title: Trophozoite stage, replicate 3

description: Laboratory strain K1.

source_name: Trophozoite stage synchronized

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles. The culture was continued for 22h after the second synchronization before harvesting of parasites

value: trophozoite


title: Control 11 follow up Normal

status: Public on Aug 02 2011

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Pooled DNA from the blood of 18 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes description =  Cancer 2008, 47(11): 994-1004

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bronchial tissue, AFB-visualized

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276

tag: case number

value: Control 11

tag: baseline/follow-up

value: follow up

tag: disease status

value: Normal

tag: tissue

value: bronchial

tag: gender

value: male

source_name: blood, pooled DNA from 19 individuals

value: blood

value: female


title: Control 12 follow up Normal

value: Control 12


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R39C59Dr420eMN10 vs. Reference

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

country: USA

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: FN mutant 6R39C59Dr420eMN10

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Qiagen DNeasy

value: Leaf sample

tag: genotype

value: fast neutron mutant

tag: phenotype

value: Mutant shows no obvious phenotype.

tag: cultivar

value: M92-220 background

source_name: FN parental line M92-220

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R39C59Dr420dMN10 vs. Reference

source_name: FN mutant 6R39C59Dr420dMN10


title: lung_4L_ 4w_rep2

type: RNA

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description: V394L/V394L GCase point-mutated mice

hyb_protocol: cRNAs were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 1.1 (GCOS 1.1) using Affymetrix default analysis settings and global scaling to the same target intensity value.

label: biotinylate

molecule: total RNA

organism: Mus musculus

source_name: 4L lung at 4 weeks

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

extract_protocol: Total RNA was extracted using TOTALLY RNA kit (Ambion Inc.) according to the manufacturer's instructions.

tag: genotype/variation

value: lung

tag: age

value: 4 weeks


title: Trophozoite stage, replicate 2

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: Laboratory strain K1.

hyb_protocol: Purified Cy3- and Cy5-labelled cDNA were mixed in a Short Oligo Hybridization Solution (Corning Inc.), and hybridized to P. falciparum spotted 70-mer oligo microarrays for 16-18 hr at 45°C. Arrays were washed at room temperature in a solution of 2x SSC (Sodium Saline Citrate) containing 0.2% SDS, and then in 0.1x SSC.

scan_protocol: The array was dried by centrifugation and immediately scanned using a GenePix 4000B scanner. The .tif images were analyzed using GenePixPro 6.1.0.4 software and data were extracted as .gpr files.

data_processing: Features flagged as bad spots (Flags <0), low intensity features (SNR 635 <3 and SNR 532 <3) and saturated features (F635 % Sat. >50 and F532 % Sat. >50) were excluded from further data analysis. The filtered features were normalized within the array by global lowess in the Aroma package in R 2.8.1 and across replicate arrays using the normalizeAcrossArrays algorithm in the Aroma package.

organism: Plasmodium falciparum

label_protocol: 10-15 µg of total RNA were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using StratascriptTM reverse transcriptase (Stratagene). The cDNA was then labelled with monoreactive Cy5 (GE Healthcare).

tag: strain

tag: developmental stage

value: trophozoite

source_name: Pooled mixed stage (ring, trophozoite, schizont)

label_protocol: 10-15 µg of pooled total RNA were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using StratascriptTM reverse transcriptase (Stratagene). The cDNA was then labelled with monoreactive Cy3 (GE Healthcare).

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles.

extract_protocol:
Parasites were harvested and liberated from erythrocytes by saponin lysis. Total RNA was extracted immediately from parasites using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommendations.

A pooled reference RNA was made by combining extracted total RNA from ring, trophozite and schizont stage parasites in equal amounts.

value: mixed (ring, trophozoite, schizont)

tag: sample type

value: reference


title: Trophozoite stage, replicate 1

description: Laboratory strain K1.

extract_protocol: Parasites were harvested and liberated from erythrocytes by saponin lysis. Total RNA was extracted immediately from parasites using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommendations.


title: lung_4L_ 4w_rep1

description: V394L/V394L GCase point-mutated mice


title: lung_4L_ 18w_rep2

description: V394L/V394L GCase point-mutated mice

source_name: 4L lung at 18 weeks

value: 18 weeks


title: Ring-stage, replicate 3

description: Laboratory strain K1.

source_name: Ring stage synchronised

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles. The culture was continued for 8h after the second synchronization before harvesting of parasites

value: ring


title: Control 10 follow up Normal

value: Control 10

value: follow up

value: Normal

value: bronchial

value: male


title: liver_9V/null_ 18w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null liver at 18 weeks

value: liver


title: Control 08 follow up Normal

value: Control 08

value: female

value: blood


title: Control 07 follow up Normal

value: Control 07


title: Ring-stage, replicate 2

description: Laboratory strain K1.


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R39C59Dr420cMN10-Rep2 vs. Reference

source_name: FN mutant 6R39C59Dr420cMN10-Rep2

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: Control 09 follow up Normal

value: Control 09


title: liver_9V/null_ 28w_rep1

description: D409V/null GCase point-mutated mice

source_name: 9V/null liver at 28 weeks

value: 28 weeks


title: liver_9V/null_ 18w_rep1

description: D409V/null GCase point-mutated mice

value: 18 weeks


title: Ring-stage, replicate 1

description: Laboratory strain K1.

value: ring

value: mixed (ring, trophozoite, schizont)

value: reference


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R39C59Dr420cMN10-Rep1 vs. Reference

source_name: FN mutant 6R39C59Dr420cMN10-Rep1


title: Control 06 follow up Squamous Metaplasia

value: Control 06

value: follow up

value: Squamous Metaplasia

value: bronchial


title: liver_9V/null_ 28w_rep2

description: D409V/null GCase point-mutated mice

value: liver


title: Control 05 follow up Normal

value: Control 05

value: Normal

value: female

value: blood

value: male


title: liver_9V/null_ 12w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null liver at 12 weeks

value: 12 weeks


title: PN 24h, replicate 5

description: Laboratory strain K1.

hyb_protocol: Purified Cy3- and Cy5-labelled cDNA were mixed in a Short Oligo Hybridization Solution (Corning Inc.), and hybridized to P. falciparum spotted 70-mer oligo microarrays for 16-18 hr at 45oC. Arrays were washed at room temperature in a solution of 2x SSC (Sodium Saline Citrate) containing 0.2% SDS, and then in 0.1x SSC.

scan_protocol: The array was dried by centrifugation and immediately scanned using a ScanArray 4000B microarray (Packard/Perkin Elmer, USA.). The .tif images were analyzed using the ScanAlyze software (author: Eisen, available from: http://www.eisenlab.org/eisen/?page_id=41) and data were extracted as .dat files.

data_processing: Features flagged as bad spots (FLAG >0) and low intensity features (CH1GTB2<0.55 and CH2GTB2<0.55) were excluded from further data analysis. The filtered features were normalized within the array by global lowess in the Aroma package in R 2.8.1 and across replicate arrays using the normalizeAcrossArrays algorithm in the Aroma package.

source_name: 24h PN treated

label_protocol: 10-15 µg of total RNA were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using StratascriptTM reverse transcriptase (Stratagene). The cDNA from the drug-treated RNA preparations was then labelled with monoreactive Cy5 (GE Healthcare).

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C. Culture synchronization was obtained by lysing mature parasites with 5% sorbitol for two consecutive cell cycles. Three culture plates (90 x 15 mm) were established, each containing 1.25% haematocrit and 15-20% parasitaemia in a total volume of 17 ml.

extract_protocol: Parasites were harvested and liberated from erythrocytes by saponin lysis. The liberated parasites were flash frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from parasites using TRIzol reagent (Invitrogen) in accordance with the manufacturer’s recommendations.

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 24h in vitro culture in the presence of IC50 concentration (11 nM) of pyronaridine (PN). The final concentration of DMSO was 0.1%

value: trophozoite

tag: treatment

value: pyronaridine

tag: treatment duration

value: 24 hrs

source_name: 24h untreated control

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 24h in vitro culture in the presence of 0.1% (v/v) DMSO.


title: Control 04 follow up Normal

value: Control 04


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R39C59Dr420aMN10 vs. Reference

source_name: FN mutant 6R39C59Dr420aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: PN 24h, replicate 3

description: Laboratory strain K1.


title: PN 24h, replicate 4

description: Laboratory strain K1.


title: liver_9V/null_ 4w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null liver at 4 weeks

value: liver

value: 4 weeks


title: Control 02 follow up Normal

source_name: Bronchial tissue, AFB-visualized

value: Control 02

value: follow up

value: Normal

value: bronchial

source_name: blood, pooled DNA from 19 individuals


title: CGH: Soy twinning phenotype FN mutant 6R39C59Dr420bMN10 vs. Reference

source_name: FN mutant 6R39C59Dr420bMN10

value: Mutant shows twinning phenotype.

source_name: FN parental line M92-220


title: PN 24h, replicate 2

description: Laboratory strain K1.

value: trophozoite


title: PN 24h, replicate 1

description: Laboratory strain K1.

