65%. The intensities of the replicated spots in each slide that passed criteria were averaged and used for normalization. We performed a global normalization among all slides so that the total slide intensity for each channel was identical among slides and channels. The ratio intensity of irs4 mutant to wild-type was used for further analysis.

organism: Candida albicans

source_name: irs4 cells

label_protocol: 20-25 µg of total RNA was used to generate labeled cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA).

extract_protocol: Strains were grown to mid-exponential phase in YPD medium at 30°C, and resuspended in fresh whole human blood. After incubation for 2 hours at 38.6°C in a 13 mL tube, cells were harvested for total RNA extraction. Candida cells were disrupted using glass beads and the Mini-beadbeater (Biospec Products, Bartlesville, OK), the total RNA was extracted using RNeasy Mini Kit (Qiagen) and the On-Column DNase digestion with the RNase free DNase Set (Qiagen) was systematically performed.

source_name: CAI-12 cells


title: Muscle 50 eccentric contractions 12 hours KO Aged 1215


title: Muscle 50 eccentric contractions 12 hours KO Adult 01031

source_name: Tibialis Anterior Muscle, Desmin Knockout, Adult


title: Muscle 50 eccentric contractions 12 hours KO Adult 0706


title: irs4 null mutant versus CAI-12 wild-type Replicate3

description: Biological replicate 3 of 3. Mutant versus wild-type

growth_protocol: Strains were grown to mid-exponential phase in YPD medium at 30°C, and resuspended in fresh whole human blood. After incubation for 2 hours at 38.6°C in a 13 mL tube, cells were harvested for total RNA extraction.


title: irs4 null mutant versus CAI-12 wild-type Replicate2

description: Biological replicate 2 of 3. Mutant versus wild-type


title: Myometrial smooth muscle cell siREST biological rep2

city: Kansas City

first: Vargheese

middle: M

last: Chennathukuzhi

state: KS

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

description: Gene expression data from primary myometrial SMCs after REST knockdown

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization.

source_name: SMCs (passage 3) prepared from normal myometrial tissue samples, treated with siREST for 48h

label_protocol: Biotinylated In-vitro Transcription using the GeneChip 3` IVT Express Kit

growth_protocol: Cells grown in DMEM with FBS (10%) for 24h were treated with scrambled control siRNA or siREST for 48h

extract_protocol: RNeasy mini-kit (Qiagen) protocol

treatment_protocol: siRNA (25nM) in Lipofectamine RNAiMAX transfection reagent (Invitrogen/ LifeTechnologies) according to manufacturer's protocol

value: Uterus, normal myometrium

value: treated with siREST for 48h


title: Muscle 50 eccentric contractions 12 hours KO Adult 01032


title: Muscle 50 eccentric contractions 12 hours WT Aged 0121


title: Muscle 50 eccentric contractions 12 hours KO Adult 0713


title: LS-89 stem_R. solanacearum inoculation_biological rep3

city: Tsukuba

first: Takeaki

last: Ishihara

state: Ibaraki

address: 3-1-1 Kannondai

department: National Agricultural Research Center

institute: National Agriculture and Food Research Organization

description: Gene expression data from R. solanacearum-inoculated LS-89 stems. RNA from 15 plants was used.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on tomato GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

organism: Solanum lycopersicum

source_name: R. solanacearum-inoculated stems of resistant cultivar LS-89, 1dpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Seedlings were raised individually in peat moss pellets and grown in a green house at 25ºC. About 30 days after sowing, seedlings at the five to six leaf-stage were used. R. solanacearum strain 8107S was grown in selective TZC medium containing 200 µg/ml streptomycin sulfate for 1 day at 30ºC, with shaking. Bacteria were collected by centrifugation and re-suspended in distilled water. The suspension was adjusted to 1e+9 cfu/ml by means of a colorimeter and then diluted to 1e+6 cfu/ml.

extract_protocol: Total RNA was isolated using an RNeasy Plant Mini Kit (Qiagen) in accordance with the manufacture's protocol.

