title: ONX eye at 21 days post-ONX, biological replicate 1

first: Amy

middle: T

last: McCurley

address: 5 Cummington Street

department: Biology

institute: Boston University

description: whole eye after ONX surgery

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

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild type adult male Danio rerio were maintained in 30 gal aquaria at 28ºC on a 14:10 light-dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and RNA was cleaned using Qiagen RNA clean-up protocol.

treatment_protocol: For optic nerve crush fish were anesthetized by immersion in 0.033% aminobenzoic acid ethylmethylester (MS222). The left optic nerve was exposed by gently pulling the eye out of the orbit and then crushing the nerve with forceps. The eye was then gently replaced in the orbit. As a SHAM control the right eye of the same fish was gently pulled out of the orbit and replaced with the nerve remaining intact. The fish were then placed in a recovery tank. At timed intervals post-crush (6 hours and 1, 4, 12, & 21 days) the fish were euthanized by overdose of MS-222 and the eyes (including retina, lens, vitreous, anterior and posterior segments) removed, flash-frozen on dry ice and stored at -70°C. For microarray analysis two biological replicates (2 pools with 5 eyes/pool for each time point) were prepared.

value: eye


title: SHAM eye at 12 days post-ONX, biological replicate 2

status: Public on Feb 01 2010

type: RNA

city: Boston

state: MA

country: USA

description: whole eye after sham surgery

label: biotin

molecule: total RNA

organism: Danio rerio

tag: tissue


title: SHAM eye at 21 days post-ONX, biological replicate 2

description: whole eye after sham surgery


title: SHAM eye at 4 days post-ONX, biological replicate 1

description: whole eye after sham surgery


title: SHAM eye at 21 days post-ONX, biological replicate 1

description: whole eye after sham surgery


title: ONX eye at 12 days post-ONX, biological replicate 2

description: whole eye after ONX surgery


title: SHAM eye at 12 days post-ONX, biological replicate 1

description: whole eye after sham surgery


title: ONX eye at 4 days post-ONX, biological replicate 1

description: whole eye after ONX surgery


title: ONX eye at 4 days post-ONX, biological replicate 2

description: whole eye after ONX surgery


title: ONX eye at 21 days post-ONX, biological replicate 2

description: whole eye after ONX surgery


title: ONX eye at 12 days post-ONX, biological replicate 1

description: whole eye after ONX surgery


title: 01-05-07-WenXie-live -WTL_M430.2

city: Pittsburgh

first: Jung Hoon

last: Lee

state: PA

address: 3501 Terrace St.

department: Pharmaceutical Sciences

institute: Univeristy of Pittsburgh

description: Gene expression data from livers of CA-AhR transgenic mice compared to WT mice

hyb_protocol: Hyb according to the standard Affymetrix protocol

scan_protocol: Scan according to the standard Affymetrix protocol

organism: Mus musculus

source_name: Liver from wild type mice

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

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

treatment_protocol: Mice were allowed for free access to food and water and maintained in a standard rodent chow diet

tag: age

value: 5-6 weeks

value: liver


title: 01-05-07-WenXie-Intestin-WTD_M430.2

description: Gene expression data from duodenums of CA-AhR transgenic mice compared to WT mice

source_name: Duodenum from wild type mice

value: duodenum


title: SHAM eye at 4 days post-ONX, biological replicate 2

description: whole eye after sham surgery


title: CoCl2 3d 5

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

country: Germany

institute: UFZ Helmholtz Centre for Environmental Research

description: Biological replicate 4 of 5, harvested after several passages.

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit following manufacturer's instructions.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1 or 10.1.1.1).

data_processing: Feature extraction files (processed signals) were used for statistics.

organism: Homo sapiens

source_name: HaCaT cells pool

label_protocol: Synthesis of cDNA, cRNA and cRNA-labeling was performed with the Agilent Low RNA Input Linear Amplification Kit according to the manufacturer’s instructions. cRNA was labelled with Cy3 (controls and treatments) and Cy5 (common reference).

growth_protocol: HaCaT cells were maintained in RPMI medium (‘Roswell Park Memorial Institute’ medium; Biochrom, Karlsruhe, Germany) supplemented with 5 % (v/v) FBS and 1% (v/v) penicillin/streptomycin. Cells were cultured in monolayers at 37°C in a humidified, 5 % (v/v) CO2-atmosphere and sub-cultured twice a week in 75 cm² flasks. Cells were seeded at densities of 200.000 cells/ml for 3d of exposure or 500.000 cells/ml for 3h of exposure, respectively in a final volume of 10 ml per 75 cm² flasks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Cells were exposed to 30 µg/ml WC (153 µM), 33 µg/ml WC-Co (153/51 µM), or 3 µg/ml (51 µM) cobalt chloride by mixing RPMI 5 % FBS with 10 fold concentrated stock solutions. Exposure was performed in the dark with 5 independent replicates (performed at different days using different cell passage numbers). Controls were performed by with the water used for the preparation of particle suspensions.

tag: cell type

value: keratinocytes (HaCaT)

tag: reference

value: common reference

source_name: HaCaT cells

tag: exposure time

value: 3 days

tag: treatment

value: CoCl2 51 µM (= 3µg/ml cobalt)


title: CoCl2 3d 1

description: Biological replicate 1 of 5, harvested after several passages.


title: WC-Co 3d 6

description: Biological replicate 5 of 5, harvested after several passages.

value: WC-Co 33 µg/ml


title: WC-Co 3d 3

description: Biological replicate 2 of 5, harvested after several passages.


title: CoCl2 3d 6


title: 01-05-07-WenXie-live -Tgl_M430.2

source_name: Liver from transgenic mice expressing constitutively activated aryl hydrocarbon receptor


title: CoCl2 3d 3


title: WC 3d 6

value: WC 30 µg/ml


title: WC-Co 3d 5


title: WC-Co 3d 4

description: Biological replicate 3 of 5, harvested after several passages.


title: 01-05-07-WenXie-Intestin-TgD_M430.2_2

source_name: Duodenum from transgenic mice expressing constitutively activated aryl hydrocarbon receptor


title: WC-Co 3d 1


title: CoCl2 3d 4


title: WC 3d 5


title: WC 3d 4


title: WC 3d 3


title: H2O 3d 4


title: H2O 3d 3


title: H2O 3d 6


title: H2O 3d 1


title: CoCl2 3h 6

value: 3 hours


title: WC 3d 1


title: H2O 3d 5


title: WC-Co 3h 6


title: CoCl2 3h 5


title: CoCl2 3h 4


title: WC-Co 3h 2


title: CoCl2 3h 2


title: CoCl2 3h 1


title: WC-Co 3h 5


title: WC 3h 5


title: H2O 3h 6


title: WC 3h 6


title: WC-Co 3h 4


title: H2O 3h 5


title: WC 3h 2


title: WC-Co 3h 1


title: WC 3h 4


title: H2O 3h 4


title: H2O 3h 2


title: WC 3h 1


title: H2O 3h 1


title: Control (rep 4)

city: New York

first: steve

last: shen

state: NY

address: 545 First Ave

department: Biochemistry

institute: New York University

description: Gene expression data from cell line

data_processing: data were processed with RMA method

organism: Rattus norvegicus

source_name: Control (rep 4)

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 was isolated from six biological replicates corresponding to Failing, Control, Failing+Captopril and Failing+Captopril+butyrate heart tissue using Trizol (Invitrogen) according to the manufacturer’s protocol, and the RNeasy mini-kit (Qiagen) was used to clean-up the RNA

tag: tissue type

value: heart


title: Control (rep 2)

description: Gene expression data from cell line

source_name: Control (rep 2)


title: frontal_cortex_HIV

city: La Jolla

first: Erick

last: Tatro

state: CA

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

description:
Pooled RNA samples from 3 subjects, average delta CT from technical triplicates reported in data table, each raw data file is from 1 technical triplicate.

Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles), FAM channel was measured.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Data for table was processed using SDS 2.3 software (Applied Biosystems, Foster City, CA) and importing files to RQ (relative quantification) Manager 2.0 software (Applied Biosystems). Normalized by subtracting RNU44-CT to get Delta CT.  Average Delta CT from technical triplicates is reported in data table, raw data (*.txt, *.sds) supplied as supplementary files (*.sds readable in SDS and RQ manager software).

label: FAM

label_protocol: not applicable

growth_protocol: not applicable

extract_protocol: MirVana (Applied Biosystems) per manufacturer's protocols of frozen tissue.

treatment_protocol: not applicable

value: brain

tag: brain region

value: frontal cortex

tag: mdd-status

value: Negative

tag: hiv-status

value: Positive


title: frontal_cortex_HIVMDD


title: miRNA parietal lobe Control number 10

status: Public on Jan 31 2010

city: Los Angeles

first: Juan

last: Nunez-Iglesias

address: 1050 Childs Way, RRI-201

department: Computational Biology

institute: University of Southern California

hyb_protocol: The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: AxoHybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device).  Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing: The values from each probe location targeting a sequence (4 locations per target) were averaged. Then they were read into R/Bioconductor, and subjected to RMA normalization (background adjustment, quantile normalization, median-polish)

source_name: Parietal lobe, Control

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining

extract_protocol: TriReagent (Sigma-Aldrich) followed by purification with Rneasy mini columns (Qiagen)

tag: gender

value: male

tag: pmi

tag: diagnosis

value: normal

tag: b&b score

value: O

value: Parietal lobe


title: miRNA parietal lobe Alzheimer's disease number 16

source_name: Parietal lobe, Alzheimer's disease

value: female

value: AD

value: VI


title: Failing (rep 6)

description: Gene expression data from cell line

source_name: Failing (rep 6)


title: miRNA parietal lobe Control number 15

value: III


title: Control (rep 6)

description: Gene expression data from cell line

source_name: Control (rep 6)


title: miRNA parietal lobe Alzheimer's disease number 3


title: miRNA parietal lobe Control number 6

value: II


title: miRNA parietal lobe Alzheimer's disease number 2

value: V-VI


title: Failing (rep 2)

description: Gene expression data from cell line

source_name: Failing (rep 2)


title: Control (rep 3)

description: Gene expression data from cell line

source_name: Control (rep 3)


title: Failing (rep 3)

description: Gene expression data from cell line

source_name: Failing (rep 3)


title: Control (rep 1)

description: Gene expression data from cell line

source_name: Control (rep 1)


title: Failing (rep 1)

description: Gene expression data from cell line

source_name: Failing (rep 1)


title: Failing (rep 5)

description: Gene expression data from cell line

source_name: Failing (rep 5)


title: miRNA parietal lobe Alzheimer's disease number 12

value: V


title: frontal_cortex_control


title: Control (rep 5)

description: Gene expression data from cell line

source_name: Control (rep 5)


title: miRNA parietal lobe Control number 18


title: Failing (rep 4)

description: Gene expression data from cell line

source_name: Failing (rep 4)


title: YAC128 mouse, 12 months of age, 1412023058_B

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

hyb_protocol: According to the manufacturer's instructions.