value: pyronaridine


title: CGH: Soy twinning phenotype FN mutant 6R18C00Br109dMN10 vs. Reference

source_name: FN mutant 6R18C00Br109dMN10


title: Control 03 follow up Normal

value: Control 03

value: male

value: blood

value: female


title: liver_9V/null_ 4w_rep1

description: D409V/null GCase point-mutated mice


title: Case 01 follow up Squamous Cell Cancer

value: Case 01

value: Squamous Cell Cancer


title: lung_9V/null_ 28w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null lung at 28 weeks

value: lung

value: 28 weeks


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R18C00Br109cMN10 vs. Reference

source_name: FN mutant 6R18C00Br109cMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R18C00Br109bMN10 vs. Reference

source_name: FN mutant 6R18C00Br109bMN10


title: PN 4h, replicate 4

description: Laboratory strain K1.

source_name: 4h PN treated

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 4h in vitro culture in the presence of IC50 concentration (11 nM) of pyronaridine (PN). The final concentration of DMSO was 0.1%

value: 4 hrs

source_name: 4h untreated control

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 4h in vitro culture in the presence of 0.1% (v/v) DMSO.


title: CGH: Soy wild type/no obvious phenotype FN mutant 6R18C00Br109aMN10 vs. Reference

source_name: FN mutant 6R18C00Br109aMN10


title: Case 06 follow up Severe Dysplasia

value: Case 06

value: follow up

value: Severe Dysplasia

value: bronchial


title: PN 4h, replicate 3

description: Laboratory strain K1.

value: trophozoite

value: pyronaridine


title: lung_9V/null_ 28w_rep1

description: D409V/null GCase point-mutated mice


title: lung_9V/null_ 18w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null lung at 18 weeks

value: 18 weeks


title: lung_9V/null_ 12w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null lung at 12 weeks

value: 12 weeks


title: lung_9V/null_ 18w_rep1

description: D409V/null GCase point-mutated mice

value: lung


title: CGH: Soy puffy shriveled leaves phenotype FN mutant 5R23C78Ar95aMN10 vs. Reference

source_name: FN mutant 5R23C78Ar95aMN10

value: Mutant shows puffy shriveled leaves phenotype.


title: PN 4h, replicate 2

description: Laboratory strain K1.


title: CQ 24h, replicate 6

description: Laboratory strain K1.

source_name: 24h CQ treated

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 24h in vitro culture in the presence of IC50 concentration (280 nM) of chloroquine (CQ). The final concentration of DMSO was 0.1%

value: chloroquine

value: 24 hrs

source_name: 24h untreated control


title: Control 23 baseline Squamous Metaplasia

value: Control 23

value: baseline

value: Squamous Metaplasia

value: male

value: blood

value: female


title: Case 03 follow up CIS

value: Case 03

value: follow up

value: CIS


title: Case 05 follow up CIS

value: Case 05

value: bronchial


title: Case 02 follow up Squamous Cell Cancer

value: Case 02

value: Squamous Cell Cancer


title: liver_9V/null_ 12w_rep1

description: D409V/null GCase point-mutated mice

source_name: 9V/null liver at 12 weeks

value: liver

value: 12 weeks


title: CGH: Soy puffy shriveled leaves phenotype FN mutant 4R47C81Cr85bMN10 vs. Reference

source_name: FN mutant 4R47C81Cr85bMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows puffy shriveled leaves phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy pale green, wrinkled phenotype FN mutant 5R15C49Dr93aMN10 vs. Reference

source_name: FN mutant 5R15C49Dr93aMN10

value: Mutant shows pale green, wrinkled phenotype.


title: CGH: Soy puffy shriveled leaves phenotype FN mutant 4R47C81Cr85aMN10 vs. Reference

source_name: FN mutant 4R47C81Cr85aMN10


title: Case 04 follow up Severe Dysplasia

source_name: Bronchial tissue, AFB-visualized

value: Case 04

value: Severe Dysplasia

value: male

source_name: blood, pooled DNA from 19 individuals

value: blood

value: female


title: CGH: Soy small not wrinkled leaves phenotype FN mutant 4R01C81Dr72iMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72iMN10

value: Mutant shows small not wrinkled leaves phenotype.

source_name: FN parental line M92-220


title: lung_9V/null_ 4w_rep2

description: D409V/null GCase point-mutated mice

source_name: 9V/null lung at 4 weeks

value: lung

value: 4 weeks


title: CQ 24h, replicate 5

description: Laboratory strain K1.

value: trophozoite

value: chloroquine

value: 24 hrs


title: CQ 24h, replicate 4

description: Laboratory strain K1.


title: CGH: Soy dwarf phenotype FN mutant 4R30C22Cr164aMN10 vs. Reference

source_name: FN mutant 4R30C22Cr164aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows dwarf phenotype.


title: lung_9V/null_ 12w_rep1

description: D409V/null GCase point-mutated mice

value: 12 weeks


title: Control 22 baseline Squamous Metaplasia

value: Control 22

value: baseline

value: Squamous Metaplasia

value: bronchial


title: CGH: Soy wrinkled leaves phenotype FN mutant 4R01C81Dr72jMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72jMN10

value: Mutant shows wrinkled leaves phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: PN 4h, replicate 1

description: Laboratory strain K1.

source_name: 4h PN treated

value: pyronaridine

value: 4 hrs

source_name: 4h untreated control


title: CQ 24h, replicate 3

description: Laboratory strain K1.

value: trophozoite


title: Control 21 baseline Squamous Metaplasia

value: Control 21

value: male

value: blood

value: female


title: CGH: Soy wrinkled leaves phenotype FN mutant 4R01C81Dr72gMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72gMN10

value: Leaf sample

value: fast neutron mutant


title: Control 20 baseline Squamous Metaplasia

value: Control 20


title: CQ 24h, replicate 1

description: Laboratory strain K1.

value: chloroquine

value: 24 hrs


title: CQ 24h, replicate 2

description: Laboratory strain K1.


title: Control 19 baseline Squamous Metaplasia

value: Control 19

value: baseline

value: Squamous Metaplasia

value: bronchial


title: CGH: Soy wrinkled leaves phenotype FN mutant 4R01C81Dr72bMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72bMN10

value: Mutant shows wrinkled leaves phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: 14-week-old Trim24-/- liver_463M

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

description: Gene expression data from 14-week-old Trim24-/- Liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

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

data_processing: Raw data were transformed with the Mas5 algorithm, which yields a normalized expression value, and "absent" and "present" calls. Target intensity was set to 100 for all chips.

label: biotin

source_name: 14-week-old Trim24-/- liver_463M

label_protocol: 100 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

growth_protocol: Generation of Trim24-/- and Trim24-/-Rara+/- mice has been described previously (Khetchoumian et al., 2007). Colonies of both lines were maintained under specific pathogen-free conditions at the Mouse Clinical Institute (MCI) of the IGBMC. Harvesting of mouse liver tissues was done as described in Khetchoumian et al. (2007). All liver samples were subjected to histopathological evaluation before analysis. All animal procedures were approved by the French Ministry of Agriculture (agreement B67-218-5) according to guidelines in compliance with the European legislation on care and use of laboratory animals.

extract_protocol:
Harvesting of mouse liver tissues was done as described in Khetchoumian et al. (2007). Livers were rapidly excised, washed in cold PBS, and frozen in liquid nitrogen and stored at - 80°C until use for RNA extraction.
Qiagen RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

tag: organ

value: Liver


title: CGH: Soy wrinkled leaves phenotype FN mutant 4R01C81Dr72fMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72fMN10


title: CGH: Soy wrinkled leaves phenotype FN mutant 4R01C81Dr72aMN10 vs. Reference

source_name: FN mutant 4R01C81Dr72aMN10


title: 14-week-old Trim24-/- liver_395M

source_name: 14-week-old Trim24-/- liver_395M


title: Control 17 baseline Squamous Metaplasia

value: Control 17

value: male


title: 14-week-old Trim24-/- liver_648M

source_name: 14-week-old Trim24-/- liver_648M


title: 14-week-old Trim24-/- liver_411M

source_name: 14-week-old Trim24-/- liver_411M


title: Control 18 baseline Squamous Metaplasia

source_name: Bronchial tissue, AFB-visualized

value: Control 18

value: blood

value: female


title: CQ 4h, replicate 2

description: Laboratory strain K1.

source_name: 4h CQ treated

treatment_protocol: Trophozoite stage (22-24h post infection) synchronized parasites were exposed to 4h in vitro culture in the presence of IC50 concentration (280 nM) of chloroquine (CQ). The final concentration of DMSO was 0.1%

value: trophozoite

value: 4 hrs


title: lung_9V/null_ 4w_rep1

description: D409V/null GCase point-mutated mice

value: lung

value: 4 weeks


title: CGH: Soy low protein phenotype FN mutant 2R38C05Cr289aMN10 vs. Reference

source_name: FN mutant 2R38C05Cr289aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows low protein phenotype.


title: Control 16 baseline Squamous Metaplasia

value: Control 16

value: baseline

value: Squamous Metaplasia

value: bronchial

source_name: blood, pooled DNA from 19 individuals


title: CGH: Soy yellow spotted leaves phenotype FN mutant 3R40C69Cr68aMN10 vs. Reference

source_name: FN mutant 3R40C69Cr68aMN10

value: Mutant shows yellow spotted leaves phenotype.

value: M92-220 background

source_name: FN parental line M92-220

value: Leaf samples

value: FN parental line M92-220.


title: Control 15 baseline Squamous Metaplasia

value: Control 15

value: male

value: blood


title: CQ 4h, replicate 1

description: Laboratory strain K1.

