title: age 45y 9031

description: whole blood


title: age 73y 9019

status: Public on Nov 21 2012

type: genomic

city: Seattle

first: Justin

last: Guinney

state: WA

address: 2606 E Roy St

country: USA

institute: Sage Bionetworks

description: whole blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified Qiagen FlexiGene DNA kit

tag: age (y)

tag: source

value: UCSD

tag: plate

tag: gender

value: M

tag: ethnicity

value: Hispanic - Mexican

tag: tissue

value: whole blood


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description: whole blood


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description: whole blood


title: age 33y 9015

description: whole blood


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description: whole blood


title: age 36y 10047

description: whole blood

value: Boston

value: F

value: Caucasian - European


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description: whole blood


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value: USC


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value: Utah


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description: whole blood


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description: whole blood


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description: whole blood


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description: whole blood


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title: GC_7d(DFOG), biological rep2

type: RNA

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

country: Japan

institute: Research Organization of Information and Systems

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: Dedifferentiated porcine follicular granulosa cells (DFOG)

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. As a last step of the extraction procedure, the RNA was purified with RNeasy Mini Kit (Qiagen).

tag: cell type

value: GC were dedifferentiated during culture in vitro, and grown to semiconfluence.


title: age 84y 1064

description: whole blood


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description: whole blood


title: age 73y 1063

description: whole blood


title: age 89y 1066

description: whole blood


title: age 96y 1058

description: whole blood


title: age 57y 1059

description: whole blood


title: GC_7d(DFOG), biological rep3


title: age 62y 1065

description: whole blood


title: age 79y 1075

description: whole blood


title: age 62y 1068

description: whole blood


title: age 73y 1057

description: whole blood


title: age 76y 1053

description: whole blood


title: age 54y 1056

description: whole blood


title: age 78y 1051

description: whole blood


title: age 88y 1049

description: whole blood


title: age 68y 1067

description: whole blood


title: GC_4d, biological rep3

source_name: Dedifferentiating porcine follicular granulosa cells (4day in culture)


title: GC_4d, biological rep2

value: Dedifferentiating porcine follicular granulosa cells (4day in culture)


title: age 76y 1060

description: whole blood


title: GC_7d(DFOG), biological rep1


title: GC_2d, biological rep3

source_name: Dedifferentiating porcine follicular granulosa cells (2day in culture)


title: age 66y 1050

description: whole blood


title: GC_4d, biological rep1


title: GC_1d, biological rep3

source_name: Dedifferentiating porcine follicular granulosa cells (1day in culture)


title: age 87y 1047

description: whole blood


title: age 73y 1046

description: whole blood


title: GC_0d, biological rep3

source_name: Porcine follicular granulosa cells

value: GC derived from ovarian follicles of porcine


title: age 67y 1054

description: whole blood


title: GC_1d, biological rep1

value: Dedifferentiating porcine follicular granulosa cells (1day in culture)


title: GC_1d, biological rep2


title: GC_2d, biological rep2

value: Dedifferentiating porcine follicular granulosa cells (2day in culture)


title: age 74y 1044

description: whole blood


title: GC_0d, biological rep2


title: GC_0d, biological rep1


title: NI VIM KD vs NI AllStars

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: siRNA KnockDown

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed on reporter and sequence level with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: naive VIM KD

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: P. acnes strain P6 (type I-2 (ST33), according to the MLST scheme of Lomholt & Kilian, 2010), an isolate from a cancerous prostate (Fassi Fehri et al. 2011), was cultured on Brucella agar plates for 3 days at 37 C under anaerobic conditions. For liquid cultures, brain heart infusion broth (BHI, Sigma–Aldrich) was used. For control experiments, P. acnes was heat-inactivated at 65 C for 20 min. The human keratinocyte cell line HaCaT (CLS) was cultured in DMEM medium (Gibco) supplemented with 10% heat-inactivated FCS. The human prostate epithelial cell line RWPE1 (ATCC CRL-11609) was cultured in keratinocyte medium supplemented with 50 μg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor (Gibco).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

treatment_protocol: HaCaT and RWPE1 cells were seeded into 12- or 24-well plates and infected with P. acnes strain P6 at a multiplicity of infection (MOI) of 50 in a humidified 5% CO2 atmosphere at 37 °C. Infections were stopped at various times, i.e. after 30min, 1 h, 2 h, 4 h, 8 h, 24 h and 48 h. For long-term infections (1-3 weeks), media were changed every third day and cells were split once a week. For RNA interference experiments RWPE1 cells were seeded into 12-well plates (1 x 105 cells/well) 1d prior to transfection. Cells were transfected with 10 nM siRNAs using HiPerFect transfection reagent (Qiagen), according to the manufacturer's instructions. Silencing efficiency on protein level was validated after 48 h by western blot. The following siRNAs were used: siVIM 5’-CAGGTTATCAACGAAACTTCT-3’ and AllStars (Qiagen Nr. 1027281).  For vimentin overexpression keratinocytes were seeded into 12-well plates (5 x 104 cells/well) 1 d prior to transfection. HaCaT cells were transfected with 1 µg of vimentin cDNA (Origene Nr. SC111054) or control GFP plasmids using 4 µl of FuGENE (Roche) according to the manufacturer's instructions. Overexpression of vimentin and GFP was determined after 48 h by western blot.

tag: cell line

value: prostate cell line RWPE1

tag: treatment

value: naive

tag: time

tag: knockdown

value: siVIM

source_name: naive AllStars

value: AllStars Qiagen negative control


title: P6 VIM KD vs P6 AllStars

description: siRNA KnockDown

source_name: P.agnes P6 infected VIM KD

value: P. agnes infected

source_name: P.agnes P6 infected AllStars


title: P6 AllStars vs P6 VIM KD

description: siRNA KnockDown


title: age 85y 1042

description: whole blood

value: UCSD


title: age 101y 1039

description: whole blood

value: whole blood


title: age 82y 1034

description: whole blood


title: age 87y 1043

description: whole blood

value: M


title: NI AllStars vs NI VIM KD

description: siRNA KnockDown


title: age 79y 1040

description: whole blood

value: F


title: age 54y 1037

description: whole blood

value: Caucasian - European


title: NI HaCaT 7d vs NI RWPE1 7d

description: 7d post infection

source_name: naive HaCaT 7d

value: keratinocyte cell line HaCaT

source_name: naive RWPE1 7d


title: NI RWPE1 24h vs P6 RWPE1 24h

description: 24h post infection

source_name: naive RWPE1 24h

source_name: P.agnes P6 infected RWPE1 24h


title: P6 HaCaT 7d vs P6 RWPE1 7d

description: 7d post infection

source_name: P.agnes P6 infected HaCaT 7d

source_name: P.agnes P6 infected RWPE1 7d


title: GC_2d, biological rep1


title: P6 RWPE1 7d vs P6 HaCaT 7d

description: 7d post infection


title: age 73y 1033

description: whole blood


title: age 77y 1045

description: whole blood


title: age 85y 1048

description: whole blood


title: age 79y 1036

description: whole blood


title: NI RWPE1 7d vs NI HaCaT 7d

description: 7d post infection


title: age 76y 1028

description: whole blood


title: P6 HaCaT 24h vs NI HaCaT 24h

description: 24h post infection

source_name: P.agnes P6 infected HaCaT 24h

source_name: naive HaCaT 24h


title: age 74y 1035

description: whole blood


title: age 79y 1032

description: whole blood


title: P6 RWPE1 24h vs P6 HaCaT 24h

description: 24h post infection


title: P6 RWPE1 24h vs NI RWPE1 24h

description: 24h post infection


title: age 92y 1019

description: whole blood


title: age 84y 1025

description: whole blood


title: age 75y 1031

description: whole blood


title: age 84y 1041

description: whole blood


title: age 74y 1026

description: whole blood


title: age 74y 1027

description: whole blood


title: age 72y 1030

description: whole blood


title: WT total testicular polysome [WT.Tpolysome.3]

city: Bethesda

first: Chon-Hwa

last: Tsai-Morris

state: Md

address: Bldg. 49, Rm 6B03, 49 Convent Drive

department: PDEGEN, NICHD, NIH

description: Gene expression data of total testicular polysomal transcripts from WT mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 7G.