treatment_protocol: Seedlings at the five to six leaf-stage were inoculated on their stems just above the cotyledon by cutting to one-third the stem depth with a knife, adding a drop of bacterial suspension or distilled water to the opening, and then clipping the wound site to avoid bending. Inoculated plants were grown in a growth chamber at 30ºC under 30,000 lux light intensity for 12 h a day.

value: stem

tag: cultivar

value: Resistant cultivar LS-89

tag: inoculum

value: R. solanacearum strain 8107S


title: Muscle 50 eccentric contractions 12 hours WT Aged 0123


title: Leiomyoma smooth muscle cell control biological rep2

description: Gene expression data from control primary leiomyoma (fibroid) SMCs

source_name: SMCs (passage 3) prepared from leiomyoma tissue samples, treated with scrambled siRNA for 48h

value: Uterus, Leiomyoma

value: treated with scrambled siRNA for 48h


title: Myometrial smooth muscle cell control biological rep2

description: Gene expression data from control primary myometrial SMCs

source_name: SMCs (passage 3) prepared from normal myometrial tissue samples, treated with scrambled siRNA for 48h


title: Leiomyoma smooth muscle cell control biological rep1


title: Myometrial smooth muscle cell siREST biological rep3


title: Muscle 50 eccentric contractions 12 hours KO Adult 01271


title: Myometrial smooth muscle cell control biological rep3


title: Myometrial smooth muscle cell siREST biological rep1


title: Leiomyoma smooth muscle cell control biological rep3


title: Myometrial smooth muscle cell control biological rep1


title: HSG IFNalpha 12hr rep3

description: 12 hours - IFNa [1000U/ml]

source_name: Human submandibular gland cell line

tag: cell line

value: HSG

tag: time

value: 12 hours

value: IFNa [1000U/ml]


title: tooth_germ-rep3

city: Boston

first: David

middle: Paul

last: Nusinow

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics

institute: Brigham and Women's Hospital

description: biological replicate 3, from the same litter as oral_tissue-rep3 (OT3).

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.8.0). It was vst transformed and quantile normalized.

source_name: non-tooth bud mandibular tissue

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: developmental stage

value: Mandibular non-tooth, non-bone oral tissue


title: LS-89 stem_R. solanacearum inoculation_biological rep2


title: Muscle 50 eccentric contractions 12 hours WT Aged 0106


title: Muscle 50 eccentric contractions 12 hours WT Adult 07273

source_name: Tibialis Anterior Muscle, Wildtype, Adult


title: Ponderosa stem_R. solanacearum inoculation_biological rep3

description: Gene expression data from R. solanacearum-inoculated Ponderosa stems. RNA from 15 plants was used.

source_name: R. solanacearum-inoculated stems of susceptible cultivar Ponderosa, 1dpi

value: Susceptible cultivar Ponderosa


title: LS-89 stem_R. solanacearum inoculation_biological rep1


title: tooth_germ-rep1

description: biological replicate 1, from the same litter as oral_tissue-rep1 (OT1).


title: Ponderosa stem_R. solanacearum inoculation_biological rep2


title: LS-89 stem_mock inoculation_biological rep3

description: Gene expression data from mock-inoculated LS-89 stems. RNA from 15 plants was used.

source_name: Water-inoculated stems of resistant cultivar LS-89, 1dpi

value: Distilled water


title: LS-89 stem_mock inoculation_biological rep1


title: Muscle 50 eccentric contractions 12 hours WT Adult 07271


title: Muscle 50 eccentric contractions 12 hours WT Adult 0629


title: oral_tissue-rep3

description: biological replicate 3, from the same litter as tooth_germ-rep3 (TG3).

source_name: lower molar tooth bud

value: Mandibular molar tooth bud


title: Muscle 50 eccentric contractions 12 hours WT Adult 07272

value: wild type


title: Ponderosa stem_mock inoculation_biological rep2

description: Gene expression data from mock-inoculated Ponderosa stems. RNA from 15 plants was used.

source_name: Water-inoculated stems of susceptible cultivar Ponderosa, 1dpi


title: tooth_germ-rep2

description: biological replicate 2, from the same litter as oral_tissue-rep2 (OT2).


