title: Control rep.3

status: Public on Jul 31 2016

type: RNA

city: Rome

first: Saveria

last: Pastore

address: via Monti di Creta 104

country: Italy

institute: Istituto Dermopatico dell'Immacolata, IRCCS

description:
replicate 3
Sample 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using Genome Studio Gene Expression Module

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal human keratinocytes_untreated

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

tag: cell line

value: primary culture

tag: cell type

value: keratinocytes

tag: treatments

value: Untreated Control, 6 hours


title: rdr126_rehydaration_Poly (A+)_rep2

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs from Poly (A+) RNA samples were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: rdr126 rehydration Poly (A+) rep2

label_protocol: 5 ng of Poly (A+) RNA fractions were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: 2-week-old rdr1/2/6 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium.

extract_protocol: Total RNA was extracted from whole plants using Plant RNA Isolation Reagent (Life technologies). 100μg total RNA was separated to Poly (A+) RNA fractions  using Ambion Poly A purist.

treatment_protocol: The plants were transferred from MS medium to plastic dish and kept for 2 hr and treated with water for 2hr

tag: tissue

value: whole plant

tag: treatment

value: rehydration


title: Control rep.1

description:
replicate 1
Sample 1


title: PD168393 and TNF alpha rep.2

description:
replicate 2
Sample 8

value: PD168393 (2 microM) and TNF alpha (50 ng/ml), 6 hours


title: PD168393 and TNF alpha rep.3

description:
replicate 3
Sample 9


title: ko-macrophage, biological rep2

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.
algorithm-name = rma-gene-default

organism: Mus musculus

source_name: peritoneal macrophage of  Prkch-/-Apoe-/- mouse

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Each mouse was maintained in SPF condition.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: Aorta and liver were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 30 ml of saline via the left ventricle. Tissues were isolated and preserved at –80°C until RNA preparation.

tag: strain

tag: genotype/variation

value: Prkch-/-Apoe-/-

tag: age

value: 17 weeks

tag: gender

value: female

tag: diet

value: regular diet

tag: fasting

tag: treatment protocol

value: no stimulation


title: TNF alpha rep.2

description:
replicate 2
Sample 5

source_name: Normal human keratinocytes_TNFalpha

value: TNF alpha (50 ng/ml), 6 hours


title: wt-liver, biological rep2

source_name: liver of Apoe-/- mouse

value: liver

value: Apoe-/-

value: 20 weeks

value: male

value: high fat diet-fed for 12 weeks

value: re-fed

value: no treatment


title: ko-macrophage, biological rep1

value: 18 weeks


title: wt-liver, biological rep1


title: rdr126_rehydaration_Poly (A+)_rep3

source_name: rdr126 rehydration Poly (A+) rep3

value: whole plant


title: TNF alpha rep.1

description:
replicate 1
Sample 4

value: primary culture

value: keratinocytes


title: PD168393 and TNF alpha rep.1

description:
replicate 1
Sample 7

value: PD168393 (2 microM) and TNF alpha (50 ng/ml), 6 hours


title: Control rep.2

description:
replicate 2
Sample 2

value: Untreated Control, 6 hours


title: wt-macrophage, biological rep3

source_name: peritoneal macrophage of  Apoe-/- mouse

value: 27 weeks

value: female


title: rdr126_dry_Poly (A+)_rep1

source_name: rdr126 dry Poly (A+)

value: drought stress


title: TNF alpha rep.3

description:
replicate 3
Sample 6

value: TNF alpha (50 ng/ml), 6 hours


title: ko-liver biological rep2

source_name: liver of Prkch-/-Apoe-/- mouse

value: liver

value: Prkch-/-Apoe-/-


title: rdr126_dry_Poly (A+)_rep3


title: wt-macrophage, biological rep2

value: Apoe-/-

value: 17 weeks

value: regular diet

value: no stimulation


title: ko-macrophage, biological rep3


title: ko-liver biological rep1

value: 20 weeks

value: male

value: high fat diet-fed for 12 weeks

value: re-fed

value: no treatment


title: wt-macrophage, biological rep1

value: 18 weeks


title: rdr126_dry_Ploy (A+)_rep2

value: whole plant


title: WT_rehydaration_Poly (A+)_rep3

source_name: WT rehydration Poly (A+) rep3

value: rehydration


title: WT_dry_Poly (A+)_rep1

source_name: WT dry Poly (A+)


title: rdr126_con_Poly (A+)_rep1

source_name: rdr126 con Poly (A+)

value: unstress condition


title: WT_rehydaration_Poly (A+)_rep2

source_name: WT rehydration Poly (A+) rep2


title: WT_dry_Poly (A+)_rep2

value: drought stress


title: rdr126_con_poly (A+)_rep3


title: WT_con_Poly (A+)_rep1

source_name: WT con Poly (A+)


title: rdr126_con_Poly (A-)_rep2

description: Poly (A-) RNA

hyb_protocol: 600 ng of cRNAs from Poly (A+) RNA sample and 3 mg of cRNAs from Poly (A-) RNA sample were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

source_name: rdr126_con_Poly (A-)

label_protocol: 5 ng of Poly (A+) RNA fraction and 1.4 μg of Poly (A-) samples were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: rdr1/2/6 (rdr1-1; rdr2-1; rdr6-15) and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium for 2 weeks. Growth chamber was set on 22 degree, 16 light 8 dark condition.

extract_protocol: Total RNA was extracted from whole plants using Plant RNA Isolation Reagent (Life technologies). 100μg total RNA was separated to Poly (A+) RNA  and Poly (A-) fractions  using Ambion Poly A purist. Poly (A-) RNA sample was prepared by depleting rRNA using Invitrogen RiboMinus Plant Kit.

treatment_protocol: The plants were transferred from MS medium to plastic dish and kept for 2 hr.

tag: genotype


title: WT_dry_Poly (A+)_rep3


title: rdr126_dry_Poly (A-)_rep2

description: Poly (A-) RNA

source_name: rdr126_dry_Poly (A-)


title: WT_rehydaration_Poly (A+)_rep1

source_name: WT rehydration Poly (A+) rep1


title: rdr126_con_Poly (A+)_rep2


title: WT_con_Poly (A+)_rep3


title: WT_dry_Poly (A-)_rep3

description: Poly (A-) RNA

source_name: WT_dry_Poly (A-)


title: rdr126_con_Poly (A-)_rep1

description: Poly (A-) RNA


title: rdr126_dry_Poly (A-)_rep1

description: Poly (A-) RNA


title: WT_dry_Poly (A-)_rep1

description: Poly (A-) RNA


title: rdr126_rehydaration_Poly (A+)_rep1

source_name: rdr126 rehydration Poly (A+) rep1


title: rdr126_con_Poly (A-)_rep3

description: Poly (A-) RNA


title: Cal/04_A11320_w15_3

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

description: Infection_Animal #_Timepoint

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 8X60K rhesus macaque (Design ID 048534) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were normalized using the quantile normalization method available in GeneData Analyst 7.6.

organism: Macaca fascicularis

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Macaques in each group (Vaccinated and Control) were intramuscularly anaesthetized with ketamine (10 mg/kg) and inoculated with a suspension containing 10^6.5 p.f.u. ml-1 of CA09 virus through a combination of intratracheal (4.5 ml), intranasal (0.5 ml per nostril), ocular (0.1 ml per eye) and oral (1 ml) routes (resulting in a total infectious dose of 10^7.4 PFU).  Bronchoalveolar lavages (BAL) were collected two weeks prior to challenge and at days 3, 7, and 10 post infection.

extract_protocol: All lysates were processed simultaneously.  RNA was extracted using QIAGEN microRNeasy spin columns per the manufacturer’s protocol.

treatment_protocol: BAL samples were mixed with Trizol and stored at -80°C until RNA isolation.

tag: vaccination status

value: Control

tag: timepoint (dpi)

tag: infection

tag: animal #

value: Bronchoaveolar lavage


title: WT_con_Poly (A+)_rep2


title: rdr126_dry_Poly (A-)_rep3

description: Poly (A-) RNA


title: Cal/04_A11310_w15_3

description: Infection_Animal #_Timepoint


title: WT_dry_Poly (A-)_rep2

description: Poly (A-) RNA


title: Cal/04_A11310_w16

description: Infection_Animal #_Timepoint


title: Pre_A11322_w13

description: Infection_Animal #_Timepoint

value: Vaccinated

value: Preinfection

value: Preinfection control


title: Pre_A11305_w13

description: Infection_Animal #_Timepoint


title: WT_con_Poly (A-)_rep3

description: Poly (A-) RNA

source_name: WT_con_Poly (A-)


title: rdr126_dry_Poly (A+)_rep3

description: Poly (A+) RNA

source_name: rdr126_dry_Poly (A+)


title: rdr126_dry_Ploy (A+)_rep2

description: Poly (A+) RNA


title: Cal/04_A11306_w16

description: Infection_Animal #_Timepoint


title: Cal/04_A11323_w16

description: Infection_Animal #_Timepoint


title: Pre_A11313_w13

description: Infection_Animal #_Timepoint


title: rdr126_dry_Poly (A+)_rep1

description: Poly (A+) RNA


title: Cal/04_A11317_w16

description: Infection_Animal #_Timepoint


title: WT_con_Poly (A-)_rep2

description: Poly (A-) RNA


title: nlp7-roots-2

city: West Lafayette

first: Anjali

middle: S

last: Iyer-Pascuzzi

state: IN

address: 915 W. State Street

department: Botany and Plant Pathology

institute: Purdue University

description: Gene expression data from 5 dai mutant roots

hyb_protocol: After fragmentation, samples were sent to Expression Analysis in Durham, NC for hybridization according to their protocols.

scan_protocol: Chips were scanned at Expression Analysis in Durham, NC according to their protocols

data_processing: Processed data attached here is with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Target intensity was set abitrarily to 250.

source_name: Arabidopsis nlp7-1_root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle amplification protocol from 1 ug total RNA.

growth_protocol: Plants were grown at 22 deg C with 16 hour days on pH 5.7 1x MS agar plates

extract_protocol: Roots were cut at the hypocotyl junction and placed into RLT buffer, then into liquid nitrogen. RNA was extracted using the RNAeasy micro kit from Qiagen.

treatment_protocol: no treatment, experiment is WT vs mutant under standard laboratory conditions

tag: ecotype

value: root


title: nlp7-roots-1


title: WT_dry_Poly (A+)_rep1

description: Poly (A+) RNA

source_name: WT_dry_Poly (A+)


title: rdr126_con_Poly (A+)_rep2

description: Poly (A+) RNA

source_name: rdr126_con_Poly (A+)


title: Cal/04_A11307_w16

description: Infection_Animal #_Timepoint


title: wt-aorta, biological rep1

description:
wt-aorta_1
Total RNA was mixed from four independent mice.

data_processing:
CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.
Algorithm: ExpressionStat 5.0

source_name: aorta of Apoe-/- mouse

value: aorta

value: Apoe-/-

value: fed


title: Cal/04_A11318_w16_4

description: Infection_Animal #_Timepoint


title: WT_con_Poly (A+)_rep3

description: Poly (A+) RNA

source_name: WT_con_Poly (A+)


title: ko-aorta, biorlogical rep1

description:
ko-aorta_1
Total RNA was mixed from four independent mice.