value: trophozoite

value: chloroquine

value: 4 hrs


title: 14-week-old WT liver_393WT

description: Gene expression data from 14-week-old Wild-Type Liver

source_name: 14-week-old WT liver_393WT

value: Liver

value: Wild-Type


title: bTC3_5d_gw8510_3.3uM_bio rep3

city: Cambridge

first: Dina

middle: A.

last: Fomina-Yadlin

state: MA

address: 7 Cambridge Center, 3112-D

institute: Broad Institute

description: Gene expression data from beta cells (bTC3) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 3

hyb_protocol: Biotinlyated cRNA targets were normalized, fragmented and hybridized to Affymetrix Mouse 430A 2.0 arrays (GPL8321) using Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)

data_processing: The data were analyzed with GenePattern (modules ExpressionFileCreator, PreProcessDataset, and GSEA) using robust multi-array (RMA) analysis for background correction, thresholding and normalization.

source_name: bTC3 cells, 5-day treatment, 3.3 uM GW8512

label_protocol: 500 ng of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688).

growth_protocol: aTC1 cells were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 ug/ml streptomycin. 24 h prior to compound treatment, 200,000 cells were plated per well in a 12-well plate in 500 ul medium.

extract_protocol: Following 5-day compound treatment, cells were lysed and RNA isolated using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: 0.5 ul GW8510, dissolved at 1000-fold desired assay concentration (3.3 uM) in DMSO, was added to begin treatment. For 5-day treatment, media was changed and new compound added on day 3. All compound treatments were performed in 0.1% final DMSO concentration. DMSO treatment was used as a vehicle control

tag: cell line

tag: compound


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R38C05Cr289eMN10 vs. Reference

source_name: FN mutant 2R38C05Cr289eMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.


title: 14-week-old WT liver_464WT

source_name: 14-week-old WT liver_464WT


title: Control 14 baseline Squamous Metaplasia

tag: case number

value: Control 14

tag: baseline/follow-up

value: baseline

value: Squamous Metaplasia

value: female


title: CGH: Soy high protein phenotype FN mutant 2R36C65Cr287gMN10 vs. Reference

source_name: FN mutant 2R36C65Cr287gMN10

tag: tissue

value: Mutant shows high protein phenotype.

value: M92-220 background

value: Leaf samples


title: Control 13 baseline Squamous Metaplasia

value: Control 13

tag: disease status

value: bronchial

tag: gender

value: male


title: CGH: Soy long stems phenotype FN mutant 3R38C99Cr148aMN10 vs. Reference

source_name: FN mutant 3R38C99Cr148aMN10

tag: genotype

tag: phenotype

value: Mutant shows long stems phenotype.

value: FN parental line M92-220.


title: 14-week-old WT liver_616WT

source_name: 14-week-old WT liver_616WT

value: Liver


title: bTC3_5d_gw8510_3.3uM_bio rep2

description: Gene expression data from beta cells (bTC3) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 2

source_name: bTC3 cells, 5-day treatment, 3.3 uM GW8511


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283kMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283kMN10

tag: cultivar


title: bTC3_5d_gw8510_3.3uM_bio rep1

description: Gene expression data from beta cells (bTC3) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 1

source_name: bTC3 cells, 5-day treatment, 3.3 uM GW8510


title: bTC3_5d_dmso_bio rep3

description: Gene expression data from beta cells (bTC3) treated with 0.1% DMSO for 5 days, biological replicate 3

source_name: bTC3 cells, 5-day treatment, DMSO

value: DMSO


title: Control 10 baseline Squamous Metaplasia

source_name: Bronchial tissue, AFB-visualized

value: Control 10

value: blood


title: 14-week-old Trim24-/- liver_466M

source_name: 14-week-old Trim24-/- liver_466M

tag: age


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283lMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283lMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.


title: 14-week-old WT liver_611WT

source_name: 14-week-old WT liver_611WT

value: Wild-Type


title: 5-week-old Trim24-/- Rara+/- liver_73R

description: Gene expression data from 5-week_old Trim24-/- Rara+/- liver

label: Biotin

source_name: 5-week-old Trim24-/- Rara+/- liver_73R

value: Trim24-/- Rara+/-


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283jMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283jMN10

source_name: FN parental line M92-220


title: Control 12 baseline Squamous Metaplasia

value: Control 12

value: baseline

value: Squamous Metaplasia

source_name: blood, pooled DNA from 19 individuals

value: female


title: 5-week-old Trim24-/- Rara+/- liver_82R

source_name: 5-week-old Trim24-/- Rara+/- liver_82R


title: bTC3_5d_dmso_bio rep2

description: Gene expression data from beta cells (bTC3) treated with 0.1% DMSO for 5 days, biological replicate 2


title: bTC3_5d_dmso_bio rep1

description: Gene expression data from beta cells (bTC3) treated with 0.1% DMSO for 5 days, biological replicate 1


title: Control 09 baseline Squamous Metaplasia

value: Control 09

value: bronchial


title: Control 11 baseline Squamous Metaplasia

value: Control 11

value: male


title: aTC1_d5_gw8510_3.3uM_bio rep3

description: Gene expression data from alpha cells (aTC1) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 3

source_name: aTC1 cells, 5-day treatment, 3.3 uM GW8512


title: 5-week-old Trim24-/- Rara+/- liver_66R

source_name: 5-week-old Trim24-/- Rara+/- liver_66R

value: Liver


title: aTC1_d5_gw8510_3.3uM_bio rep2

description: Gene expression data from alpha cells (aTC1) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 2

source_name: aTC1 cells, 5-day treatment, 3.3 uM GW8511


title: CGH: Soy twinning phenotype FN mutant 2R29C14Cr283gMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283gMN10

value: Mutant shows twinning phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy twinning phenotype FN mutant 2R29C14Cr283eMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283eMN10

value: Leaf sample

value: fast neutron mutant


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R36C65Cr287cMN10 vs. Reference

source_name: FN mutant 2R36C65Cr287cMN10

value: Mutant shows no obvious phenotype.


title: 5-week-old Trim24-/- liver_37KO

description: Gene expression data from 5-week_old Trim24-/- liver

source_name: 5-week-old Trim24-/- liver_37KO


title: Control 07 baseline Squamous Metaplasia

value: Control 07

value: blood


title: 5-week-old Trim24-/- Rara+/- liver_54R

source_name: 5-week-old Trim24-/- Rara+/- liver_54R

value: Trim24-/- Rara+/-


title: Control 06 baseline Squamous Metaplasia

source_name: Bronchial tissue, AFB-visualized

value: Control 06

value: baseline

value: Squamous Metaplasia


title: aTC1_d5_gw8510_3.3uM_bio rep1

description: Gene expression data from alpha cells (aTC1) treated with 3.3 uM GW8510 in 0.1% DMSO for 5 days, biological replicate 1

source_name: aTC1 cells, 5-day treatment, 3.3 uM GW8510


title: aTC1_d5_dmso_bio rep3

description: Gene expression data from alpha cells (aTC1) treated with 0.1% DMSO for 5 days, biological replicate 3

source_name: aTC1 cells, 5-day treatment, DMSO

value: DMSO


title: 5-week-old Trim24-/- liver_6KO

source_name: 5-week-old Trim24-/- liver_6KO


title: Control 05 baseline Squamous Metaplasia

value: Control 05

value: bronchial

value: female


title: Control 04 baseline Squamous Metaplasia

value: Control 04

value: male


title: 5-week-old Trim24-/- liver_8KO

source_name: 5-week-old Trim24-/- liver_8KO

value: Liver


title: 14-week-old WT liver_613WT

source_name: 14-week-old WT liver_613WT

value: Wild-Type


title: CQ 4h, replicate 3

description: Laboratory strain K1.

source_name: 4h CQ treated

tag: strain

value: trophozoite

value: chloroquine

value: 4 hrs

source_name: 4h untreated control


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283cMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283cMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows no obvious phenotype.

value: M92-220 background

source_name: FN parental line M92-220

value: Leaf samples

value: FN parental line M92-220.


title: 5-week-old Trim24-/- liver_1KO

source_name: 5-week-old Trim24-/- liver_1KO


title: aTC1_d5_dmso_bio rep2

description: Gene expression data from alpha cells (aTC1) treated with 0.1% DMSO for 5 days, biological replicate 2

value: DMSO


title: aTC1_d5_dmso_bio rep1

description: Gene expression data from alpha cells (aTC1) treated with 0.1% DMSO for 5 days, biological replicate 1


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283bMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283bMN10


title: Control 03 baseline Squamous Metaplasia

description: Pooled DNA from the blood of 18 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes description =  Cancer 2008, 47(11): 994-1004

value: Control 03

value: baseline

value: Squamous Metaplasia

source_name: blood, pooled DNA from 19 individuals

value: blood


title: human DLBCL tumoral sample, miRNA expr, case 36

city: Madrid

first: Santiago

last: Montes-Moreno

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Pathology

country: Spain

institute: CNIO

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_4.txt

hyb_protocol: 100 ng of total RNA were hybridized on an Agilent 8x15K Human miRNA one-color microarray for detecting 470 human and 64 viral miRNAs, following the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Between-array median normalization was carried out to render miRNA expression datasets comparable using Genespring GX9 software.

source_name: human DLBCL tumoral sample

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: total RNA was isolated by Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was checked using total RNA (small fraction chip) with the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA) and by 1% agarose electrophoresis, following the standard procedure.