scan_protocol: According to the manufacturer's instructions using the BeadExpress platform.

data_processing: The BeadStudio software was used to quantile normalize and background correct the scanned microarray image data. The data was then exported into R using the beadarray package (http://bioconductor.org/packages/2.3/bioc/html/beadarray. To avoid negative values, intensities are shifted by the sample minimum.

label_protocol: Biotinylated antisense RNA was generated using the Illumina Totalprep RNA amplification kit

extract_protocol: Striatal tissue was collected from 12 and 24 month old YAC128 mice and wildtype littermates. Animals were anaesthetized using Avertine and tissue was collected in RNAlater (Ambion) and stored at -80 prior to RNA isolation. Homogenization of tissue was performed using a Fastprep Homogenizer (ThermoScientific). Total RNA from mouse striatum was extracted using the Qiagen RNeasy mini kit and eluted in 30 microliters RNase free water according to manufacturer's instructions. Total RNA was quantified using the Nanodrop spectrophotometer (ThermoScientific) and the integrity of the total RNA was determined electrophoretically on the RNA Nano Assay Chip run on the Bioanalyzer 2100 (Agilent Tech).

value: 12 months

value: whole striatum

tag: genotype


title: WT mouse, 12 months of age, 1412023059_A

value: WT


title: WT mouse, 12 months of age, 1412023058_E


title: WT mouse, 12 months of age, 1412023058_F


title: YAC128 mouse, 12 months of age, 1412023058_A


title: YAC128 mouse, 24 months of age, 1692176113_B

value: 24 months


title: WT mouse, 24 months of age, 1692176113_A


title: WT mouse, 24 months of age, 1692176113_C


title: WT mouse, 24 months of age, 1692176102_A


title: YAC128 mouse, 24 months of age, 1692176102_F


title: YAC128 mouse, 24 months of age, 1692176102_E


title: Uninfected vs live M. bovis infected for two hours 3

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

country: United Kingdom

institute: The Roslin Institute

description: Biological replicate 5 of 5

hyb_protocol: cDNA was resuspended in SlideHyb™ Glass Array Hybridization buffer #3 (Ambion). Pre-processing, hybridization, for 3hrs at 65°C, 3 hrs at 55°C and 12hrs at 50°C, and washing was performed in a Tecan HS400™ Hybridization station.

scan_protocol: Scanned on a GenePix 4000A scanner.

data_processing: Data were processed using the R package limma.  Background was subtracted and loess normalization applied.

label: Alexa Fluor 647

organism: Bos taurus

source_name: Alveolar macrophages

label_protocol: 10μg total RNA reverse transcribed using Superscript Plus Indirect cDNA labelling system (Invitrogen) with Oligo dT primers. cDNA was labelled with Alexa Fluor dyes 555 and 647.

growth_protocol: Alveolar macrophages harvested from cattle aged 6-12 months, cells cultured in RPMI-1640 + Glutamax, 10% heat-inactivaled foetal calf serum (FCS), 5x 10(5) beta-mercaptoethanol, 1x penicillin/streptomycin, 2.5μg/ml fungizone for 24 hours, media then changed to as before except 3% FCS and no penicillin/streptomycin and cultured for a further 24 hours.

extract_protocol: Cells lysed with 4M guanidine thiocyantae, homogenised using 20g needle and bacteria removed by pelleting. RNA then extracted using Qiagen Rneasy Maxi kit according to manufacturer's instructions.

treatment_protocol: Cells were uninfected or infected with either live or heat-killed M. bovis for two or four hours.

tag: animal number

value: Alveolar macrophages

tag: infection type

value: Uninfected

tag: infection time

value: 0 hours

label: Alexa Fluor 555

tag: infection

value: Live M. bovis

value: 2 hours


title: WT mouse, 24 months of age, 1692176102_D

tag: age

tag: tissue


title: YAC128 mouse, 12 months of age, 1412023058_C


title: YAC128 mouse, 24 months of age, 1692176102_C


title: YAC128 mouse, 24 months of age, 1692176102_B


title: YAC128 mouse, 12 months of age, 1412023059_C


title: YAC128 mouse, 12 months of age, 1412023058_D


title: WT mouse, 12 months of age, 1412023059_B


title: Live M. bovis infected for two hours vs heat-killed M. bovis infected for two hours 2

description: Biological replicate 5 of 5

tag: cell type

value: Heat-killed M. bovis


title: Uninfected vs heat-killed M. bovis infected for four hours 5

description: Biological replicate 4 of 5

value: 4 hours


title: Live M. bovis infected for four hours vs heat-killed M. bovis infected for four hours 2

description: Biological replicate 5 of 5


title: Heat-killed M. bovis infected for two hours vs uninfected 3

description: Biological replicate 5 of 5


title: Heat-killed M. bovis infected for four hours vs uninfected 2

description: Biological replicate 5 of 5


title: Uninfected vs heat-killed M. bovis infected for two hours 2

description: Biological replicate 4 of 5


title: Heat-killed M. bovis infected for four hours vs live M. bovis infected for four hours 3

description: Biological replicate 4 of 5


title: Heat-killed M. bovis infected for two hours vs live M. bovis infected for two hours 3

description: Biological replicate 4 of 5


title: Live M. bovis infected for four hours vs uninfected 3

description: Biological replicate 4 of 5


title: Live M. bovis infected for two hours vs uninfected 2

description: Biological replicate 4 of 5


title: Live M. bovis infected for two hours vs heat-killed M. bovis infected for two hours 1

description: Biological replicate 3 of 5


title: Uninfected vs heat-killed M. bovis infected for four hours 2

description: Biological replicate 3 of 5


title: Heat-killed M. bovis infected for four hours vs live M. bovis infected for four hours 2

description: Biological replicate 3 of 5


title: Heat-killed M. bovis infected for two hours vs uninfected 2

description: Biological replicate 3 of 5


title: Uninfected vs live M. bovis infected for two hours 2

description: Biological replicate 3 of 5


title: Live M. bovis infected for four hours vs uninfected 2

description: Biological replicate 3 of 5


title: Heat-killed M. bovis infected for two hours vs live M. bovis infected for two hours 2

description: Biological replicate 2 of 5


title: Uninfected vs heat-killed M. bovis infected for four hours 3

description: Biological replicate 3 of 5


title: Live M. bovis infected for four hours vs heat-killed M. bovis infected for four hours 1

description: Biological replicate 2 of 5


title: NB06 Non-malignant bone_replicate 3

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

country: Australia

institute: University of Queensland

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers, as described by the manufacturer. Washing was performed following solutions and protocols recommended by Agilent.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log of ratio of processed test signal/processed reference signal using GeneSpring version 7.2.

source_name: Total RNA from non-malignant bone labelled with AlexFluor647

label_protocol: 20 ug of total RNA incubated with 5 ug anchored oligo(dT)12-18 primer 70oC/10 min. Reverse transcription performed at 42oC/2 h with 0.65 uL aminoallyl dNTP - 25 mM dATP, dGTP, dCTP, 7.5 mM dTTP, 15 mM aminoallyl d-UTP, and 400 U Superscript II. The RNA was labelled at room temperature/1 hour with AlexaFluor555 or AlexaFluor647 in the presence of 0.3M NaHCO3 and DMSO.

extract_protocol: Total RNA extracted from 100 mg of tumour biopsy with 900 uL Trizol and 100 uL 2M acetic acid.

treatment_protocol: Biopsies were removed from patients and immediately frozen in dry ice, before long-term storage at -80oC.

value: Male

value: 71 years

source_name: Total RNA pooled from 8 cancer cell lines

tag: cell lines

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: NB08 Non-malignant bone_replicate 4

value: 56 years


title: NB04 Non-malignant bone_replicate 2

value: Female

value: 75 years

tag: bone

value: femur head


title: OSN23 A Biopsy_poor_rep1

source_name: Total RNA from osteosarcoma biopsy of poor responder labelled with AlexaFluor647

value: 16 years

value: left calcaneum


title: OSR21 A Biopsy_good_rep1

source_name: Total RNA from osteosarcoma biopsy of good responder labelled with AlexFluor647

value: 18 years

value: right 8th rib


title: OSN23 B Biopsy_poor_dye-swap_rep2

source_name: Total RNA from osteosarcoma biopsy of poor responder labelled with AlexaFluor555


title: NB03 Non-malignant bone_replicate 1

value: 49 years


title: OSR22 A Biopsy_good_rep1

value: 15 years

value: left femur


title: NB09 Non-malignant bone_replicate 5

value: 79 years


title: OSR22 B Biopsy_good_dye-swap_rep2

source_name: Total RNA from osteosarcoma biopsy of good responder labelled with AlexFluor555


title: Heat-killed M. bovis infected for two hours vs uninfected 1

description: Biological replicate 2 of 5

value: Alveolar macrophages

value: Heat-killed M. bovis

value: 2 hours

value: Uninfected

value: 0 hours


title: OSN20 A Biopsy_poor_rep1

value: Male

value: 67 years

value: right pelvis

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: OSN20 B Biopsy_poor_dye-swap_rep2


title: Uninfected vs live M. bovis infected for four hours 2

description: Biological replicate 5 of 5

value: Live M. bovis

value: 4 hours


title: OSN19  Biopsy_poor_1

value: 17 years

value: left tibia


title: Heat-killed M. bovis infected for four hours vs live M. bovis infected for four hours 1

description: Biological replicate 1 of 5


title: Heat-killed M. bovis infected for two hours vs live M. bovis infected for two hours 1

description: Biological replicate 1 of 5


title: Live M. bovis infected for two hours vs uninfected 1

description: Biological replicate 1 of 5


title: Uninfected vs heat-killed M. bovis infected for two hours 1

description: Biological replicate 1 of 5


title: Heat-killed M. bovis infected for four hours vs uninfected 1

description: Biological replicate 2 of 5


title: Uninfected vs live M. bovis infected for two hours 1

description: Biological replicate 2 of 5


title: Uninfected vs heat-killed M. bovis infected for four hours 1

description: Biological replicate 1 of 5


title: Uninfected vs live M. bovis infected for four hours 1

description: Biological replicate 2 of 5


title: Live M. bovis infected for four hours vs uninfected 1

description: Biological replicate 1 of 5


title: OSR17 B Biopsy_good_dye-swap_rep 2

value: Female

value: 14 years


title: OSN16 B Biopsy_poor_dye-swap_rep 2


title: OSN15 A Biopsy_poor_rep 1

value: 18 years

value: right femur


title: OSN18 B Biopsy_poor-dye-swap_rep2

value: 24 years

value: left femur


title: OSN18 A Biopsy_poor_rep1


title: OSR17 A Biopsy_good_rep 1


title: OSN15 B Biopsy_poor_dye-swap_rep 2


title: OSN14 A Biopsy_poor_rep 1


title: OSN16 A Biopsy_non-metastatic_rep 1


title: OSN13 B Biopsy_poor_dye-swap_rep 2

value: 15 years


title: Uninfected vs heat-killed M. bovis infected for four hours 4

description: Biological replicate 4 of 5

value: Alveolar macrophages

value: Uninfected

value: Heat-killed M. bovis


title: OSR12 A Biopsy_good_rep 1

value: Male

value: right tibia


title: MaF pre-iPSC9P2, Vc+, D4

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: Gene expression data from MaF pre-iPSC9P2, Vc+, D4.