source_name: aorta of Prkch-/-Apoe-/- mouse

value: Prkch-/-Apoe-/-

value: 20 weeks

value: male

value: high fat diet-fed for 12 weeks


title: rdr126_con_Poly (A+)_rep1

description: Poly (A+) RNA

value: whole plant


title: rdr126_con_poly (A+)_rep3

description: Poly (A+) RNA


title: Pre_A11320_w13

description: Infection_Animal #_Timepoint


title: Cal/04_A11309_w16_4

description: Infection_Animal #_Timepoint


title: WTCol-roots-1

description: Gene expression data from 5 dai WT roots

source_name: Arabidopsis Col-0_root

value: wild type


title: WT_dry_Poly (A+)_rep3

description: Poly (A+) RNA


title: WT_dry_Poly (A+)_rep2

description: Poly (A+) RNA


title: 98326 Gfi1-KDxNup98_RNA

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

department: Hematology

country: Germany

institute: University Hospital Essen

description: Gene expression array from bone marrow cellsof adult mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MG-430_2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

label: Biotin

source_name: bone marrow cells from mouse

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions of Rneasy Kit Qiagen

treatment_protocol: After collecting whole bone marrow cells, cells were treated with erylyse and resuspend in RLT-buffer

value: Vav-1 Nup98/HoxD13 tg

value: Gfi1 KD

tag: cell type

value: bone marrow cell


title: 101367 Gfi1-KIxNup98_RNA

value: Gfi1 KI


title: NP7

city: Leioa

first: Ibon

last: Cancio

address: B/sarriena s/n

country: Spain

institute: UPV/EHU

description:
thicklip grey mullet
Liver_inmmature

hyb_protocol: 200 ng of labeled cRNA were mixed with fragmentation buffer and blocking agent and fragmented by incubation at 60ºC for 30 minutes following protocol.; They were mixed with 2X GEX Hybridization buffer HI-RPM, and hybridize at 65ºC for 17h 45 min. Different tissue and sex samples were hybridized to different slides and arrays to avoid signal intensity differences due to hybridization/washing artifacts, spatial differences, etc

scan_protocol: Scan Area: Default: (61x 21.6 mm); Scan Resolution: 5 mm; Green Channel; eXtended Dynamic Range (XDR): Selected; XDR High: 100% PMT; XDR Low: 10% PMT

data_processing: Image Analysis with Feature Extraction Software (FE; version:9.5.3.1 ); quatile normalization; Data statistical analysis made in TIGR MultiExperiment Viewer (MEV) : MeV 4.0

organism: Chelon labrosus

source_name: Liver

label_protocol: 1st step: double stranded cDNA synthesis using MMLV-RT and Oligo dT-T7Promoter primer; 2nd Step: In vitro transcription and Cy-3 labeling of ds cDNA using the antisense T7 Promoter Primer,T7 RNA Polymerase and Cy-3-CTP; QuickAmp Labeling Kit one-color (Cy3-CTP included); 200 ng of purified total RNA were used in the labeled cRNA synthesis reaction.; Sample F-L-1 was labeled twice as a control

growth_protocol: environmental samples, field samples

extract_protocol: Extraction method: Trizol (Invitrogen) and further column purification (RNeasy Mini kit, QIAGEN)

treatment_protocol: Total RNA extracted from liver tissue

value: Liver

tag: developmental stage

value: immature

value: NP


title: 1PA2

description:
thicklip grey mullet
Liver_inmmature

treatment_protocol: Total RNA extracted from liver tissues comparission

tag: tissue

tag: sample time

value: First sampling (day 5)

tag: geographic source

value: inner part of the harbour (Pasaia_AZTI)


title: Cal/04_A11323_w15_3

description: Infection_Animal #_Timepoint

value: Control

value: Bronchoaveolar lavage


title: 1PA4

description:
thicklip grey mullet
Liver_inmmature


title: NP5

description:
thicklip grey mullet
Liver_inmmature

tag: treatment


title: TGFb+

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

hyb_protocol: The samples were hybridized to miRCURY LNA microRNA Array according to the manufacturer's protocol.

scan_protocol: The miRNA arrays were scanned using a GenePix 4000B scanner (Molecular Devices), and data were analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics).

data_processing: The quantified signals were background corrected and normalized with quantile normalization.

source_name: MS1 cells, TGFb+

label_protocol: MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturer's recommendations.

growth_protocol: MS1 cells were cultured under standard conditions.

extract_protocol: Total RNA was prepared using miRNeasy Mini kit (Qiagen).

treatment_protocol: MS1 cells were treated with/without TGF-b for 72 hours.

tag: cell line

value: endothelial cell line

value: transforming growth factor-beta (TGF-b)


title: WT_con_Poly (A+)_rep1

description: Poly (A+) RNA

value: unstress condition


title: WTCol-roots-2

tag: genotype/variation

value: root


title: WT_con_Poly (A+)_rep2

description: Poly (A+) RNA

value: whole plant


title: TGFb-

source_name: MS1 cells, TGFb-


title: Pre_A11323_w13

description: Infection_Animal #_Timepoint

value: Preinfection

value: Preinfection control


title: Cal/04_A11317_w16_4

description: Infection_Animal #_Timepoint

value: Vaccinated


title: NP2

description:
thicklip grey mullet
Liver_inmmature


title: NP1

description:
thicklip grey mullet
Liver_inmmature


title: Cal/04_A11312_w16_4

description: Infection_Animal #_Timepoint


title: 100249 Gfi1-KDxNup98-RNA

tag: strain

value: Vav-1 Nup98/HoxD13 tg

value: Gfi1 KD

value: bone marrow cell


title: Pre_A11321_w13

description: Infection_Animal #_Timepoint


title: 87515 Gfi1-KIxNup98_RNA

value: Gfi1 KI


title: 104678 Gfi1-KDxNup98-RNA


title: 1PA3

description:
thicklip grey mullet
Liver_inmmature

value: Liver

value: immature


title: BAP5

description:
thicklip grey mullet
Liver_inmmature

value: BAP


title: NP4

description:
thicklip grey mullet
Liver_inmmature

value: NP


title: NP3

description:
thicklip grey mullet
Liver_inmmature


title: BAP2

description:
thicklip grey mullet
Liver_inmmature


title: BAP3

description:
thicklip grey mullet
Liver_inmmature


title: BAP9

description:
thicklip grey mullet
Liver_inmmature


title: BAP7

description:
thicklip grey mullet
Liver_inmmature


title: M-A-4_NC

description:
thicklip grey mullet
US45102972_252114610005_S02_GE1-v5_95_Feb07_2_2
Liver_male_adult_Arriluze

hyb_protocol: 600 ng of labeled cRNA were mixed with fragmentation buffer and blocking agent and fragmented by incubation at 60ºC for 30 minutes following protocol.; They were mixed with 2X GEX Hybridization buffer HI-RPM, and hybridize at 65ºC for 17h 45 min. Different tissue and sex samples were hybridized to different slides and arrays to avoid signal intensity differences due to hybridization/washing artifacts, spatial differences, etc

source_name: Liver, field sample

treatment_protocol: Total RNA extracted from 2 tissues comparission (Gonad,liver) and gender hepatic and gonad comparission (female, male, intersex)

tag: Sex

value: male

value: adult


title: CD4

description:
thicklip grey mullet
Liver_inmmature

value: CD


title: 91897 Gfi1-KIxNup98_RNA


title: CD9

description:
thicklip grey mullet
Liver_inmmature


title: BAP4

description:
thicklip grey mullet
Liver_inmmature


title: Cal/04_A11317_w15_3

description: Infection_Animal #_Timepoint

value: Bronchoaveolar lavage


title: Cal/04_A11322_w15_3

description: Infection_Animal #_Timepoint


title: WT_con_Poly (A-)_rep1

description: Poly (A-) RNA

value: unstress condition


title: CD6

description:
thicklip grey mullet
Liver_inmmature


title: Pre_A11318_w13

description: Infection_Animal #_Timepoint


title: Cal/04_A11306_w15_3

description: Infection_Animal #_Timepoint


title: Cal/04_A11312_w16

description: Infection_Animal #_Timepoint

value: Control


title: Pre_A11317_w13

description: Infection_Animal #_Timepoint

value: Preinfection


title: Cal/04_A11318_w16

description: Infection_Animal #_Timepoint


title: CD7

description:
thicklip grey mullet
Liver_inmmature


title: F-A-5_NC

description:
thicklip grey mullet
US45102972_252114610005_S02_GE1-v5_95_Feb07_1_4
Liver_female_adult_Arriluze

value: female


title: F-A-6_NC

description:
thicklip grey mullet
US45102972_252114610005_S02_GE1-v5_95_Feb07_2_1
Liver_female_adult_Arriluze


title: CD2

description:
thicklip grey mullet
Liver_inmmature


title: ACETONE 8

description:
thicklip grey mullet
Liver_inmmature

value: acetone


title: ACETONE 9

description:
thicklip grey mullet
Liver_inmmature


title: CD1

description:
thicklip grey mullet
Liver_inmmature


title: ACETONE 7

description:
thicklip grey mullet
Liver_inmmature


title: ACETONE 2

description:
thicklip grey mullet
Liver_inmmature


title: ACETONE 4

description:
thicklip grey mullet
Liver_inmmature


title: ACETONE 1

description:
thicklip grey mullet
Liver_inmmature


title: M-A-3_NC

description:
thicklip grey mullet
US45102972_252114610004_S01_GE1-v5_95_Feb07_2_3
Liver_male_adult_Arriluze


title: I-GO-2_NC

description:
thicklip grey mullet
US45102972_252114610005_S02_GE1-v5_95_Feb07_1_3
Gondad_intersex male_adult_Ondarrua

source_name: Gonad, field sample

value: Gondad

value: intersex male


title: I-L-1_NC

description:
thicklip grey mullet
US45102972_252114610004_S01_GE1-v5_95_Feb07_2_4
Liver_intersex male_adult_Ondarrua


title: CONTROL 7

description:
thicklip grey mullet
Liver_inmmature

value: control


title: CONTROL 6

description:
thicklip grey mullet
Liver_inmmature


title: Cal/04_A11322_w16_4

description: Infection_Animal #_Timepoint

value: Vaccinated


title: M-A-2_NC

description:
thicklip grey mullet
US45102972_252114610003_S01_GE1-v5_95_Feb07_1_4
Liver_male_adult_Arriluze

value: Liver


title: F-A-4_NC

description:
thicklip grey mullet
US45102972_252114610004_S01_GE1-v5_95_Feb07_2_2
Liver_female_adult_Arriluze


title: 2PD7

description:
thicklip grey mullet
Liver_inmmature

value: immature

value: Second sampling (day 21)

value: outer part of the harbour (Pasaia_Donibane)


title: Pre_A11310_w13

description: Infection_Animal #_Timepoint

value: Preinfection control


title: CONTROL 5

description:
thicklip grey mullet
Liver_inmmature


title: 2PD6

description:
thicklip grey mullet
Liver_inmmature


title: CONTROL 4

description:
thicklip grey mullet
Liver_inmmature


title: CONTROL 3

description:
thicklip grey mullet
Liver_inmmature


title: CONTROL 2

description:
thicklip grey mullet
Liver_inmmature


title: M-A-1_NC

description:
thicklip grey mullet
US45102972_252114610003_S01_GE1-v5_95_Feb07_1_3
Liver_male_adult_Arriluze

value: male

value: adult


title: 2PD5

description:
thicklip grey mullet
Liver_inmmature


title: F-A-3_NC

description:
thicklip grey mullet
US45102972_252114610003_S01_GE1-v5_95_Feb07_1_2
Liver_female_adult_Arriluze