tag: case id

value: tumoral sample

tag: cell type

value: diffuse large B cell lymphoma (DLBCL)

tag: status os (0 alive; 1 death)

tag: status pfs (0

tag: time os (months)

tag: time pfs (months)


title: 5-week-old WT liver_90WT

description: Gene expression data from 5-week_old Wild-type liver

source_name: 5-week-old WT liver_90WT

tag: organ

value: Liver

value: Wild-Type


title: 5-week-old WT liver_44WT

source_name: 5-week-old WT liver_44WT


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R14C98Cr134cMN10 vs. Reference

source_name: FN mutant 2R14C98Cr134cMN10


title: Case 06 baseline Squamous Metaplasia

source_name: Bronchial tissue, AFB-visualized

tag: case number

value: Case 06

value: bronchial

value: female

value: male


title: seedling in far-red treated with mock, biological rep3

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

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

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

data_processing: Raw microarray data were normalized using the robust multiarray analysis (RMA) algorithm in the BIOCONDUCTOR affy package. Then the microarray data were analyzed using Significance Analysis of Microarrays (SAM) method with default parameters as well as a manual setting of false discovery threshold (FDR) < 0.027 in D and <0.022 in FR.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings growing in far-red light for 4 days and  treated with mock for 2 hours

label_protocol: RNA quality was assessed with an Agilent 2100 Bioanalyzer, and hybridization to the Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays was performed according to the manufacturer’s instructions.

growth_protocol: FHY3p:FHY3-GR fhy3-4 transgenic seedlings grown in D or continuous FR light for 4 d

extract_protocol: total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: treated with 10 μM dexamethasone (DEX) or MOCK (equal volume of ethanol) for 2 h

tag: developmental stage

value: seedling

value: 4 days

tag: genotype/variation

value: FHY3p:FHY3-GR fhy3-4 transgenic line


title: Case 01 baseline Squamous Metaplasia

value: Case 01

tag: baseline/follow-up

tag: disease status

tag: tissue


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283aMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283aMN10

value: Leaf sample

tag: genotype

value: fast neutron mutant

tag: phenotype

value: Mutant shows no obvious phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: Control 08 baseline Squamous Metaplasia

value: Control 08

value: baseline

value: Squamous Metaplasia

tag: gender

value: blood


title: 5-week-old WT liver_45WT

source_name: 5-week-old WT liver_45WT

value: Liver

tag: age

value: Wild-Type


title: Control 01 baseline Squamous Metaplasia

value: Control 01

value: bronchial

value: male

value: female


title: human DLBCL tumoral sample, miRNA expr, case 35

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_4.txt

tag: case id

value: tumoral sample

value: diffuse large B cell lymphoma (DLBCL)


title: Case 05 baseline Squamous Metaplasia

value: Case 05


title: 5-week-old WT liver_2WT

source_name: 5-week-old WT liver_2WT


title: CGH: Soy low protein, high oil, low seed composition phenotype FN mutant 2R14C98Cr134aMN10 vs. Reference

source_name: FN mutant 2R14C98Cr134aMN10

value: Leaf sample

value: fast neutron mutant

value: Mutant shows low protein, high oil, low seed composition phenotype.

tag: cultivar


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R42C85Cr275jMN10 vs. Reference

source_name: FN mutant 1R42C85Cr275jMN10

value: Mutant shows no obvious phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R48C22Cr26aMN10 vs. Reference

source_name: FN mutant 1R48C22Cr26aMN10


title: CGH: Soy twinning phenotype FN mutant 2R29C14Cr283fMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283fMN10

value: Mutant shows twinning phenotype.


title: human DLBCL tumoral sample, miRNA expr, case 33

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_2.txt

tag: cell type

tag: status os (0 alive; 1 death)


title: human DLBCL tumoral sample, miRNA expr, case 34

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_3.txt

tag: status pfs (0

tag: time os (months)


title: human DLBCL tumoral sample, miRNA expr, case 32

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_3.txt

tag: time pfs (months)


title: human DLBCL tumoral sample, miRNA expr, case 31

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_2.txt


title: Case 02 baseline Squamous Metaplasia

tag: case number

value: Case 02

value: baseline

value: Squamous Metaplasia

value: blood


title: Control 02 baseline Squamous Metaplasia

value: Control 02

value: bronchial

value: male


title: Case 04 baseline Squamous Metaplasia

value: Case 04

value: female


title: Case 03 baseline Squamous Metaplasia

value: Case 03


title: CGH: Soy wild type/no obvious phenotype FN mutant 2R29C14Cr283dMN10 vs. Reference

source_name: FN mutant 2R29C14Cr283dMN10

value: Leaf sample

value: fast neutron mutant

source_name: FN parental line M92-220


title: Phaeodactylum_Cadmium1.2mg_24h_rep2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description:
Reference=Cy3
Raw data file: 24t Cd 1.2mg vs H cy5(II).gpr

hyb_protocol: Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 825 ng cRNA from HL exposed cells were mixed with 825 ng cRNA from low light acclimated cells from the corresponding time point. The cRNA mixture was fragmented and hybridized on 4x44K Phaeodactylum tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in a rotary oven (10 rpm, 65°C, 17 h). The slides were washed with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325), Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), acetonitrile (VWR International) and Stabilization and Drying Solution (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slides were scanned at 5 micrometer resolution on an Agilent DNA microarray scanner (Agilent Technologies). The resulting images were processed using GenePix 5.1 software (Axon Instruments, Union City, USA).

data_processing:
The GenePix processed data were filtered to remove spots that had been flagged ‘Absent’, ‘Not Found’ or ‘Bad’, by the GenePix program or by manual flagging. Spots with more than 50% saturated pixels, or had median foreground intensity less than the local median background intensity were excluded from the analysis. No background subtraction was performed. For making statistical inference about differentially regulated genes the Limma package and the R statistical data analysis program package (R 2.10.1) was used. The limma approach is based on fitting a linear model to the expression data of each probe on a microarray. In this experiment each treatment consists of 3 sets of biological replicates (cadmium treatment and control samples) which are dye swapped and adjusted for probe-specific dye effects. Data were normalized using the global loess method.
Data were analyzed using the Limma package and the R statistical data analysis program (R 2.10.1). Values in matrix table are given as log2 ratios (treatment/reference). Spots where both cy3 and cy5 signals were below background threshold are registered as blank entries.

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum, Cadmium 1.2 mg, 24 h

label_protocol: Total RNA was isolated from three biological replicas of each treatment (0.12mg and 1.23mg Cd2+) as well as controll samples (non-treated). The RNA (0.36 - 1 μg) was reverse transcribed, amplified and labelled using the Quick Amp Labelling Kit, Two-Color (Agilent p/n 5190-0444).

growth_protocol: Axenic P. tricornutum cells were transferred from f/2 medium to artificial seawater base AK modified with added f/2-medium nutrients. No EDTA was used; Fe-EDTA was replaced with an equal molar amount of ferric chloride. The prepared artificial seawater was sterile filtrated through a 0.2 µm pore filter before nutrients were added by sterile filtration through 0.2 µm pore filter. The cultures were maintained at 14±1°C under continuous cool white fluorescent light (54 µmol photons m-2s-1) on a rotary table and acclimated for one week prior to the exposure to cadmium.  Axenity was monitored by occasional inoculation into peptone-enriched f/2 medium to check for bacterial growth.

extract_protocol: Diatom cultures were centrifuged at 4000 g for 10 min at 15°C. The supernatant was removed and the cell pellet was resuspended in 1 ml f/2 medium. The suspension was transferred to 2 ml tubes and centrifuged at 18000 g for 1 min at 4°C. Supernatants were removed and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: Cells for the experiments were grown in batch cultures; all vessels were acid washed and rinsed with Milli-Q water prior to use. The cells were first grown axenically in a batch culture to reach an approximate density of 106 cells ml-1, then aliquots were transferred to 75 cm2 sterile Falcon polystyrene flasks to reach cell densities of 1 - 3 x 106 cells ml-1 on the day of the experiment. Cadmium was added as CdCl2 to final Cd2+ concentrations of 123 µg/l and 1230 µg/l from 1000x stock solutions.

tag: clone

source_name: Phaeodactylum, reference, 24 h


title: Phaeodactylum_Cadmium1.2mg_24h_rep3

description:
Reference=Cy5
Raw data file: 24t Cd 1.2mg vs H cy3(III).gpr


title: CGH: Soy stunted spindley plants phenotype FN mutant 1R40C35Cr273hMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273hMN10

value: Mutant shows stunted spindley plants phenotype.


title: Phaeodactylum_Cadmium0.12mg_24h_rep3

description:
Reference=Cy5
Raw data file: 24t Cd 0.12mg vs H cy3(III).gpr

source_name: Phaeodactylum, Cadmium 0.12 mg, 24 h


title: Phaeodactylum_Cadmium1.2mg_24h_rep1

description:
Reference=Cy3
Raw data file: 24t Cd 1.2mg vs H cy5(I).gpr


title: human DLBCL tumoral sample, miRNA expr, case 28

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_1.txt

source_name: human DLBCL tumoral sample

value: tumoral sample

value: diffuse large B cell lymphoma (DLBCL)


title: human DLBCL tumoral sample, miRNA expr, case 30

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_4.txt


title: human DLBCL tumoral sample, miRNA expr, case 26

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_3.txt


title: CGH: Soy high protein phenotype FN mutant 1R42C85Cr275gMN10 vs. Reference

source_name: FN mutant 1R42C85Cr275gMN10

value: Mutant shows high protein phenotype.

