title: K14E6 transgenic mice RNA pool biological replicate 3

city: Mexico City

first: Laura

middle: I

last: Uribe

state: DF

address: Periferico Sur 4124 Col. Ex rancho de Anzaldo

department: Research

country: Mexico

institute: INMEGEN

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

scan_protocol: Genechips were scanned using the GCOS software and the Affymetrix Genechip Scanner 3000  7G.

data_processing: The data was analyzed using Partek Genomic Suite. Raw intensity probes wer imported by setting up RMA background correction and the differential gene expression intensities were calculated with the default  one way ANOVA parameters.

source_name: RNA from skin tissue of 3 K14E6 transgenic mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed and treated according to the American Association of Laboratory Animal Care (AALAC) regulations. All mice procedures were performed according to the protocol approved by the Research Unit for Laboratory Animal Care Committee (UPEAL-CINVESTAV-IPN, Mexico; NOM-062-ZOO-1999)

extract_protocol: RNA was extracted using the TRIzol reagent as per  manufacturers instructions and a second round of purification was performed using the Rnaeasy Mini Kit columns (Qiagen).

treatment_protocol: Three 6-week-old virgin female mice were used for each biological replicate. After sacrifice, mice dorsal skin were shaved and a 0.5 cm biopsy was disected. The tissue sample was immediately liquid nitrogen frozen for later RNA isolation.

tag: genotype/variation

value: K14E6 transgenic mice

tag: tissue

value: skin

tag: age

value: female

tag: strain

value: FVB


title: Eahy2.Can.1H.Cy3

status: Public on Jul 27 2010

type: RNA

city: Milwaukee

first: Jenifer

last: Coburn

state: WI

address: 8701 Watertown Plank Rd.

department: ID/CBID

country: USA

institute: Medical College of Wisconsin

description: Eahy, Canicola vs Patoc, 1 hr, Cy3

hyb_protocol: The two differently labeled cDNAs were mixed and hybridized using Pronto Microarray Hybridization Kit in a hybridization chamber (Corning, Corning, NY), with the same array slide for 38 to 42 hr according to manufacturer’s instruction.   After a series of washes using the buffers provided in the kit, slides were spun dry.

scan_protocol: The slides were scanned under two laser channels in a Scanarray 4000 scanner (Packard Bioscience, Meriden, CT).

data_processing:
Images were overlaid and analyzed using Imagene (BioDiscovery, El Segundo, CA). Raw gene expression was imported from Imagene to GeneSifter (GeneSifter.Net, VizX Labs, Seattle, WA) for analysis.
Data from 3 biological replicate experiments were normalized using Lowess normalization and by the median of the raw intensities for all spots in each sample for each array.
Each channel from the dual-channel hybridized array was analyzed independantly. The same raw data file is therefore associated with two Samples.

molecule: total RNA

organism: Homo sapiens

source_name: infected with L. interrogans 1 hr

label_protocol: 5 to 20 mg of total RNA from uninfected control and infected samples was used to generate cDNA labeled with aminoallyl (aa)-dUTP through a reverse transcription reaction using anchored oligo(dT) primers.  The purified aa-dUTP-labeled cDNAs were coupled in 10 µl 0.1 M NaHCO3 with either Cy3 or Cy5 NHS-ester dye. Cy-dye labeled cDNA was purified using a Cyscribe GFX column (Amersham Biosciences, Piscataway, NJ).

extract_protocol: Cells were washed with phosphate buffered saline (PBS) and harvested for RNA isolation.  The RNA was purified using RNeasy kit (Qiagen, Valencia, CA) with DNase digestion according to manufacturer’s manual. The quality of RNA was checked using a Bioanalyzer (Agilent, Santa Clara, CA).