data_processing: The data were analyzed with GCOS 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: Biotin

organism: Mus musculus

source_name: WT mouse testis polysome

label_protocol: 1 μg of total RNA was reverse transcribed by using either one step (polysome or germ cells) or two steps (GRTH/IgG immunoprecipitated samples) target labeling procedure followed by fragmentation of the cRNA and hybridization to the chips.

growth_protocol: Adult GRTH wild type and GRTH-/- male mice were housed in temperature and light-controlled conditions

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

treatment_protocol: Testiuclar polysome were obtained by sucrose gradient fraction. Cells were purified by centrifugal elutriation.

value: male

tag: developmental stage

value: adult

tag: strain

tag: genotype/variation

value: WT

value: testicular polysome


title: WT total testicular polysome [WT.Tpolysome.1]

description: Gene expression data of IgG immunoprecipitated polysomal transcripts from WT mouse


title: NI HaCaT 24h vs NI RWPE1 24h

description: 24h post infection


title: WT total testicular polysome [WT.Tpolysome.2]


title: GRTH IgG polysome.2 [WT.IgG.2]

source_name: WT mouse IgG testicular polysome


title: GRTH IgG polysome.1 [WT.IgG.1]

description: Gene expression data GRTH immunoprecipitated polysomal transcripts from WT mouse


title: NI RWPE1 24h vs NI HaCaT 24h

description: 24h post infection


title: GRTH KO.total testicular polysome [KO.Tpolysome.3]

description: Gene expression data of total testicular polysomal transcripts from GRTH KO mouse

source_name: GRTH KO mouse testis polysome

value: GRTH null


title: NI HaCaT 24h vs P6 HaCaT 24h

description: 24h post infection


title: GRTH KO.total testicular polysome [KO.Tpolysome.1]


title: age 79y 1021

description: whole blood


title: P6 HaCaT 24h vs P6 RWPE1 24h

description: 24h post infection


title: GRTH IP polysome.2 [WT.GRTHIP.2]

source_name: WT mouse GRTH IP testicular polysome


title: age 60y 1020

description: whole blood


title: age 80y 1018

description: whole blood


title: GRTH KO.total testicular polysome [KO.Tpolysome.2]


title: liver_HFHP_12w_pool

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.3).

source_name: liver tissue, after 12 weeks on the high protein - high fat diet, pooled RNA of n=5 mice

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Male C57BL/6J mice aged 8 weeks were purchased from Charles River (L'Arbresle, France ) and housed in pairs in the light and temperature-controlled animal facility of Wageningen University (12:12 h reversed light/dark cycle, 20±2 °C). Mice were fed standard lab chow (RMH-B) and had free access to feed and weter.

extract_protocol: Total RNA was prepared from liver tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, liver RNA of 5 mice per group was subsequently pooled at a concentration of 500 ng/mouse.

treatment_protocol: At 10 weeks of age mice were stratified according to their bodyweight into 9 diet groups (n=10 per group). All groups received a low fat-normal protein diet (LF-NP, 10 and 15 energy% from fat and protein, respectively) as run-in two weeks prior to the dietary intervention. One group was sacrificed after the run-in period to serve as reference group. The other groups either continued on the LF-NP diet or were switched to a high fat-normal protein (HF-NP, 35 and 15 energy% from fat and protein, respectively), a low fat-high protein (LF-HP, 10 and 50 energy% from fat and protein, respectively) or a high fat-high protein (HF-HP, 35 and 50 energy% from fat and protein, respectively) diet which they received for 1 or 12 weeks. The week prior to sacrifice mice were habituated to a modified feeding schedule. Food was removed at the beginning of the light phase. One hour after beginning of the dark phase, mice received a calibrated meal of 12.1 kJ to be consumed during 2 hours before getting ad libitum access to their habitual diet. The day of sacrifice, mice received the calibrated meal at the habitual time and were anaesthetised with Isoflurane two hours later, whereafter the liver was removed.

tag: age

value: 22 weeks

value: liver

tag: diet

value: HF-HP


title: age 93y 1023

description: whole blood


title: GRTH IP polysome.1 [WT.GRTHIP.1]


title: age 68y 1022

description: whole blood


title: GRTH KO Leydig cells [KO.LC.2]

description: Gene expression data of Leydig cell transcripts from GRTH KO mouse

source_name: GRTH KO mouse Leydig cells

value: purified Leydig cells


title: age 71y 1016

description: whole blood


title: age 56y 1029

description: whole blood


title: Berry_treated_148DAFB_vs_untreated_110DAFB_BioRep1_swap

city: Legnaro

first: Alessandro

last: Botton

state: Padova

address: Agripolis - viale dell'università 16

department: Agronomy, Food, Natural resources, Animals and Environment

country: Italy

institute: University of Padova

description: Comparison between gene expression profiles of NAA-treated berries at 148 DAFB (harvest of the treated) and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 1 (dye swapped)

hyb_protocol: The pre-hybridization and hybridization steps were carried out in Corning® hybridization chambers with some drops of 0.3× SSC to maintain internal humidity and salts concentration, immersed in a water bath at 48 °C. The microarray was pre-hybridized for 2 h with a solution containing 5× SSC, 0.1% SDS, 1× Denhardt's, and 100 ng/μl DNA carrier. Then the slides were washed once with 0.2× SSC solution and isopropanol, and dried by centrifuging for 2 min at 2000 rpm. Before hybridization, probes were mixed to have an equal amount of each fluorescent dye, ethanol precipitated with ammonium acetate (final 2 M) and resuspended in 37 μl of hybridization solution (5× SSC, 0.1% SDS, 25% formamide, and 40 ng/μl DNA carrier). The probe was denaturated for 30 s, distributed on the spotted area of the slide, and covered with a glass cover slip. After 48 h of hybridization the slides were washed once in 1× SSC 0.2% SDS and in 0.1× SSC 0.2% SDS for 5 min and twice in 0.2× SSC for 5 min to eliminate completely SDS residues that may cause shadows on the spotted area.

scan_protocol: The microarrays were scanned with a two-channel confocal microarray scanner (ScanArray® Lite, Perkin-Elmer) using its dedicated software (ScanArray Express 3.0.0., Perkin-Elmer). The laser power was set between 67 and 79% of maximum and the photomultiplier tube (PMT) was set between 69 and 79% of maximum. The excitation/emission settings were 543/570 nm for Cy3 and 633/670 nm for Cy5. After laser focusing and balancing of the two channels, scans were conducted at a resolution of 5 μm. For any scan, two separate 16-bit TIFF images were produced.

data_processing: Raw hybridization data were quality-filtered, background-subtracted, and intra-array normalized with the loess method. Calculations were all carried out with the package limma and other basic statistical functions of R for Mac OS X v2.13.1 (http://www.r-project.org/).

label: chA: Cy5

organism: Vitis vinifera

source_name: Whole deseeded berry, NAA-treated, at 148DAFB

label_protocol: Total RNA was converted into target cDNA by reverse transcription using the SuperScriptTM Indirect cDNA Labeling System (Invitrogen, USA) following the manufacturer's instructions.

extract_protocol: Total RNA was extracted from whole berries using the perchlorate method of Davies and Robinson (1996) modified by Rizzini et al. (2009).