title: 2PD4

description:
thicklip grey mullet
Liver_inmmature


title: Cal/04_A11322_w16

description: Infection_Animal #_Timepoint

value: Bronchoaveolar lavage


title: Cal/04_A11315_w16

description: Infection_Animal #_Timepoint


title: Cal/04_A11321_w15_3

description: Infection_Animal #_Timepoint


title: Cal/04_A11318_w15_3

description: Infection_Animal #_Timepoint


title: Cal/04_A11305_w15_3

description: Infection_Animal #_Timepoint


title: 2PD3

description:
thicklip grey mullet
Liver_inmmature


title: F-A-2_NC

description:
thicklip grey mullet
US45102972_252114610003_S01_GE1-v5_95_Feb07_1_1
Liver_female_adult_Arriluze


title: 2PD2

description:
thicklip grey mullet
Liver_inmmature


title: 2PA7

description:
thicklip grey mullet
Liver_inmmature

value: inner part of the harbour (Pasaia_AZTI)


title: F-A-1_NC

description:
thicklip grey mullet
US45102972_252114610002_S01_GE1-v5_95_Feb07_2_4
Liver_female_adult_Arriluze


title: 2PA4

description:
thicklip grey mullet
Liver_inmmature


title: Cal/04_A11323_w16_4

description: Infection_Animal #_Timepoint

value: Control


title: 2PA5

description:
thicklip grey mullet
Liver_inmmature


title: 2PA3

description:
thicklip grey mullet
Liver_inmmature


title: 2PA1

description:
thicklip grey mullet
Liver_inmmature


title: I-L-2_NC

description:
thicklip grey mullet
US45102972_252114610002_S01_GE1-v5_95_Feb07_2_1
Liver_ Intersex male_adult_Ondarrua

value: Intersex male


title: 2PA2

description:
thicklip grey mullet
Liver_inmmature


title: 1PD8

description:
thicklip grey mullet
Liver_inmmature

value: First sampling (day 5)


title: 1PD5

description:
thicklip grey mullet
Liver_inmmature


title: M-A-5_NC

description:
thicklip grey mullet
US45102972_252114610001_S01_GE1-v5_95_Feb07_1_2
Liver_male_adult_Arriluze

value: female


title: 1PD4

description:
thicklip grey mullet
Liver_inmmature


title: I-GO-1_NC

description:
thicklip grey mullet
US45102972_252114610002_S01_GE1-v5_95_Feb07_2_2
Gonad_intersec male_adult_Ondarrua

value: Gonad

value: intersec male


title: 1PD3

description:
thicklip grey mullet
Liver_inmmature


title: 1PD2

description:
thicklip grey mullet
Liver_inmmature


title: 1PD1

description:
thicklip grey mullet
Liver_inmmature


title: 1PA5

description:
thicklip grey mullet
Liver_inmmature


title: F-GI-2_NC

source_name: Gill, field sample

extract_protocol: Total RNA extracted from several tissues comparison (Gonad, brain, gill, gonad). Extraction method: Trizol (Invitrogen) and further column purification (RNeasy Mini kit, QIAGEN)

value: Gill

tag: gender


title: F-B-5_NC

source_name: Brain, field sample

value: Brain


title: F-B-6_NC


title: F-GI-6_NC


title: F-GI-3_NC


title: F-GI-1_NC


title: F-GI-5_NC


title: F-B-4_NC


title: F-GI-4_NC


title: 1PA8

description:
thicklip grey mullet
Liver_inmmature

value: Liver


title: F-B-3_NC


title: F-GO-6_NC


title: F-GO-4_NC


title: F-GO-5_NC


title: F-B-1_NC


title: F-GO-2_NC


title: Spleen_40ukg/g_rep6

description: C6 (Dieta 40%)

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 600 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 17 hours at 10 rpm in the hybridization oven.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent Technologies), with ozone-barrier slide covers (Agilent P/N G2505-60550). Profiles AgilentG3_GX_1Color.  SCAN C SETTINGS.  Dye Channel:Green.  Scan Region:61 x 21,6 mm.  Scan resolution (um):3.  Tiff:20 bit.

data_processing:
Images (.tiff images) were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies).  Feature Extraction protocol for data extraction: GE1_107_Sep09.  Design File/Grid Template: 035147_D_F_20110629.  QC Metric Set: GE1_QCMT_Sep09.
Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 12.6 (Agilent Technologies).That file contains the summarized data per biological feature and per sample.  Preprocessing:  First we transform all Feature Extraction flags to Absent/Marginal/Present calls (Compromised/Not Detected/Detected Flags in the new GeneSpring versions), the same way as we did with the Tissue Experiment:  Feature is NOT Positive and significant: ABSENT (Compromised).  Feature is NOT uniform: ABSENT (Compromised).  Feature is NOT well above background: MARGINAL (Not Detected).  Feature is Saturated: MARGINAL (Not Detected).  Feature is Population outlier: ABSENT (Compromised).  Threshold raw signals (lineal data) to 1.  Summarization: calculate the geometric mean of replicated probes The resulted summarized lineal data is the “Raw Signal” in result files. Gene Spring uses the “gProcessedSignals” from Feature Extraction txt Raw Data Files).Log base2 transformation.  Intra-chip normalization: quantile normalization.  Baseline to Mean of Control (Dieta 0) Samples.  Filter Probesets based on Present/Absent calls: Use flag spot information in data files. Entities retained in which 100 % of samples in 1 out of any 3 conditions (DIETA 0, DIETA 20%, DIETA 40%) have Present (Detected) or Marginal (Not Detected) Flag.

organism: Anguilla anguilla

source_name: spleen, pool of 3

label_protocol: One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) Version 6.5 May 2010. Samples are retrotranscribed (first strand synthesis) and labeled using Low imput Quick Amp Labeling kit, One color (Agilent Technologies, Cat. Nº 5190-2305) following manufacturer instructions.  First, total RNA is retrotranscribed with AffinityScript Reverse Transcriptase (AffinityScript RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT is in vitro transcribed by T7 RNA pol in the presence of either Cy3-CTP or Cy5-CTP fluorophores to generate amplified and labeled cRNA.  Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).  Amount of nucleic acid labeled: 50 ng.  After labeling and purification, cRNA is quantify with NanoDrop ND-1000 spectrophotometer in order to determine the yield and specific activity of each reaction.  Yield: ug of cRNA. Should be > 0.825 ug.  Specific activity: pmol Cy3 per ug of cRNA. Should be > 6.

extract_protocol: Extraction method: TRIzol (Invitrogen)

treatment_protocol: Elvers (1.7 ± 0.2 g) obtained from local fishermen (Delta del Ebro, Spain) were fed at different doses of LPSp (0, 20 and 40 μg LPSp kg BW-1 day-1) for a period of 70 days (4 replicates per dietary group). LPSp was added to the diet (52% protein, 24% fat, 9% ash) by top coating the pellets with the lyophilized powder of LPSp dissolved in 2% fish oil (diets manufactured by ALLERQUA, Denmark). The trial was conducted in 100 L tanks (40 L functional volume) connected to a recirculation unit (IRTAmar®) and water quality was as follows: temperature, 21 ± 0.5 ºC; pH, 7.5 ± 0.1; photoperiod, 12 L:12 D and oxygen at saturation levels.

value: spleen

value: elver

tag: diet

value: LPSp

tag: dose


title: Spleen_40ukg/g_rep2

description: C2 (Dieta 40%)


title: Spleen_40ukg/g_rep5

description: C5 (Dieta 40%)


title: 1PA7

description:
thicklip grey mullet
Liver_inmmature

value: immature


title: F-GO-3_NC


title: Spleen_20ug/kg_rep4

description: B4 (Dieta 20%)


title: Spleen_40ukg/g_rep7

description: C7 (Dieta 40%)


title: Spleen_40ukg/g_rep4

description: C4 (Dieta 40%)


title: Spleen_20ug/kg_rep7

description: B7 (Dieta 20%)


title: Spleen_40ukg/g_rep1

description: C1 (Dieta 40%)


title: Spleen_20ug/kg_rep2

description: B2 (Dieta 20%)


title: Spleen_20ug/kg_rep6

description: B6 (Dieta 20%)


title: F-L-5_NC

source_name: Liver_field sample


title: Cal/04_A11309_w16

description: Infection_Animal #_Timepoint

tag: vaccination status

tag: timepoint (dpi)


title: F-B-2_NC


title: Spleen_40ukg/g_rep3

description: C3 (Dieta 40%)


title: F-GO-1_NC


title: Spleen_20ug/kg_rep5

description: B5 (Dieta 20%)


title: F-L-4_NC


title: F-L-3_NC


title: Spleen_20ug/kg_rep3

description: B3 (Dieta 20%)


title: Spleen_controlDiet_rep7

description: D7 (Dieta 0)

value: control


title: Spleen_controlDiet_rep6

description: D6 (Dieta 0)


title: F-L-2_NC

value: adult


title: Spleen_20ug/kg_rep1

description: B1 (Dieta 20%)


title: Spleen_controlDiet_rep5

description: D5 (Dieta 0)


title: Spleen_controlDiet_rep3

description: D3 (Dieta 0)


title: Spleen_controlDiet_rep2

description: D2 (Dieta 0)


title: F-L-1_NC


title: Liver_Oil_14d_7

hyb_protocol: 600 ng of labeled cRNA were mixed with fragmentation buffer and blocking agent and fragmented by incubation at 60ºC for 30 minutes following protocol.; They were mixed with 2X GEX Hybridization buffer HI-RPM, and hybridize at 65ºC for 17h 45 min. Different samples wererandomly  hybridized to different slides and arrays to avoid signal intensity differences due to hybridization/washing artifacts, spatial differences, etc

data_processing: Image Analysis with Feature Extraction Software (FE; version:9.5.3.1 ); quantile normalization; average of copied probes; Data statistical analysis made in TIGR MultiExperiment Viewer (MEV) : MeV 4.0

organism: Scophthalmus maximus

source_name: Liver sample, oil treated group, 14 days of exposure

growth_protocol: Juvenile turbots, S. maximus (n = 500; weight 358 ± 93 g, length 28 ± 2 cm, mean ± SD) were purchased from a fish farm (France Turbot, Tredarzec, France). Before starting the experiment, they were acclimatized for 20 days in two laboratory tanks of 1000 L (control tank and treatment tank). They were fed daily with dried pellets (Aquaculture food Le Gouessant®, Lamballe, France, 4.5 mm diameter, total protein 54% of dry matter and crude fat 12% of dry matter). Running seawater was supplied at a flow rate of 5 L min−1 in both tanks. Water was taken from Sea of Iroise, France, and sterilized by means of UV-rays and filters system. Experiments were performed in the facilities of Cedre (Brest, France).   The light regime was set according to the season: 14 h light, 10 h dark. Water salinity (35–36‰), water pH (7.98 ± 0.06), oxygen concentration (228 ± 18 μmol L−1) and sea water temperature (16 ± 2 °C) were measured daily. During the experiment, turbots were fed twice per day with dried pellets. Additional information in Ruiz et al, 2012.

treatment_protocol: Turbots were exposed for 14 days to 10% of the water soluble fraction (WSF) of heavy fuel oil no. 6 using a continuous flow-through system with water aeration described by Aas et al. (2000). The system made it possible to expose fish to relative stable concentrations of dispersed crude oil, similar to those reported after accidental oil spills such as Prestige and Exxon Valdez shipwrecks: 2090 ng L−1 (González et al., 2006) and 6000 ng L−1 (Short and Harris, 1996), respectively. The experimental system consisted of a 2 m high column, which was filled with glass beads coated with oil and seawater was running through the column from top to bottom, to produce the WSF of the oil, which was diluted ten times before being administered to the animals. Additional information in Ruiz et al, 2012.