tag: cell type

value: macrovascular cell line

tag: cell line

tag: replicate

value: replicate experiment 2


title: FvB non transgenic control mice RNA pool biological replicate 3

label: biotin

organism: Mus musculus

source_name: RNA from skin tissue of 3 FvB non transgenic mice

value: FvB non transgenic mice

tag: gender


title: Eahy1.uninf.3H.Cy5

description: Eahy, Patoc vs. uninfected, 3 hr, Cy5

source_name: uninfected 3 hr

value: replicate experiment 1


title: Eahy2.uninf.1H.Cy3

description: Eahy, Canicola vs. uninfected, 1 hr, Cy3

source_name: uninfected 1 hr


title: FvB non transgenic control mice RNA pool biological replicate 2


title: Eahy1.Patoc.3H.Cy3

description: Eahy, Patoc vs. uninfected, 3 hr, Cy3

source_name: infected with L. biflexa 3 hr


title: Eahy2.Pat.1H.Cy5

description: Eahy, Canicola vs Patoc, 1 hr, Cy5

source_name: infected with L. biflexa 1 hr


description:
K14E6 Δ146-151 transgenic mice RNA pool biological replicate 1
The background mice information is the following:

*FVB Inbred Mice Characteristics
Coat: Albino
Litter average: 8.5
Haplotype: /H-2^q /

Swiss background mouse with good reproductive characteristicsInbr. F38.Albino,/A,B,c,D,P/. Origin: Outbred N:GP (NIH General Purpose) Swiss mice established at the National Institutes of Health in 1935

source_name: RNA from skin tissue of 3 K14E6 Δ146-151 transgenic mice

value: K14E6 Δ146-151 transgenic mice


title: Eahy1.Can.3H.Cy5

description: Eahy, Canicola vs. uninfected, 3 hr, Cy5

source_name: infected with L. interrogans 3 hr


title: Eahy1.uninf1H.Cy5

description: Eahy, Patoc vs. uninfected, 1 hr, Cy5


description:
K14E6 Δ146-151 transgenic mice RNA pool biological replicate 3
The background mice information is the following:

*FVB Inbred Mice Characteristics
Coat: Albino
Litter average: 8.5
Haplotype: /H-2^q /

Swiss background mouse with good reproductive characteristicsInbr. F38.Albino,/A,B,c,D,P/. Origin: Outbred N:GP (NIH General Purpose) Swiss mice established at the National Institutes of Health in 1935


description:
K14E6 Δ146-151 transgenic mice RNA pool biological replicate 2
The background mice information is the following:

*FVB Inbred Mice Characteristics
Coat: Albino
Litter average: 8.5
Haplotype: /H-2^q /

Swiss background mouse with good reproductive characteristicsInbr. F38.Albino,/A,B,c,D,P/. Origin: Outbred N:GP (NIH General Purpose) Swiss mice established at the National Institutes of Health in 1935


title: Eahy1.uninf.3H.Cy3

description: Eahy, Canicola vs. uninfected, 3 hr, Cy3


title: Eahy1.Pat.3H.Cy5

description: Eahy, Canicola vs Patoc, 3 hr, Cy5


title: Eahy1.Can.1H.Cy5

description: Eahy, Canicola vs. uninfected, 1 hr, Cy5


title: Eahy1.Pat.1H.Cy5

description: Eahy, Canicola vs Patoc, 1 hr, Cy5


title: Eahy1.Can.3H.Cy3

description: Eahy, Canicola vs Patoc, 3 hr, Cy3


title: Mouse Neuro2A neuroblastoma cells (B) transfected by Scramble (red) or by Malat1 antisense oligonucleotides (green)

status: Public on Jul 26 2010

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

country: France

institute: École Normale Supérieure

description: Technical replicate 1 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65¡C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37¡C. The array slides are then air dryed and ready for scaning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample B) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-5 (red).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal calf serum to 70% confluence.

extract_protocol: Hot phenol extract procedure followed by RNEasy Mini Kit purification step (Quiagen)

treatment_protocol: Neuro2A cells transfected overnight with SCR control mixed LNA/DNA oligonucleotides complexed with Lipofectamine 2000.

tag: sample

value: B agent:Scramble_oligodexoxynucleotides

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample B) transfected by Malat1 ASO labeled with Cyanine-3 (green).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

treatment_protocol: Neuro2A cells transfected overnight with AS4 Malat1-antisense mixed LNA/DNA oligonucleotides complexed with Lipofectamine 2000.

value: B agent:Malat1_ASO


title: Mouse Neuro2A neuroblastoma cells (B) transfected by Malat1 antisense (red) or by Scramble oligonucleotides (green)

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample B) transfected by Malat1 ASO labeled with Cyanine-5 (red).