value: M92-220 background

value: Leaf samples

value: FN parental line M92-220.


title: seedling in dark treated with DEX, biological rep4

source_name: Arabidopsis thaliana seedlings growing in dark for 4 days and  treated with DEX for 2 hours

tag: developmental stage

value: seedling

value: 4 days

tag: genotype/variation

value: FHY3p:FHY3-GR fhy3-4 transgenic line


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R42C85Cr275cMN10 vs. Reference

source_name: FN mutant 1R42C85Cr275cMN10

value: Mutant shows no obvious phenotype.


title: CGH: Soy stunted spindley plants phenotype FN mutant 1R40C35Cr273fMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273fMN10


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R40C35Cr273cMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273cMN10


title: human DLBCL tumoral sample, miRNA expr, case 25

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_2.txt


title: human DLBCL tumoral sample, miRNA expr, case 29

description: US22502553_251643611739_S01_miRNA-v1_95_May07_2_2.txt


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R40C35Cr273dMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273dMN10


title: human DLBCL tumoral sample, miRNA expr, case 24

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_1.txt


title: human DLBCL tumoral sample, miRNA expr, case 27

description: US22502553_251643611739_S01_miRNA-v1_95_May07_1_4.txt


title: Blad_wt2

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: based on Affymetrix protocols

scan_protocol: based on Affymetrix protocols

data_processing: data processed/normalized by algorithm:RMA

source_name: bladder urothelium

label_protocol: based on Affymetrix protocols

extract_protocol: Total RNA from E14.5 whole bladders isolated from Klf5D/D and Klf5+/+ShhGfpCre+ embryos (n=3 samples/genotype, each sample a pool of two bladders) was isolated using the Qiagen MicroRNA Kit.

value: E14 Bladder

value: Klf5+/+ShhGfpCre+ (control)


title: CGH: Soy wrinkled leaves phenotype FN mutant 1R38C92Cr272jMN10 vs. Reference

source_name: FN mutant 1R38C92Cr272jMN10

value: Mutant shows wrinkled leaves.

tag: culitvar


title: human DLBCL tumoral sample, miRNA expr, case 23

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_3.txt

tag: tissue


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R40C35Cr273gMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273gMN10

tag: genotype


title: Blad_klf5_mut3

value: Klf5 ∆/∆


title: human DLBCL tumoral sample, miRNA expr, case 22

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_2.txt


title: Phaeodactylum_Cadmium0.12mg_24h_rep2

description:
Reference=Cy3
Raw data file: 24t Cd 0.12mg vs H cy5(II).gpr


title: Blad_wt1


title: Bcl11b-4

city: La Jolla

first: Elizabeth

last: Thomas

state: CA

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

description: replicate 4

hyb_protocol: Samples were hybridized onto the Illumina Sentrix BeadChip Array MouseRef-8 v2 for 18 hours at 58°C (protocol available at http://www.illumina.com/products/mouseref-8_expression_beadchip_kits_v2.ilmn).

scan_protocol: BeadChip Arrays were scanned using the Illumina BeadArray Reader with default settings.

data_processing: Data normalization was performed using GenomeStudio Gene Expression Module v1.0 with quantile normalization.

label_protocol: Biotin-labeled

extract_protocol: RNA  from striatal cells was extracted using RNAeasy mini kit (Qiagen) with DNase I treatment to eliminate genomic DNA contamination

value: STHdh striatal cells


title: Blad_wt3


title: Phaeodactylum_Cadmium0.12mg_24h_rep1

description:
Reference=Cy5
Raw data file: 24t Cd 0.12mg vs H cy3(I).gpr


title: Bcl11b-3

description: replicate 3


title: human DLBCL tumoral sample, miRNA expr, case 21

description: US22502553_251643611738_S01_miRNA-v1_95_May07_2_1.txt


title: Bcl11b-2

description: replicate 2


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R36C56Cr267IMN10 vs. Reference

source_name: FN mutant 1R36C56Cr267IMN10

value: Leaf sample

value: fast neutron mutant

tag: phenotype


title: Blad_klf5_mut2


title: human DLBCL tumoral sample, miRNA expr, case 20

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_3.txt

value: tumoral sample


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R40C35Cr273eMN10 vs. Reference

source_name: FN mutant 1R40C35Cr273eMN10


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R38C92Cr272iMN10 vs. Reference

source_name: FN mutant 1R38C92Cr272iMN10

source_name: FN parental line M92-220


title: CGH: Soy high protein phenotype FN mutant 1R36C56Cr267dMN10 vs. Reference

source_name: FN mutant 1R36C56Cr267dMN10


title: shZBP-89, biological rep2

city: Boston

first: Andrew

middle: Jonghan

last: Woo

address: 1 Blackfan Circle, Karp Res Bldg

department: Hematology / Oncology

institute: Children's Hospital Boston / Harvard Medical School

hyb_protocol: According to standard Affymetrix protocols.

data_processing: dCHIP program using Affymetrix default analysis settings and global scaling as normalization method

source_name: erythroblast transduced with shZBP-89

growth_protocol: De-identified cryogenically preserved primary human CD34+  (hCD34+) cells were obtained from the Yale Center of Excellence in Molecular Hematology (New Haven, Connecticut).  They were prepared by magnetically sorting mononuclear samples of G-CSF mobilized peripheral blood from donors.  For erythroid ex vivo differentiation, hCD34+ progenitor stem cells were expanded for 6 days in StemSpan SFEM Medium with 1X CC100 cytokine mix (StemCell Technologies Inc.) and 2% P/S.  On day 6 of expansion, cells were reseeded into erythroid differentiation medium (StemSpan SFEM Medium containing 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM β-estradiol)

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy Plus Mini Kit according to the manufacturer's instructions.

treatment_protocol: Expanding hCD34+ cells were seeded in fresh medium 24 hrs post-transduction, and cultured for an additional 24 hrs prior to the start of selection with puromycin.  The empty pLKO.1ps vector and shZBP-89 in the same vector backbone are used.

value: Erythroid progenitors on day 6 of differentiation

value: transduced with lentivirus expressing short hairpins against ZBP-89


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R38C92Cr272hMN10 vs. Reference

source_name: FN mutant 1R38C92Cr272hMN10

value: M92-220 background


title: PcDNA3.1-4

description: replicate 4

source_name: wild-type

value: wild-type


title: human DLBCL tumoral sample, miRNA expr, case 18

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_4.txt

source_name: human DLBCL tumoral sample

value: diffuse large B cell lymphoma (DLBCL)


title: shZBP-89, biological rep1

scan_protocol: According to standard Affymetrix protocols.


title: Bcl11b-1

description: replicate 1


title: human DLBCL tumoral sample, miRNA expr, case 17

description: US22502553_251643611602_S01_miRNA-v1_95_May07_2_1.txt


title: Empty vector, biological rep2

source_name: erythroblast transduced with empty vector

label_protocol: According to standard Affymetrix protocols.

value: transduced with control empty vector


title: CGH: Soy less dense, longer stems phenotype FN mutant 1R26C94Cr17bMN10 vs. Reference

source_name: FN mutant 1R26C94Cr17bMN10

value: Mutant shows less dense, longer stems phenotype.

value: Leaf samples

value: FN parental line M92-220.


title: Empty vector, biological rep1


title: human DLBCL tumoral sample, miRNA expr, case 19

description: US22502553_251643611738_S01_miRNA-v1_95_May07_1_2.txt


title: human DLBCL tumoral sample, miRNA expr, case 16

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_4.txt


title: Blad_klf5_mut1

value: E14 Bladder


title: Node_10

city: Leeds

first: Rosalyn

last: Jewell

address: Leeds Cancer Research UK Centre, LIMM, Cancer Genetics Building, St James;s University Hospital, Beckett Street

department: Section of Epidemiology and Biostatistics

country: United Kingdom

institute: University of Leeds

hyb_protocol: A PCR reaction was then performed with Cy3 and Cy5 labelled universal PCR primers and the double stranded PCR products were isolated and hybridised at 45°C for 18 hours to the Illumina DASL 502 gene Human Cancer Panel.

scan_protocol: After hybridisation the arrays were scanned using the BeadArray™ scanner and analysed by BeadStudio v3 software (Illumina, USA).

data_processing: The data were normalized using Beadstudio software (Illumina, USA) before exporting to STATA version 10 for statistical analyses. The normalisation methods used were background correction, cubic spline smoothing and plate scaling. Studies were normalized separately before samples were compared across studies. The mean gene expression across 3 probes targeting each gene was used for analysis.

label: Cy3 and Cy5

source_name: Malignant melanoma

label_protocol: 200ng total RNA was converted into cDNA using biotinylated random hexamers and oligo-deoxythymidine 18 primers, and Illumina-supplied reagents according to manufacturer’s instructions. Pairs of query oligos were then annealed to complementary sequences (~50 bases) flanking the specific cDNA target site. The biotinylated cDNA was then bound to streptavidin-conjugated paramagnetic particles and mis-hybridised and non-hybridised oligos were washed away. Hybridised oligos were then extended and ligated to generate amplifiable templates.