treatment_protocol: One-hundred bunches from fifty homogeneous plants (two bunches per plant) were treated in planta with a synthetic auxin (naphtalenacetic acid, NAA, 200 mg/L; SIGMA-N640) at the pre-véraison stage corresponding to fifty-three days after full bloom (DAFB).

tag: organ

value: whole berry (deseeded)

label: chB: Cy3

source_name: Whole deseeded berry, untreated, at 110DAFB


title: age 77y 1013

description: whole blood

tag: age (y)


title: liver_HFNP_12w_pool

source_name: liver tissue, after 12 weeks on the normal protein - high fat diet, pooled RNA of n=5 mice

value: HF-NP


title: Berry_treated_148DAFB_vs_untreated_110DAFB_BioRep2

description: Comparison between gene expression profiles of NAA-treated berries at 148 DAFB (harvest of the treated) and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 2

label: chA: Cy3

label: chB: Cy5


title: Berry_treated_148DAFB_vs_untreated_110DAFB_BioRep1

description: Comparison between gene expression profiles of NAA-treated berries at 148 DAFB (harvest of the treated) and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 1


title: Berry_treated_110DAFB_vs_untreated_110DAFB_BioRep2

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 2

source_name: Whole deseeded berry, NAA-treated, at 110DAFB


title: age 73y 1009

description: whole blood

tag: source

value: UCSD


title: liver_LFHP_12w_pool

source_name: liver tissue, after 12 weeks on thehigh protein - low fat diet, pooled RNA of n=5 mice

value: LF-HP


title: WT Leydig cells [WT.LC.2]

description: Gene expression data of Leydig cell transcripts from WT mouse

source_name: WT mouse Leydig cells


title: age 82y 1011

description: whole blood

tag: plate

value: M

value: whole blood


title: GRTH KO Leydig cells [KO.LC.1]

tag: gender


title: age 68y 1017

description: whole blood

tag: ethnicity

value: Caucasian - European


title: liver_HFHP_1w_pool

source_name: liver tissue, after 1 week on the high protein - high fat diet, pooled RNA of n=5 mice

value: 13 weeks

tag: tissue


title: liver_LFNP_12w_pool

source_name: liver tissue, after 12 weeks on the normal protein - low fat diet, pooled RNA of n=5 mice

value: male

value: LF-NP


title: age 75y 1008

description: whole blood

value: F


title: age 48y 1012

description: whole blood


title: age 73y 1007

description: whole blood


title: age 83y 1010

description: whole blood


title: WT Leydig cells [WT.LC.1]

value: adult

value: WT

tag: cell type


title: age 54y 1014

description: whole blood


title: Berry_treated_110DAFB_vs_untreated_110DAFB_BioRep1_swap

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 1 (dye swapped)


title: age 63y 1015

description: whole blood


title: Berry_treated_60DAFB_vs_treated_110DAFB_BioRep2

description: Comparison between gene expression profiles of treated berries at 60 and 110 DAFB - Biological replicate 2

source_name: Whole deseeded berry, NAA-treated, at 60DAFB


title: liver_HFNP_1w_pool

source_name: liver tissue, after 1 week on the normal protein - high fat diet, pooled RNA of n=5 mice


title: GRTH KO round spermatids [KO.RS.3]

description: Gene expression data of round spermatid transcripts from GRTH KO mouse

source_name: GRTH KO mouse round spesrmatids

value: GRTH null

value: purified round spermatids


title: Panc-1+ve SQ2 target study

city: Suwon

first: pooja

last: Dua

address: Chun-chun Dong, Jang-an Gu

department: Chemistry

country: South Korea

institute: Sungkyunkwan University

description: Pancreatic cancer cells

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Panc-1-ve cells (Panc-1 cells that do not bind to aptamer SQ2)

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

growth_protocol: Capan1 and Panc-1 cells were cultures in accordance with ATCC culture conditions. See www.atcc.org. Panc-1 +ve and Panc-1-ve cells were cultured in DMEM with 10% serum. HPDE was cultured in keratinocyte serum free medium supplemented with growth factors as described Furukawa, T. etal Am J Pathol, 148: 1763-1770, 1996.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA)

tag: phenotype

value: Pancreatic carcinoma

tag: cell line

value: Panc-1-ve cells


title: WT round spermatids [WT.RS.3]

description: Gene expression data of round spermatid transcripts from WT mouse

source_name: WT mouse round spesrmatids


title: Berry_treated_60DAFB_vs_treated_110DAFB_BioRep1_swap

description: Comparison between gene expression profiles of treated berries at 60 and 110 DAFB - Biological replicate 1 (dye-swapped)

value: whole berry (deseeded)


title: Berry_treated_110DAFB_vs_untreated_110DAFB_BioRep1

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 110 DAFB (harvest of the control untreated) - Biological replicate 1


title: age 62y 1005

description: whole blood


title: liver_LFHP_1w_pool

source_name: liver tissue, after 1 week on the high protein - low fat diet, pooled RNA of n=5 mice

value: liver

tag: time


title: Panc-1-ve  SQ2 target study

description: Pancreatic cancer cells

source_name: Panc-1+ve cells (Panc-1 cells that binds to aptamer SQ2)

value: Panc-1+ve cells

value: Panc-1 cells that binds to aptamer SQ2


title: age 64y 1004

description: whole blood

value: UCSD


title: liver_LFNP_1w_pool

source_name: liver tissue, after 1 week on the normal protein - low fat diet, pooled RNA of n=5 mice


title: GRTH KO round spermatids [KO.RS.2]


title: liver_LFNP_0w_pool

source_name: liver tissue, baseline (t=0), pooled RNA of n=5 mice

value: 12 weeks


title: age 87y 1006

description: whole blood

value: Caucasian - European

value: whole blood


title: Berry_treated_60DAFB_vs_treated_110DAFB_BioRep1

description: Comparison between gene expression profiles of treated berries at 60 and 110 DAFB - Biological replicate 1


title: Berry_treated_60DAFB_vs_untreated_60DAFB_BioRep2_swap

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 3 days after the treatment (60 DAFB) - Biological replicate 2 (dye-swapped)

source_name: Whole deseeded berry, untreated, at 60DAFB


title: GRTH KO round spermatids [KO.RS.1]

value: male


title: WT round spermatids [WT.RS.2]


title: Panc-1  SQ2 target study

description: Pancreatic cancer cells

source_name: Panc-1 cells (ATCC)

value: Panc-1 cells


title: Capan-1 SQ2 target study

description: Pancreatic cancer cells

source_name: Capan1 cells (ATCC)

value: Pancreatic adenocarcinoma

value: Capan1 cells


title: WT round spermatids [WT.RS.1]

value: adult

value: WT


title: age 66y 1003

description: whole blood

value: F


title: age 89y 1002

description: whole blood


title: Berry_treated_60DAFB_vs_untreated_60DAFB_BioRep2

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 3 days after the treatment (60 DAFB) - Biological replicate 2


title: age 67y 1001

description: whole blood


title: Cerebral Palsy, Gracilis, Patient Replicate 10

city: San Diego

first: Lucas

middle: Robert

last: Smith

state: CA

address: 3350 La Jolla Village Drive Mail Code 151

department: Bioengineering

institute: University of California San Diego

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45oC on GeneChip Human Genome U133A Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GeneSpring Software (Affymetrix, version 11.5) was used for primary analysis.  Genes were denoted as present if they had a MAS5 present call on 10/40 chips.  The concordance of 3 summarization algorithms were used: MAS5, RMA, and GC-RMA.  Significantly altered genes were determined by a 2x2 ANOVA within GeneSpring on patient group (cerebral palsy or control patients) and muscle (gracilis or semitendinosus) with a False Discovery Rate set at 1%.  This analysis was performed on each of the three summarization algorithms and the overlap of all 3 was used as the significantly different gene set. The RMA and GCRMA in log2 format values are linked to the Series record.