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample B) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-3 (green).


title: Eahy1.Patoc.1H.Cy3

description: Eahy, Patoc vs. uninfected, 1 hr, Cy3


title: Eahy1.Can.1H.Cy3

description: Eahy, Canicola vs Patoc, 1 hr, Cy3


title: Mouse Neuro2A neuroblastoma cells (A) transfected by Scramble (red) or by Malat1 antisense oligonucleotides (green)

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample A) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-5 (red).

value: A agent:Scramble_oligodexoxynucleotides

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample A) transfected by Malat1 ASO labeled with Cyanine-3 (green).

value: A agent:Malat1_ASO


title: Eahy1.uninf.1H.Cy3


title: Mouse Neuro2A neuroblastoma cells (C) transfected by Scramble (red) or by Malat1 antisense oligonucleotides (green)

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample C) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-5 (red).

value: C agent:Scramble_oligodexoxynucleotides

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample C) transfected by Malat1 ASO labeled with Cyanine-3 (green).

value: C agent:Malat1_ASO


title: aHDF L351P

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Gene expression after 2 days retroviral transduction into aHDF

scan_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).

data_processing: Data were analyzed with GeneSpring GX 11. The parameters for normalization are as follows:  Data transformation: Set measurement less than 0.01 to 0.01  Per chip: Normalize to 50th percentile

source_name: adult human dermal fibroblast, retroviral infection, day2

growth_protocol: aHDFs were cultivated with 10% FBS/DMEM, passage by Trypsin.

extract_protocol: Total RNA was isolated with Trizol.

treatment_protocol: Transduction of indicated genes were done by retroviral infection.

tag: transduction of gene

value: dermal fibroblasts


title: 137A

city: rochester

first: keyi

last: liu

address: 1425 portland ave

institute: Rochester General Research Institute

description:
3 technical replicates: 137A_H010, 137A_H011, 137A_H012

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.

hyb_protocol: 10 μg Cy5-labeled aRNA was hybridized to Human OneArray glass slide containing 30,968 human genome probes and 1,082 experimental control probes according to the manufacturer's standard protocols (PhalanxBio, CA, USA). The Human OneArray slide was prehybridized for 2 h at 42C with OneArray Pre-hybridization buffer and then hybridized for 16 h at 42C with OneArray hybridization buffer. The slides were then washed according to the manufacturer’s instruction (PhalanxBio Inc, CA, USA).

scan_protocol: The arrays were scanned at 5 μm resolution using a Molecular Dynamics Axon 4100A scanner. Raw intensity signals for each microarray were captured and computed using the GenePixPro™ Software. Raw data formats were stored in TIFF images and GPR data files.

data_processing: The data from all microarrays in each experimental set was then analyzed using Omicsoft Array Studio software; control and missing features were removed, and the remaining signals were quantile normalized. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques.

source_name: PBMC, Spn-AOM

label_protocol: 10 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA Amplification Kit (Cat. No. 1753) (Applied Biosystems) according to the instructions. The aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Lifesciences). RNA was purified and fragmented using Ambion’s RNA Fragmentation Reagents.

growth_protocol: Blood was collected from children with acute otitis media caused by S. pneumoniae and their pre-infection healthy stage.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll gradient and total RNA was extracted from PBMCs using the QIAamp RNA blood Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions.

value: blood

value: peripheral blood mononuclear cells (PBMCs)

tag: patient

tag: infection stage

value: Streptococcus pneumoniae acute otitis media (Spn-AOM)


title: 110V1

description:
3 technical replicates: 110V1_H001, 110V1_H002, 110V1_H003

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.

source_name: PBMC, pre-infection

value: pre-infection


title: 110A1

description:
3 technical replicates: 110A1_H004, 110A1_H005, 110A1_H006

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: Mouse Neuro2A neuroblastoma cells (A) transfected by Malat1 antisense (red) or by Scramble oligonucleotides (green)

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample A) transfected by Malat1 ASO labeled with Cyanine-5 (red).