extract_protocol: Cores of tissue were taken using a tissue microarray core. These were de-waxed using xylene and two changes of absolute ethanol. RNA was extracted using the column based technique Roche High Pure Paraffin RNA kit and treated with Dnase I according to the kit protocol. Quality control procedures included running samples on the ND-1000 spectrophotometer, the Agilent 2100 Bioanalyzer and performing quantitaive RT-PCR of RPL13a.

tag: replicate samples

value: Unique sample

tag: study type

value: Study 2

tag: sample type

value: Node


title: PcDNA3.1-1

description: replicate 1

value: STHdh striatal cells


title: PcDNA3.1-3

description: replicate 3


title: CGH: Soy less dense, longer stems phenotype FN mutant 1R26C94Cr17aMN10 vs. Reference

source_name: FN mutant 1R26C94Cr17aMN10

value: Leaf sample

tag: cultivar


title: Liver_2000 pmm CLOF_treatment group 8_replicate 8C_Cy5

city: Logan

first: Abby

middle: D

last: Benninghoff

state: UT

address: 4815 Old Main Hill

department: Animal, Dairy and Veterinary Sciences

institute: Utah State University

hyb_protocol: For detection of gene expression on the OSUrbt array, the Genisphere 3DNA Array 900 kit (Hatfield, PA) was used in a dye-swap, reference sample design following the supplier’s protocol. During reverse transcription (SuperScript II, Invitrogen) of total RNA (1 μg) using the supplied Genisphere oligo d(T) primers, each biological sample was tagged separately with a capture sequence for one of two fluorescent dendromer reagents, Cy3 or Cy5. Each reverse transcription reaction also included spiked in mRNA corresponding to the SpotReport Alien Oligo controls. Corresponding reference RNA was reverse transcribed with the capture sequence for the opposite reagent (Cy3 or Cy5). To account for any differences in dye labeling efficiency, technical replicates were performed for two of the three biological replicates in which the capture sequence tags were swapped between the sample and reference. Following reverse transcription, equal amounts of capture sequence-tagged sample and reference cDNA were combined and treated with RNase cocktail (Ambion, Austin, TX) to degrade any remaining RNA. Hybridization of cDNA and capture reagents to the OSUrbt arrays was performed as described previously (Benninghoff et al., 2008). Briefly, sterile 20x SSC was prepared with 3 M sodium chloride and 0.3 M sodium citrate at a pH of 7.0; appropriate dilutions were made with sterile water for hybridization wash buffers. Sodium dodecyl sulfate (SDS) was also added to some hybridization wash buffers at a 0.1% (w/v) final concentration. Prior to hybridization, arrays were pre-washed with gentle mixing on a rocking platform twice in 0.1% SDS for 5 min at room temperature (RT), twice in 2x SSC, 0.1% SDS for 10 min at 47°C, once in 0.1x SSC at RT for 5 min and once in ultra-pure water for 5 min. Slides were dried by centrifugation. cDNA was hybridized to the arrays in formamide-based hybridization buffer (25% formamide, 4x SCC, 0.5% SDS and 2x Denhardt’s solution, Genisphere, Inc.) for 16 hrs at 47°C in a Hybex Microarray Incubation System (SciGene Corporation, Sunnyvale, CA). Post hybridization, the arrays were rinsed in 2x SCC, 0.1% SDS for 10 min at 47°C in the Hybex water bath. Then, arrays were washed with gentle mixing twice in 2x SSC, 0.1% SDS for 5 min at 47°C, twice in 1x SSC for 5 min at RT and twice in 0.1x SCC for 5 min at RT. Slides were dried by centrifugation and pre-warmed to 49°C. Next, the 3DNA Cy3/Cy5 capture reagent mixture was hybridized to the arrays for 3 hrs at 49°C in the dark. After this second hybridization, the arrays were rinsed, washed and dried again as previously described in SCC buffers containing 100 μM DTT in the dark.

scan_protocol: Within 24 hrs of hybridization, array images at a resolution of 5 μm were obtained using the Axon GenePix Pro 4200A scanner (Molecular Devices Corp., Sunnyvale, CA) with a1% saturation tolerance and 90% laser power and at 543 nm and 633 nm excitation wavelengths for Cy3 and Cy5, respectively.

data_processing: Array image files were processed with ratio-centering, and spot intensities were quantified using GenePix Pro software (Molecular Devices). For each array feature, raw median signal values were background-corrected and LOWESS normalized using BioArray Software Environment (BASE) (Saal et al. 2002). Statistical analyses of gene expression were performed using the normalized, geometric mean expression values for each biological replicate to compare experimental treatments to the control (MultiExperiment Viewer, MeV) (Saeed et al. 2003); a statistically significant change in gene expression was inferred when p < 0.05 (Welch’s t-test, between subjects and assuming unequal variances). Multiple criteria were used to reduce the original raw data sets to subsets of genes considered as significantly regulated by any one of the experimental treatments. These criteria included filters for statistical significance (P-value < 0.05 by Welch’s t-test with unequal variance), spot consistency (>1.5-fold change in 9 out of the 10 biological and technical replicate features) and mean fold change (>2-fold).

organism: Oncorhynchus mykiss

source_name: Liver total RNA from trout fed Clofibrate diet

label_protocol: Labeled using Genisphere Array 900 kit adapted from manufacturer's protocol.

growth_protocol: Mt. Shasta strain rainbow trout were hatched and reared at the Sinnhuber Aquatic Research Laboratory at Oregon State University in Corvallis, Oregon. Fish were maintained in flow-through 375-l tanks at 12 °C with activated carbon water filtration on a 12:12 hr light:dark cycle.

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Approximately 3500 fry were initiated at 10 weeks post spawn with an aqueous exposure to 10 ppb AFB1 or 0.01% EtOH (non-initiated sham controls) for 30 min; a second cohort of about 1000 fry was AFB1- or sham-initiated at 15 weeks of age. To determine whether the expected tumor-promoting effects of PFOA and related compounds are carcinogen- or target organ-dependent, a third cohort of about 1000 fry was initiated at 10 weeks post spawn with a 30-min aqueous exposure to 35 ppm MNNG, a multi-organ carcinogen in trout, or 0.01% DMSO (non-initiated sham control). After initiation, fry were fed Oregon Test Diet (OTD), a semi-purified casein-based diet, for one month. Then, within each initiation cohort, trout were randomly distributed into dietary treatment groups with 125 animals assigned to duplicate tanks (250 fish/treatment). In the first cohort, fish were fed experimental diets containing 5 ppm E2, 2000 ppm PFOA (approximately 50 mg/kg bw/day), 2000 ppm FtOH or 2000 ppm CLOF ad libitum (2.8-5.6% of body weight) five days per week for six months. PFNA and PFDA experimental diets were initially administered at 2000 ppm based upon prior testing of PFOA without significant mortality. Due to an unexpected number of mortalities in the PFNA and PFDA treatment groups early in the study, diet concentrations adjusted as follows: at 2 weeks into experimental diet administration, PFNA concentration was reduced to 200 ppm (5 mg/kg/day) and at four weeks into the diet administration, PFNA was reduced to 1000 ppm PFNA (25 mg/kg/day) for the remainder of the exposure period. (Note: Animals were sacrificed to obtain RNA for the microarray study prior to any reductions in diet test chemical concentrations.)  In the second cohort (AFB1 at 15 weeks), trout were fed 100 ppm PFOS (2.5 mg/kg/day); this lower test concentration of PFOS was selected based upon observed lethal toxicity at the 2000 ppm diet level (unpublished data). All experimental diets were prepared monthly, stored frozen at -20°C and then thawed to 4°C a few days prior to feeding. Most test compounds were added directly to the oil portion of the OTD diet, though 8:2FtOH was incorporated into the diet via an oil-in-water emulsification. At conclusion of the 6-month promotion diet period, animals were once again fed standard OTD for the remainder of the study.

tag: strain

value: Mt. Shasta

tag: age

value: 4 months

source_name: Liver total RNA reference pool


title: human DLBCL tumoral sample, miRNA expr, case 15

description: US22502553_251643611602_S01_miRNA-v1_95_May07_1_1.txt

tag: case id

value: tumoral sample

tag: cell type

tag: status os (0 alive; 1 death)

tag: status pfs (0


title: PcDNA3.1-2

description: replicate 2


title: CGH: Soy wrinkled leaves phenotype FN mutant 1R25C64Cr16aMN10 vs. Reference

source_name: FN mutant 1R25C64Cr16aMN10

value: fast neutron mutant

value: Mutant shows wrinkled leaves phenotype.


title: CGH: Soy low protein phenotype FN mutant 1R36C56Cr267cMN10 vs. Reference

source_name: FN mutant 1R36C56Cr267cMN10

value: Mutant shows low protein phenotype.

value: M92-220 background


title: Liver_2000 pmm CLOF_treatment group 8_replicate 8B_Cy3


title: human DLBCL tumoral sample, miRNA expr, case 14

description: US22502553_251643611601_S01_miRNA-v1_95_May07_2_4.txt

value: diffuse large B cell lymphoma (DLBCL)

tag: time os (months)

tag: time pfs (months)


title: Node_24


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R24C99Cr262aMN10 vs. Reference

source_name: FN mutant 1R24C99Cr262aMN10

value: Mutant shows no obvious phenotype.