source_name: Gracilis Mucle, Cerebral Palsy

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

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

tag: subject

tag: disease

value: CP

tag: muscle

value: GR

value: M

tag: gmfcs

tag: popliteal angle


title: Cerebral Palsy, Semitendinosus, Patient Replicate 10

source_name: Semitendinosus Muscle, Cerebral Palsy

value: ST

tag: age


title: Cerebral Palsy, Semitendinosus, Patient Replicate 9


title: Berry_treated_60DAFB_vs_untreated_60DAFB_BioRep1_swap

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 3 days after the treatment (60 DAFB) - Biological replicate 1 (dye swapped)

tag: organ

value: whole berry (deseeded)


title: HPDE SQ2 target study

description: Normal pancreatic ductal cells

source_name: Human pancreatic ductal cell line (HPDE) developed by Ming S.Taso

value: normal pancreatic ductal cells


title: Berry_treated_60DAFB_vs_untreated_60DAFB_BioRep1

description: Comparison between gene expression profiles of NAA-treated and untreated berries at 3 days after the treatment (60 DAFB) - Biological replicate 1


title: GRTH KO spermatocytes [KO.SP.4]

description: Gene expression data of spermatocyte transcripts from KO mouse

source_name: GRTH KO mouse spermatocytes

tag: developmental stage

tag: strain

tag: genotype/variation

value: GRTH null

value: purified spermatocytes


title: Cerebral Palsy, Gracilis, Patient Replicate 9

tag: gender


title: GRTH KO spermatocytes [KO.SP.3]


title: GRTH KO spermatocytes [KO.SP.1]


title: GRTH KO spermatocytes [KO.SP.2]


title: WT spermatocytes [WT.SP.4]

description: Gene expression data of spermatocyte transcripts from GRTH WT mouse

source_name: WT mouse spermatocytes


title: WT spermatocytes [WT.SP.3]


title: Panc-1+ve  siALPPL2 48h study

description: ALPPL2 positive pancreatic carcinoma cells with siRNA mediated ALPPL2 knockdown

source_name: Panc-1+ve cells (ALPPL2 expressing Panc-1 cells)

growth_protocol: Panc-1 +ve cells were cultured in DMEM with 10% FCS under 5% CO2 containing humified conditions.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) 48 h post transfection.

treatment_protocol: Panc1+ve cells were either treated with lipofectamine 2000 or transfected with 10nM of siALPPL2-2 (5' CACCACGCCCUUUGCUUUA 3' ), siALPPL2-3 (5' GGCCCAUGAGUCAGAGAGG 3') and siGFP control (5' GGCUACGUCCAGGAGCGCA3') in DMEM with 10% FCS in accordance with the standard transfection protocol. See www.invitrogen.com

value: Pancreatic carcinoma cells

value: ALPPL2 expressing

tag: treatment


title: Cerebral Palsy, Gracilis, Patient Replicate 8


title: Cerebral Palsy, Semitendinosus, Patient Replicate 8


title: Cerebral Palsy, Semitendinosus, Patient Replicate 6


title: Panc-1+ve L2K  48h study

description: ALPPL2 positive pancreatic carcinoma cells

value: Lipofectamine 2000


title: WT spermatocytes [WT.SP.2]

description: Gene expression data of spermatocyte transcripts from WT mouse

value: male


title: Cerebral Palsy, Gracilis, Patient Replicate 7


title: Cerebral Palsy, Semitendinosus, Patient Replicate 7


title: Panc-1+ve  siALPPL2-2 48h study


title: Panc-1+ve siGFP  48h study

value: siGFP


title: WT spermatocytes [WT.SP.1]


title: Cerebral Palsy, Gracilis, Patient Replicate 6


title: brain metastatic 131/4-5B2 vs poorly metastatic WM239 replicate #4

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

description: VALUE in data table represents Cy5/Cy3

hyb_protocol: Probes were denatured for 3 min at 95°C.The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer (Roche) with yeast tRNA (Invitrogen) and salmon sperm DNA (Invitrogen) in a microslides box hybridization chamber. Slides were washed 3 times in 0.1 X SSC-0.1% SDS at 50°C and 4 times in 0.1X SSC. Slides were dried by centrifugation.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

source_name: brain metastatic 131/4-5B2

label_protocol: 20 µg of total RNA were primed with 2 µl of 3.0ug/ul (dT)20VN DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3h in the presence of 600 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, with 50 µM amino-allyl-dUTP. The reaction was purified on an Amersham CyScribe GFX column following manufacturer's instructions. The aa-cDNA was labeled with monoreactive Cy dye(GE Healthcare) for 1h at room temperature and purified on an Amersham CyScribe GFX column following manufacturer's instructions.

extract_protocol: Total RNA extracted using Qiagen Rneasy kit following manufacturer's instructions

value: brain metastatic 131/4-5B2

source_name: poorly metastatic WM239

value: poorly metastatic WM239


title: brain metastatic 131/4-5B2 vs poorly metastatic WM239 replicate #2

description: VALUE in data table represents Cy3/Cy5


title: Cerebral Palsy, Semitendinosus, Patient Replicate 5


title: brain metastatic 131/4-5B2 vs poorly metastatic WM239 replicate #1

description: VALUE in data table represents Cy3/Cy5


title: brain metastatic 131/4-5B2 vs highly metastatic variant 113/6-4 replicate #4

description: VALUE in data table represents Cy5/Cy3

source_name: metastatic 113/6-4L

value: metastatic 113/6-4L


title: brain metastatic 131/4-5B2 vs poorly metastatic WM239 replicate #3

description: VALUE in data table represents Cy5/Cy3


title: Cerebral Palsy, Semitendinosus, Patient Replicate 3


title: Cerebral Palsy, Semitendinosus, Patient Replicate 4


title: Cerebral Palsy, Gracilis, Patient Replicate 3


title: Cerebral Palsy, Gracilis, Patient Replicate 4


title: wt dss 6 days 80_3

city: La Jolla

first: Laia

last: Egea

address: 9500 Gilman Dr

department: Medicine

institute: UCSD

hyb_protocol: 1650ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). 5 µm scanning in green at 10% and 100% PMT

data_processing: Slide design ID was 26655 and the protocol used for extraction was GE1_107_Sep09. Version 10.7.3.1. of feature extraction. The data were normalized using the multi-loess method described in this paper: Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil, J. Mol. Endocrinology, 33, 1 (2004)

source_name: colon crypts from 1.5%DSS treated wt mice for 6 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150ng RNA using the Quick Amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA (isolated by RNeasy kit; Qiagen following the manufacturer's intructions) was prepared from isolated crypts of WT and GM-CSF-/- mice colons before or after 1.5% DSS treatment for 6 days. .

treatment_protocol: Colitis was induced by allowing mice to drink 1.5% (w/v) Dextran sodium sulfate (DSS) (m. w. 36-50 kDa, MP Biomedicals) dissolved in the drinking water ad libitum for 6 days. Untreated mice were administered water only.