value: liver

value: juvenile

value: oil

tag: days of exposure


title: Eel_Liver_time2_Do (SAMPLE 30)

description: hepatic Total RNA

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent Technologies), with ozone-barrier slide covers (Agilent P/N G2505-60550). Profiles AgilentG3_GX_1Color.  SCAN C SETTINGS.  Dye Channel: Green.  Scan Region: 61 x 21,6 mm.  Scan resolution (um): 3.  Tiff: 20 bit.

data_processing:
Images (.tiff images) were quantified using Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies).Software (ver. 10.7.3.1) (Agilent Technologies).  Feature Extraction protocol for data extraction: GE1_107_Sep09.  Design File/Grid Template: 035147_D_F_20110629.  QC Metric Set: GE1_QCMT_Sep09.   The processed signal is corrected for background and microarray processing artifacts (Spatial detrending). For background correction it uses the negative control feature data, which corresponds to sequences with no expected hybridization, and it is an indication of unspecific binding or hybridization. The most significant data are:Standard deviation of the spot signal (feature and background).  Flagging of those features with anomalous data (non-uniform outliers, which are features with high standard deviation of the spot signal, saturated features, and population outliers for replicated features).  Calculation and correction of the systematic error.
Raw data processed on GeneSpring GX 12.6 (Agilent Technologies). File contains the summarized data per biological feature and per sample.Preprocessing:  First we transform all Feature Extraction flags to Absent/Marginal/Present calls (Compromized/Not Detected/Detected Flags in the new GeneSpring versions).  Feature is NOT Positive and significant: ABSENT (Compromized).  Feature is NOT uniform: ABSENT (Compromized).  Feature is NOT well above background: MARGINAL (Not Detected).  Feature is Saturated: MARGINAL (Not Detected).  Feature is Population outlier: ABSENT (Compromized).  Threshold raw signals (lineal data) to 1.  Summarization: calculate the geometric mean of replicated probes The resulted summarized lineal data is the “Raw Signal” in result files. Gene Spring uses the “gProcessedSignals” from Feature Extraction txt Raw Data Files).  Log base2 transformation.  Intra-chip normalization: quantile normalization.  Baseline to Control Samples. Mean of T0 UP samples.  Filter Probesets based on Present/Absent calls: Use flag spot information in data files. Entities retained in which 100 % of samples in 1 out of any 5 conditions (T0 UP, T1 UP, T1 DOWN, T2 UP, T2 DOWN) have Present or Marginal Flag.  There are 61.377 Biological Features or probes in the microarray design, and after filtering 42.469 have been retained.

label_protocol: Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) Version 6.5 May 2010. Samples are retrotranscribed (first strand synthesis) and labeled using Low imput Quick Amp Labeling kit, One color (Agilent Technologies, Cat. Nº 5190-2305) following manufacturer instructions.First, total RNA is retrotranscribed with AffinityScript Reverse Transcriptase (AffinityScript RT), an engineered thermostable mutant derived from Moloney Murine Leukemia Virus (MMLV) reverse transcriptase, using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT is in vitro transcribed by T7 RNA pol in the presence of either Cy3-CTP or Cy5-CTP fluorophores to generate amplified and labeled cRNA. Labeled samples were purified with silica-based RNeasy spin columns (Qiagen).  Amount of nucleic acid labeled: 50 ng.  After labeling and purification, cRNA is quantify with NanoDrop ND-1000 spectrophotometer in order to determine the yield and specific activity of each reaction.  Yield: ug of cRNA. Should be > 0.825 ug.  Specific activity: pmol Cy3 per ug of cRNA. Should be > 6.  All the labeled samples were above those limits.

extract_protocol: TRIzol total RNA extraction method (Invitrogen)

tag: agent

value: SMURFFIT-KAPPA paper industry effluent

tag: time

value: T2 (after 15 days of exposure)

tag: location

value: Downstream

tag: group


title: Liver_Oil_14d_6

tag: tissue

tag: developmental stage


title: Liver_Oil_14d_5

tag: treatment


title: Eel_Liver_time2_Do (SAMPLE 28)

description: hepatic Total RNA


title: Eel_Liver_time2_Do (SAMPLE 29)

description: hepatic Total RNA


title: T3-H5

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep5.

hyb_protocol: 200 ng of labeled cRNA were mixed with fragmentation buffer and blocking agent and fragmented by incubation at 60ºC for 30 minutes following protocol. They were mixed with 2X GEX Hybridization buffer HI-RPM, and hybridized at 65ºC for 17h 45 min.

scan_protocol: Scan area: default (61x 21.6 mm); Scan resolution: 5 mm; Green channel; eXtended Dynamic Range (XDR): selected; XDR high: 100% PMT; XDR low: 10% PMT.

data_processing: Image analysis with Feature Extraction Software (FE; version:9.5.3.1 ); quantile normalization; data statistical analysis made in TIGR MultiExperiment Viewer (MEV): MeV 4.0. The following step after quantile normalization step: Baseline to median of control samples. Control samples : T1-C samples, Sample A signal for gene X= normalized signal for gene X in Sample A (log2)   median normalized  signal for gene X in control samples (log2).

source_name: Liver, high dose TBT, week 3

label_protocol: 1st step: double stranded cDNA synthesis using MMLV-RT and Oligo dT-T7Promoter primer; 2nd Step: In vitro transcription and Cy-3 labeling of ds cDNA using the antisense T7 Promoter Primer, T7 RNA Polymerase and Cy-3-CTP; QuickAmp Labeling Kit one-color (Cy3-CTP included); 200 ng of purified total RNA were used in the labeled cRNA synthesis reaction.

growth_protocol: Environmental samples, field samples.

extract_protocol: Total RNA was extracted from hepatic tissues. Extraction method: Trizol (Invitrogen) and further column purification (RNeasy Mini kit, QIAGEN).

treatment_protocol: TBT exposure; control, low dose (10ng/L), and high dose (500ng/L). Sampling times: 1 day (T1), 1 week (T2), and 3 weeks (T3).

value: high dose tributyltin (TBT)

tag: exposure time

value: week 3


title: Spleen_controlDiet_rep4

description: D4 (Dieta 0)


title: T3-H6

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep6.


title: Spleen_controlDiet_rep1

description: D1 (Dieta 0)


title: Eel_Liver_time2_Do (SAMPLE 27)

description: hepatic Total RNA


title: T3-H7

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep7.


title: T3-H4

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep4.


title: Eel_Liver_time2_Do (SAMPLE 26)

description: hepatic Total RNA


title: Liver_Oil_14d_3


title: Eel_Liver_time2_UP (SAMPLE 21)

description: hepatic Total RNA

value: Upstream


title: T3-H2

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep2.


title: Eel_Liver_time2_UP (SAMPLE 23)

description: hepatic Total RNA


title: Liver_Oil_14d_4


title: Eel_Liver_time2_UP (SAMPLE 22)

description: hepatic Total RNA


title: T3-H1

description:
thicklip grey mullet
T3=2 weeks; H=high dose; Rep1.


title: Eel_Liver_time2_UP (SAMPLE 24)

description: hepatic Total RNA


title: Eel_Liver_time2_UP (SAMPLE 20)

description: hepatic Total RNA


title: Eel_Liver_time2_Do (SAMPLE 25)

description: hepatic Total RNA


title: Liver_Control_14d_8

source_name: Liver sample, control group, 14 days of exposure


title: Liver_Oil_14d_1


title: T3-L6

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep6.

source_name: Liver, low dose TBT, week 3

value: low dose tributyltin (TBT)


title: T3-L7

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep7.


title: T3-L5

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep5.


title: Eel_Liver_time1_Do (SAMPLE 14)

description: hepatic Total RNA

value: T1 (after 3 days of exposure)


title: Eel_Liver_time1_Do (SAMPLE 18)

description: hepatic Total RNA


title: Eel_Liver_time1_Do (SAMPLE 17)

description: hepatic Total RNA


title: Eel_Liver_time2_UP (SAMPLE 19)

description: hepatic Total RNA


title: Eel_Liver_time1_Do (SAMPLE 13)

description: hepatic Total RNA


title: Eel_Liver_time1_Do (SAMPLE 16)

description: hepatic Total RNA


title: Liver_Control_14d_7


title: Liver_Control_14d_5


title: Eel_Liver_time1_Do (SAMPLE 15)

description: hepatic Total RNA


title: Eel_Liver_time1_UP (SAMPLE 12)

description: hepatic Total RNA


title: Liver_Control_14d_3


title: Liver_Control_14d_4


title: Eel_Liver_time1_UP (SAMPLE 9)

description: hepatic Total RNA


title: T3-L4

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep4.


title: Eel_Liver_time1_UP (SAMPLE 11)

description: hepatic Total RNA


title: Eel_Liver_time1_UP (SAMPLE 10)

description: hepatic Total RNA


title: T3-L2

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep2.


title: Eel_Liver_time1_UP (SAMPLE 7)

description: hepatic Total RNA


title: T3-L3

description:
thicklip grey mullet
T3=2 weeks; L=low dose; Rep3.


title: Eel_Liver_time0 (SAMPLE 5)

description: hepatic Total RNA

value: ToUP


title: Liver_Styrene_7d_5

source_name: Liver sample, treated group, 7 days of exposure

treatment_protocol: Turbots were exposed to styrene for 7 days. Then fish were maintained for another 7 days in clean water for the recovery. The styrene exposure system was built in order to perform a controlled exposure to the chemical in a realistic way, simulating the possible concentration present in the sea surface after a styrene spill. The experimental system was composed of a mixing tank connected to an exposure tank and a degassing column. In the mixing tank, which had a capacity of 316 L, a slick of styrene was placed in contact with the aqueous phase and dissolved slowly. Then, contaminated water containing the dissolved fraction of the slick was pumped to the exposure tank (300 L) where turbots were maintained. Styrene disappeared rapidly from water and, therefore, the concentration remaining in the exposure tank would be similar to that appearing in seawater immediately after a spill. The exposure tank was connected to a system of waste water recuperation by overflow. During the experimentation, a water flow of 1.3 L min−1 was pumped and sent on a degassing column before being directed to the mixing tank. A second circuit ensured a renewal of fresh sea water to maintain the nitrate and nitrite concentrations stable. In addition, the oxygen saturation of water was maintained into this tank by a compressor, which injected air via diffuser. The degassing column favored the gaseous exchange, allowed water oxygenation by percolation on glass beads and allowed elimination of dissolved carbon dioxide produced by organisms (carbon dioxide transfer from water to air). During the experimentation, both mixing and exposure tanks were kept covered to avoid cross contamination from the styrene exposure tank to the control tank. The concentration of styrene was monitored in seawater during the experiment. Fish samples were collected before the exposure (T0), after 3 and 7 days of exposure and after 7 days of recovery in clean water. Muscle tissues of 10 control and 10 styrene-exposed turbots were collected after 7 days of exposure to determine the level of styrene in fish. Styrene concentration was measured in muscle because xenobiotic metabolism in this organ is much slower than in liver and, thus, styrene accumulation in muscle could better reflect environmental exposure. Livers of 6-7 turbots per experimental group at each sampling time were dissected out, immersed individually in RNA later® and frozen in liquid nitrogen for transcription studies. Livers, gonads and blood samples of 12 turbots per experimental group were collected and processed individually at each sampling time for liver AOX activity, plasma vitellogenin levels and histopathological analysis of liver and gonad. For lysosomal membrane stability test a small piece of the liver obtained from 5 fish per experimental group were rapidly frozen in liquid nitrogen and stored at −80 ◦C until sectioning. Additional information in Ruiz et al, 2012.