title: human DLBCL tumoral sample, miRNA expr, case 13

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_3.txt


title: Node_23


title: Liver_2000 ppm CLOF_treatment group 8_replicate 8B_Cy5


title: CGH: Soy low oil phenotype FN mutant 1R24C99Cr262hMN10 vs. Reference

source_name: FN mutant 1R24C99Cr262hMN10

value: Mutant shows no oil phenotype.

value: Leaf samples


title: human DLBCL tumoral sample, miRNA expr, case 12

description: US22502553_251643611600_S01_miRNA-v1_95_May07_2_2.txt


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R12C79Cr12eMN10 vs. Reference

source_name: FN mutant 1R12C79Cr12eMN10

value: FN parental line M92-220.


title: CGH: Soy spindly chlorotic FN mutant 1R12C79Cr12fMN10 vs. Reference

source_name: FN mutant 1R12C79Cr12fMN10

value: Mutant shows spindly chlorotic.

source_name: FN parental line M92-220


title: Liver_2000 ppm CLOF_treatment group 8_replicate 8A_Cy3


title: Node_22

value: Unique sample

value: Study 2


title: human DLBCL tumoral sample, miRNA expr, case 11

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_4.txt


title: CGH: Soy spindly chlorotic FN mutant 1R12C79Cr12dMN10 vs. Reference

source_name: FN mutant 1R12C79Cr12dMN10

value: Mutant shows spindly chlorotic phenotype.


title: Node_9

value: Node


title: Liver_2000 ppm CLOF_treatment group 8_replicate 8A_Cy5

value: Mt. Shasta


title: Liver_2000 ppm FTOH_treatment group 7_replicate 7C_Cy5

source_name: Liver total RNA from trout fed FtOH diet

value: 4 months


title: Node_24 (rep)

value: Replicate sample


title: Node_21


title: human DLBCL tumoral sample, miRNA expr, case 10

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_3.txt

value: tumoral sample


title: human DLBCL tumoral sample, miRNA expr, case 9

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_2.txt


title: Liver_2000 ppm FTOH_treatment group 7_replicate 7B_Cy3


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R12C79Cr12cMN10-Rep2 vs. Reference

source_name: FN mutant 1R12C79Cr12cMN10-Rep2

value: Leaf sample

value: fast neutron mutant


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R12C79Cr12cMN10-Rep1 vs. Reference

source_name: FN mutant 1R12C79Cr12cMN10-Rep1

value: M92-220 background


title: human DLBCL tumoral sample, miRNA expr, case 8

description: US22502553_251643611600_S01_miRNA-v1_95_May07_1_1.txt

source_name: human DLBCL tumoral sample

value: diffuse large B cell lymphoma (DLBCL)


title: Node_20


title: Liver_2000 ppm FTOH_treatment group 7_replicate 7B_Cy5


title: human DLBCL tumoral sample, miRNA expr, case 7

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_4.txt


title: Liver_2000 ppm FTOH_treatment group 7_replicate 7A_Cy3


title: Node_19


title: Node_8


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R07C24Cr123bMn10 vs. Reference

source_name: FN mutant 1R07C24Cr123bMn10

value: Mutant shows no obvious phenotype.


title: Node_18

source_name: Malignant melanoma


title: Liver_2000 ppm FTOH_treatment group 7_replicate 7A_Cy5


title: human DLBCL tumoral sample, miRNA expr, case 6

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_3.txt


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R07C24Cr123eMn10 vs. Reference

source_name: FN mutant 1R07C24Cr123eMn10


title: Liver_2000 ppm PFOS_treatment group 6_replicate 6C_Cy5

source_name: Liver total RNA from trout fed PFOS diet

value: 5 months

source_name: Liver total RNA reference pool (time-matched)


title: human DLBCL tumoral sample, miRNA expr, case 5

description: US22502553_251643611593_S01_miRNA-v1_95_May07_2_1.txt


title: Node_7 (rep)


title: human DLBCL tumoral sample, miRNA expr, case 4

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_4.txt


title: human DLBCL tumoral sample, miRNA expr, case 3

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_3.txt


title: Node_17


title: Node_7


title: Liver_2000 ppm PFOS_treatment group 6_replicate 6B_Cy3


title: Liver_2000 ppm PFOS_treatment group 6_replicate 6B_Cy5


title: Liver_2000 ppm PFOS_treatment group 6_replicate 6A_Cy3


title: Node_16


title: human DLBCL tumoral sample, miRNA expr, case 2

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_2.txt


title: Node_15


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R03C32Cr6bMN10 vs. Reference

source_name: FN mutant 1R03C32Cr6bMN10

value: Leaf samples


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R03C32Cr6dMN10 vs. Reference

source_name: FN mutant 1R03C32Cr6dMN10

value: FN parental line M92-220.


title: human DLBCL tumoral sample, miRNA expr, case 1

description: US22502553_251643611593_S01_miRNA-v1_95_May07_1_1.txt


title: Liver_2000 ppm PFDA_treatment group 5_replicate 5C_Cy5

source_name: Liver total RNA from trout fed PFDA diet

source_name: Liver total RNA reference pool


title: CGH: Soy wild type/no obvious phenotype FN mutant 1R03C32Cr6cMN10 vs. Reference

source_name: FN mutant 1R03C32Cr6cMN10


title: Node_14


title: Node_6


title: Liver_2000 ppm PFDA_treatment group 5_replicate 5B_Cy3


title: Node_13


title: Node_5

value: Study 1


title: Liver_2000 ppm PFDA_treatment group 5_replicate 5B_Cy5


title: CGH: Soy high protein and oil seed composition FN mutant 1R07C24Cr123dMn10 vs. Reference

source_name: FN mutant 1R07C24Cr123dMn10

value: Mutant shows high protein and oil seed composition.


title: CGH: Soy copper leaf pigmentation FN mutant R56C58BBM08YB#1 vs. Reference

source_name: FN mutant R56C58BBM08YB#1

value: Mutant shows copper leaf pigmentation.  Mutant was known as "VP06" in Bolon et al. (Plant Physiol. 156:240-253)

source_name: FN pooled reference

value: 30 pooled soybean fast neutron mutants


title: Liver_2000 ppm PFDA_treatment group 5_replicate 5A_Cy5


title: CGH: Soy abnormal floral meristem development FN mutant 2R01C00CMN09NSFBV vs. Reference

source_name: FN mutant 2R01C00CMN09NSFBV

value: Mutant shows abnormal floral meristem development.  Mutant was known as "VP07" in Bolon et al. (Plant Physiol. 156:240-253)


title: Node_4

value: Unique sample

value: Node


title: Node_12


title: Liver_2000 ppm PFNA_treatment group 4_replicate 4C_Cy5

source_name: Liver total RNA from trout fed PFNA diet

value: Mt. Shasta

value: 4 months


title: Node_3


title: CGH: Soy thick twisted petioles FN mutant 4R17C93DMN09NSFBV vs. Reference

source_name: FN mutant 4R17C93DMN09NSFBV

value: Leaf sample

value: Mutant shows thick twisted petioles.  Mutant was known as "VP09" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy short petioles, crinkled leaves FN mutant 6R44C72DMN09NSFBV vs. Reference

source_name: FN mutant 6R44C72DMN09NSFBV

value: fast neutron mutant

value: Mutant shows short petioles, crinkled leaves .  Mutant was known as "VP05" in Bolon et al. (Plant Physiol. 156:240-253)

value: M92-220 background


title: Node_2


title: Liver_2000 ppm PFNA_treatment group 4_replicate 4B_Cy3


title: CGH: Soy fused trifoliates FN mutant 4R20C91DMN09NSFBV vs. Reference

source_name: FN mutant 4R20C91DMN09NSFBV

value: Mutant shows fused trifoliates.  Mutant was known as "VP08" in Bolon et al. (Plant Physiol. 156:240-253)


title: Liver_2000 ppm PFNA_treatment group 4_replicate 4B_Cy5


title: Node_11

source_name: Malignant melanoma


title: CGH: Soy short trichomes FN mutant R59C46CSCW08YB#1 vs. Reference

source_name: FN mutant R59C46CSCW08YB#1

value: Mutant shows short trichomes.  Mutant was known as "VP02" in Bolon et al. (Plant Physiol. 156:240-253)

value: Leaf samples


title: Liver_2000 ppm PFNA_treatment group 4_replicate 4A_Cy3


title: Liver_2000 ppm PFNA_treatment group 4_replicate 4A_Cy5


title: Node_1

value: Study 1


title: Liver_2000 ppm PFOA_treatment group 3_replicate 3C_Cy5

source_name: Liver total RNA from trout fed PFOA diet


title: CGH: Soy yellow leaf pigmentation FN mutant R69C54BBM08YB#1 vs. Reference

source_name: FN mutant R69C54BBM08YB#1

value: Mutant shows yellow leaf pigmentation.  Mutant was known as "VP04" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy chimeric leaf pigmentation FN mutant 1R19C96CMN09NSFBV vs. Reference

source_name: FN mutant 1R19C96CMN09NSFBV

value: Mutant shows chimeric leaf pigmentation.  Mutant was known as "VP03" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy short trichomes FN mutant R55C01CSCW08YB#1sg vs. Reference

source_name: FN mutant R55C01CSCW08YB#1sg

value: Mutant shows short trichomes.  Mutant was known as "VP01" in Bolon et al. (Plant Physiol. 156:240-253)

value: 30 pooled soybean fast neutron mutants


title: Liver_2000 ppm PFOS_treatment group 6_replicate 6A_Cy5

source_name: Liver total RNA from trout fed PFOS diet

value: 5 months

source_name: Liver total RNA reference pool (time-matched)