tag: genotype

value: wild type

value: DSS

tag: tissue

value: colon crypts

value: 8 weeks


title: gmcsf ko dss 6 days 79_2

source_name: colon crypts from 1.5%DSS treated gmcsf ko mice for 6 days

value: GMCSF KO

value: water


title: Cerebral Palsy, Gracilis, Patient Replicate 5

value: CP

value: GR

value: M


title: brain metastatic 131/4-5B2 vs highly metastatic variant 113/6-4 replicate #2

description: VALUE in data table represents Cy3/Cy5

tag: cell type


title: gmcsf ko water 6 days 80_2

source_name: colon crypts from untreated gmcsf ko mice


title: Cerebral Palsy, Semitendinosus, Patient Replicate 2

value: ST


title: brain metastatic 131/4-5B1 vs poorly metastatic WM239 replicate #3

description: VALUE in data table represents Cy5/Cy3

source_name: brain metastatic 131/4-5B1

value: brain metastatic 131/4-5B1


title: brain metastatic 131/4-5B2 vs highly metastatic variant 113/6-4 replicate #3

description: VALUE in data table represents Cy5/Cy3


title: wt water 6 days 79_3

source_name: colon crypts from untreated wt mice


title: brain metastatic 131/4-5B1 vs poorly metastatic WM239 replicate #4

description: VALUE in data table represents Cy5/Cy3


title: wt water 6 days 80_1


title: wt dss 6 days 79_1


title: brain metastatic 131/4-5B1 vs poorly metastatic WM239 replicate #2

description: VALUE in data table represents Cy3/Cy5


title: gmcsf ko dss 6 days 80_4


title: Cerebral Palsy, Semitendinosus, Patient Replicate 1


title: Cerebral Palsy, Gracilis, Patient Replicate 1


title: gmcsf ko dss 6 days 78_4


title: brain metastatic 131/4-5B1 vs poorly metastatic WM239 replicate #1

description: VALUE in data table represents Cy3/Cy5


title: Typically Developing Control, Semitendinosus, Patient Replicate 10

source_name: Semitendinosus Muscle, Control

value: TD

value: F


title: brain metastatic 131/4-5B2 vs highly metastatic variant 113/6-4 replicate #1

description: VALUE in data table represents Cy3/Cy5


title: brain metastatic 131/4-5B1 vs highly metastatic variant 113/6-4 replicate #4

description: VALUE in data table represents Cy5/Cy3


title: brain metastatic 131/4-5B1 vs highly metastatic variant 113/6-4 replicate #3

description: VALUE in data table represents Cy5/Cy3


title: Cerebral Palsy, Gracilis, Patient Replicate 2


title: wt dss 6 days 78_3

value: male


title: Typically Developing Control, Gracilis, Patient Replicate 10

source_name: Gracilis Mucle, Control


title: brain metastatic 131/4-5B1 vs highly metastatic variant 113/6-4 replicate #2

description: VALUE in data table represents Cy3/Cy5


title: Typically Developing Control, Semitendinosus, Patient Replicate 8


title: Typically Developing Control, Semitendinosus, Patient Replicate 9


title: Typically Developing Control, Semitendinosus, Patient Replicate 7


title: wt water 6 days 78_1


title: brain metastatic 131/4-5B1 vs highly metastatic variant 113/6-4 replicate #1

description: VALUE in data table represents Cy3/Cy5


title: gmcsf ko water 6 days 78_2


title: Typically Developing Control, Gracilis, Patient Replicate 9


title: Typically Developing Control, Gracilis, Patient Replicate 8


title: metastatic 113/6-4L vs poorly metastatic WM239 replicate #3

description: VALUE in data table represents Cy5/Cy3


title: brain stem  control/experimental replicate 1 (1BS)

city: Urbana

first: Yibayiri

middle: Osee

last: Sanogo

state: IL

address: 505 S. Goodwin

department: Integrative Biology

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Samples representing individual brain parts were labeled using either Cy3 or Cy5 dyes and competitively hybridized to the arrays. We used a loop design in the microarray experiment and controlled for dye effect by performing dye swaps. For hybridization, 900 ng cRNA of samples from control and experimental groups labeled with different dyes were mixed, fragmented and hybridized onto an Agilent 4_44K oligonucleotide microarray

scan_protocol: The microarray slides were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) and expression feature were extracted using GenePix Pro 6.0 software (Molecular Devices)

data_processing: As preprocessing methods of gene expression intensities, we used within array loess normalization without background correction. For the between array normalization, we used the Aquantile method. Since the Aquantile method does not take into account weighted values, we manually replaced the A values with NA (non available) for zero weights.

organism: Gasterosteus aculeatus

source_name: brain stem control

label_protocol: The samples were labeled using the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) following the manufacturer's instructions.

growth_protocol: The fish were maintained in our laboratory in 104L tanks under 8:16h light/dark photoperiod during the winter period (November to March). An average of 10% of the water in the tanks was recycled each day. The adult fish were fed ad libitum with a mixture of bloodworms, serpula and mysis

extract_protocol: Each fish brain parts were individually dissected and placed immediately on ice in 500ml of TRIzol¨ Reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated immediately from individual brains using TRIzol¨ Reagent according to the manufacturer's recommendation followed by on column purification with RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: Fish in the control and experimental groups were paired and matched by size whereas the intruders were always smaller in size than the resident fish. The intruder was gently netted and introduced into the tank of the resident male. The interaction between the resident fish and the intruder was video-recorded for 15 minutes and the videos were later scored for the number of orients, approaches, chases and bites directed toward the intruder by the focal fish.

value: Adult

value: Male

tag: origin

value: Balvormie pond in Western Scotland

tag: stress

value: control

source_name: brain stem experimental

value: intrusion into their territory


title: brain stem  control/experimental replicate 5 (5BS)


title: metastatic 113/6-4L vs poorly metastatic WM239 replicate #4

description: VALUE in data table represents Cy5/Cy3

value: metastatic 113/6-4L

value: poorly metastatic WM239


title: Typically Developing Control, Gracilis, Patient Replicate 7

tag: subject


title: brain stem  control/experimental replicate 3 (3BS)


title: metastatic 113/6-4L vs poorly metastatic WM239 replicate #2

description: VALUE in data table represents Cy3/Cy5


title: brain stem  control/experimental replicate 2 (2BS)


title: Typically Developing Control, Gracilis, Patient Replicate 6

tag: disease


title: cerebellum control/experimental replicate 5 (5C)

source_name: cerebellum control

source_name: cerebellum experimental


title: metastatic 113/6-4L vs poorly metastatic WM239 replicate #1

description: VALUE in data table represents Cy3/Cy5


title: cerebellum control/experimental replicate 4 (4C)


title: Typically Developing Control, Semitendinosus, Patient Replicate 5

tag: muscle


title: cerebellum control/experimental replicate 2 (2C)


title: Typically Developing Control, Semitendinosus, Patient Replicate 6

tag: gmfcs


title: Typically Developing Control, Gracilis, Patient Replicate 5

tag: popliteal angle


title: Typically Developing Control, Semitendinosus, Patient Replicate 4

tag: age


title: cerebellum control/experimental replicate 3 (3C)


title: Typically Developing Control, Semitendinosus, Patient Replicate 3


title: cerebellum control/experimental replicate 1 (1C)


title: Typically Developing Control, Gracilis, Patient Replicate 3


title: Typically Developing Control, Semitendinosus, Patient Replicate 2


title: diencephalon control/experimental replicate 4 (4D)

source_name: diencephalon control

source_name: diencephalon experimental


title: diencephalon control/experimental replicate 3 (3D)


title: diencephalon control/experimental replicate 5 (5D)


title: diencephalon control/experimental replicate 2 (2D)


title: Typically Developing Control, Gracilis, Patient Replicate 2


title: telencephalon control/experiemntal replicate 5 (5T)

source_name: telencephalon control

source_name: telencephalon experimental


title: gmcsf ko water 6 days 79_4

value: GMCSF KO

value: DSS

value: colon crypts

value: 8 weeks


title: telencephalon control/experiemntal replicate 1 (1T)


title: telencephalon control/experiemntal replicate 4 (4T)


title: Typically Developing Control, Gracilis, Patient Replicate 1

value: GR

value: M


title: HEK293T cell culture,control,biological rep 5

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell line


title: telencephalon control/experiemntal replicate 2 (2T)


title: Typically Developing Control, Semitendinosus, Patient Replicate 1

value: ST


title: diencephalon control/experimental replicate 1 (1D)


title: Typically Developing Control, Gracilis, Patient Replicate 4

value: TD


title: telencephalon control/experiemntal replicate 3 (3T)


title: wavy-REP1

city: Campus de Cantoblanco

first: Antonio

last: Leyva

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

country: Spain

institute: CNB-CSIC

description: Gene expression data from whole plant (actin2-5 mutant)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

organism: Arabidopsis thaliana

source_name: wavy mutant

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild-type and actin2-5 seedlings were grown on half strength Murashige & Skoog medium for 8 days before harvest and storage at -80 ºC

extract_protocol: RNA was isolated with TriReagent and Plant RNA Isolation Aid (Ambion), followed by cleanup with RNeasy Mini Kit (Qiagen).