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: MaF pre-iPSC9P2, Vc treated, lysed on D4

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: MaF pre-iPSCs were cultured on feeder in mESC medium with or without Vc. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Vc was added to mESC medium at a final concentration of 50 μg/ml. One day after pre-iPSCs were plated onto feeder (D2), media were changed to mESC medium with or without Vc. Vc was continuously added in the Vc treatment group.

value: MaF pre-induced pluripotent stem cells

tag: treatment

value: vitamin C

tag: time

value: Day 4


title: MaF pre-iPSC9P2, Vc-, D5

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D5.

source_name: MaF pre-iPSC9P2, Vc untreated, lysed on D5

value: Day 5


title: SKO-transduced MEFs, Vc+, D10

description: Gene expression data from SKO-transduced MEFs, Vc+, D10.

source_name: SKO-transduced MEFs, Vc treated, lysed on D10

growth_protocol: MEFs were cultured in DMEM+10% FBS+NEAA+GlutaMax+penicillin/streptomycin (P/S); after two-rounds of infections, GFP- or SKO-transduced MEFs were cultured in mESC standard medium (DMEM+15% FBS+NEAA+GlutaMax+Sodium pyruvate+P/S+β-mercaptoethanol+1,000U/ml LIF) with or without Vc.

treatment_protocol: Vc was added to mESC medium at a final concentration of 50 μg/ml. At D2 after the 2nd infection, transduced MEFs were changed to mESC medium with or without Vc. Vc was continuously added in the Vc treatment group.

value: MEF

tag: transduction

value: SKO (sox2, klf4 and oct4)

value: Day 10


title: OSR12 B Biopsy_good_dye-swap_rep 2

tag: gender

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: MaF pre-iPSC9P2, Vc-, D4

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D4.

source_name: MaF pre-iPSC9P2, Vc untreated, lysed on D4


title: MaF pre-iPSC9P2, Vc+, D6

description: Gene expression data from MaF pre-iPSC9P2, Vc+, D6.

source_name: MaF pre-iPSC9P2, Vc treated, lysed on D6

value: Day 6


title: OSN11 A Biopsy_poor_rep 1

value: Female

value: 29 years

value: sacrum


title: MaF pre-iPSC9P2, Vc+, D5

description: Gene expression data from MaF pre-iPSC9P2, Vc+, D5.

source_name: MaF pre-iPSC9P2, Vc treated, lysed on D5


title: MaF pre-iPSC9P2, Vc-, D3

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D3.

source_name: MaF pre-iPSC9P2, Vc untreated, lysed on D3

value: Day 3


title: OSN13 A Biopsy_poor_rep 1

value: 15 years

value: right femur


title: MaF pre-iPSC9P2, Vc+, D3

description: Gene expression data from MaF pre-iPSC9P2, Vc+, D3.

source_name: MaF pre-iPSC9P2, Vc treated, lysed on D3


title: MaF pre-iPSC9P2, Vc-, D6

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D6.

source_name: MaF pre-iPSC9P2, Vc untreated, lysed on D6


title: OSN10 B Biopsy_poor_dye-swap_rep 2

value: 7 years

value: tibia


title: OSN14 B Biopsy_poor_dye-swap_rep 2

value: Male

value: 18 years

value: left tibia


title: OSN11 B Biopsy_poor_dye-swap_rep 2


title: SKO-transduced MEFs, Vc+, D8

description: Gene expression data from SKO-transduced MEFs, Vc+, D8.

source_name: SKO-transduced MEFs, Vc treated, lysed on D8

value: vitamin C

value: Day 8


title: SKO-transduced MEFs, Vc+, D6

description: Gene expression data from SKO-transduced MEFs, Vc+, D6.

source_name: SKO-transduced MEFs, Vc treated, lysed on D6

value: MEF

value: SKO (sox2, klf4 and oct4)


title: OSN10 A Biopsy_poor_rep 1

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: OSR21 B Biopsy_good_dye-swap_rep2

value: right 8th rib


title: SKO-transduced MEFs, Vc+, D5

description: Gene expression data from SKO-transduced MEFs, Vc+, D5.

source_name: SKO-transduced MEFs, Vc treated, lysed on D5

value: Day 5


title: OSR9 B Biopsy_good_dye-swap_rep 2

value: Female

value: 13 years

source_name: Total RNA pooled from 8 cancer cell lines


title: OSU8 B Biopsy_unknown_dye-swap_rep 2

source_name: Total RNA from osteosarcoma biopsy, unknown response, labelled with AlexFluor555

value: 37 years

value: right tibia


title: SKO-transduced MEFs, Vc-, D10

description: Gene expression data from SKO-transduced MEFs, Vc-, D10.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D10

value: Day 10


title: SKO-transduced MEFs, Vc+, D4

description: Gene expression data from SKO-transduced MEFs, Vc+, D4.

source_name: SKO-transduced MEFs, Vc treated, lysed on D4

value: Day 4


title: OSU8 A Biopsy_unknown_rep 1

source_name: Total RNA from osteosarcoma biopsy, unknown response, labelled with AlexFluor647


title: OSR9 A Biopsy_good_rep 1

source_name: Total RNA from osteosarcoma biopsy of good responder labelled with AlexFluor647

value: right femur


title: SKO-transduced MEFs, Vc-, D8

description: Gene expression data from SKO-transduced MEFs, Vc-, D8.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D8


title: SKO-transduced MEFs, Vc+, D3

description: Gene expression data from SKO-transduced MEFs, Vc+, D3.

source_name: SKO-transduced MEFs, Vc treated, lysed on D3

value: Day 3


title: OSN7  Biopsy_poor_1

source_name: Total RNA from osteosarcoma biopsy of poor responder labelled with AlexaFluor647

value: 27 years

value: right humerus


title: SKO-transduced MEFs, Vc-, D6

description: Gene expression data from SKO-transduced MEFs, Vc-, D6.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D6

value: Day 6


title: OSN6 B Biopsy_poor_dye-swap_rep 2

source_name: Total RNA from osteosarcoma biopsy of poor responder labelled with AlexaFluor555

value: 15 years


title: OSN5 B Biopsy_poor_dye-swap_rep 2

value: Male

value: 12 years

value: left femur


title: SKO-transduced MEFs, Vc-, D5

description: Gene expression data from SKO-transduced MEFs, Vc-, D5.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D5

value: MEF

value: SKO (sox2, klf4 and oct4)


title: OSN5 A Biopsy_poor_rep 1

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: SKO-transduced MEFs, Vc-, D3

description: Gene expression data from SKO-transduced MEFs, Vc-, D3.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D3


title: GFP-transduced MEFs, Vc+, D3

description: Gene expression data from GFP-transduced MEFs, Vc+, D3.

source_name: GFP-transduced MEFs, Vc treated, lysed on D3

value: GFP control

value: vitamin C


title: OSN4 A Biopsy_poor_rep 1

value: 14 years


title: GFP-transduced MEFs, Vc-, D3

description: Gene expression data from GFP-transduced MEFs, Vc-, D3.

source_name: GFP-transduced MEFs, Vc untreated, lysed on D3


title: OSN3 B Biopsy_poor_dye-swap_rep 2

value: Female

value: 19 years


title: OSN4 B Biopsy_poor_dye-swap_rep 2

value: right femur


title: OSN3 A Biopsy_poor_rep 1


title: OSN2 A Biopsy_poor_rep 1

value: 39 years

value: left pelvis


title: OSN2 B Biopsy_poor_dye-swap_rep 2


title: SKO-transduced MEFs, Vc-, D4

description: Gene expression data from SKO-transduced MEFs, Vc-, D4.

source_name: SKO-transduced MEFs, Vc untreated, lysed on D4

value: Day 4


title: Ad-MyD88 infected bmDC Replicate 1

status: Public on Jan 29 2010

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Biological replicate 1 of 3. Ad-MyD88 infected bmDCs, harvested 16 hours post-infection

hyb_protocol: Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon GenePix Pro 4000A scanner. Image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Ad-MyD88 infected bmDCs

label_protocol: 10 µg of total RNA was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols

extract_protocol: Total RNA extracted using TriReagent following manufacturer's instructions.  The RNA was further assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol:
Bone-marrow cultured Dendritic cells were prepared from the bone marrow of C57Bl/6 mice by culturin RBC-depleted bone marrow cells in complete media ( RPMI 1640, 10% FBS, 2mM L-glutamine, 1mM Sodium Pyruvate, 7mM HEPES, 50um beta-mercaptoethanol, .1mM Non-essential amino acids) with GM-CSF (10ng/ml) and IL-4 (10ng/ml) for 10 days).
Cultured into DCs over the course of 10 days and then infected with 20000vp/cell for 16 hrs.

tag: passage

value: Bone Marrow derived Dendritic cells (bmDCs)

tag: strain

source_name: Total RNA from Murine Universal RNA (Stratagene, La Jolla, CA)

tag: reference

value: Multiple cell lines spanning multiple tissue types


title: OSN1 A Biopsy_poor_rep 1

value: 76 years

value: left tibia

source_name: Total RNA pooled from 8 cancer cell lines


title: Ad-MyD88 infected bmDC Replicate 3

description: Biological replicate 3 of 3. Ad-MyD88 infected bmDCs, harvested 16 hours post-infection

growth_protocol: Bone-marrow cultured Dendritic cells were prepared from the bone marrow of C57Bl/6 mice by culturin RBC-depleted bone marrow cells in complete media ( RPMI 1640, 10% FBS, 2mM L-glutamine, 1mM Sodium Pyruvate, 7mM HEPES, 50um beta-mercaptoethanol, .1mM Non-essential amino acids) with GM-CSF (10ng/ml) and IL-4 (10ng/ml) for 10 days).