value: styrene


title: Eel_Liver_time1_UP (SAMPLE 8)

description: hepatic Total RNA


title: Liver_Styrene_7d_6


title: Eel_Liver_time0 (SAMPLE 6)

description: hepatic Total RNA


title: T3-C4

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep4.

source_name: Control liver, week 3


title: T3-C3

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep3.


title: 66 (T3_Hg)

hyb_protocol: All cRNA labelled samples purified and quantified using RNeasy spin columns (Qiagen) and NanoDrop ND-1000 spectophotometer respectively. As a result yield and specific activity of each reaction was measured and all of them were above following limits 0.825 ug yield and 6 pmol Cy3 per μg of cRNA. Finally, 50 ng of labelled cRNA were obtained. Hybridization step was performed in a SureHyb hybridization chamber (Agilent), a total of 600ng of labelled cRNA was used in a volume of 40 μL. They were incubated in the hybridization oven at 10 rpm, 65 oC for 17 hours. Slides were washed using GE wash buffer 1 (1 minute), GE wash buffer 2 (37 oC, 1 minute), and acetonitrile wash (10 seconds). Finally, scanning process was performed on a G2565 DNA microarray scanner (Agilent) with ozone barrier slide cover using following settings: Green channel dye, 61*21.6 mm scan region, scan resolution of 3 μm and 20 bit Tiff.

scan_protocol: Feature Extraction software v. 10.7.3.1 (Agilent) was used to feature signal intensity extraction. It was subsequently processed on GeneSpring GX 12.6 (Agilent Technologies).

data_processing: As preprocessing, first all Feature Extraction flags were transformed to Absent/Marginal/Present calls (Compromized/Not Detected/Detected Flags in the new GeneSpring versions), as follows: Feature is NOT Positive and significant: ABSENT (Compromized);Feature is NOT uniform: ABSENT (Compromized);Feature is NOT well above background: MARGINAL (Not Detected);Feature is Saturated: MARGINAL (Not Detected); Feature is Population outlier: ABSENT (Compromized);Threshold raw signals (lineal data) to 1.  After that a geometric mean of replicated probes was calculated and the resulted Raw Signal was transformed as Log2. Furthermore, an intra-chip normalization was done based on quantile normalization. Finally a baseline was performed with the mean value of control samples.

source_name: Hg treatment, T3

label_protocol: The hybridization step was performed using the One-Color Microarray-Based Gene Expression Analysis “Low Input Quick Amp Labeling” protocol (Agilent, version 6.5, May, 2010) following manufacturer’s instructions. Total RNA was used as starting material to produce cRNA, which was in vitro synthesized using QuickAmp Labelling Kit one-color (Agilent). At first step, it was retrotranscribed using AffinityScript reverse transcriptase, an MMLV reverse transcriptase and Oligo dT primers coupled to T7 promoter. After that, in vitro transcription and Cy-3 labelling of ds cDNA was performed using the antisense T7 Promoter Primer, T7 RNA Polymerase and Cy-3-CTP.

extract_protocol: Liver (100 mg) was gridded in TRizol® (Invotrgen) using Precellys homogenizer (Bertin technologies, France) and Precellys lysing kit MK28-R (Bertin; 2*5000, 30sec). After that, RNA was extracted following TRIzol® (Invitrogen) manufacturers´s instructions and purified using RNAsy Kit (Qiagen) with the additional DNAse treatment (Qiagen) on columns. RNA quantity and quality was measured using Epoch TM Take 3 TM spectrophotometer (Biotek) and 2100 bioanalyzer (Agilent) respectively. RIN values above 8 were discharged.

treatment_protocol: An exposure laboratory experiment was performed in the “Ur Biologia eta Experimentazio Zerbitzua” (UBEZ) of the University of the Basque Country (UPV/EHU) A total of 84 eels, 20.23 ± 2.84 cm in length, were acclimatized to laboratory conditions for 2 weeks in a 10 L water glass tanks under controlled conditions: 12 h light/dark cycle at 18oC, conductivity 600 μS. During this period animals were fed with commercial flakes. Ammonium, nitrites and nitrates kits (Sera GmbH) were used to systematically asses the levels of nitrogenous compounds which were maintained at 0-0.5mg/l; 0-0.5 mg/l, and 5-10 mg/l, respectively. When highest concentrations within those ranges were achieved seawater was partially replaced.  A day before exposure experiment, animals were placed in 4 aquaria with 8 L of water at 600 μS. In each aquarium 21 eels were randomly distributed and exposed to: metal-mercury (Hg) (Fluka-Sigma-Aldrich) at a concentration of 100μg/L; and to a phitosterol, β-sitosterol (Sigma) at a concentration of 150 μg/ L. The last compound needed ethanol (0.01%) as vehicle. In addition to an ethanol control group, a water control (600μS) without contaminant was also prepared.

value: Hg treatment

value: T3 (9 days)


title: Eel_Liver_time0 (SAMPLE 4)

description: hepatic Total RNA

value: control

value: immature


title: T3-C7

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep7.

value: liver


title: Eel_Liver_time0 (SAMPLE 3)

description: hepatic Total RNA


title: 44 (T3_Hg)


title: Liver_Styrene_7d_1

value: juvenile


title: Liver_Styrene_7d_3


title: Liver_Styrene_7d_4


title: T3-C1

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep1.


title: 73 (T3_Hg)


title: 41 (T3_C)

source_name: control group, T3

value: control group


title: 18 (T3_C)


title: 35 (T2_Hg)

source_name: Hg treatment, T2

value: T2 (6 days)


title: 12 (T2_Hg)


title: Liver_Control_7d_5

source_name: Liver sample, control group, 7 days of exposure


title: 20 (T3_Hg)


title: Eel_Liver_time0 (SAMPLE 1)

description: hepatic Total RNA


title: T3-C2

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep2.


title: Eel_Liver_time0 (SAMPLE 2)

description: hepatic Total RNA


title: 19 (T3_Hg)


title: Liver_Styrene_7d_2


title: 65 (T3_C)


title: Liver_Control_7d_7


title: 59 (T2_Hg)


title: 34 (T2_C)

source_name: control group, T2


title: 17 (T3_C)


title: 42 (T3_C)


title: T2-H6

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep6.

source_name: Liver, high dose TBT, week 1

value: week 1


title: T2-H4

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep4.


title: Liver_Control_7d_2


title: T2-H7

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep7.


title: 58 (T2_Hg)


title: Liver_Control_7d_6


title: 33 (T2_C)


title: Liver_Control_7d_4


title: T2-H5

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep5.


title: Liver_Styrene_3d_4

source_name: Liver sample, treated group, 3 days of exposure


title: T2-L4

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep4.

source_name: Liver, low dose TBT, week 1


title: 57 (T2_C)


title: T2-H1

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep1.


title: T2-L5

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep5.


title: 11 (T2_Hg)


title: T2-L6

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep6.


title: 9 (T2_C)


title: 3 (T1_Hg)

source_name: Hg treatment, T1

value: T1 (3 days)


title: 10 (T2_C)


title: Liver_Styrene_3d_2


title: T2-L2

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep2.


title: 52 (T1_Hg)


title: 49 (T1_C)

source_name: control group, T1


title: T2-H3

description:
thicklip grey mullet
T2=1 week; H=high dose; Rep3.

value: high dose tributyltin (TBT)


title: T2-L1

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep1.


title: 4 (T1_Hg)


title: 1 (T1_C)


title: 50 (T1_C)


title: Liver_Control_7d_3


title: Liver_Styrene_3d_1


title: 28 (T1_Hg)


title: Liver_Control_3d_7_2

source_name: Liver sample, control group, 3 days of exposure


title: 70 (T3_bS)

source_name: b-sitosterol, T2

value: b-sitosterol


title: Liver_Control_3d_5_2


title: Liver_Styrene_3d_7


title: Liver_Styrene_3d_3


title: Liver_Styrene_3d_5


title: T2-L3

description:
thicklip grey mullet
T2=1 week; L=low dose; Rep3.


title: 27 (T1_Hg)


title: 48 (T3_bS)


title: 26 (T1_C)


title: 69 (T3_C+)

source_name: Ethanol (b-sitosterol dissolvent), T2

value: Ethanol (b-sitosterol dissolvent)


title: 76 (T3_C+)


title: T2-C2

description:
thicklip grey mullet
T2=1 week; C=control; Rep2.

source_name: Control liver, week 1


title: T3-C5

description:
thicklip grey mullet
T3=2 weeks; C=control; Rep5.

value: week 3


title: 71 (T3_bS)


title: T2-C1

description:
thicklip grey mullet
T2=1 week; C=control; Rep1.


title: 25 (T1_C)


title: Liver_Control_3d_2_2


title: Liver_Control_3d_6_2


title: Liver_Control_3d_1BIS


title: T2-C7

description:
thicklip grey mullet
T2=1 week; C=control; Rep7.


title: T1-H7

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep7.

source_name: Liver, high dose TBT, day 1

value: day 1


title: 24 (T3_bS)


title: T2-C5

description:
thicklip grey mullet
T2=1 week; C=control; Rep5.


title: 47 (T3_bS)


title: T1-H6

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep6.


title: T2-C4

description:
thicklip grey mullet
T2=1 week; C=control; Rep4.


title: 23 (T3_bS)


title: T1-H5

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep5.


title: 40 (T2_bS)


title: 75 (T3_C+)


title: 61 (T2_C+)


title: Liver_Control_3d_4_2


title: Liver_Oil_3d_7

source_name: Liver sample, oil treated group, 3 days of exposure

treatment_protocol: Turbots were exposed for 3 days to 10% of the water soluble fraction (WSF) of heavy fuel oil no. 6 using a continuous flow-through system with water aeration described by Aas et al. (2000). The system made it possible to expose fish to relative stable concentrations of dispersed crude oil, similar to those reported after accidental oil spills such as Prestige and Exxon Valdez shipwrecks: 2090 ng L−1 (González et al., 2006) and 6000 ng L−1 (Short and Harris, 1996), respectively. The experimental system consisted of a 2 m high column, which was filled with glass beads coated with oil and seawater was running through the column from top to bottom, to produce the WSF of the oil, which was diluted ten times before being administered to the animals. Additional information in Ruiz et al, 2012.

value: oil treated


title: Liver_Control_3d_3


title: T2-C6

description:
thicklip grey mullet
T2=1 week; C=control; Rep6.


title: Liver_Oil_3d_5


title: T1-H4

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep4.


title: 68 (T3_C+)


title: 60 (T2_C+)


title: Liver_Oil_3d_3


title: 46 (T3_C+)


title: T1-H3

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep3.


title: 22 (T3_C+)


title: 63 (T2_bS)


title: mAst-E2-3

city: Aurora

first: Diana

last: Cittelly

state: CO

department: Pathology

institute: University of Colorado AMC

hyb_protocol: Samples were hybridized using the Gene Atlas Microarray System (Affymetrix) hybridization chamber; 20 hours at 48 C

scan_protocol: Samples were scanned and imaged using the Gene Atlas Microarray System Fludics and Imaging equipment (Affymetrix)

data_processing: CEL files were processed in Partek Genomic Suite using RMA Quantile normalization; intensity values were scaled by log2 transformation

label_protocol: Fragmented ssDNA was labeled with the Affymetrix WT Terminal Labeling and Hybridization kit according to the instructions, using Affymetrix proprietary biotinylated labeling reagent.

extract_protocol: Sorted human cells were collected in lysis buffer and RNA extracted using RNAqueous-Micro Total RNA Kit (Ambion).