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample A) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-3 (green).


title: 69V1

description:
3 technical replicates: 69V1_H010, 69V1_H011, 69V1_H012

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: 69A

description:
3 technical replicates: 69A_H013, 69A_H014, 69A_H015

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: 137V2

description:
3 technical replicates: 137V2_H007, 137V2_H008, 137V2_H009

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: 149A

description:
3 technical replicates: 149A_H004, 149A_H005, 149A_H006

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: K14E6 transgenic mice RNA pool biological replicate 2

source_name: RNA from skin tissue of 3 K14E6 transgenic mice

value: K14E6 transgenic mice

value: skin

value: female

value: FVB


title: aHDF L420P

label_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).


title: aHDF V394D

hyb_protocol: erformed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).


title: aHDF W136E


title: Roseburia Inulinivorans_starch3_inulin5_B

status: Public on Jul 24 2010

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

description: Strain Roseburia inulinivorans A2-194 was isolated from a human faecal sample in 1997, and is a member of the Firmicutes

hyb_protocol: Hybridization was done in the GeneTAC hybridization station (Genomic Solutions) with agitation and using circulating buffers. Slides were first blocked in buffer (180mM succinic anhydride, 44mM sodium borate in 1-methyl-2-pyrrolidone), washed in deionised water at 98°C (2× 1min) and finally in 95 % ethanol (1 min) at room temperature. After drying the slides were pre-hybridized at 50°C for 30 min (in 10 mg ml17 fraction V BSA, 3.5× SSC and 0.1% SDS), washed again in deionised water, dried and immediately hybridized. The hybridization solution (labelled cDNA mixed with 10µg Human Cot-1 DNA (Invitrogen), 15.4 µg yeast tRNA, 8 µl poly dA, 14.4 µl 20× SSC and 2.4 µl 100× Denhardt’s solution) was first boiled for 2 min and cooled to 45°C before adding 1.4 µl 5% SDS and incubating at 65°C for 30 min. This solution was then added to the array slides which were hybridized for 16 h at 65°C before washing at room temperature in medium  stringency buffer (0.1 % SDS, 0.5× SSC) for 5 min, followed by two high stringency washes (0.1 % SDS, 0.1× SSC) of 5 min each.

scan_protocol: The fluorescence of each spot was measured in two channels using a GeneTAC LS IV (Genomic Solutions) utilising GeneTac Integrator version 3.0.1 software.

data_processing: The microarray data were log2-transformed and normalised by Loess normalisation to remove intensity dependent dye-effects. As each clone was represented by three spots we calculated the median of the three log2(Cy5/Cy3) values, a robust measure of relative gene expression. In total the fluorescence of 12 hybridising spots were compared for each clone. P-values were calculated by applying a one-sample t-test to the two log-ratios from the two replicate experiments, while the two dye-swapped arrays within each experiment were combined by averaging.

organism: Roseburia inulinivorans DSM 16841

source_name: mRNA extracted from Roseburia Inulinivorans grown on starch at OD 0.4

label_protocol: The purified RNA (1 ug) was labelled by reverse transcription (Amersham Cyscribe first-strand cDNA labelling kit), employing random nonamer extension incorporating either dCTP-Cy3 dye.

growth_protocol: Routine anaerobic culturing of R. inulinivorans A2-194 was in M2GSC medium (39). Growth on single carbon sources utilised basal YCFA medium (3) supplemented with 0.5 % w/v of the specific substrate (amylopectin starch, Sigma).

extract_protocol: RNA was purified from mid-exponential phase (OD650 = 0.4) cultures on basal YCFA supplemented with starch using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion).