value: Murine Universal RNA (Stratagene, La Jolla, CA)


title: P90/P30 expression_e

status: Public on Jan 30 2010

city: Houston

first: Richard

last: Kellermayer

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization of the arrays was carried out  according to the Agilent Chip-on-chipmammalian protocol (version 9.1, 2006)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Probe ratios were calculated for P90/P30 comparisons in each of the 4 arrays separately.

source_name: P30 animal

label_protocol: total RNA (0.4ug) samples were processed and labelled with Cy3 (Quick Amp labelling kit, two color, Agilent technologies)

extract_protocol:
tissue_isolation_protocol: Colonic mucosa was sheared by microscope slide and flash frozen on dry ice
Total RNA was extracted by Qiagen Rneasy mini kit (Cat.no.74106)

value: 30 postnatal days

value: colonic mucosa

source_name: P90 animal

label_protocol: total RNA (0.4ug) samples were processed and labelled with Cy5 (Quick Amp labelling kit, two color, Agilent technologies)

value: 90 postnatal days


title: OSN1 B Biopsy_poor_dye-swap_rep 2

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: P90/P30 expression_k


title: Mock control bmDC Replicate 3

description: Biological replicate 3 of 3. Mock control treated bmDCs, harvested 16 hours post-infection

source_name: Mock treated bmDCs

value: Mock


title: Ad-GFP control infected bmDC Replicate 3

description: Biological replicate 3 of 3. Ad-GFP control infected bmDCs, harvested 16 hours post-infection

source_name: Ad-GFP infected bmDCs

value: Ad-GFP


title: Ad-GFP control infected bmDC Replicate 2

description: Biological replicate 2 of 3. Ad-GFP control infected bmDCs, harvested 16 hours post-infection


title: P90/P30 expression_b


title: Ad-MyD88 infected bmDC Replicate 2

description: Biological replicate 2 of 3. Ad-MyD88 infected bmDCs, harvested 16 hours post-infection


title: Ad-GFP control infected bmDCs Replicate 1

description: Biological replicate 1 of 3. Ad-GFP control infected bmDCs, harvested 16 hours post-infection


title: Mock vs D-Psicose in shoot of rice, replicate 1

city: Miki-cho

first: Kazuya

last: Akimitsu

state: Kagawa

address: 2393 Ikenobe

department: Agriculture

country: Japan

institute: Kagawa University

description:
Biological replicate 1 of 3.
D-Psicose_Rep1

hyb_protocol: Cy3- and Cy5-labeled samples (500 μl) were equally mixed and used for hybridization. Hybridization was conducted at 65°C, 10 rpm, 17h.

scan_protocol: The plate was washed with SSC series, removed excess of buffer with N2 gas and scanned with an Agilent Microarray Scanner (Agilent Technologies).

data_processing: Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

organism: Oryza sativa

source_name: Rice shoot, treated with D-Psicose at 2-leaf stage

label_protocol: Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Seeds were germinated in 0.2% Benlate for 1 day and deionized water for 1 day at 30°C under dark, and grown for 5 days on water.

extract_protocol: Qiagen RNeasy Plant Mini Kit following manufacturer's instructions.

treatment_protocol: Seedlings of two-leaf-stage rice plants were cultured in Kimura-B liquid medium with or without 0.5 mM D-Psicose for 2 days.

tag: cultivar

value: Nipponbare

tag: developmental stage

value: 2-leaf stage

value: shoot

value: D-Psicose

tag: treatment time

value: 2 days

source_name: Rice shoot, non-sugar-treated at 2-leaf stage

value: no sugar


title: Mock control MEF Replicate 3

description: Biological replicate 3 of 3. Mock control treated MEFs, harvested 16 hours post-infection

source_name: Mock treated MEFs

growth_protocol: Grown in DMEM with 20%FBS and Pen.Step and then serum starved in .2% FBS for 48 hrs. before treatment

treatment_protocol: serum starved for 48 hrs. and then mock infected for 16 hrs.

value: Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos

source_name: Murine Universal RNA (Stratagene, La Jolla, CA)


title: Mock vs D-Psicose in shoot of rice, replicate 2

description:
Biological replicate 2 of 3.
D-Psicose_Rep2


title: P90/P30 expression_a


title: Mock vs D-Psicose in shoot of rice, replicate 3

description:
Biological replicate 3 of 3.
D-Psicose_Rep3


title: Mock control MEF Replicate 2

description: Biological replicate 2 of 3. Mock control treated MEFs, harvested 16 hours post-infection

value: Multiple cell lines spanning multiple tissue types


title: Ad-MyD88 infected MEF Replicate 3

description: Biological replicate 3 of 3. Ad-MyD88 infected MEFs, harvested 16 hours post-infection

source_name: Ad-MyD88 infected MEFs

treatment_protocol: serum starved for 48 hrs. and then infected at MOI of 300 for 16 hrs.


title: Ad-MyD88 infected MEF Replicate 1

description: Biological replicate 1 of 3. Ad-MyD88 infected MEFs, harvested 16 hours post-infection


title: Mock control MEF Replicate 1

description: Biological replicate 1 of 3. Mock control treated MEFs, harvested 16 hours post-infection


title: Control 360 min - Combined data (3 reps)

status: Public on Jan 10 2010

city: Lincoln

first: James

middle: L

last: Van Etten

state: NE

address: 4240 Fair Street

department: Plant Pathology

institute: University of Nebraska-Lincoln

description: 4 technical replicate, 3 independent biological replicates

hyb_protocol: Arrays were hybridized (42ºC) for 16 hours in a Corning hybridization chamber (Corning, Lowell, MA).  Slides were washed twice (42ºC) in 2x SSC (1x SSC is 0.15 M sodium chloride/0.015 M sodium citrate), 0.5% SDS for 15 min followed by two washes in 0.5x SSC, 0.5% SDS for 15 min

scan_protocol: Slides were subjected to fluorescence detection with Axon 4000B scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Midas v2.19 (TM4) software was used for : low intensity filter (<10,000), normalization of the intensities between the two channels using Lowess (Locfit), and SD regularization across blocks. In TMEV v4.1 (TM4), all time points from each set of experiments were loaded and columns (experiments) were normalized, ANOVA was used to detect genes that display statistically significant variation in expression in at least one of the experimental time points.

organism: Paramecium bursaria Chlorella virus 1

source_name: non-treated control for aphidicolin-treated Chlorella NC64A infected with PBCV-1

label_protocol: 20 ug of total RNA was reverse-transcribed using oligo(dT) as primers and cDNAs were labeled with either Cy3 or Cy5-dUTP (GE Healthcare, Piscataway, NJ) using the SuperScript Indirect cDNA Labeling System (Invitrogen) following the supplier’s directions

growth_protocol: Log phase Chlorella NC64A cells were concentrated to 1 x 10*8 cells/ml with fresh MBBM media.

extract_protocol: Total RNA extracted using Absolutely RNA Miniprep Kit (Stratagene, La Jolla, CA) following manufacturer's instructions

treatment_protocol: Non-treated, infected control cells  competitively hybridized against aphidicolin-treated, infected cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.).

tag: cell line

value: Chlorella NC64A


title: Mutant biological rep1

status: Public on Jan 22 2010

city: Charlottesville

first: Timothy

middle: P

last: Bender

state: VA

address: 345 Crispell Dr

department: Microbiology

institute: University of Virginia

description: Gene expression data from DP thymocytes.

hyb_protocol: Hybridization was performed for 16 hrs per standard Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner

data_processing: GeneChIP Operating Software (GCOS)

source_name: Mybf/w Cd4-Cre Tcra-/- DP, biological rep1

label_protocol: Biotinylated cRNA was prepared per standard Affymetrix protocol

extract_protocol: 2-10 ug of total RNA was extracted using the Rneasy Kit (Qiagen). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer.

treatment_protocol: Tcra-/- thymocytes were freshly harvested and positively selected for the DP subset over anti-CD4 magnetic columns (Miltenyi).

tag: genotype/variation

value: c-Myb deficient


title: Control 240 min - Combined data (3 reps)


title: Ad-GFP control infected MEF Replicate 1

description: Biological replicate 1 of 3. Ad-GFP control infected MEFs, harvested 16 hours post-infection

source_name: Ad-GFP infected MEFs


title: Ad-GFP control infected MEF Replicate 3

description: Biological replicate 3 of 3. Ad-GFP control infected MEFs, harvested 16 hours post-infection


title: Ad-MyD88 infected MEF Replicate 2

description: Biological replicate 2 of 3. Ad-MyD88 infected MEFs, harvested 16 hours post-infection


title: tumor control rep1

status: Public on Jan 15 2010

city: Heidelberg

first: Silke

last: Wolterink

address: INF 580

department: Translationale Immunologie

institute: DKFZ Heidelberg

description: Isotyp treated mice 3 times weekly

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation by Chipster

source_name: SKOV3ip tumor after 26 days

label_protocol: Standard Illumina labelling protocol

growth_protocol: 6 week old female Balb/c nude were inoculated with 7*10^6 SKOV3ip cells intraperitoneal. Therapy started on day three after tumor inoculation. After 26 days mice were sacrified and intraperitoneal tumor was isolated.

extract_protocol: Tumor samples from mice were treated in a tissue homogenizer and total RNA was extracted by using RNeasy® mini kit (Qiagen Inc., Valencia, CA, USA) according to the manufacture’s instructions. The concentration and quality of total RNA was verified by electrophoresis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). RNA concentrations were determined using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). All of the RNA samples were stored at −80 °C until used for microarray analysis

treatment_protocol: Tumor-bearing mice were treated 3 times weekly with 200µg L1-9.3/Igg2a or isotype control.

value: human ovarian carcinoma

value: Balb/c nude mice

tag: age

value: 6 weeks

value: SKOV3ip intraperitoneal

value: female

tag: mouse id


title: Mutant biological rep2

source_name: Mybf/w Cd4-Cre Tcra-/- DP, biological rep2


title: Ad-GFP control infected MEF Replicate 2

description: Biological replicate 2 of 3. Ad-GFP control infected MEFs, harvested 16 hours post-infection

tag: cell type

tag: tissue


title: Control biological rep2

source_name: Mybf/f Cd4-Cre Tcra-/- DP, biological rep2

value: c-Myb sufficient


title: tumor control rep2

description: Isotyp treated mice 3 times weekly


title: Mutant biological rep3

source_name: Mybf/w Cd4-Cre Tcra-/- DP, biological rep3


title: Mutant biological rep4

source_name: Mybf/w Cd4-Cre Tcra-/- DP, biological rep4


title: Control biological rep3

source_name: Mybf/f Cd4-Cre Tcra-/- DP, biological rep3


title: Control 120 min - Combined data (3 reps)


title: Control biological rep4

source_name: Mybf/f Cd4-Cre Tcra-/- DP, biological rep4


title: Control biological rep1

source_name: Mybf/f Cd4-Cre Tcra-/- DP, biological rep1


title: tumor L1-9.3/IgG2a rep 1

description: L1-9.3/IgG2a treated mice 3 times weekly


title: OSN6 A Biopsy_poor_rep 1

source_name: Total RNA from osteosarcoma biopsy of poor responder labelled with AlexaFluor647

value: Female

value: 15 years

tag: bone

value: right humerus

source_name: Total RNA pooled from 8 cancer cell lines

tag: cell lines

value: HDF, COLO-16, LNCap, DU145, SK-BR3, U2OS, HT29, DG75


title: tumor L1-9.3/IgG2a rep 2


title: Control 60 min - Combined data (3 reps)


title: Control 40 min - Combined data (3 reps)


title: Control 90 min - Combined data (3 reps)


title: Control 20 min - Combined data (3 reps)


title: 360 min - Replicate 4 (III)

description: Technical replicate 4 of 4 (Biological replicate 3 of 3)

source_name: Chlorella NC64A infected with PBCV-1 (MOI=5)

treatment_protocol: Cells were infected with PBCV-1 with MOI = 5.