title: wavy-REP3


title: HEK293T cell culture,control,biological rep 6

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 6


title: wavy-REP2


title: HEK293T cell culture,control,biological rep 4

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 4


title: WildType-REP3

description: Gene expression data from whole plant (wild type)

source_name: Wild Type Columbia

value: Wild Type

tag: ecotype

value: Columbia


title: 071-052_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo

status: Public on Nov 20 2012

first: Daniel

middle: Edward

last: Zak

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

description:
probe group file: BrainArray version 9: HsEx10stv2_Hs_ENTREZG
meta-probeset file: BrainArray version 9: HsEx10stv2_Hs_ENTREZG

hyb_protocol: Samples were hybridized according to the Whole Transcript Sense Target Labeling protocol: *Heat cocktails at 99° for 5 minutes, 42° for 5 minutes, and then centrifuged at 13,200g for 1 minute. *Transfer 200uL of hyb solution to each array. *Hybridize 16 hours at 45° at 60rpm. *Wash and stain using fluidics protocol FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Microarrays were normalized at the gene level using the BrainArray custom CDF (Entrez Gene, Version 9) for probeset definitions and RMA as implemented in the justRMA function of the Bioconductor package affy for background adjustment, quantile normalization and summarization.

source_name: PBMC obtained after in vivo vaccination for varying times with MRKAd5/HIV

label_protocol: Total RNA samples were labeled as described in the Whole Transcript Sense Target Labeling protocol (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Blood was collected immediately before vaccination and at 4-6, 24, 72, and 168 hours post-vaccination. PBMC RNA was extracted using the RNeasy Protect Cell protocol (Qiagen)

treatment_protocol: At the start of the trial (Day 0), all volunteers were intramuscularly vaccinated with 1.5x10^10 genomes of the MRKAd5/HIV vaccine

tag: human subject anonymized id

tag: pre-existing serum ad5 neutralizing antibody titer (merck assay)

tag: pre-existing serum ad5 neutralizing antibody titer class

tag: time post vaccination or treatment

tag: vaccine or treatment

tag: in vivo or in vitro

value: in vivo


title: Core 3 synthase vs vector control replicate 1

city: Omaha

first: prakash

last: Radhakrishnan

address: 985950 Nebraska Medical Center

department: Eppley Cancer Center

institute: University of Nebraska Medical Center

description: biological replicate 1

hyb_protocol: Amino Allyl MessageAmp II aRNA Amplification and Hybridization for Phalanx OneArray Slides protocol

scan_protocol: Images were quantified using GenePix 4000B

data_processing: Methods/Results: The gene expression data was preprocessed and analyzed using the Bioconductor LIMMA Package in R. Several filters and normalization were applied prior to analysis. Median background was subtracted. Intensity filter was applied if either the red and green channels are below 100 intensities, or the spot is flagged with bad quality. The Log2 transformation was applied to all ratios. Two-step normalization was then done to “center” each array using lowess smoother within array and Aquartile normalization between arrays. Genes were excluded if the percent of spots missing or filtered out exceeded 50% (more than two arrays). Empty spots and control spots have been excluded. Duplicate spots for the same genes were averaged together. A total of 14360 genes were remained for analysis. The LIMMA (Linear Models for Microarray Analysis) method was fit on the normalized data to compare the intensities between the treated and control samples. The Benjamini Hochberg approach was used to control the false discovery rate (FDR). Ninety genes were claimed to be differentially expressed with the FDR less than 0.1. These genes are presented in Analysed_data_from_three_replicates_with_p-values.xls file. The result file contains the unique ID, gene name, the normalized value from each array, the average fold change in the treated samples compared to the control sample, and the FDR adjusted p value. The genes have been sorted by original ranking of the p-value.  References: 1. Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273. 2. Smyth GK: Linear models and empirical bayes methods for Assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3:Article 3. Benjamini, Yoav; Hochberg, Yosef (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B,  57 (1): 289–300.

source_name: FG Pancreatic Cancer cells with Core 3 synthase

growth_protocol: Generation of stable expression of Core 3 synthase: Core 3 synthase and vector control expressing FG cells were generated by transfection of retroviral vector (PLVX puro) alone or core 3 synthase insert containing vector into phoenix cells using Lipofectamine 2000 (Invitrogen) following manufacturer instructions. Viral supernatant was collected from these packaging cells after 48 h of post-transfections. The vector alone and core 3 synthase insert containing viral particles were used to transduce the FG cells. After 48 h of transduction, the cells were selected and maintained with Puromycin (3μg/μl).  The expression of core 3 synthase was verified by RT-PCR and western blot.

extract_protocol: Total RNA was isolated from FG vector control and FG Core 3 synthase expressing cells in triplicate using Tri Reagent according to manufacturer instruction (Molecular Research Center, Cincinnati, OH, USA). The RNA quality was first checked by Nanodrop Spectrophotometer and followed by Bio-analyzer. Thus, the extracted RNA was used for microarray analysis.

value: FG

tag: transfection

value: Core 3 synthase stable expression vector

source_name: FG Pancreatic cancer cells with PLVX puro vector

value: PLVX puro vector control


title: Core 3 synthase vs vector control replicate 2

description: biological replicate 2

label_protocol: Amino Allyl MessageAmp II aRNA Amplification and Hybridization for Phalanx OneArray Slides protocol


title: RR2_nsrR_Cy3_ch1_wt_Cy5_ch2_7DS13315878_rep1

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner at 10?m resolution, 95% laser power, PMT for low scan set to where maximal intensity of spots was 75% of saturation; PMT for high scan was 20% higher than low scan PMT. Image acquisition with ScanArray Express 3.0.1 software, spot quantification using MolecularWare AnalyzerDG Pro version 2.50.

data_processing: used values for median measurements for spot and background in high PMT setting; normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: 14028s nsrR mutant

label_protocol: Standard labeling using Cy3-dUTP with reverse transcriptase and random hexamers

growth_protocol: aerobically  in LB to mid-log phase (OD600~0.5) at 37°C

extract_protocol: 1Vol culture was mixed with 2Vol RNAprotect reagent (Qiagen, Valencia, CA, USA) and RNA immediately purified using the Qiagen RNeasy midi kit (Qiagen).

tag: genotype/variation

value: nsrR mutant

source_name: 14028s wild type

label_protocol: Standard labeling using Cy5-dUTP with reverse transcriptase and random hexamers

value: wild type


title: WildType-REP1

tag: genotype


title: Core 3 synthase vs vector control replicate 3

description: biological replicate 3


title: 071-052_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: 071-052_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-052_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: RR2_wt_Cy3_ch1_nsrR_Cy5_ch2_7DS1331587_rep1

description: biological replicate


title: RR2_nsrR_Cy3_ch1_wt_Cy5_ch2_7DS13322028_rep2

description: biological replicate


title: WildType-REP2


title: 071-052_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: RR2_wt_Cy3_ch1_nsrR_Cy5_ch2_7DS13322029_rep2

description: biological replicate


title: anti338miR2 biological replicate 2

city: Lausanne

first: Cécile

last: Jacovetti

address: rue du Bugnon 9

department: DBCM

country: Switzerland

institute: University of Lausanne

hyb_protocol: samples were hybridized on  RaGene V1.0 affymetrix Chip  according to the manufacturer's instructions.