source_name: mRNA extracted from Roseburia Inulinivorans grown on inulin at OD 0.4

label_protocol: The purified RNA (1 ug) was labelled by reverse transcription (Amersham Cyscribe first-strand cDNA labelling kit), employing random nonamer extension incorporating dCTP-Cy5 dye.

growth_protocol: Routine anaerobic culturing of R. inulinivorans A2-194 was in M2GSC medium (39). Growth on single carbon sources utilised basal YCFA medium (3) supplemented with 0.5 % w/v of the specific substrate (inulin -Dahlia, Sigma).

extract_protocol: RNA was purified from mid-exponential phase (OD650 = 0.4) cultures on basal YCFA supplemented with inulin using the RNeasy RNA purification kit (Qiagen), and the mRNA component enriched using the MICROBExpress system (Ambion).


title: Roseburia Inulinivorans_inulin3_starch5_A

source_name: mRNA extracted from Roseburia Inulinivorans grown on Inulin at OD 0.4


title: Mouse Neuro2A neuroblastoma cells (C) transfected by Malat1 antisense (red) or by Scramble oligonucleotides (green)

description: Technical replicate 1 of 2.

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample C) transfected by Malat1 ASO labeled with Cyanine-5 (red).

source_name: Total RNA extracted from Neuro2A neuroblastoma cells (Sample C) transfected by Scramble oligodexoxynucleotides labeled with Cyanine-3 (green).


title: arpe cells_treated-rep1

city: Bethesda

first: Cynthia

last: Jawoski

state: MD

address: bldg 6, room 136

department: NEI

institute: NIH

description: ARPE cells treated with PDTC are c ompared with untreated cells.

hyb_protocol: MiRNAs were incubated with hubridization solution at 75-80 degrees C for 10 min athen loaded onto array.  Arrays were mounted with Maui Mixer SL and hybridized overnight (16-20 h) at 52 degrees C withy conwtant mixing.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner (Molecular Devices).

data_processing:
The scanned array images were annotated and analyzed using the GenePix® software and the .GAL file containing the array list (NCode™_Multi_Species_20141.GAL). The data output file is saved as a .Gpr file and exported as a .Txt file.   The .Txt files were transferred to individual worksheets in a Summary Excel file, individually sorted by name for easy access and analysis using Microsoft Excel.
Blanks, empty spots and dye markers have been removed in all worksheets.  The array data were checked to ensure the mean backgrounds were below 50 for both the A3 and A5 channels.  The results were also checked for the presence of signal for the NCode™ Multi-Species miRNA Microarray Controls for both the A3 and A5 channels. The experiment passed internal QC specifications for N-Code™ microRNA expression profiling.
Stataistical analysis performed using algorithms in Microsoft Excel to determine mean, std dev. Etc.

source_name: ARPE cells

label_protocol: PolyA-tailed miRNA was labeled with Alexa Fluor 3 (A3) or Alexa Fluor5 (A50 using the Ncode miRNA labeling system  (Cat # 25-0888).

growth_protocol: Cells were grown until semi-confulent.

extract_protocol: Total RNA was isolated using TRIzol reagaent.  Small RNA was enriched.

treatment_protocol: Treated cells were exposed to 100 uM PDTC (pyrrolidine dithiocarbamate) for 24 h.

tag: agent

value: control

value: PDTC


title: arpe cells_untreated-rep1


title: aHDF c-Myc

value: c-Myc


title: 149V1

description:
3 technical replicates: 149V1_H001, 149V1_H002, 149V1_H003

30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.


title: Roseburia Inulinivorans_starch3_inulin5_A


title: Roseburia Inulinivorans_inulin3_starch5_B


title: aHDF Mock

value: Mock


title: aHDF L-Myc

value: L-Myc


title: uterine_leiomyoma_patient_B4

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

hyb_protocol: 10 micrograms of biotin labeled cRNA was hybridized for 16 hr to the Affymetrix array. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Total RNA from uterine leiomyoma tumor

label_protocol: Affymetrix One-cycle labeling protocol was used to prepare biotin labeled cRNAs for array hybridizations

extract_protocol: Total RNA was extracted from tissues using Ambion RNAqueous® Kit according to manufacturer's instructions.