tag: infected cell

value: chlorella-like green alga, Chlorella NC64A

tag: time

value: 360 min

source_name: RNA control (III)

tag: control composition

value: a pool of transcripts obtained by mixing equal amounts of total RNA from each time point


title: Aphid 120 min - Combined data (3 reps)

source_name: aphidicolin-treated Chlorella NC64A infected with PBCV-1

treatment_protocol: Cells were infected with PBCV-1 with MOI = 5. Aphidicolin (20 ug/ml) was added to treated cells 15 prior to infection.


title: 360 min - Replicate 3 (III)

description: Technical replicate 3 of 4 (Biological replicate 3 of 3)


title: Aphid 90 min - Combined data (3 reps)


title: Aphid 240 min - Combined data (3 reps)


title: Aphid 360 min - Combined data (3 reps)


title: 360 min - Replicate 2 (III)

description: Technical replicate 2 of 4 (Biological replicate 3 of 3)


title: Aphid 20 min - Combined data (3 reps)


title: 240 min - Replicate 3 (III)

value: 240 min


title: Aphid 60 min - Combined data (3 reps)


title: 120 min - Replicate 3 (III)

value: 120 min


title: 120 min - Replicate 4 (III)


title: 240 min - Replicate 4 (III)


title: 360 min - Replicate 1 (III)

description: Technical replicate 1 of 4 (Biological replicate 3 of 3)


title: 120 min - Replicate 2 (III)


title: 90 min - Replicate 4 (III)

value: 90 min


title: 240 min - Replicate 1 (III)


title: 240 min - Replicate 2 (III)


title: 90 min - Replicate 2 (III)


title: Aphid 40 min - Combined data (3 reps)

value: Chlorella NC64A


title: 90 min - Replicate 1 (III)


title: 60 min - Replicate 4 (III)

value: 60 min


title: Mock control bmDC Replicate 1

description: Biological replicate 1 of 3. Mock control treated bmDCs, harvested 16 hours post-infection

source_name: Mock treated bmDCs

tag: infection

value: Mock

tag: passage

value: Bone Marrow derived Dendritic cells (bmDCs)

source_name: Total RNA from Murine Universal RNA (Stratagene, La Jolla, CA)

value: Multiple cell lines spanning multiple tissue types


title: 120 min - Replicate 1 (III)


title: 40 min - Replicate 1 (III)

value: 40 min


title: 60 min - Replicate 2 (III)


title: 40 min - Replicate 3 (III)


title: 40 min - Replicate 4 (III)


title: 60 min - Replicate 1 (III)


title: 40 min - Replicate 2 (III)


title: 20 min - Replicate 3 (III)

value: 20 min


title: 20 min - Replicate 1 (III)


title: 360 min - Replicate 4 (II)

description: Technical replicate 4 of 4 (Biological replicate 2 of 3)

source_name: RNA control (II)


title: 20 min - Replicate 2 (III)


title: 360 min - Replicate 3 (II)

description: Technical replicate 3 of 4 (Biological replicate 2 of 3)


title: 90 min - Replicate 3 (III)


title: 360 min - Replicate 2 (II)

description: Technical replicate 2 of 4 (Biological replicate 2 of 3)


title: 360 min - Replicate 1 (II)

description: Technical replicate 1 of 4 (Biological replicate 2 of 3)


title: 240 min - Replicate 4 (II)


title: 240 min - Replicate 3 (II)


title: 240 min - Replicate 2 (II)


title: 20 min - Replicate 4 (III)


title: 120 min - Replicate 4 (II)


title: 120 min - Replicate 3 (II)


title: 120 min - Replicate 2 (II)


title: 90 min - Replicate 4 (II)


title: 90 min - Replicate 3 (II)


title: 120 min - Replicate 1 (II)


title: 90 min - Replicate 2 (II)


title: Mock control bmDC Replicate 2

description: Biological replicate 2 of 3. Mock control treated bmDCs, harvested 16 hours post-infection

tag: strain

tag: reference

value: Murine Universal RNA (Stratagene, La Jolla, CA)


title: 60 min - Replicate 3 (II)


title: 60 min - Replicate 2 (II)


title: 60 min - Replicate 4 (II)


title: 90 min - Replicate 1 (II)


title: 40 min - Replicate 2 (II)


title: 60 min - Replicate 1 (II)


title: 20 min - Replicate 4 (II)


title: 40 min - Replicate 4 (II)


title: 40 min - Replicate 3 (II)


title: 20 min - Replicate 3 (II)


title: 360 min - Replicate 2 (I)

description: Technical replicate 2 of 4 (Biological replicate 1 of 3)

source_name: RNA control (I)


title: 20 min - Replicate 2 (II)


title: 360 min - Replicate 1 (I)

description: Technical replicate 1 of 4 (Biological replicate 1 of 3)


title: 360 min - Replicate 4 (I)

description: Technical replicate 4 of 4 (Biological replicate 1 of 3)


title: 120 min - Replicate 4 (I)


title: 240 min - Replicate 3 (I)

description: Technical replicate 3 of 4 (Biological replicate 1 of 3)


title: 240 min - Replicate 4 (I)


title: 240 min - Replicate 1 (I)


title: 360 min - Replicate 3 (I)


title: 120 min - Replicate 3 (I)


title: 240 min - Replicate 2 (I)


title: 120 min - Replicate 2 (I)


title: 40 min - Replicate 1 (II)


title: 20 min - Replicate 1 (II)


title: 90 min - Replicate 3 (I)


title: 120 min - Replicate 1 (I)


title: 90 min - Replicate 4 (I)


title: 90 min - Replicate 1 (I)


title: 60 min - Replicate 4 (I)


title: 60 min - Replicate 2 (I)


title: 90 min - Replicate 2 (I)


title: 60 min - Replicate 1 (I)


title: 40 min - Replicate 4 (I)


title: 40 min - Replicate 3 (I)


title: 40 min - Replicate 1 (I)


title: 20 min - Replicate 3 (I)


title: 40 min - Replicate 2 (I)


title: 20 min - Replicate 1 (I)


title: 20 min - Replicate 4 (I)


title: 20 min - Replicate 2 (I)


title: H2O2_rep2

status: Public on Jan 04 2010

city: Worcester

first: Jessica

last: Lopes da Rosa-Spiegler

address: 364 Plantation street

institute: University of Massachusetts Medical School

description: Analysis compared steady-state RNA levels of log-phase wt and rtt109-/- cells treated with hydrogen peroxide

hyb_protocol: DNA oligonucleotide C.  albicans microarray slides were purchased from The Genome Center at Washington University (http://genome.wustl.edu/services/microarray/candida_albicans).   Hybridization and washing were performed per the labeling manufacturer’s instructions (Genisphere).

scan_protocol: Scanning was performed immediately after washing using GenePix software at a PTM ranging from 490-630 (Cy3; 532nm) and 650-960 (Cy5; 635nm).

data_processing: Limma package (limma_2.18.0) from Bioconductor was used for preprocessing and model fitting. A linear model was fit to the background-corrected, loess-normalized and log-transformed expression data. The dye effect and mutant effect were tested as explanatory variables to determine whether the expression level of each gene differed between mutant and wild type samples, after the dye effect was removed statistically. Three features for each gene were printed on the array, resulting in three estimated log-fold changes for each gene. Genes with at least one feature having a p-value < 0.01 for mutant effect and a fold change ≥2 were considered potentially differentially expressed in mutant and were included for subsequent Gene Ontology (GO) enrichment test.     The gene and GO term association list was downloaded from http://www.candidagenome.org (version 1.633 and taxon: 5476) with duplicates removed. All the ancestor GO terms were added to the association list using GO.db package (GO.db_2.2.11) from Bioconductor. GO enrichment analysis was performed using the hypergeometric test in R (V 2.9.0). GO terms with at least ten associated genes in the genome and a p-value adjusted using the Benjamini-Hochberg method  < 0.01 were considered significantly enriched.

organism: Candida albicans

source_name: Log-phase culture grown in YPD, then treated with 0.4 mM H2O2 for 10 minutes

label_protocol: 10 μg RNA was labeled by reverse transcription using the 3DNA Array 350 system (Genisphere).

growth_protocol: In the first (YPD) experiment, wild-type and rtt109 -/- cultures were grown at 30°C in 50 ml YPD to a matching O.D. 600 nm for each of the four biological replicates, with the final O.D. 600 nm ranging from 0.6-0.9 for the different experiments. Pellets were flash frozen with liquid nitrogen and stored at -80°C until further processing.

extract_protocol: RNA was purified by acid-phenol extraction followed by ethanol, ammonium acetate precipitation as previously described (Sexton et al., Yeast 24, 847 (2007))

treatment_protocol: In the second (H2O2) experiment, RNA was analyzed from H2O2-exposed cells. In this case, the final O.D. 600nm ranged from 0.5-0.9 before exposure to 0.4 mM H2O2 in YPD for 10 minutes at 30°C. The cells were immediately centrifuged into a pellet and flash frozen with liquid nitrogen for storage. RNA was then prepared and analyzed as above.

tag: agent/stress

value: SC5314 (wild-type)


title: YPD_rep2

description: Analysis compared steady-state RNA levels of log-phase wt and rtt109-/- cells

source_name: Log-phase culture grown in YPD


title: YPD_rep1


title: H2O2_rep4

description: Analysis compared steady-state RNA levels of log-phase wt and rtt109-/- cells treated with hydrogen peroxide; dye-swap


title: YPD_rep4

description: Analysis compared steady-state RNA levels of log-phase wt and rtt109-/- cells; dye-swap


title: Colonic mucosal cells #1

status: Public on Jan 03 2010

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

description: Manufacturer's scanner and feature extraction - normalization software

hyb_protocol: Agilent 44K hybridization, 17 hrs

scan_protocol: Agilent scanner and Feature Extraction Software

data_processing:
All microarrays are scanned and the intensities normalized over background using a microarray scanner from Agilent Technologies including proprietary software. All microarray data sets (single channel) are imported into the microarray data analysis software Genespring 7.3 (Agilent, USA) and normalized intensities compared. Each individual normalized intensity was divided by the median of intensity of all 15 data points and the statistical significance of difference of the mean calculated using Genespring 7.3 microarray analysis software (Agilent). A p-value of less than < 0.05 was considered as a significant difference.