scan_protocol: microarrays were scanned with GeneChip® Scanner 30007G (Affymetrix)

data_processing: Expression values were normalized using RMA expression summary algorithms implemented in R (version 2.9.2) within the Affy package. Values are in log2

organism: Rattus norvegicus

source_name: INS832/13 cells

label_protocol: 100ng of total RNA was submitted to WT expression kit (Ambion ) for sample processing

extract_protocol: total RNA was extracted with miRNeasy kit (Qiagen)

treatment_protocol: INS832/13 cells were treated with an antimiR338 or a scrambled anti-miR (the control).

value: INS832/13 pancreatic carcinoma cell line

value: miR-338-3p blockade


title: RR2_wt_Cy3_ch1_nsrR_Cy5_ch2_7DS13322030_rep3

description: biological replicate


title: 071-048_Ad5Titer_220_time_024hr_vaccine_MRKAd5_exp_vivo


title: RR2_nsrR_Cy3_ch1_wt_Cy5_ch2_7DS13322031_rep3

description: biological replicate


title: CT2 biological replicate 2

value: control


title: anti338miR3 biological replicate 3


title: 071-050_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: 071-048_Ad5Titer_220_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-050_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: wedge excision right middle lobe: adenocarcinoma in situ (AIS).

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description: reference raw data file: US22502676_252252210525_S01_CGH_105_Dec08_1_1.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505C micro-array scanner. Image data acquisition was performed in feature extraction software v10.7.3.1 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. A moving average of 5 data points was used. The normalization method used was median normalization, performed in R.

source_name: Lung tissue

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).

tag: gender

tag: tissue

value: wedge excision right middle lobe:adenocarcinoma in situ (AIS).

source_name: Normal lung tissue

value: normal lung


title: wedge excision apex left upper lobe: papillary adenocarcinoma.

value: wedge excision apex left upper lobe:papillary adenocarcinoma.


title: CT1 biological replicate 1


title: 071-050_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo

city: Seattle


title: 071-048_Ad5Titer_220_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-046_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-050_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: CT3 biological replicate 3


title: lobectomy material of the right upper lobe: mixed papillary adenocarcinoma/AIS.

value: M

value: lobectomy material of the right upper lobe:mixed papillary adenocarcinoma/AIS.


title: 071-046_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: 071-050_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: Large White sample replicate 18

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

description: Large White sample replicate 18 of 20

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample and 300 ng of cyanine 5-labeled reference sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red reference signal. Limma package and the normalizeWithinArrays procedure were used.

source_name: Longissimus muscle of LW pig

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

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

tag: breed

value: Large white

value: skeletal muscle

tag: pig live weight

tag: rearing conditions

value: Alternative

source_name: reference pool composed of an equal amount of total RNA isolated from all 40 samples


title: 071-046_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo

value: in vivo


title: Large White sample replicate 16

description: Large White sample replicate 16 of 20


title: Large White sample replicate 20

description: Large White sample replicate 20 of 20


title: Large White sample replicate 19

description: Large White sample replicate 19 of 20


title: 071-048_Ad5Titer_220_time_072hr_vaccine_MRKAd5_exp_vivo


title: Large White sample replicate 17

description: Large White sample replicate 17 of 20


title: 071-048_Ad5Titer_220_time_000hr_vaccine_MRKAd5_exp_vivo


title: anti338miR1 biological replicate 1


title: Large White sample replicate 15

description: Large White sample replicate 15 of 20


title: Large White sample replicate 13

description: Large White sample replicate 13 of 20


title: Large White sample replicate 8

description: Large White sample replicate 8 of 20

value: Conventional


title: Large White sample replicate 12

description: Large White sample replicate 12 of 20


title: Large White sample replicate 11

description: Large White sample replicate 11 of 20


title: Large White sample replicate 9

description: Large White sample replicate 9 of 20


title: Large White sample replicate 10

description: Large White sample replicate 10 of 20


title: Large White sample replicate 6

description: Large White sample replicate 6 of 20


title: Large White sample replicate 14

description: Large White sample replicate 14 of 20


title: 071-046_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: 071-044_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-044_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: 071-035_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-044_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-035_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-035_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: 071-046_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-044_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: 071-025_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: Large White sample replicate 5

description: Large White sample replicate 5 of 20


title: Large White sample replicate 3

description: Large White sample replicate 3 of 20


title: Large White sample replicate 1

description: Large White sample replicate 1 of 20


title: 071-044_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: 071-035_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: Large White sample replicate 2

description: Large White sample replicate 2 of 20


title: 071-035_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: Large White sample replicate 7

description: Large White sample replicate 7 of 20


title: 071-025_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 20

description: Basque sample Replicate 20 of 20

source_name: Longissimus muscle of B pig

value: Basque


title: Large White sample replicate 4

description: Large White sample replicate 4 of 20


title: 071-025_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 19

description: Basque sample Replicate 19 of 20


title: Basque sample Replicate 18

description: Basque sample Replicate 18 of 20


title: Basque sample Replicate 16

description: Basque sample Replicate 16 of 20


title: 071-025_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 11

description: Basque sample Replicate 11 of 20


title: Basque sample Replicate 13

description: Basque sample Replicate 13 of 20


title: 071-008_Ad5Titer_707_time_072hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 17

description: Basque sample Replicate 17 of 20


title: Basque sample Replicate 15

description: Basque sample Replicate 15 of 20


title: 071-025_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-015_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo


title: 071-015_Ad5Titer_0_time_006hr_vaccine_MRKAd5_exp_vivo


title: 071-015_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo


title: 071-015_Ad5Titer_0_time_072hr_vaccine_MRKAd5_exp_vivo


title: 071-008_Ad5Titer_707_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-008_Ad5Titer_707_time_024hr_vaccine_MRKAd5_exp_vivo


title: 071-015_Ad5Titer_0_time_168hr_vaccine_MRKAd5_exp_vivo


title: 071-008_Ad5Titer_707_time_006hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 9

description: Basque sample Replicate 9 of 20


title: 14days gestant female, biological replicate 1

hyb_protocol: Hybridization was performed according to microRNA Labeling & Hybridization Kit.

scan_protocol: Microarrays were scanned with Agilent High-Resolution Microarray Scanner.

data_processing: Data were imported into GeneSpringGX (Agilent Technologies) and quantile normalized. Values are in log2.

source_name: islets of 14 days gestant female rat

label_protocol: 100ng of total RNA was submitted to microRNA Labeling & Hybridization Kit.

extract_protocol: Total RNA was extracted with miRNeasy kit QIAGEN following manufacturer's instructions.

value: female

value: islets


title: 14days gestant female, biological replicate 4


title: 14days gestant female, biological replicate 3


title: 14days gestant female, biological replicate 2


title: Basque sample Replicate 14

description: Basque sample Replicate 14 of 20


title: control female, biological replicate 4

source_name: islets of control female rat


title: Basque sample Replicate 6

description: Basque sample Replicate 6 of 20


title: Basque sample Replicate 12

description: Basque sample Replicate 12 of 20


title: 071-008_Ad5Titer_707_time_000hr_vaccine_MRKAd5_exp_vivo


title: Basque sample Replicate 8

description: Basque sample Replicate 8 of 20


title: Basque sample Replicate 10

description: Basque sample Replicate 10 of 20


title: Basque sample Replicate 5

description: Basque sample Replicate 5 of 20


title: Basque sample Replicate 7

description: Basque sample Replicate 7 of 20


title: Basque sample Replicate 4

description: Basque sample Replicate 4 of 20


title: control female, biological replicate 3


title: control female, biological replicate 1


title: control female, biological replicate 2


title: Basque sample Replicate 3

description: Basque sample Replicate 3 of 20


title: Basque sample Replicate 1

description: Basque sample Replicate 1 of 20


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_120mM NaCl replicate 3

city: Chania

first: Maria

middle: E.