tag: race

value: African American

value: uterine leiomyoma tumor


title: uterine_leiomyoma_patient_B8


title: uterine_leiomyoma_patient_B5


title: normal_myometrium_patient_B4

source_name: Total RNA from normal myometrium

value: normal myometrium


title: uterine_leiomyoma_patient_B3


title: uterine_leiomyoma_patient_B2


title: normal_myometrium_patient_B2


title: normal_myometrium_patient_B3


title: normal_myometrium_patient_B5


title: normal_myometrium_patient_B8


title: Muscle Saline 15d rep3

city: Urbana

first: Diana

last: Cheng

state: IL

address: 1115 Plant Sciences Laboratory, 1201 South Dorner Drive

department: Natural Resources and Environmental Sciences

institute: University of Illinois Urbana Champaign

description: replication 3

hyb_protocol: After the quality control assessment, 1.5 µg of cRNA from each experimental sample along with hybridization controls were hybridized for 16 hours to the MouseWG-6 v2.0 Expression BeadChips (Illumina, Inc., San Diego, CA) in the 58 °C Illumina Hybridization Oven. Washing, staining with streptavidin-Cy3 (GE Healthcare Bio-Sciences, Piscataway, NJ), and scanning were performed according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (revision A).  Two BeadChips were used in this study, each containing six arrays.

scan_protocol: The arrays were scanned using an Illumina BeadArray Reader.  Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The raw bead-level files were processed with Illumina® BeadStudio 3.1.3, Gene Expression Module v3.4.0 (Illumina), without background correction or normalization, to get one value per beadtype for each array.  These beadtype values were normalized and analyzed in R (R Development Core Team) using the beadarray package (Dunning et al., 2007) from the Bioconductor Project (Gentleman et al., 2004).  Background fluorescence was corrected by subtracting the mean of the negative control beadtypes; negative and zero values after background correction were set to 0.5.  Quantile normalization was performed and data were log2 transformed.  Differential expression was assessed using a linear model using the limma package (Smyth, 2005), which uses an empirical Bayes correction (Smyth, 2004) that helps to improve power by borrowing information across beadtypes. BeadStudio’s Detection p-values were used to filter out 21,572 beadtypes that were not detected (p > 0.05) above the negative controls in any of the 12 samples.  The remaining 23,709 beadtypes were input to Ingenuity Pathways Analysis as the reference set.

source_name: Mouse triceps brachii

label_protocol: 300 ng of high quality total RNA were primed with an oligo(dT) primer bearing a T7 promoter, and reverse transcribed in the first-strand cDNA synthesis using the Illumina® TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX). Single stranded cDNA was then converted into double stranded cDNA according to the manufacturer’s instructions. The double-stranded cDNA was purified and served as a template in the 14-hour in vitro transcription (IVT) reaction. Prior to hybridization, the synthesized biotin labeled cRNA was cleaned up using the same Amplification Kit.

growth_protocol: Animals were individually housed in plastic cages in a temperature controlled room (22 °C) with 12:12 hour light-dark cycles and given ad libitum access to food (AIN-93G) and water.

extract_protocol: Total RNA was extracted from triceps (ca. 100 mg) by homogenization with 1 mL TriReagent (St. Louis, MO) for 3 min at 30Hz using a Tissuelyser II (Qiagen, Gaithersburg, MD).  Total RNA was treated with DNase I and purified using an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.  Quantity and purity of RNA was determined using the NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA).  RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Total RNA was pooled into groups containing three individual biological replicates (except for one pool of saline infused group B which had two replicates).  Each pool contained an equal quantity of RNA (1 μg) from each individual animal.  Three pools were analyzed per treatment using Illumina’s MouseWG-6 v2.0 Expression BeadChips (San Diego, CA).