Raw data files contain data for both Cy3 and Cy5.  However, each channel was analyzed individually.  Thus, one raw data file may apply to two different samples.

source_name: Colonic mucosal cells

label_protocol: Low RNA Input Fluor Linear Amplification Kit (Agilent Technologies, USA)

extract_protocol: NucleoSpin RNA II (BD Biosciences, USA)

value: Sprague Dawley

tag: gender

value: male

value: Colonic mucosal cell suspension


title: Colonic mucosal cells #2


title: YPD_rep3


title: Ileal mucosal cells #1

source_name: Ileal mucosal cells

value: Ileal mucosal cell suspension


title: H2O2_rep1


title: Ileal mucosal cells #3

source_name: Ileal mucosal cell


title: Ileal mucosal cells #2


title: Jejunal mucosal cells #1

source_name: Jejunal mucosal cells

value: Jejunal mucosal cell suspension


title: Jejunal mucosal cells #3


title: Duodenal mucosal cells #3

source_name: Rat duodenal mucosa

value: Duodenal mucosal cell suspension


title: Colonic mucosal cells #3


title: Jejunal mucosal cells #2


title: Duodenal mucosal cells #1


title: Gastric mucosa cells #2

source_name: Rat gastric mucosa

value: Gastric mucosal cell suspension


title: retinal pigmented epithelium_adult_Wild type_tech rep3

status: Public on Jan 01 2010

city: Baltimore

first: Laszlo

last: Hackler

state: MD

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

hyb_protocol: Manual hybridization overnight at 55C in sealed hybridization chambers.

scan_protocol: Arrays were scanned with a ScanArray ExpressHT microarray scanner (Perkin Elmer).

data_processing: Raw images were analyzed using ImaGene v5.6 software (BioDiscovery), low quality spots with quality and low intensity flags were discarded. Background corrected intensity was used to calculate relative expression ratio. The data from each array was normalized by the global Lowess method and the green (reference) channel (Gquantile) method was applied for between array normalization in BioConductor.

source_name: cells from the retinal pigmented epithelium

label_protocol: Approximately 15ng of total RNA from LCM samples was amplified with two rounds of in vitro transcription (IVT), in case of the reference sample; 2µg total RNA was used with one round of IVT, using the BioArray High Yield kit (ENZO LifeSciences). Cy3 and Cy5 fluorescent dyes were incorporated during the final IVT step resulting in fluorescently labeled cRNA for hybridization on microarrays.

extract_protocol: Total RNA was purified with the RNeasy Micro kit (Qiagen) according to the manufacturer’s protocol.

value: retina

value: retinal pigmented epithelial cells

tag: genome/variation

value: wild type

value: 3 months

source_name: adult retina - reference


title: Duodenal mucosal cells #2


title: 60 min - Replicate 3 (III)

description: Technical replicate 3 of 4 (Biological replicate 3 of 3)

source_name: Chlorella NC64A infected with PBCV-1 (MOI=5)

value: chlorella-like green alga, Chlorella NC64A

value: 60 min

value: a pool of transcripts obtained by mixing equal amounts of total RNA from each time point


title: retinal pigmented epithelium_adult_Wild type_tech rep1


title: retinal pigmented epithelium_adult_Wild type_tech rep2


title: photoreceptor layer_adult_Wild type_biological rep3_tech rep3

source_name: cells from the photoreceptor layer of the adult retina

value: photoreceptor cells


title: Gastric mucosal cells #3


title: photoreceptor layer_adult_Wild type_biological rep3_tech rep2


title: Gastric mucosal cells #1

source_name: rat gastric mucosa


title: photoreceptor layer_adult_Wild type_biological rep2_tech rep1


title: photoreceptor layer_adult_Wild type_biological rep1_tech rep1


title: photoreceptor layer_adult_Wild type_biological rep1_tech rep2


title: photoreceptor layer_adult_Wild type_biological rep3_tech rep1


title: photoreceptor layer_adult_Nrlnull_biological rep2_tech rep1

source_name: cells from the photoreceptor layer of the Nrl null adult retina

value: C57BL/6 Nrl KO

value: Nrl null


title: photoreceptor layer_adult_Wild type_biological rep2_tech rep3


title: photoreceptor layer_adult_Nrlnull_biological rep2_tech rep2


title: photoreceptor layer_adult_Nrlnull_biological rep1_tech rep2


title: photoreceptor layer_adult_Nrlnull_biological rep1_tech rep1


title: photoreceptor layer_adult_Wild type_biological rep2_tech rep2


title: photoreceptor layer_adult_Wild type_biological rep1_tech rep3


title: inner nuclear layer_adult_Wild type_biological rep3_tech rep3

source_name: cells from the inner nuclear layer of the adult retina

value: inner nuclear cells


title: photoreceptor layer_adult_Nrlnull_biological rep2_tech rep3


title: inner nuclear layer_adult_Wild type_biological rep2_tech rep3


title: inner nuclear layer_adult_Wild type_biological rep1_tech rep3


title: inner nuclear layer_adult_Wild type_biological rep2_tech rep1


title: inner nuclear layer_adult_Wild type_biological rep3_tech rep1


title: inner nuclear layer_adult_Wild type_biological rep2_tech rep2


title: inner nuclear layer_adult_Wild type_biological rep3_tech rep2


title: inner nuclear layer_adult_Wild type_biological rep1_tech rep1


title: ganglion cell layer_adult_Wild type_biological rep3_tech rep2

source_name: cells from the ganglion cell layer of the adult retina

value: ganglion cells


title: inner nuclear layer_adult_Wild type_biological rep1_tech rep2


title: ganglion cell layer_adult_Wild type_biological rep3_tech rep1


title: ganglion cell layer_adult_Wild type_biological rep2_tech rep1


title: ganglion cell layer_adult_Wild type_biological rep2_tech rep3


title: ganglion cell layer_adult_Wild type_biological rep2_tech rep2


title: ganglion cell layer_adult_Wild type_biological rep1_tech rep1


title: ganglion cell layer_adult_Wild type_biological rep1_tech rep3


title: ganglion cell layer_adult_Wild type_biological rep1_tech rep2


title: H2O2_rep3

tag: genotype/variation

value: SC5314 (wild-type)


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 3

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

institute: Hoffman-La Roche

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat 230 2.0 whole genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Chips were pre-processed using robust multichip analysis. Normalized data were fit to  a linear model with dose and time contrasts using the GLM procedure of SAS 9.1 (SAS Institute, Carey NC).

source_name: Heart, colchicine, 2 mg/kg, 24hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix 3' IVT express kit).

extract_protocol: Total RNA was extracted using Qiagen's RNAeasy kit according to the manufacturer's instructions.

treatment_protocol: Vinblastine (0.5 and 3 mg/kg;  Sigma-Aldrich, Saint-Louis, MO), vincristine (0.1 and 1 mg/kg;  Mayne Pharma, Inc., Lake Forest, IL) and colchicine (0.2 and 2 mg/kg;  Sigma Aldrich) in 0.9% saline or 0.9% saline (n=6 rats/group/time-point) were administered intra-venously.

value: Wistar (Crl:Wi(Han))

value: male

value: heart

tag: treatment

value: colchicine

tag: treatment dosage

value: 2 mg/kg

tag: treatment time


title: 60 min - Replicate 3 (I)

source_name: RNA control (I)


type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

description: SPF32 strain grown to post-exponential phase, replicate 2.

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461)

data_processing: VALUE is log2 ratio of Ch1 over Ch2. Values for both channel have been background substracted and % total normalised.

label: AlexaFluor 546.

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: Total RNA isolated from strain SPF32 grown to post-exponential phase.

label_protocol: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461).

extract_protocol: TRIzol reagent (Invitrogen).

label: AlexaFluor 647.

molecule: genomic DNA

source_name: Genomic DNA used as reference channel.

label_protocol: 5 ugh of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1).

extract_protocol: Wizard Genomic Purification Kit (Promega).


description: KS79 strain grown to post-exponential phase, replicate 2.

source_name: Total RNA isolated from strain KS79 grown to post-exponential phase.


description: SPF32 strain grown to post-exponential phase, replicate 3.


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 5

tag: tissue


description: SPF32 strain grown to post-exponential phase, replicate 1.


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 4


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 4

source_name: Heart, colchicine, 2 mg/kg, 6hr


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 2


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 6


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 2


description: KS79 strain grown to post-exponential phase, replicate 3.


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 5


title: Rat treated with 2 mg/kg of Colchicine for 24hr, 1


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 6


description: KS79 strain grown to post-exponential phase, replicate 1.