title: LS-89 stem_mock inoculation_biological rep2


title: Ponderosa stem_mock inoculation_biological rep3


title: Muscle 50 eccentric contractions 12 hours WT Adult 0701

value: tibialis anterior


title: Water deficit response of Valencia leaf grafted onto tetraploid rootstock, Replicate 3

status: Public on Oct 05 2012

city: Seville

first: Jose

middle: M.

last: Colmenero-Flores

address: Av. Reina Mercedes 10

department: Plant Biotechnology

institute: IRNAS (CSIC)

description:
4x rootstock Rep3
Control vs. Water deficit Valencia leaf grafted onto tetraploid rootstock, Replicate 3

hyb_protocol: Cy5-labelled cDNA from individual samples was mixed with equal amount of Cy3-labeled reference sample (40-60 pmoles of each dye) in 55μl hybridization solution containing 3XSSC, 0.1% SDS and 0.1mg/ml salmon sperm DNA. The hybridization mix was denatured at 95ºC for 60 seconds and applied to a microarray slide previously prehybridized. Slide prehybridization consisted on 60 min incubation at 50ºC in 3x SSC, 0.1% SDS and 0.1mg/ml BSA, washing twice with SSC (0.1x) and one with distilled water, followed by drying through 5 min centrifugation at 1000 rpm. The slide was placed in a hybridization chamber (Olympus) and incubated overnight (14-16h) in a bath at 50 ºC. After hybridization, slides were washed by stepwise incubations in 2x SSC + 0.1% SDS buffer at 42ºC for 5 min, 0.1x SSC + 0.1% SDS buffer at 28ºC for 5 min (twice), 0.1x SSC at 28ºC for 1 min (five times), and finally in 0.01x SSC buffer at 28ºC for some seconds. Drying was achieved by centrifugation at 1000 rpm for 5 min.

scan_protocol: A GenePix 4000B microarray scanner (Axon Instruments, Inc.) and the GenePix Pro 4.1 acquisition software were used to scan the chips at 5-10 µm resolution. Photomultiplier gains for the two channels were adjusted so that the ratio of total intensities was approximately 1 and the percentage of saturated spots was about 1%. High-resolution tiff images were generated and used for quantification of gene expression data. Spot positions were identified on the color images and quality flags were assigned to individual spots both automatic and manually.  Only spots with background-subtracted foreground intensity greater than two in at least one channel were used, and only microarrays with optimal hybridization data were pre-processed and normalized for further analyses

data_processing:
Raw data were imported into the R computing environment for pre-processing, visualization, and statistical analysis. To identify probes showing significant differential gene expression between samples, the Linear Models in Microarrays (LIMMA; Smyth, 2005) software package was used. Pre-processing and normalization of two-color microarray data including signal intensity, background correction, uniformity of the expression ratio over the chip surface (within-array normalization), and normality of M-value distributions were evaluated according to Smyth and Speed (2003).
M-value was defined as the logarithm in base-2 of water-deficit versus control expression ratio. Reproducibility between replicates that were assessed indicated that the experimental system provided consistent signals in spots corresponding to the same gene and acceptable low variability between biological replicates (not shown). P-values associated to the statistical analysis of differential expression obtained from Limma analysis are corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) procedure (Benjamini & Hochberg, 1995). Differences in gene expression were considered to be significant when the M-value was higher than 0.7 (absolute value) and the FDR-adjusted P-value was smaller than 0.05.

organism: Citrus limonia

label_protocol: the Cy-labelled cDNA of control leaves was hybridized with labelled cDNA from water-stressed samples. To avoid Cy3 and CY5 dye-related artefacts, control and water-stressed cDNA samples were dye-swapped and used to hybridize four slides corresponding to different combinations of the four biological replicates obtained from every treatment

growth_protocol: Autotetraploid (4x) (IVIA-516) of Rangpur lime (RL, Citrus limonia, Osbeck) were investigated, Seeds were planted in substrate (sand, turf and peat, 1:1:1) in a greenhouse for 4 months, Usinfg flow cytometry and SSRs markers, the conformity of the plant material was verified, and 4x one-year-old seedlings were grafted with 2x Valencia Delta sweet orange (V, Citrus sinensis, IVIA 363). Trees were grown in the greenhouse for two years. Since V/4xRL trees grew slower than V/2xRL, trees were pruned to equalize tree size. Trees were then transplanted in new 4L pots containing fresh commercial soil and regular fertilization was applied. Four months after pruning, twelve V/4xRL uniform trees presenting therefore a similar number of leaves for V/2xRL and V/4xRL trees were selected to investigate water deficit tolerance.