treatment_protocol: Adult mice were given a continuous infusion of saline or 20-hydroxyecdysone (5 mg/kg/day) for 5 or 15 days via subcutaneously implanted Alzet® osmotic pumps.

value: male

value: 12 weeks

value: triceps brachii


title: Muscle Saline 15d rep2

description: replication 2


title: Gene expression profiles of HL-60 cells exposed to benzoquinone (IC50) [sample 3]

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

country: South Korea

institute: Korea Institute of Science and Technology

description: HL-60 cells were treated with 11.87 µM benzoquinone for 3 h, and the RNA was subjected to microarray analysis.

hyb_protocol: Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) or Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62℃ for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58℃, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

data_processing: The fluorescent intensity of each spot was calculated by local median background subtraction. The robust scatter-plot smoother LOWESS function was used to perform intensity dependent normalization for the gene expression. Scatter plot analysis was made by Microsoft Excel 2003. Significance Analysis of Microarray (SAM) was performed for the selection of the genes with significant gene expression changes (Tusher et al., 2001). Computing a p-value for each gene assessed the statistical significance of the differential expression of genes. To determine the p-value, a permutation procedure was used and for each permutation, two-sample t statistics were computed for each gene. Genes were considered differentially expressed when logarithmic gene expression ratios in three independent hybridizations were more than 1.5 or less than 0.66, i.e., 1.5-fold difference in expression level, and when the p-values were less than 5.

source_name: HL-60 cells treated with DMSO for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 44 K whole human genome microarray (Agilent Technologies. Inc). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy3 dye for the controls (DMSO).

extract_protocol: Total RNA was extracted from the HL-60 cells treated to DMSO for 3 h using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: human promyelocytic leukemia cells

tag: treatment

value: DMSO

tag: treatment time

value: 3 h

source_name: HL-60 cells treated with benzoquinone (IC50) for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 44 K whole human genome microarray (Agilent Technologies. Inc). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy5 dye for the treated samples.

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of benzene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

tag: treament

value: benzoquinone

tag: treament dose

tag: treament time

value: 3 hr


title: Muscle Saline 15d rep1

description: replication 1

tag: age

tag: tissue


title: Gene expression profiles of HL-60 cells exposed to benzoquinone (IC50) [sample 1]

tag: cell type


title: Gene expression profiles of HL-60 cells exposed to hydroquinone (IC50) [sample 3]

description: HL-60 cells were treated with 180 µM hydroquinone for 3 h, and the RNA was subjected to microarray analysis.

tag: cell line

source_name: HL-60 cells treated with hydroquinone (IC50) for 3 h

value: hydroquinone


title: Muscle 20E 15d rep2

description: replication 2

tag: strain


title: Muscle Saline 5d rep3

description: replication 3

tag: gender


title: Muscle 20E 15d rep1

description: replication 1


title: Muscle 20E 15d rep3

description: replication 3


title: Gene expression profiles of HL-60 cells exposed to hydroquinone (IC50) [sample 2]


title: Gene expression profiles of HL-60 cells exposed to benzoquinone (IC50) [sample 2]


title: Muscle Saline 5d rep2

description: replication 2


title: Muscle Saline 5d rep1

description: replication 1


title: Gene expression profiles of HL-60 cells exposed to hydroquinone (IC50) [sample 1]


title: Muscle 20E 5d rep3

description: replication 3


title: Muscle 20E 5d rep2

description: replication 2


title: 3T3_Mn_tech_rep6

city: Quebec

first: Jacques

last: Couet

address: 2725 chemin Sainte-Foy

country: Canada

institute: Centre de Recherche de l'Hopital Laval

hyb_protocol: The lyophilized biotin-labeled cRNA preparations were hybridized to BeadChip Illumina MouseWG-6 v2.0 expression beadchip microarrays (Illumina) according to Illumina’s protocol (11286340 rev. A), using 750 ng cRNA per array. After hybridization and washes, arrays were incubated in streptavidin-Cy3 solution

scan_protocol: Cy3 fluorescence signals were read on a BeadArray reader (Illumina)