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 1


title: Rat treated with 2 mg/kg of Colchicine for 6hr, 3


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 4

source_name: Heart, colchicine, 0.2 mg/kg, 24hr

value: 0.2 mg/kg


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 6


title: 16j Ssa family 9_infected_replicate 1

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

institute: Fisheries & Oceans Canada

description: no additional information

hyb_protocol: Hybridization, including washes and drying steps, were carried out on a HS400 automated hybridization station (Tecan, Switzerland) using a reference design. Slides where washed 3 times in 0.1x SSC, 0.2 % SDS at 23°C for 30s, 2 times in 0.2X SSC at 23°C for 30s, followed by a 1h pre-hybridization at 49°C in 5x SSC, 0.01% SDS, 1% BSA and washed with post hybridization buffer (2X SSC, 0.014% SDS) at 49°C for 1 min. Slides were then hybridized for 16 hours using a temperature shift that varied between 49°C and 53°C every hour with a hybridization mix composed of 20 µl of Alexa555 labeled cDNA (experimental samples), 20 µl of Alexa647 labeled cDNA (Reference RNA), 120µl of SlideHybTM Glass Array Hybridization Buffer # 3 (Ambion, CA, USA) and 1.5µl of a custom oligo LNA dT blocker consisting of a 20mer thymine (T) sequence where every second base is an LNA-thymine. The hybridization mix was pre-heated at 90°C for 5 min and then cooled to 49°C prior to being injected on the slides. Following hybridization, slides where washed 4 times with post hybridization buffer at 49°C, 39°C, 30°C, 30°C respectively, followed by 2 washes at room temperature in 1X SSC and 0.2X SSC and then dried with nitrogen.

scan_protocol: Microarray slides were scanned at a resolution of 10µm using a ScanArray Gx microarray scanner (Perkin Elmer, MA, USA). PMT were adjusted to obtain an equal amount of signal from each dye

data_processing: Numerical intensities and descriptive statitistics as well as flag value for each spot were extracted using the SpotReader feature extraction software (Niles Scientific, CA, USA). Flag values computed were then used to filter out genes that had missing values (-50,-75,-100 flag values) on more than 40 percent of the total number of slides used in each statistical analysis performed. Background corrected median value for each spot remaining after filtering were log2 transformed and normalized using a global Loess method. Resulting values were expressed as normalized log2 ratios (log2 value of the experimental sample minus the log2 value of the reference sample) for each spot. A Significance Analysis of Microarray (SAM) test was used to identify gene differentially expressed by comparing the log2 ratios of infected fish (n=~8) to those of control fish (n=~8)  for each time-point.

label: Alexa 555

organism: Salmo salar

source_name: Head-kidney_infected_9 (16j)

label_protocol: Experimentals RNA's from infected and control Atlantic salmon were labeled with Alexa 555 using the Superscript Plus Direct Labeling System (Invitrogen, CA, USA) following the manufacturer's protocol. The reference RNA was labeled in Alexa 647 using the same protocol.

extract_protocol: Total RNA from RNAlater preserved salmon head-kidney samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the Absolutely RNA Miniprep kits (Stratagene, CA, USA) and following the manufacturer’s protocol. A DNase digestion step was performed on each sample to eliminate possible traces of residual genomic DNA. RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA). Only RNA samples with RNA quality indicator (RQI) values above 8 were hybridized on microarray slides. RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

value: Head-kidney

value: 16 days

value: ISAV-infected

label: Alexa 647

source_name: Salmo salar reference RNA

tag: reference source

value: pooled total RNA from 18 healthy Atlantic salmon

value: Reference RNA


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 5


title: 16j Ssa family 9_infected_replicate 3

description: no additional information


title: 16j Ssa family 9_infected_replicate 2

description: no additional information


title: 16j Ssa family 8_infected_replicate 3

description: no additional information

source_name: Head-kidney_infected_8 (16j)


title: 16j Ssa family 8_infected_replicate 2

description: no additional information


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 3


title: 16j Ssa family 9_infected_replicate 4

description: no additional information


title: 16j Ssa family 9_control_replicate 2

description: no additional information

source_name: Head-kidney_control_9 (16j)

value: control


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 2


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 6

source_name: Heart, colchicine, 0.2 mg/kg, 6hr


title: 16j Ssa family 9_control_replicate 3

description: no additional information


title: 16j Ssa family 8_infected_replicate 1

description: no additional information


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 5


title: Rat treated with 0.2 mg/kg of Colchicine for 24hr, 1


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 3


title: 16j Ssa family 9_control_replicate 1

description: no additional information


title: 16j Ssa family 8_control_replicate 4

description: no additional information

source_name: Head-kidney_control_8 (16j)


title: 16j Ssa family 8_control_replicate 2

description: no additional information


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 2


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 4


title: Rat treated with 0.2 mg/kg of Colchicine for 6hr, 1


title: 16j Ssa family 8_control_replicate 1

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 4

source_name: Heart, vincristine, 1 mg/kg, 24hr

value: vincristine

value: 1 mg/kg


title: 7j Ssa family 9_infected_replicate 4

description: no additional information

source_name: Head-kidney_infected_9 (7j)

value: 7 days


title: 16j Ssa family 8_control_replicate 3

description: no additional information


title: 7j Ssa family 9_infected_replicate 3

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 5


title: 7j Ssa family 9_infected_replicate 2

description: no additional information


title: 7j Ssa family 9_infected_replicate 1

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 2


title: ganglion cell layer_adult_Wild type_biological rep3_tech rep3

value: retina

tag: cell type

value: ganglion cells

value: wild type

tag: age

value: 3 months

source_name: adult retina - reference


title: 7j Ssa family 8_infected_replicate 3

description: no additional information

source_name: Head-kidney_infected_8 (7j)

tag: time


title: 7j Ssa family 9_control_replicate 4

description: no additional information

source_name: Head-kidney_control_9 (7j)


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 3

value: Wistar (Crl:Wi(Han))

value: male

value: heart


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 6

source_name: Heart, vincristine, 1 mg/kg, 6hr


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 5


title: 7j Ssa family 8_infected_replicate 2

description: no additional information


title: 7j Ssa family 8_infected_replicate 1

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 1


title: 7j Ssa family 9_control_replicate 2

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 3


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 1


title: Rat treated with 0.1 mg/kg of Vincristine for 24hr, 5

source_name: Heart, vincristine, 0.1 mg/kg, 24hr

value: 0.1 mg/kg


title: 7j Ssa family 9_control_replicate 1

description: no additional information

value: Head-kidney


title: 7j Ssa family 8_control_replicate 3

description: no additional information

source_name: Head-kidney_control_8 (7j)


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 2


title: 7j Ssa family 9_control_replicate 3

description: no additional information


title: Rat treated with 0.1 mg/kg of Vincristine for 24hr, 3


title: 7j Ssa family 8_infected_replicate 4

description: no additional information


title: 3j Ssa family 9_infected_replicate 4

description: no additional information

source_name: Head-kidney_infected_9 (3j)

value: 3 days


title: 7j Ssa family 8_control_replicate 1

description: no additional information


title: Rat treated with 0.1 mg/kg of Vincristine for 24hr, 2


title: Rat treated with 0.1 mg/kg of Vincristine for 6hr, 4

source_name: Heart, vincristine, 0.1 mg/kg, 6hr


title: 7j Ssa family 8_control_replicate 2

description: no additional information


title: 3j Ssa family 9_infected_replicate 3

description: no additional information

value: ISAV-infected


title: 3j Ssa family 9_infected_replicate 2

description: no additional information

value: pooled total RNA from 18 healthy Atlantic salmon


title: Rat treated with 0.1 mg/kg of Vincristine for 24hr, 1


title: Rat treated with 0.1 mg/kg of Vincristine for 24hr, 4


title: Rat treated with 0.1 mg/kg of Vincristine for 6hr, 5


title: 3j Ssa family 9_infected_replicate 1

description: no additional information

value: Reference RNA


title: 3j Ssa family 8_infected_replicate 4

description: no additional information

source_name: Head-kidney_infected_8 (3j)


title: Rat treated with 0.1 mg/kg of Vincristine for 6hr, 3


title: 3j Ssa family 8_infected_replicate 3

description: no additional information


title: Rat treated with 0.1 mg/kg of Vincristine for 6hr, 2


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 5

source_name: Heart, vinblastine, 3 mg/kg, 24hr

value: vinblastine

value: 3 mg/kg


title: 3j Ssa family 8_infected_replicate 1

description: no additional information

source_name: Salmo salar reference RNA


title: Rat treated with 1 mg/kg of Vincristine for 24hr, 6

value: vincristine

value: 1 mg/kg


title: Rat treated with 0.1 mg/kg of Vincristine for 6hr, 1


title: 3j Ssa family 8_control_replicate 2

description: no additional information

source_name: Head-kidney_control_8 (3j)

value: control


title: 3j Ssa family 9_control_replicate 2

description: no additional information

source_name: Head-kidney_control_9 (3j)


title: 3j Ssa family 8_control_replicate 4

description: no additional information


title: 3j Ssa family 9_control_replicate 4

description: no additional information


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 1


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 4


title: 3j Ssa family 8_control_replicate 3

description: no additional information


title: 3j Ssa family 9_control_replicate 1

description: no additional information


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 2


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 3


title: 3j Ssa family 8_control_replicate 1

description: no additional information


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 5

source_name: Heart, vinblastine, 3 mg/kg, 6hr


title: 3j Ssa family 9_control_replicate 3

description: no additional information


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 4


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 6


title: 3j Ssa family 8_infected_replicate 2

description: no additional information


title: Rat treated with 3 mg/kg of Vinblastine for 24hr, 6


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 3


title: 24h Ssa family 9_infected_replicate 4

description: no additional information

source_name: Head-kidney_infected_9 (24h)


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 2


title: 24h Ssa family 8_infected_replicate 3

description: no additional information

source_name: Head-kidney_infected_8 (24h)


title: 24h Ssa family 9_infected_replicate 3

description: no additional information


title: 24h Ssa family 8_infected_replicate 2

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 1

source_name: Heart, vinblastine, 0.5 mg/kg, 24hr

value: 0.5 mg/kg


title: 24h Ssa family 8_infected_replicate 1

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 2


title: 24h Ssa family 9_control_replicate 4

description: no additional information

source_name: Head-kidney_control_9 (24h)


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 6


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 3

source_name: Heart, vinblastine, 0.5 mg/kg, 6hr


title: 24h Ssa family 9_control_replicate 1

description: no additional information


title: Rat treated with 1 mg/kg of Vincristine for 6hr, 4


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 4


title: 24h Ssa family 9_infected_replicate 1

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 6


title: 24h Ssa family 8_control_replicate 4

description: no additional information

source_name: Head-kidney_control_8 (24h)


title: 24h Ssa family 9_control_replicate 2

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 5


title: Rat treated with 0.5 mg/kg of Vinblastine for 24hr, 3


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 4


title: 24h Ssa family 8_control_replicate 3

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 2


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 5


title: Rat treated with 3 mg/kg of Vinblastine for 6hr, 1


title: 24h Ssa family 8_control_replicate 2

description: no additional information


title: 24h Ssa family 9_infected_replicate 2

description: no additional information


title: 24h Ssa family 9_control_replicate 3

description: no additional information


title: Rat treated with 0.5 mg/kg of Vinblastine for 6hr, 1


title: Rat treated with Saline (vehicle) for 24hr, 5

source_name: Heart, saline, 24hr

value: saline


title: Rat treated with Saline (vehicle) for 24hr, 4


title: 6h Ssa family 9_infected_replicate 3

description: no additional information

source_name: Head-kidney_infected_9 (6h)


title: 6h Ssa family 9_infected_replicate 2

description: no additional information


title: 6h Ssa family 9_infected_replicate 1

description: no additional information


title: 6h Ssa family 8_infected_replicate 3

description: no additional information

source_name: Head-kidney_infected_8 (6h)


title: Rat treated with Saline (vehicle) for 24hr, 3


title: Rat treated with Saline (vehicle) for 24hr, 1


title: Rat treated with Saline (vehicle) for 6hr, 5

source_name: Heart, saline, 6hr


title: 6h Ssa family 8_infected_replicate 1

description: no additional information


title: 6h Ssa family 8_infected_replicate 2

description: no additional information


title: 6h Ssa family 9_control_replicate 2

description: no additional information

source_name: Head-kidney_control_9 (6h)


title: 6h Ssa family 9_infected_replicate 4

description: no additional information


title: Rat treated with Saline (vehicle) for 6hr, 4


title: Rat treated with Saline (vehicle) for 6hr, 2


title: 6h Ssa family 8_control_replicate 4

description: no additional information

source_name: Head-kidney_control_8 (6h)


title: 6h Ssa family 9_control_replicate 3

description: no additional information


title: Rat treated with Saline (vehicle) for 6hr, 3


title: 6h Ssa family 9_control_replicate 1

description: no additional information


title: 6h Ssa family 8_control_replicate 3

description: no additional information


title: Rat treated with Saline (vehicle) for 6hr, 1


title: 0h Ssa family 9_control_replicate 4

description: no additional information

source_name: Head-kidney_control_9 (0h)


title: 0h Ssa family 9_control_replicate 2

description: no additional information

source_name: Salmo salar reference RNA


title: 0h Ssa family 9_control_replicate 1

description: no additional information

source_name: Head-kidney_control_8 (0h)


title: 6h Ssa family 8_control_replicate 2

description: no additional information


title: 6h Ssa family 8_control_replicate 1

description: no additional information


title: 0h Ssa family 9_control_replicate 3

description: no additional information


title: 0h Ssa family 8_control_replicate 3

description: no additional information


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 6

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 6.