tag: cell line

value: MDA231-derived brain trophic 231BR cells

value: E-treated, with astrocytes


title: 62 (T2_bS)


title: mAst-E2-2


title: 16 (T2_bS)


title: 37 (T2_C+)


title: 15 (T2_bS)


title: 39 (T2_bS)


title: Liver_Oil_3d_8


title: Liver_Oil_3d_6


title: Liver_Oil_3d_4


title: Liver_Oil_3d_2


title: mAst-OH2

value: OH-treated, with astrocytes


title: T1-H1

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep1.


title: T1-H2

description:
thicklip grey mullet
T1=1 day; H=high dose; Rep2.


title: mAst-OH1


title: 38 (T2_C+)


title: T1-L4

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep4.

source_name: Liver, low dose TBT, day 1

value: low dose tributyltin (TBT)


title: mAst-OH3


title: Liver_Oil_3d_1


title: T1-L7

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep7.

value: immature


title: T1-L6

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep6.

value: liver


title: 13 (T2_C+)


title: OH3

source_name: 231BR-OH-treated-no astrocytes

value: OH-treated, no astrocytes


title: mAst-E2-1


title: 14 (T2_C+)


title: 56 (T1_BS)

source_name: b-sitosterol, T1


title: Liver_Control_3d_8

value: juvenile

value: control


title: Liver_Control_3d_7


title: Bortezomib responsive

city: Chengdu

first: Li

last: Zhang

state: Sichuan

address: No. 37 Guo Xue Xiang

department: Department of Hematology

country: China

institute: West China Hospital, Sichuan University

description: MiRNA

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.
After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: exosomes

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: serum

tag: serum component

value: exosomes

tag: drug resistance status

value: Bortezomib-response


title: Bortezomib resistance

description: MiRNA

value: Bortezomib-resistance


title: Liver_Control_3d_6


title: T1-L5

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep5.


title: 55 (T1_BS)

value: b-sitosterol

value: T1 (3 days)


title: OH2


title: T1-C7

description:
thicklip grey mullet
T1=1 day; C=control; Rep7.

source_name: Control liver, day 1

value: day 1


title: E2-3

source_name: 231BR-E-treated-no astrocytes

value: E-treated, no astrocytes


title: Liver_Control_3d_2


title: 7 (T1_BS)


title: Liver_Control_3d_5


title: Liver_Control_3d_4


title: 8 (T1_BS)


title: OH1

value: MDA231-derived brain trophic 231BR cells


title: 32 (T1_BS)


title: 31 (T1_BS)


title: 53 (T1_C+)

source_name: Ethanol (b-sitosterol dissolvent), T1

value: Ethanol (b-sitosterol dissolvent)


title: E2-2


title: T1-L1

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep1.


title: 30 (T1_C+)


title: Liver_Control_3d_1


title: T1-C5

description:
thicklip grey mullet
T1=1 day; C=control; Rep5.


title: 54 (T1_C+)


title: T1-C6

description:
thicklip grey mullet
T1=1 day; C=control; Rep6.


title: T1-L2

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep2.


title: T1-L3

description:
thicklip grey mullet
T1=1 day; L=low dose; Rep3.


title: E2-1


title: T1-C4

description:
thicklip grey mullet
T1=1 day; C=control; Rep4.


title: 29 (T1_C+)


title: T1-C1

description:
thicklip grey mullet
T1=1 day; C=control; Rep1.


title: 6 (T1_C+)


title: T1-C2

description:
thicklip grey mullet
T1=1 day; C=control; Rep2.


title: 5 (T1_C+)


title: MCF7_Ag-30_24h_rep3

status: Public on Jul 30 2016

city: Wageningen

first: Meike

last: van der Zande

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

hyb_protocol: 750 ng of each labeled cRNA sample was hybridized overnight at 58 °C onto the Illumina HumanHT-12 v4 Expression BeadChip.

scan_protocol: the BeadChip was washed and incubated with Streptavidin-Cy3 and the chips were scanned using the Illumina iScan array scanner (Illumina, San Diego, USA). Primary gene expression of the scanned BeadChip arrays was performed using Illumina’s Genomestudio v 2011.1 software with the default settings advised by Illumina.

data_processing: Normalization and analysis of the datasets was performed using MadMax. A variance Stabilization and Normalization (VSN) method was used to obtain expression values. After background subtraction the spot intensities were floored to 40, followed by 2 log mean centering and calculation of 2 log rations of treatments versus the average of the control samples.

source_name: MCF-7, 30nm AgNP exposure, 24h

label_protocol: Biotin (biotin-16-UTP) labeled cRNA was amplified from the total RNA using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Life Technologies, Bleiswijk, the Netherlands).

growth_protocol: Both cell types were seeded at a density of ~40,000 ells/cm2 in a 6-well plate, and grown towards a confluency of ~60%.

extract_protocol: cells were washed to remove remaining nanoparticles, resuspended in 600 µl RLT buffer (RNeasy, Qiagen, Venlo, the Netherlands) containing 1% β-mercapto ethanol (Sigma). The lysate was further purified using the Qiashredder, followed by the RNeasy Mini Kit, including DNase treatment (Qiagen, Venlo, The Netherlands). RNA concentration and purity was determined using the Nanodrop ND1000 spectrophotometer (Isogen, De Meern, The Netherlands) and the Shimadzu MultiNA (Tokyo, Japan) and Agilent Bioanalyzer was used to analyze the quality and integrity of the RNA samples.

treatment_protocol: Cells were exposed for 6h or 24h at 37°C (95% RH, 5% CO2) to Ag-20, Ag-30, Ag-60, or Ag-110 AgNPs at a concentration of 25 µg/ml, or to AgNO3 at a concentration of 1.5 µg/ml (n=3)

tag: cell type

value: MCF-7 (ATCC)

tag: exposure duration

tag: exposure material

value: 30nm AgNPs

tag: exposure dose

value: 25 µg/ml


title: MCF7_Ag-110_24h_rep3

source_name: MCF-7, 110nm AgNP exposure, 24h

value: 110nm AgNPs


title: MCF7_Ag-110_24h_rep2


title: MCF7_Ag-60_24h_rep3

source_name: MCF-7, 60nm AgNP exposure, 24h

value: 60nm AgNPs


title: MCF7_Ag-60_24h_rep2


title: MCF7_Ag-30_24h_rep2


title: MCF7_Ag-110_24h_rep1


title: FIO rep2

city: Postgraduate Institute of Medical Education & Research

first: sanjay

middle: kumar

last: bhadada

state: sec-12, chandigarh

address: room no: 2, 4th floor, Block:F,Nehru hospital

department: Endocrinology

country: India

institute: Postgraduate Institute of Medical Education and Research

description: 40 year old Male patient with FIO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human PrimeView 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: The data were analyzed with Expression Console and Gene springGX 12.0 using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: RNA/Trans-Iliec Bone

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

extract_protocol: Total RNA prepared using Trizol extraction Method

value: Trans-Iliac Bone biopsy

tag: age

tag: gender

value: male

tag: disease state

value: Fibrogenesis imperfecta ossium


title: MCF7_AgNO3_24h_rep3

source_name: MCF-7, AgNO3 exposure, 24h

value: 1.5 µg/ml


title: MCF7_Ag-20_24h_rep2

source_name: MCF-7, 20nm AgNP exposure, 24h

value: 20nm AgNPs


title: control rep2

description: 35 year old Male without any Bone, Metabolic or Inflammatory disease, presented with Post-traumatic fracture.

value: control


title: MCF7_Ag-110_6h_rep3

source_name: MCF-7, 110nm AgNP exposure, 6h


title: MCF7_ctrl_24h_rep2

source_name: MCF-7, ctrl, 24h


title: MCF7_Ag-110_6h_rep2


title: MCF7_Ag-60_6h_rep2

source_name: MCF-7, 60nm AgNP exposure, 6h


title: MCF7_Ag-110_6h_rep1


title: MCF7_ctrl_24h_rep1


title: MCF7_Ag-60_24h_rep1


title: control rep1


title: MCF7_Ag-60_6h_rep1


title: MCF7_AgNO3_24h_rep1


title: MCF7_Ag-20_24h_rep3


title: MCF7_Ag-30_24h_rep1


title: MCF7_Ag-60_6h_rep3


title: MCF7_Ag-30_6h_rep3

source_name: MCF-7, 30nm AgNP exposure, 6h


title: MCF7_AgNO3_24h_rep2


title: MCF7_ctrl_24h_rep3


title: FIO rep1

description: 40 year old Male patient with FIO


title: MCF7_Ag-30_6h_rep2


title: MCF7_Ag-20_6h_rep3

source_name: MCF-7, 20nm AgNP exposure, 6h


title: MCF7_AgNO3_6h_rep4

source_name: MCF-7, AgNO3 exposure, 6h


title: MCF7_AgNO3_6h_rep2


title: MCF7_Ag-30_6h_rep1


title: MCF7_ctrl_6h_rep3

source_name: MCF-7, ctrl, 6h


title: MCF7_Ag-20_6h_rep2


title: MCF7_AgNO3_6h_rep3


title: MCF7_ctrl_6h_rep2


title: MCF7_AgNO3_6h_rep1


title: Caco2_Ag-110_24h_rep3

source_name: Caco-2, 110nm AgNP exposure, 24h

value: Caco-2 (HTB-37TM; ATCC)


title: MCF7_Ag-20_6h_rep1


title: Caco2_Ag-110_24h_rep1


title: MCF7_ctrl_6h_rep1


title: Caco2_Ag-110_24h_rep2


title: Caco2_Ag-60_24h_rep1

source_name: Caco-2, 60nm AgNP exposure, 24h


title: Caco2_Ag-60_24h_rep2


title: BS90 septic injury 12h biological replicate 2

city: Albuquerque

first: Coen

middle: M

last: Adema

state: NM

address: 1 University of New Mexico

department: CETI Biology MSC03 2020

institute: University of New Mexico

hyb_protocol: Probes (experimental and URR) were combined in GEx hybridization buffer (Agilent Gene Expression Hybridization Kit), and samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers and incubated in a rotary oven, 65C, 17h)

scan_protocol: Scanned on an Agilent G2505C DNA Microarray Scanner. Agilent Feature Extraction (version 10.5.1.1) was used for data extraction from the generated image files and to generate QC reports for each array.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Biomphalaria glabrata

source_name: pool of 5 snails, bacterial injection,  12h

label_protocol: 50 ng of total RNA was reverse transcribed (Affinityscript RT) and used as template for cRNA synthesis by T7 RNA polymerase in presence of  Cy3 or Cy5-labeled CTP (Labelit). Labeled cRNA was purified (RNAeasy minikit, Qiagen) and specific activity determined with a nanodrop 100.

growth_protocol: BB02 and BS90 strain Biomphalaria glabrata snails were lab-reared (lettuce ad libitum, 12 h light: 12 h dark schedule). Adult snails of 10-12mm shell diameter were used for this study.

extract_protocol: Total RNA eas extracted using Trizol following manufacturer's instructions.  Sample quality was determined with Agilent Bioanalyzer and NanoDrop spectrophotometer. Biological replicates were pooled from 5 individuals.