title: Liver_2000 ppm PFDA_treatment group 5_replicate 5A_Cy3

source_name: Liver total RNA reference pool

source_name: Liver total RNA from trout fed PFDA diet


title: CGH: Soy hypernodulating FN mutant R01M08DMN10NSFBV vs. Reference

source_name: FN mutant R01M08DMN10NSFBV

value: Mutant shows hypernodulating.  Mutant was known as "RN03" in Bolon et al. (Plant Physiol. 156:240-253)


title: Primary_10

value: Unique sample

value: Study 2

value: Primary


title: Primary_9


title: Liver_2000 ppm PFOA_treatment group 3_replicate 3B_Cy3

value: Mt. Shasta

value: 4 months


title: Primary_8


title: CGH: Soy No nodules FN mutant R01M04DMN10NSFBV vs. Reference

source_name: FN mutant R01M04DMN10NSFBV

value: Leaf sample

value: fast neutron mutant

value: Mutant shows No nodules.  Mutant was known as "RN01" in Bolon et al. (Plant Physiol. 156:240-253)

source_name: FN pooled reference


title: Liver_2000 ppm PFOA_treatment group 3_replicate 3B_Cy5


title: Primary_7


title: CGH: Soy high seed protein FN mutant R15C01p33a02 vs. Reference

source_name: FN mutant R15C01p33a02

value: Mutant shows high seed protein.  Mutant was known as "PO08" in Bolon et al. (Plant Physiol. 156:240-253)

value: M92-220 background


title: Liver_2000 ppm PFOA_treatment group 3_replicate 3A_Cy3


title: Liver_2000 ppm PFOA_treatment group 3_replicate 3A_Cy5


title: Primary_5

value: Study 1


title: Primary_6


title: CGH: Soy high seed protein, high protein/oil, chimeric leaves FN mutant R60C28p35c02 vs. Reference

source_name: FN mutant R60C28p35c02

value: Mutant shows high seed protein, high protein/oil, chimeric leaves.  Mutant was known as "PO03" in Bolon et al. (Plant Physiol. 156:240-253)

value: Leaf samples


title: CGH: Soy high seed oil, high seed protein+oil FN mutant R51C43p26e06 vs. Reference

source_name: FN mutant R51C43p26e06

value: Mutant shows high seed oil, high seed protein+oil .  Mutant was known as "PO07" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy low seed protein FN mutant R29C32p13i08 vs. Reference

source_name: FN mutant R29C32p13i08

value: Mutant shows low seed protein.  Mutant was known as "PO06" in Bolon et al. (Plant Physiol. 156:240-253)

value: 30 pooled soybean fast neutron mutants


title: Primary_4

source_name: Malignant melanoma


title: Liver_5 ppm Estradiol_treatment group 2_replicate 2C_Cy5

source_name: Liver total RNA from trout fed Estradiol diet


title: CGH: Soy low seed oil, low protein+oil FN mutant R60C52p28b09 vs. Reference

source_name: FN mutant R60C52p28b09

value: Mutant shows low seed oil, low protein+oil .  Mutant was known as "PO05" in Bolon et al. (Plant Physiol. 156:240-253)


title: Liver_5 ppm Estradiol_treatment group 2_replicate 2B_Cy5


title: WT technical replicate 2

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

institute: Institute for Research in Biomedicine (IRB, Barcelona)

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and1  min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 110%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Primary human keratinocytes

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: Primary human keratinocytes

tag: genotype/variation

value: Cbx4 WT


title: Liver_5 ppm Estradiol_treatment group 2_replicate 2B_Cy3


title: Primary_3 (rep)

value: Replicate sample

value: Primary


title: Liver_5 ppm Estradiol_treatment group 2_replicate 2A_Cy3

value: Mt. Shasta

value: 4 months


title: CGH: Soy high seed protein FN mutant R32C17p18e09 vs. Reference

source_name: FN mutant R32C17p18e09

value: Leaf sample

value: fast neutron mutant

value: Mutant shows high seed protein.  Mutant was known as "PO01" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy high seed proten/oil FN mutant R62C02p30a01 vs. Reference

source_name: FN mutant R62C02p30a01

value: Mutant shows high seed protein/oil.  Mutant was known as "PO02" in Bolon et al. (Plant Physiol. 156:240-253)

value: M92-220 background


title: Primary_3

value: Unique sample

value: Study 1


title: WT technical replicate 1


title: Primary_2


title: Liver_5 ppm Estradiol_treatment group 2_replicate 2A_Cy5


title: AS technical replicate 3

value: Cbx4 SUMO mutant


title: CGH: Soy late maturity FN mutant R32C17p18idm vs. Reference

source_name: FN mutant R32C17p18idm

value: Mutant shows late maturity.  Mutant was known as "LM05" in Bolon et al. (Plant Physiol. 156:240-253)

value: Leaf samples


title: Primary_1


title: Liver_Control_treatment group 1_replicate 1B_Cy3

source_name: Liver total RNA from trout fed control diet


title: CGH: Soy late maturity FN mutant R29C32p13jdm vs. Reference

source_name: FN mutant R29C32p13jdm

value: Mutant shows late maturity.  Mutant was known as "LM07" in Bolon et al. (Plant Physiol. 156:240-253)

value: 30 pooled soybean fast neutron mutants


title: Liver_Control_treatment group 1_replicate 1B_Cy5

source_name: Liver total RNA reference pool


title: Liver_Control_treatment group 1_replicate 1A_Cy3


title: CGH: Soy tall plant FN mutant R01M05DMN10NSFBV vs. Reference

source_name: FN mutant R01M05DMN10NSFBV

value: Mutant shows tall plant.  Mutant was known as "RN02" in Bolon et al. (Plant Physiol. 156:240-253)


title: AS technical replicate 1

value: Primary human keratinocytes


title: CGH: Soy late maturity FN mutant R06C50p07idm vs. Reference

source_name: FN mutant R06C50p07idm

value: Mutant shows late maturity.  Mutant was known as "LM06" in Bolon et al. (Plant Physiol. 156:240-253)


title: Liver_Control_treatment group 1_replicate 1C_Cy5

value: Mt. Shasta


title: AS technical replicate 2


title: Ctrl technical replicate 3

value: pBABE control


title: Liver_Control_treatment group 1_replicate 1A_Cy5

value: 4 months


title: Ctrl technical replicate 2


title: 14178311 - V2TS-7 repet1 vs LUC repet1

status: Public on Aug 01 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Determine the level of expression in transgenic plants expressing geminiviral gene silencing suppressors.

hyb_protocol: LUC repet1 Cy5 / V2TS-7 repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

source_name: LUC repet1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=MS+Kanamycine  hygrometry=not controlled  Temperature=22ºC  Light=16h light-8h darkness

extract_protocol: LUC repet1:32ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: original entry

value: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: Columbia

value: wild type

value: whole plant

source_name: V2TS-7 repet1

extract_protocol: V2TS-7 repet1:29ug. (Qiagen_RNeasy.pdf)

value: arabidopsis thaliana (columbia)  mutant (v2 overexpressing line) -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: V2 overexpressing line


title: tri-culture fed by 40µmol TCE_rep3

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using the MAS5 algorithm and R statistical program . Each microarray was normalized by global scaling the signal intensities to a value of 2500.

organism:
Nitratidesulfovibrio vulgaris str. Hildenborough
Methanobacterium congolense
Dehalococcoides mccartyi 195

source_name: 195/DVH/MC tri-culture grown on 3rd day

label_protocol: One µg of cDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: 15 replicates of 100mL culture were grown to early exponential phase when 90% of the given amount of trichloroethene was dechlorinated. For strain 195 on 7th day, for co-culture fed by 78µmol TCE on 5th day, for co-culture fed by 40µmol TCE on 3rd day, and for tri-culture fed by 40µmol TCE on 3rd day.  500mL cells were collected by filtration as one biological replicate. Three biological replicates were prepared.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit (Qiagen,Valencia, CA) according to the manufacturer’s instructions. cDNA was synthesized according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

tag: bacteria

value: tri-culture

tag: agent

value: TCE

tag: tce concentration

tag: time

value: 3rd day


title: 14178314 - V2TS-7 repet2 vs LUC repet2

hyb_protocol: LUC repet2 Cy5 / V2TS-7 repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: LUC repet2

extract_protocol: LUC repet2:26ug. (Qiagen_RNeasy.pdf)

tag: genotype

tag: tissue

source_name: V2TS-7 repet2

extract_protocol: V2TS-7 repet2:16ug. (Qiagen_RNeasy.pdf)


title: tri-culture fed by 40µmol TCE_rep2

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: Ctrl technical replicate 1


title: tri-culture fed by 40µmol TCE_rep1


title: 14178315 - V2TS-7 repet3 vs LUC repet3

hyb_protocol: LUC repet3 Cy5 / V2TS-7 repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: LUC repet3

extract_protocol: LUC repet3:21ug. (Qiagen_RNeasy.pdf)

tag: cultivar

source_name: V2TS-7 repet3

extract_protocol: V2TS-7 repet3:12ug. (Qiagen_RNeasy.pdf)


title: 14178310 - LUC repet1 vs V2TS-7 repet1

hyb_protocol: V2TS-7 repet1 Cy5 / LUC repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.