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: Local background was removed from spot signal intensity and the noise signal was estimated by recording the average signal intensity of 10 negative controls printed on the chip. Normalisation of signal intensity was carried out by calculating the fold increase over the noise signal value.

source_name: Total RNA isolated from strain JR32 grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, OD600 = 0.7.

source_name: Genomic DNA used as reference channel.


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 4

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 4.


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 5

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 5.


title: 0h Ssa family 8_control_replicate 2

description: no additional information


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 1

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 1.


title: 0h Ssa family 8_control_replicate 1

description: no additional information


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 5

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 5.

source_name: Total RNA isolated from strain JR32 grown at 30 ¼C to exponential phase, OD600 = 0.7.


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 4

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 4.


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 6

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 6.


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 3

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 3.


title: JR32 strain grown at 30 degrees C to exponential phase and exposed to 37 degrees C for 30 min, replicate 2

description: JR32 strain grown at 30 ¼C to exponential phase and exposed to 37 ¼C for 30 min, replicate 2.


title: IL-17-producing hybridoma S2-1

city: Fukuoka

first: Kensuke

last: Shibata

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using robust spline normalization in R

source_name: IL-17-producing hybridoma

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

growth_protocol: hybridomas were maintained in RPMI supplimented with 10% fetal calf serum.

extract_protocol: RNA was extracted with Rneasy Mini Kit(QIAGEN). Quality control was performed with Agilent Bioanalyser.

value: hybridoma


title: IL-17-producing hybridoma S2-2


title: IL-17-non-producing hybridoma DE3-3

source_name: IL-17-non-producing hybridoma


title: IL-17-producing hybridoma S2-3


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 3

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 3.


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 2

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 2.


title: IL-17-non-producing hybridoma DE3-1


title: JR32 strain grown at 30 degrees C to exponential phase, replicate 1

description: JR32 strain grown at 30 ¼C to exponential phase, replicate 1.


description: LM1376 strain grown to post-exponential phase, replicate 6.

source_name: Total RNA isolated from strain LM1376 grown to post-exponential phase.


description: LM1376 strain grown to post-exponential phase, replicate 5.


description: LM1376 strain grown to post-exponential phase, replicate 4.


description: LM1376 strain grown to post-exponential phase, replicate 2.


description: LM1376 strain grown to exponential phase, replicate 5.

source_name: Total RNA isolated from strain LM1376 grown to exponential phase, OD600 = 0.7.


description: LM1376 strain grown to exponential phase, replicate 4.


description: LM1376 strain grown to exponential phase, replicate 2.


description: LM1376 strain grown to exponential phase, replicate 1.


description: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 5.

source_name: Total RNA isolated from strain JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min.


description: LM1376 strain grown to exponential phase, replicate 3.


description: LM1376 strain grown to post-exponential phase, replicate 3.


description: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 6.


description: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 4.


description: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 2.


description: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 3.


title: Rat treated with Saline (vehicle) for 24hr, 6

source_name: Heart, saline, 24hr

value: Wistar (Crl:Wi(Han))


title: JR32 strain grown to post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 1

description: JR32 strain grown to post-post-exponetial phase, exposed to 100 mM NaCl for 10 min, replicate 1.

source_name: Total RNA isolated from strain JR32 strain grown to post-post-exponetial phase, exposed to 100 mM NaCl for 10 min.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 6.

source_name: Total RNA isolated from strain JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 4.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 3.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 5.


description: LM1376 strain grown to post-exponential phase, replicate 1.


description: LM1376 strain grown to exponential phase, replicate 6.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 2.

source_name: Total RNA isolated from strain JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 4.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 6.


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 6.

source_name: Total RNA isolated from strain JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 1.


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 2.


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 3.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 3.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 5.


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 1.


description: JR32 strain grown to exponential phase, exposed to 100 mM NaCl for 10 min, replicate 2.


description: JR32 strain grown to post-exponential phase, replicate 5.

source_name: Total RNA isolated from strain JR32 grown to post-exponential phase.


title: Rat treated with Saline (vehicle) for 24hr, 2

value: male


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 5.


description: JR32 strain grown to exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 4.


description: JR32 strain grown to post-exponential phase, replicate 3.


description: JR32 strain grown to post-exponential phase, exposed to 0.1 mM H2O2 for 10 min, replicate 1.


description: JR32 strain grown to post-exponential phase, replicate 6.


description: JR32 strain grown to post-exponential phase, replicate 1.


description: JR32 strain grown to exponential phase, replicate 6.

source_name: Total RNA isolated from strain JR32 grown to exponential phase, OD600 = 0.7.


description: JR32 strain grown to exponential phase, replicate 5.


description: JR32 strain grown to post-exponential phase, replicate 4.


title: RAW 264.7 – infected with Brucella melitensis for 4hrs – replicate date 06012004

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin - Madison

description: See other fields

hyb_protocol: Labeled cRNA was hybridized to GeneChip® Test3 arrays and Murine Genome U74Av2 microarrays (Affymetrix). GeneChip® hybridization, washing and scanning was performed by the University of WI –Biotechnology Center, Gene Expression Center (University of WI, Madison) utilizing all Affymetrix protocols and procedures.  Washing and streptavidin-phycoerythrin staining was completed on a GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000 and signal output analysis completed with MAS5.0 as a part of GCOS v1.1.1 (Affymetrix).

data_processing: Signal output analysis completed with MAS5.0 as a part of GCOS v1.1.1 (Affymetrix).  For statistical analysis arrays were compiled and processed with EBarrays, a statistical analysis package in the comprehensive R archive network.

label: Biotin

source_name: RAW 264.7, infected with Brucella melitensis, 4 hours

label_protocol: Target RNA was prepared according to protocols in the Affymetrix GeneChip® Expression Analysis technical manual (Affymetrix, Santa Clara, CA).  In vitro synthesis of biotin-labeled cRNA was completed with Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix).  In vitro transcription clean up was completed over an RNeasy spin column (Qiagen).  Labeled cRNA mixed with fragmentation buffer was incubated at 94°C for 35 minutes.  Final RNA concentration in fragmentation buffer ranged from 0.5-1.1 μg/μL.  Visual confirmation of isolation and fragmentation was completed with agarose gel electrophoresis.

growth_protocol:
RAW 264.7 (TIB-71, ATCC) mouse macrophage (Mφ) cell line was maintained at 37°C with 5% CO2 in RPMI 1640 (Invitrogen) supplemented with 10% Fetal Bovine Serum, 0.2mM L-glutamine, antibiotic-antimycotic (100 U/mL penicillin G, 100 μg/mL streptomycin, 0.25 μg/mL amphotericin B, Gibco), 1mM sodium pyruvate (SAFC Biosciences), and MEM amino acids (Hyclone).  Macrophages were subcultured as necessary by removing old media, washing with PBS, adding fresh media, scraping cells and diluting cells 1:3 to 1:20.
B. melitensis, B. neotomae, B. ovis were grown in 12- by 75-mm tubes on a shaker platform in BBL Brucella broth (BD Bioscience).  Cultures for infection were grown at 37°C for 2 days prior to infection.

extract_protocol: Total RNA was isolated from macrophage cultures utilizing RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol with the following modifications.  Cells were lysed in RLT and then centrifuged to remove intact bacterial cells.  RNA from two independent infections was pooled for each target preparation.  DNase treated RNA was converted to double stranded cDNA using a synthesis kit (Gibco) except that T-7-(dT)24 oligomer (Genset Corp.) was used.  The double stranded cDNA was isolated with the GeneChip® Sample cleanup module.

treatment_protocol: RAW 264.7 cells for microarray were plated in 75cm2 flasks 12-24hr prior to infection, in supplemented RPMI 1640 without antibiotics at an approximate concentration of 5x 10^6 cells per flask.  Macrophage cells were washed once with PBS prior to infection and 5 mL fresh media added.  One mL of actively growing Brucella culture was added to the macrophages (MOI ~1000:1).  Infections were allowed to incubate for 4 hours at 37°C with 5% CO2.  Cells were washed once with PBS to remove extracellular bacteria and then cells were lysed for RNA collection (RNeasy Mini Kit (Qiagen, Valencia, CA)).

tag: designation

value: RAW 264.7 macrophages

tag: atcc

tag: growth properties

value: adherent

value: Abelson murine leukemia virus-induced tumor

tag: antigen expression

value: BALB/c mice

tag: bacteria

value: Brucella melitensis, Gram negative, facultative intracellular pathogen


description: JR32 strain grown to exponential phase, replicate 3.

tag: strain


description: JR32 strain grown to exponential phase, replicate 2.


description: JR32 strain grown to exponential phase, replicate 4.


description: JR32 strain grown to exponential phase, replicate 1.


title: RAW 264.7 – infected with Brucella melitensis for 4hrs – replicate date 10142003

description: See other fields

scan_protocol: GeneChips were scanned with HP 2500 GeneArray Scanner and signal output analysis completed with MAS5.0 as a part of GCOS v1 (Affymetrix).

data_processing: Signal output analysis completed with MAS5.0 as a part of GCOS v1 (Affymetrix).  For statistical analysis arrays were compiled and processed with EBarrays, a statistical analysis package in the comprehensive R archive network.