value: adult

value: whole body

tag: strain

source_name: snails URR, pooled RNA samples for maximum feature reactivity

value: BB02 BS90 Mline


title: Caco2_Ag-60_24h_rep3


title: BS90 septic injury 12h biological replicate 1

description: pooled RNA samples for maximum feature reactivity


title: Caco2_Ag-30_24h_rep3

source_name: Caco-2, 30nm AgNP exposure, 24h


title: Caco2_AgNO3_24h_rep2

source_name: Caco-2, AgNO3 exposure, 24h


title: Caco2_AgNO3_24h_rep1


title: Caco2_Ag-20_24h_rep1

source_name: Caco-2, 20nm AgNP exposure, 24h


title: Caco2_Ag-20_24h_rep3


title: Caco2_AgNO3_24h_rep3


title: Caco2_Ag-30_24h_rep2


title: Caco2_Ag-20_24h_rep2


title: Caco2_ctrl_24h_rep3

source_name: Caco-2, ctrl, 24h


title: Caco2_ctrl_24h_rep2


title: control_knee joint cartilage_male_8 weeks

city: guanghzou

first: hua

last: wang

state: guangdong

address: gongzhou dadao bei

department: cell biology

institute: southern medical university

description: miRNA expression in knee joint cartilage

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

data_processing: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were  normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

source_name: knee joint cartilage, eight weeks old

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: All mice were housed in a pathogen-free animal facility.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: knee articular cartilage from 2 months old Col2a1Tsc1KO and control mice was peeled off and washed in sterile and RNase free 0.1M PBS buffer.

tag: genotype

value: wildtype

value: knee joint cartilage

value: 8 weeks old


title: BS90 injury 12h biological replicate 3

source_name: pool of 5 snails, wounded with hypodermic needle, 12h


title: Col2a1Tsc1KO_knee joint cartilage_male_8 weeks

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

value: Col2a1; Tsc1 KO


title: Caco2_Ag-110_6h_rep1

source_name: Caco-2, 110nm AgNP exposure, 6h

value: 25 µg/ml


title: Caco2_ctrl_24h_rep1


title: Caco2_Ag-110_6h_rep2

value: 110nm AgNPs


title: Caco2_Ag-110_6h_rep3


title: Caco2_Ag-60_6h_rep3

source_name: Caco-2, 60nm AgNP exposure, 6h

value: 60nm AgNPs


title: BS90 injury 12h biological replicate 2


title: Caco2_Ag-30_6h_rep2

source_name: Caco-2, 30nm AgNP exposure, 6h

value: 30nm AgNPs


title: Caco2_Ag-30_6h_rep1


title: Caco2_Ag-60_6h_rep2


title: BS90 untreated biological replicate 1

source_name: pool of 5 snails, sham exposed, 12h


title: Caco2_Ag-30_6h_rep3


title: Caco2_AgNO3_6h_rep3

source_name: Caco-2, AgNO3 exposure, 6h


title: Caco2_Ag-60_6h_rep1


title: Caco2_Ag-20_6h_rep1

source_name: Caco-2, 20nm AgNP exposure, 6h


title: Caco2_AgNO3_6h_rep1


title: BS90 untreated biological  replicate 2


title: Caco2_AgNO3_6h_rep2


title: Caco2_Ag-20_6h_rep2


title: Caco2_ctrl_6h_rep3

source_name: Caco-2, ctrl, 6h


title: Caco2_Ag-20_6h_rep3


title: Caco2_ctrl_6h_rep1


title: Caco2_ctrl_6h_rep2


title: Caco2_Ag-30_24h_rep1


title: MCF7_Ag-20_24h_rep1

source_name: MCF-7, 20nm AgNP exposure, 24h

value: MCF-7 (ATCC)


title: Paraquat-incubated Aag2 Cell Replicate 2

status: Public on Jul 29 2016

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

description: Biological replicate 2 of 4

hyb_protocol: The hybridizations were conducted on an Agilent-based microarray platform using custom-designed whole-genome 8 x 60K A. aegypti microarrays and reagents from Agilent Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned with an Agilent High Resolution Scanner (Agilent Technologies Inc., Santa Clara, CA, USA). Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Background-subtracted median fluorescent values were normalized according to a LOWESS normalization method, using MIDAS software. Low-intensity and flagged probes were excluded during the normalization procedure. The probes representing the same gene had their signals averaged to a single expression value per gene. Probes with more than more than one missing value for heme or paraquat were not analyzed. Differential expression analysis was done using the Significance Analysis of Microarrays (SAM) method (samr R package).

organism: Aedes aegypti

source_name: Pooled Control Aag2 Cell Samples

label_protocol: Two micrograms of total RNA were used for probe synthesis of cy3- and cy5-labeled cRNA using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies Inc., Santa Clara, CA, USA) according to the manufacturer’s protocol.

growth_protocol: Aag2 cells were maintained at 28°C in Schneider´s Drosophila medium with L-glutamine (Invitrogen-GIBCO, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum.

extract_protocol: Cells were submitted to total RNA extraction using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Cells were incubated with the heme solution diluent (0.1 M NaOH, 0.01 M phosphate buffer, used as control), 50 µM Heme (Hemin, Frontier Scientific Inc., Logan, UT, USA), or 100 µM paraquat (ChemService, West Chester, PA, USA), for 6 hours.

value: Aag2 (Grace - 1966)

value: embryonic

source_name: Paraquat-incubated Aag2 cells


title: 6mo_Control3

city: New York

first: Josefa

last: Sullivan

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with GeneSpring version 13.0 using Affymetrix default analysis settings and RMA summarization algorithm with quantile normalization. The baseline was transformed to the median of all samples and data was trimmed arbitrarily to exclude raw expression below 20

source_name: striatal tissue

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

growth_protocol: not applicable

extract_protocol: Total RNA was isolated using Trizol LS as per the manufacturer's protocol

treatment_protocol: WT or dKO

value: WT


title: Paraquat-incubated Aag2 Cell Replicate 1

description: Biological replicate 1 of 4


title: Heme-incubated Aag2 Cell Replicate 1

description: Biological replicate 1 of 4

source_name: Heme-incubated Aag2 cells


title: 6mo_Mut1

value: Ezh1; Ezh2 Camk Cre


title: 6mo_Mut5


title: 6mo_Mut2


title: 3mo_Mut3


title: 6mo_Control2


title: Heme-incubated Aag2 Cell Replicate 4

description: Biological replicate 4 of 4


title: 3mo_Mut2


title: 6mo_Control4


title: 6mo_Mut6


title: 3mo_Control4


title: 3mo_Control1


title: 6mo_Mut3


title: 6mo_Control1


title: 6wk_Mut3


title: 3mo_Mut1


title: 3mo_Control2


title: 3mo_Control3


title: Paraquat-incubated Aag2 Cell Replicate 3

description: Biological replicate 3 of 4


title: Heme-incubated Aag2 Cell Replicate 3

description: Biological replicate 3 of 4


title: 6mo_Mut4


title: 6wk_Mut2


title: Heme-incubated Aag2 Cell Replicate 2

description: Biological replicate 2 of 4


city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: FFPE from non-progressive T1G3 bladder cancer: B1887

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: Bladder,FFPE

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: RNA were extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol

tag: liver sample group

value: non-progressive T1G3 bladder cancer

tag: ID


title: 6wk_Control2


title: 4689

city: Boston

first: Iris

last: Jaffe

state: MA

address: 800 Washington Street

institute: Tufts Medical Center

description: aortic miRNA expression data

hyb_protocol: Reverse-transcribed aortic miRNA was hybridized to Mouse miRNA2.0 microarrays (Affymetrix, Santa Clara, CA) at the Boston University Medical School Center for Genetics and Genomics.

scan_protocol: standard protocol

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package included within in the Bioconductor software suite (version 2.10.0). Affymetrix probeset mapping (also obtained from Bioconductor version 2.10.0) was used to normalize the miRNA 2.0 microarray. Differential miRNA expression was assessed with the limma package by creating linear models or using the empirical Bayes (moderated) t test. Correction for multiple hypothesis testing was accomplished using the Benjamini-Hochberg false discovery rate (FDR). All microarray analyses were performed using the R environment for statistical computing (version 2.12.0).

source_name: AORTA

label_protocol: standard protocol

extract_protocol: Total aortic miRNA was extracted from 3 or 12 month old mice using QIAzol, followed by column purification.

value: male

value: MR-knockout

value: young


title: Paraquat-incubated Aag2 Cell Replicate 4

description: Biological replicate 4 of 4

tag: tissue


description: FFPE from non-progressive T1G3 bladder cancer: B1885


title: 6wk_Mut1


title: 4703

description: aortic miRNA expression data


title: 6wk_Control1


description: FFPE from non-progressive T1G3 bladder cancer: B1880


title: 4691

description: aortic miRNA expression data


title: 410

description: aortic miRNA expression data

value: aged


title: 9

description: aortic miRNA expression data


title: 4693

description: aortic miRNA expression data

value: wildtype


title: 6wk_Control3


title: 4690

description: aortic miRNA expression data


description: FFPE from non-progressive T1G3 bladder cancer: B1871


description: FFPE from non-progressive T1G3 bladder cancer: B1870


title: 194

description: aortic miRNA expression data


title: progressive T1G3 bladder cancer: B1851

description: FFPE from progressive T1G3 bladder cancer: B1851

value: progressive T1G3 bladder cancer


title: 4705

description: aortic miRNA expression data


description: FFPE from non-progressive T1G3 bladder cancer: B1872


title: progressive T1G3 bladder cancer: B1849

description: FFPE from progressive T1G3 bladder cancer: B1849


title: progressive T1G3 bladder cancer: B1847

description: FFPE from progressive T1G3 bladder cancer: B1847


title: 409

description: aortic miRNA expression data


description: FFPE from non-progressive T1G3 bladder cancer: B1873


title: progressive T1G3 bladder cancer: B1867

description: FFPE from progressive T1G3 bladder cancer: B1867


title: progressive T1G3 bladder cancer: B1865

description: FFPE from progressive T1G3 bladder cancer: B1865


description: FFPE from non-progressive T1G3 bladder cancer: B1752


title: progressive T1G3 bladder cancer: B1680b

description: FFPE from progressive T1G3 bladder cancer: B1680b


title: BS90 injury 12h biological replicate 1

value: adult

value: whole body

source_name: snails URR, pooled RNA samples for maximum feature reactivity

value: BB02 BS90 Mline


title: 192

description: aortic miRNA expression data


title: progressive T1G3 bladder cancer: B1679

description: FFPE from progressive T1G3 bladder cancer: B1679


title: 182

description: aortic miRNA expression data


title: progressive T1G3 bladder cancer: B1845

description: FFPE from progressive T1G3 bladder cancer: B1845


title: 8

description: aortic miRNA expression data


title: progressive T1G3 bladder cancer: B1666

description: FFPE from progressive T1G3 bladder cancer: B1666


title: progressive T1G3 bladder cancer: B1665C

description: FFPE from progressive T1G3 bladder cancer: B1665C


title: pDC_CTRL_NST_P11

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

description:
Sample name: pDC_CTRL_NST.P11.224.2.1
Gene expression after cell purification

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 8x60K V2  using Agilent’s recommended hybridization chamber and oven. The samples were randomly distributed for the labeling approach and the subsequent  hybridization. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1  for 1 min at room temperature followed by a second wash with preheated Agilent Gene  Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The raw data was extracted with the Agilent Feature Extraction Software and was quantile normalized using R. The limma R package was used for the selection of differentially expressed genes.

source_name: Resting plasmacytoid dendritic cells from healthy seronegative individuals

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Peripheral blood dendritic cells were first enriched by incubation with anti-CD304 (BDCA-4/Neuropilin-1)-coated magnetic beads (for pDC), followed by purification of mDC using anti-CD1c (BDCA-1) beads, both from Miltenyi Biotec. To ensure high purity necessary for microarray experiments, enriched cells were further purified by flow cytometry (FACSAria; BD-Biosciences) after staining with CD11c-APC, HLA-DR-PerCP-Cy5.5, Lin-FITC and CD123-PE antibodies (BD-Biosciences). Dead cells were excluded by using the Sytox Blue (Life Technologies) cell death marker and in the Lin-HLA-DR+ gate, pDC were defined as CD11c-CD123+, while mDC were defined as CD11c+CD123-.