last: Manioudaki

address: Makedonias 1

department: Horticultural Genetics and Biotechnology

country: Greece

institute: MAICH

description: CH_t_45ps rep3

hyb_protocol: Fluorescent samples were combined and purified using the PureLink™ PCR purification System. The only modification was the use of 20μl Low temp Hybridization buffer as elution buffer. The probe was supplemented with 3.5 μl of 5 mg/ml Salmon sperm DNA and 2 μl of yeast tRNA. The mixture was heated at 60oC for 5 minutes and was kept at 45oC before hybridization. The probes were placed onto the array; the slides in a sealed hybridization cassette and submerged in a 43oC water bath for 18 hours. The slides were then placed in washing solution 1 (1X SSC, 0.03% SDS) and then transferred to washing solution 2 (0.2X SSC) for 5 min with agitation followed by washing solution 3 (0.05X SSC).

scan_protocol: Microarrays were scanned with an Axon microarray scanner (model GenePix 4000B).

data_processing: The scanned images were analyzed using GenePix Pro 6.0 software. Spots were flagged as ‘not found’, ‘absent’ or ‘bad’.  The default local background subtraction method was used. Feature data were extracted from the raw images as GenePix Results files (.gpr) and converted to TIGR MultiExperiment Viewer (.mev) files using the ExpressConverter V2.1 tool implemented in the TM4 microarray software suite.  The Integrated Intensity Value (IIV) for each spot was subsequently used as input for the normalization pipeline in MIDAS V2.21 software which included the following steps (1) locally weighted scatterplot smoothing regression (LOWESS) normalization in block mode (2) in-slide replicate analysis and (3) low-intensity filtering that removes intensity values <10000. Low-quality array elements were eliminated by applying background checking for both channels with a signal/noise threshold of 2.0 and usage of flags for both channels. One bad tolerance policy parameter was set to generous.

label: Alexa 555

organism: Olea europaea

source_name: Olive cv. Chondrolia Chalkidikis roots 45days_post-120mM NaCl-stress

label_protocol: 15 μg of intact total RNA were labeled with SuperScript™ Plus Direct cDNA Labeling System (Invitrogen) using Alexa Fluor®-labeled nucleotides

growth_protocol: One year-old, self-rooted trees of Olea europaea L., cv. Chondrolia Chalkidikis obtained from a commercial nursery and grown under identical conditions were transplanted in plastic bags containing a 1:1 mixture of perlite:sand. The young trees were irrigated daily with 150ml of half-strength Hoagland solution for one month and 35 of those of similar growth were selected for the salinity experiment while another 35 for the un-treated control. Totally 70 young trees per cultivar were used for the experiment.

extract_protocol: Four young trees were used to collect root tissue at each point of treatment. The root tissue was washed repeatedly with deionised water, sterilized with 0.5% sodium hypochloride, immediately ground with liquid nitrogen and stored at a -80°C freezer. Total RNA was extracted according to the method of Bachem et al., 1998 and concentrated using the NucleoSpin® RNA Clean-up XS kit.

treatment_protocol: Plants were irrigated daily with 150ml of half-strength Hoagland solution containing in addition 0 (control) and 120 mM/l NaCl for 15, 45, 90 days through salt stress experiment and with half strength Hoagland solution for 15 and 45 days through post-stress period.

tag: cultivar

value: Chondrolia Chalkidikis (salt sensitive)

value: root


title: Basque sample Replicate 2

description: Basque sample Replicate 2 of 20


title: 7098_Ad5Titer_0_treatment_2E4vppc_vaccine_MRKAd5_exp_vitro.CEL

source_name: PBMC derived from independent donors and stimulated for 24hrs in vitro with MRKAd5 empty vector

growth_protocol: PBMC from healthy Ad5-seronegative individuals were in RPMI containing 10% FCS.

extract_protocol: Cells were frozen in RNAprotect cell reagent (Qiagen) for RNA purification.

treatment_protocol: PBMC were stimulated with 20,000 viral particles/cell of MRKAd5 empty vector or GTS buffer (mock)  for 24hrs in vitro.

value: MRKAd5 at 20000 virus particles/cell

value: in vitro


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_120mM NaCl replicate 1

description: CH_t_45ps rep1

label: Alexa 647


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_120mM NaCl replicate 2

description: CH_t_45ps rep2


title: 7098_Ad5Titer_0_treatment_Mock_vaccine_MRKAd5_exp_vitro.CEL

value: Mock


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_120mM NaCl replicate 4

description: CH_t_15ps rep4

source_name: Olive cv. Chondrolia Chalkidikis roots 15days_post-120mM NaCl-stress


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_120mM NaCl replicate 3

description: CH_t_15ps rep3


title: C57BL6_Infected3

city: Worcester MA

first: Ricardo

last: Gazzinelli

address: 364 Plantation Street, LRB

department: Infectious Diseases and Immunology

institute: University of Massachussetts Medical School

description: Gene expression data from hearts of mice infected with a Y strain of T. cruzi at day 18 post-infection.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0. GeneChips were washed and stained in a fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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, and confirmation by analysis using RMA from the Bioconductor affy package. MAS5 data was used to form the conclusions of this study (RMA was for secondary confirmation only).

source_name: Infected C57BL6 mouse at day 18 post-infection with T. cruzi

label_protocol: Biotin-labeled RNA fragments were prepared according to the standard protocol (Expression Anakysis Technical Manual, 2005, Affymetrix)

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

treatment_protocol: Hearts of mice were extracted at day 18 post-infection with T cruzi.

tag: strain

value: Cardiac tissue


title: C57BL6_Control2

description: Gene expression data from hearts of uninfected mice

source_name: Non-infected C57BL mouse control


title: 071-052_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL

source_name: PBMC obtained after in vivo vaccination for varying times with MRKAd5/HIV


title: C57BL6_Control1


title: C57BL6_Infected1


title: 071-050_Ad5Titer_0_time_000hr_vaccine_MRKAd5_exp_vivo.CEL


title: Olive_cultivar Chondrolia Chalkidikis_45days of post-stress_120mM NaCl replicate 4

description: CH_t_45ps rep4


title: C57BL6_Control3


title: 3609_Ad5Titer_0_treatment_2E4vppc_vaccine_MRKAd5_exp_vitro.CEL


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_120mM NaCl replicate 1

description: CH_t_15ps rep1


title: C57BL6_Infected2


title: 3609_Ad5Titer_0_treatment_Mock_vaccine_MRKAd5_exp_vitro.CEL


title: 3096_Ad5Titer_0_treatment_2E4vppc_vaccine_MRKAd5_exp_vitro.CEL


title: 071-046_Ad5Titer_0_time_024hr_vaccine_MRKAd5_exp_vivo.CEL


title: 2286_Ad5Titer_0_treatment_Mock_vaccine_MRKAd5_exp_vitro.CEL


title: 3096_Ad5Titer_0_treatment_Mock_vaccine_MRKAd5_exp_vitro.CEL


title: 2286_Ad5Titer_0_treatment_2E4vppc_vaccine_MRKAd5_exp_vitro.CEL


title: Olive_cultivar Chondrolia Chalkidikis_15days of post-stress_120mM NaCl replicate 2

description: CH_t_15ps rep2