extract_protocol: Four independent biological replicates (leaf) per tree combination (V/2xRL and V/4xRL) and condition (Control and after 24 d of water deficit) were selected randomly among six independent biological leaf samples replicates that were harvested from each tree combination (from 9.00–12.00 AM of the day) for microarray and q-RT PCR experiments. Total RNA purification and a quality assessment were performed according to Brumos et al. (2009). Prior microarray hybridization, total RNA was retrotranscribed to cDNA and labelled with the Cy3 and Cy5 fluorophores, following the indirect method,described by Forment et al. (2005).

treatment_protocol: Trees were regularly watered at field capacity for two weeks prior to applying the water deficit, Each pot of the first set of trees was enclosed in a plastic bag. Water requirements to maintain control trees at field capacity were estimated. Six V/2xRL and six V/4xRL were assigned as control trees. The water deficit was applied by ceasing watering of six tree combinations of V/2xRL and six V/4xRL for 24 days after bagging the pots

source_name: 302F_water stressed


title: oral_tissue-rep2

description: biological replicate 2, from the same litter as tooth_germ-rep2 (TG2).


title: Water deficit response of Valencia leaf grafted onto tetraploid rootstock, Replicate 4

description:
4x rootstock Rep4
Control vs. Water deficit Valencia leaf grafted onto tetraploid rootstock, Replicate 4

source_name: 305F_water stressed


title: Water deficit response of Valencia leaf grafted onto tetraploid rootstock, Replicate 2

description:
4x rootstock Rep2
Control vs. Water deficit Valencia leaf grafted onto tetraploid rootstock, Replicate 2

source_name: 301F_water stressed


title: Ponderosa stem_R. solanacearum inoculation_biological rep1


title: Water deficit response of Valencia leaf grafted onto diploid rootstock, Replicate 4

description:
2x/RL Rep4
Control vs. Water deficit Valencia leaf grafted onto diploid rootstock, Replicate 4

source_name: 405F_water stressed

growth_protocol: Diploid (2x) (IVIA-334) Rangpur lime (RL, Citrus limonia, Osbeck) were investigated, Seeds were planted in substrate (sand, turf and peat, 1:1:1) in a greenhouse for 4 months, Usinfg flow cytometry and SSRs markers, the conformity of the plant material was verified, 2x one-year-old seedlings were grafted with 2x Valencia Delta sweet orange (V, Citrus sinensis, IVIA 363). Trees were grown in the greenhouse for two years. Since V/4xRL trees grew slower than V/2xRL, trees were pruned to equalize tree size. Trees were then transplanted in new 4L pots containing fresh commercial soil and regular fertilization was applied. Four months after pruning, Twelve V/2xRL uniform trees presenting therefore a similar number of leaves for V/2xRL and V/4xRL trees were selected to investigate water deficit tolerance.


title: Water deficit response of Valencia leaf grafted onto diploid rootstock, Replicate 3

description:
2x/RL Rep3
Control vs. Water deficit Valencia leaf grafted onto diploid rootstock, Replicate 3

source_name: 401F_water stressed


title: Water deficit response of Valencia leaf grafted onto tetraploid rootstock, Replicate 1

description:
4x rootstock Rep1
Control vs. Water deficit Valencia leaf grafted onto tetraploid rootstock, Replicate 1

source_name: 303F_water stressed


title: oral_tissue-rep1

description: biological replicate 1, from the same litter as tooth_germ-rep1 (TG1).


title: Water deficit response of Valencia leaf grafted onto diploid rootstock, Replicate 1

description:
2x/RL Rep1
Control vs. Water deficit Valencia leaf grafted onto diploid rootstock, Replicate 1

source_name: 404F_water stressed


title: Ponderosa stem_mock inoculation_biological rep1


title: Water deficit response of Valencia leaf grafted onto diploid rootstock, Replicate 2

description:
2x/RL Rep2
Control vs. Water deficit Valencia leaf grafted onto diploid rootstock, Replicate 2

source_name: 406F_water stressed


title: P128N

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

hyb_protocol: Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland) for 16 hours, followed by stringency washes. Subsequently, slides were dried and scanned.