extract_protocol: Cell pellets were resuspended in Amplification Buffer (Miltenyi Biotec) before freezing them. Later, samples were sent to Miltenyi Biotec and the SuperAmp technology (Miltenyi Biotec) was used to amplify mRNA before transcriptomic analysis.

treatment_protocol: After purification, a cell aliquot was left un-stimulated while the other was stimulated for 2 hrs at 37 ºC with 1 µg/ml poly(I:C) (Amersham) + 250 µg/ml DEAE-Dextran (Sigma) in case of mDC or 5 µg/ml of Imiquimod (Invivogen) in case of pDC.

tag: individual

value: healthy seronegative individuals

value: peripheral blood

value: plasmacytoid DC

tag: protocol

value: non-stimulated


title: pDC_CTRL_ST_P10

description:
Sample name: pDC_CTRL_ST.P10.238.1.3
Gene expression after 2h stimulation with Imiquimod

source_name: Activated plasmacytoid dendritic cells from healthy seronegative individuals

value: stimulated with Imiquimod


title: pDC_CTRL_ST_P9

description:
Sample name: pDC_CTRL_ST.P9.225.1.4
Gene expression after 2h stimulation with Imiquimod


title: pDC_CHR_NST_P7

description:
Sample name: pDC_CHR_NST.P7.223.2.3
Gene expression after cell purification

source_name: Resting plasmacytoid dendritic cells from HCV chronically infected patients

value: HCV chronically infected patient


title: pDC_CHR_ST_P6

description:
Sample name: pDC_CHR_ST.P6.225.1.3
Gene expression after 2h stimulation with Imiquimod

source_name: Activated plasmacytoid dendritic cells from HCV chronically infected patients


title: pDC_CHR_NST_P5

description:
Sample name: pDC_CHR_NST.P5.224.2.3
Gene expression after cell purification


title: pDC_AR_ST_P13

description:
Sample name: pDC_AR_ST.P13.238.1.4
Gene expression after 2h stimulation with Imiquimod

source_name: Activated plasmacytoid dendritic cells from acute HCV resolving patients

value: acute HCV resolving patient


title: pDC_CTRL_ST_P11

description:
Sample name: pDC_CTRL_ST.P11.223.2.4
Gene expression after 2h stimulation with Imiquimod


title: pDC_CTRL_NST_P12

description:
Sample name: pDC_CTRL_NST.P12.239.1.2
Gene expression after cell purification


description: FFPE from non-progressive T1G3 bladder cancer : B1655

value: non-progressive T1G3 bladder cancer


title: pDC_CTRL_NST_P10

description:
Sample name: pDC_CTRL_NST.P10.238.2.2
Gene expression after cell purification


title: pDC_CTRL_ST_P12

description:
Sample name: pDC_CTRL_ST.P12.225.1.1
Gene expression after 2h stimulation with Imiquimod


title: pDC_AR_ST_P14

description:
Sample name: pDC_AR_ST.P14.238.2.4
Gene expression after 2h stimulation with Imiquimod


title: pDC_CHR_ST_P8

description:
Sample name: pDC_CHR_ST.P8.224.1.4
Gene expression after 2h stimulation with Imiquimod


title: pDC_ANR_ST_P4

description:
Sample name: pDC_ANR_ST.P4.239.1.1
Gene expression after 2h stimulation with Imiquimod

source_name: Activated plasmacytoid dendritic cells  from patients with hepatitis C virus infection

value: patient with hepatitis C virus infection


title: progressive T1G3 bladder cancer: B1674

description: FFPE from progressive T1G3 bladder cancer: B1674


title: pDC_CHR_ST_P5

description:
Sample name: pDC_CHR_ST.P5.224.1.3
Gene expression after 2h stimulation with Imiquimod


title: progressive T1G3 bladder cancer: B1668

description: FFPE from progressive T1G3 bladder cancer: B1668


title: pDC_CHR_NST_P8

description:
Sample name: pDC_CHR_NST.P8.224.2.4
Gene expression after cell purification


title: pDC_AR_NST_P14

description:
Sample name: pDC_AR_NST.P14.224.1.1
Gene expression after cell purification

source_name: Resting plasmacytoid dendritic cells  from acute HCV resolving patients


title: pDC_CTRL_NST_P9

description:
Sample name: pDC_CTRL_NST.P9.225.2.4
Gene expression after cell purification


title: pDC_CHR_NST_P6

description:
Sample name: pDC_CHR_NST.P6.225.2.3
Gene expression after cell purification


title: pDC_CHR_ST_P7

description:
Sample name: pDC_CHR_ST.P7.238.1.2
Gene expression after 2h stimulation with Imiquimod


title: pDC_ANR_ST_P2

description:
Sample name: pDC_ANR_ST.P2.224.2.2
Gene expression after 2h stimulation with Imiquimod


title: pDC_AR_NST_P13

description:
Sample name: pDC_AR_NST.P13.238.2.3
Gene expression after cell purification


title: pDC_ANR_ST_P1

description:
Sample name: pDC_ANR_ST.P1.223.2.1
Gene expression after 2h stimulation with Imiquimod


title: pDC_ANR_NST_P4

description:
Sample name: pDC_ANR_NST.P4.223.2.2
Gene expression after cell purification

source_name: Resting plasmacytoid dendritic cells  from patients with hepatitis C virus infection


title: pDC_ANR_NST_P3

description:
Sample name: pDC_ANR_NST.P3.238.1.1
Gene expression after cell purification


title: pDC_ANR_ST_P3

description:
Sample name: pDC_ANR_ST.P3.225.2.2
Gene expression after 2h stimulation with Imiquimod


title: pDC_ANR_NST_P1

description:
Sample name: pDC_ANR_NST.P1.224.1.2
Gene expression after cell purification


title: Rat cochlea - 3 day treated with ototoxic drugs and Antioxidant protection 3

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Ototoxic treated plus antioxidant

data_processing: The open source NormFinder v.5 software [44] was used to identify a pair of stable genes, which were used as reference genes for the normalisation of the data. Genes selected from NormFinder were Idh1 and Prnp for the 5-day dataset; Txnip and Idh1 for 23-day dataset; Xirp1 and Txnrd2 for the combined 5 and 23 days dataset. Normalisation was performed using the rank normalisation method and the data subsequently filtered to discard the genes whose expression was undetermined (Ct values > 35) in at least 90 % of the samples in the dataset.

organism: Rattus norvegicus

source_name: Cochlea

label_protocol: Genes involved in oxidation were studied with the “Rat oxidative stress and antioxidant defense RT2 profiler PCR array” (PARN-065, SABiosciences Corp., Frederick, MD, USA). It includes a panel of 84 target genes and 5 housekeeping genes that are listed in Supplementary file 1. First-strand cDNA was synthesised using the RT2 first strand kit (C-03, SABiosciences Corp.) and PCR arrays were then processed on an Applied Biosystems 7900HT Real-Time PCR System, to obtain the Ct values.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro Kit after cochleae homogenisation.

treatment_protocol: Two month-old male Wistar rats (n=36) were distributed in two groups, one receiving resveratrol plus NAC (n=20) and the control group receiving vehicle (n=16). Two days after the beginning of the treatment, a gelatin sponge embedded in a concentrated solution of kanamycin and furosemide (200 mg/ml and 50 mg/ml, respectively, in 0.1 M PBS pH 8.5) was located by bullostomy in the middle ear, close to the round window. The contralateral left ears were used as controls for the corresponding experimental conditions.

value: cochlea

tag: treatment

value: treated with antioxidant drugs prior Ototoxic administration

tag: time

value: 3 days


title: mDC_CTRL_NST_P9

description:
Sample name: mDC_CTRL_NST.P9.222.1.4
Gene expression after cell purification

source_name: Resting myeloid dendritic cells from healthy seronegative individuals

value: myeloid DC


title: mDC_CTRL_ST_P10

description:
Sample name: mDC_CTRL_ST.P10.222.2.4
Gene expression after 2h stimulation with poly(I:C)

source_name: Activated myeloid dendritic cells from healthy seronegative individuals

value: stimulated with poly(I:C)


title: pDC_ANR_NST_P2

description:
Sample name: pDC_ANR_NST.P2.225.1.2
Gene expression after cell purification


title: Rat cochlea - 3 day treated with ototoxic drugs and Antioxidant protection 5

description: Ototoxic treated plus antioxidant


title: mDC_CHR_ST_P5

description:
Sample name: mDC_CHR_ST.P5.221.1.3
Gene expression after 2h stimulation with poly(I:C)

source_name: Activated myeloid dendritic cells from HCV chronically infected patients


title: mDC_CTRL_NST_P10

description:
Sample name: mDC_CTRL_NST.P10.223.1.2
Gene expression after cell purification


title: mDC_CHR_ST_P6

description:
Sample name: mDC_CHR_ST.P6.222.1.3
Gene expression after 2h stimulation with poly(I:C)


title: Rat cochlea - 3 day treated with ototoxic drugs and Antioxidant protection 6

description: Ototoxic treated plus antioxidant


title: mDC_AR_NST_P14

description:
Sample name: mDC_AR_NST.P14.220.2.1
Gene expression after cell purification

source_name: Resting myeloid dendritic cells from acute HCV resolving patients


title: mDC_CTRL_NST_P11

description:
Sample name: mDC_CTRL_NST.P11.221.1.1
Gene expression after cell purification


title: mDC_AR_ST_P14

description:
Sample name: mDC_AR_ST.P14.239.2.1
Gene expression after 2h stimulation with poly(I:C)

source_name: Activated myeloid dendritic cells from acute HCV resolving patients


title: mDC_CHR_ST_P7

description:
Sample name: mDC_CHR_ST.P7.223.1.1
Gene expression after 2h stimulation with poly(I:C)


title: mDC_CHR_ST_P8

description:
Sample name: mDC_CHR_ST.P8.220.2.4
Gene expression after 2h stimulation with poly(I:C)


title: mDC_CTRL_NST_P12

description:
Sample name: mDC_CTRL_NST.P12.222.1.1
Gene expression after cell purification


title: mDC_CHR_NST_P8

description:
Sample name: mDC_CHR_NST.P8.221.1.4
Gene expression after cell purification

source_name: Resting myeloid dendritic cells from HCV chronically infected patients


title: mDC_CTRL_ST_P11

description:
Sample name: mDC_CTRL_ST.P11.220.1.4
Gene expression after 2h stimulation with poly(I:C)


title: Contralateral rat choclea -3 days not treated 3

description: control

value: untreated


title: Rat cochlea - 3 day treated with ototoxic drugs and Antioxidant protection 2

description: Ototoxic treated plus antioxidant


title: Contralateral rat choclea -3 days not treated 2

description: control


title: mDC_CHR_NST_P6

description:
Sample name: mDC_CHR_NST.P6.222.2.3
Gene expression after cell purification


title: mDC_CTRL_ST_P12

description:
Sample name: mDC_CTRL_ST.P12.221.2.1
Gene expression after 2h stimulation with poly(I:C)


title: mDC_AR_ST_P13

description:
Sample name: mDC_AR_ST.P13.222.2.1
Gene expression after 2h stimulation with poly(I:C)


title: mDC_CHR_NST_P5

description:
Sample name: mDC_CHR_NST.P5.221.2.3
Gene expression after cell purification


title: mDC_AR_NST_P13

description:
Sample name: mDC_AR_NST.P13.239.1.3
Gene expression after cell purification