scan_protocol: The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA) to generate Tagged Image File Format (TIFF) images. The analysis was performed using the relevant GenePix® Array Lists (GAL files) (www.exiqon.com). Image analysis: The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.

data_processing: Data processing and normalization: Low-level analysis was performed in the R statistical computing environment, including importing and pre-processing of the data using the LIMMA package (available at http://bioconductor.org). After excluding flagged spots from the analysis, the “normexp” background correction method, plus offset=50 was applied. The intensities were log2 transformed and quantile normalized as implemented in LIMMA. Log2 intensities (single channel analysis) of four intra-slide replicates were averaged.

source_name: rectal, normal

label_protocol: One µg of total RNA from each sample was labeled using the miRCURY™ LNA microRNA Power labeling kit (Exiqon) following a two-step protocol: First, Calf Intestinal Alkaline Phosphatase (CIAP) was applied to remove terminal 5'phosphates; second, fluorescent labels were attached enzymatically to the 3'-end of the microRNAs. Sample-specific RNA was labeled with Hy3 (green channel) fluorophore.

extract_protocol: RNA was extracted using TRIZOL (Invitrogen, Carlsbad, CA). Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: normal rectal mucosa

tag: t (tumor) or n (normal)

value: N

tag: patient identifier


title: P050N


title: P110N


title: P108N


title: P081N2

description: Technical replicate 2 of 2.


title: P097N


title: P096N


title: P093N


title: P095N


title: P094N


title: P090N


title: P092N


title: P089N


title: 1443

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: aCGH analysis

hyb_protocol: Labelled DNAs were hybridized to whole-genome oligonucleotide 2x105K or 4x44K microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNAs (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the following settings: Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100% . Microarray performance was assessed by QC metric tool.

data_processing:
The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies) applying Z-Score algorithm.

Z-score data is not available for GEO submission.

source_name: tumor sample

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI)  were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was extracted overnight with lysis buffer containing K proteinase (0.2 mg/ml) followed by standard phenol/chloroform extraction. DNA content and quality were measured by Biophotometer (Eppendorf)

value: Neuroblastoma

tag: tumor stage

tag: patient nationality

value: Italian

value: male

tag: group

value: long-survivor

source_name: reference

value: Normal Reference DNA


title: 1702

description: aCGH analysis

tag: gender


title: 1404

description: aCGH analysis

value: female


title: P083N


title: P084N


title: 1119

description: aCGH analysis


title: 1985

description: aCGH analysis


title: 1409

description: aCGH analysis


title: 1341

description: aCGH analysis


title: P076N


title: P081N

description: Technical replicate 1 of 2.


title: 2121

description: aCGH analysis


title: 1387

description: aCGH analysis


title: 1428

description: aCGH analysis


title: 1726

description: aCGH analysis


title: P097T

source_name: rectal, tumor

value: rectal tumor

value: T


title: 662

description: aCGH analysis

value: short-survivor


title: P095T


title: P094T


title: P096T


title: P093T


title: P084T


title: P081T


title: P089T


title: P076T


title: P090T


title: P083T


title: P054T


title: P052T


title: P042T


title: P043T


title: P049T

description: Technical replicate 1 of 2.


title: P046T


title: P050T


title: P048T


title: P040T


title: P044T


title: P038T


title: P092T


title: P055N


title: P055T


title: P052N


title: P046N


title: P049N


title: P044N


title: P042N


title: P040N


title: P038N


title: P123N


title: P043N


title: P125N


title: P049T2

description: Technical replicate 2 of 2.


title: P124N


title: P120N


title: P122N


title: P119N


title: P048N


title: P118N


title: P054N


title: P116N


title: P115N


title: P117N


title: P123T


title: P128T


title: P125T


title: P114N


title: P122T


title: P124T


title: P120T


title: P119T


title: P118T


title: GRSPaV-free_berries_rep3

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: berries from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: The study was carried out in a vineyard planted in 2002 in Albenga (Liguria), North-West Italy, where a row was established with the white grape cultivar Bosco (V. vinifera L.). Vines were grafted onto 1103 P rootstock, spaced 2.10 m between rows and 1.00 m between plants for a total plant density of about 4700 vines/hectare. Vines were vertically trained and one-cane pruned (Guyot), leaving 12 buds per vine.

extract_protocol: Samples from each organ were arbitrary pooled in 3 independent biological replicates and total RNA was extracted according to the method described by Gambino et al. (2008) [PMID:    16240119].

treatment_protocol: Grapevine rupestris stem pitting-associated virus (GRSPaV) infection. All the plants of ‘Bosco’ derived by vegetative propagation from a single mother plant originally infected by GRSPaV and further subjected to sanitation. The in vitro thermotherapy and meristem tip culture sanitation techniques successfully eliminated most of the viruses present in the mother vine, but they did not provide satisfactory results in the eradication of GRSPaV, leaving some plants still infected by the virus.   The sanitary status of all plants of ‘Bosco’ was tested in 2010 by multiplex RT-PCR (Gambino and Gribaudo, 2006), in order to detect the most important 9 viruses that commonly affect grapevine in Italy and in other viticultural countries: Arabis mosaic virus (ArMV), Grapevine fanleaf virus (GFLV), Grapevine virus B (GVB), Grapevine fleck virus (GFkV), GLRaV-1,-2,-3, GVA and GRSPaV. The multiplex RT-PCR analyses were repeated in 2011 to confirm the sanitary status of plants selected for the trial.

value: Bosco

tag: treatment

value: GRSPaV-free

value: berries


title: P116T


title: P115T


title: P117T


title: P114T


title: P113N


title: GRSPaV-free_berries_rep2

source_name: berries from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2


title: P107N


title: P111N


title: GRSPaV-infected_berries_rep2

source_name: berries from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2

value: GRSPaV-infected


title: GRSPaV-infected_berries_rep3

source_name: berries from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3


title: P112N


title: P106N


title: P104N


title: P102N


title: P103N


title: P100N


title: P110T


title: P112T


title: P107T


title: P108T


title: P106T


title: GRSPaV-free_leaves_rep2

source_name: leaves from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2

value: leaves


title: GRSPaV-free_leaves_rep3

source_name: leaves from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3


title: GRSPaV-infected_leaves_rep3

source_name: leaves from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3


title: GRSPaV-infected_leaves_rep2

source_name: leaves from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2


title: GRSPaV-infected_berries_rep1

source_name: berries from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: GRSPaV-free_leaves_rep1

source_name: leaves from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: GRSPaV-infected_leaves_rep1

source_name: leaves from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: P104T


title: GRSPaV-free_berries_rep1

source_name: berries from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: Control, biological rep. 3

source_name: SK-BR-3 breast cancer cells stably transfected with empty vector

value: tumor

tag: origin

value: luminal-like

tag: transfector

value: empty vector


title: GRSPaV-free_petioles_rep3

source_name: petioles from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3

tag: tissue

value: petioles


title: P103T


title: P101N

source_name: rectal, normal

value: normal rectal mucosa

value: N


title: P113T


title: GRSPaV-free_petioles_rep2

source_name: petioles from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2


title: P102T

source_name: rectal, tumor


title: P101T


title: P100T


title: P074N


title: P072N


title: P067N


title: P071N


title: P070N


title: P066N


title: Cologne_251275011698

description: aCGH analysis

source_name: tumor sample

value: Neuroblastoma

value: German

value: long-survivor

source_name: reference


title: Cologne_251275011687

description: aCGH analysis

value: Normal Reference DNA


title: GRSPaV-free_petioles_rep1

source_name: petioles from grapevine plants non-infected (e.g. control) by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: GRSPaV-infected_petioles_rep3

source_name: petioles from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 3


title: GRSPaV-infected_petioles_rep2

source_name: petioles from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 2


title: GRSPaV-infected_petioles_rep1

source_name: petioles from grapevine plants infected by Grapevine rupestris stem pitting-associated virus (GRSPaV), replicate 1


title: Cologne_251275011672

description: aCGH analysis


title: P060N


title: P065N