data_processing:
Raw fluorescence data were processed and normalized with the lumi package (FlexArray microarray analysis software, version 1.3.1), using RMA background adjustment, VST variance stabilization, and Robust Spline Normalization algorithms.
Differential expression was determined according to the SAM statistical method (Tusher et al, 2001; Proc. Natl. Acad. Sci. USA 98:5116-5121)

source_name: 3T3 fibroblasts from mouse embryo, cultured with Mn

label_protocol: Total RNA extracts were treated for double-stranded cDNA synthesis and labeling of cRNA with biotin according to the Eberwine method (Van Gelder et al 1990), using the Illumina TotalPrep RNA Amplification kit reagents and protocol (Ambion cat no IL1791)

growth_protocol: BALB/3T3 mouse fibroblast cells (ATCC number CL-163, Clone A31) were chosen for the experiment since a tissue culture model using this cell line was previously developed in our laboratory. Fibroblasts are of the three types of cell that constructs the adventitial layer of artery, this cell line is also known to be easy to handle, can proliferate rapidly, and maintain its viability at higher passage number. In the experiments, cells at population doubling number of 5 were used and cultured with Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% foetal bovine serum (Lonza) and 1% antibiotic/antimycotic (PenStrep) at 37oC in a humidified incubator at 5% CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), and further purified on column with RNeasy MinElute (Qiagen). RNA concentration and integrity were assessed by UV spectrophotometry (Nanodrop ND-1000, Thermo Scientific) and microfluidic electrophoresis (Bioanalyzer 2100, Agilent), respectively

treatment_protocol: About 250 ul DMEM containing 200 cells/ul were placed within each well of 24-well cell culture plate. Cells were then incubated overnight allowing stable cell adhesions to the plate. In the experiment, metal powders of pure iron, pure manganese, and iron manganese alloy were used. Powders of pure iron and manganese were obtained from GoodFellow Inc., while powder of iron manganese alloy was prepared by means of mechanical filing and sieving that produced <53 mm in diameter of iron particles. Powders were chosen in order to create an extreme condition of high surface area in contact with culture medium. Prior to the exposure, powders of metals were sterilized under UV light for 30 minutes. Powders were then placed above the fibroblasts monolayer using tissue culture inserts and followed by the addition of another 250 uL DMEM. At least six replicates were applied to each kind of metal powder as well as control group (none of metal powders were given). Fibroblasts were incubated for 24 hours following the previous metal exposures with pure iron, manganese, and iron manganese alloy powders, the exposure amount of each metal was obtained respectively as follow: 3,25 mg/ml (w/v), 0,5 mg/ml (w/v), and 5 mg/ml (w/v).

value: BALB/c

value: Mn


title: 3T3_Mn_tech_rep5


title: 3T3_Mn_tech_rep2


title: 3T3_Fe_tech_rep5

source_name: 3T3 fibroblasts from mouse embryo, cultured with Fe

value: Fe


title: 3T3_Fe_tech_rep2


title: 3T3_Mn_tech_rep3


title: 3T3_Fe-35Mn alloy_tech_rep5

source_name: 3T3 fibroblasts from mouse embryo, cultured with Fe-35Mn alloy

value: Fe-35Mn alloy


title: 3T3_Fe-35Mn alloy_tech_rep2


title: 3T3_Fe-35Mn alloy_tech_rep4


title: 3T3_Fe-35Mn alloy_tech_rep1


title: 3T3_Fe-35Mn alloy_tech_rep6


title: 3T3_Ctrl_tech_rep5

source_name: 3T3 fibroblasts from mouse embryo, cultured without metal

value: Ctrl


title: 3T3_Ctrl_tech_rep3


title: 3T3_Fe-35Mn alloy_tech_rep3


title: Muscle 20E 5d rep1

description: replication 1


title: p4_10s035_MES_20090326.gpr

city: Portland

first: Suzy

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

description: Cy3= Julidochromis marlieri male aRNA Cy5= Julidochromis marlieri female aRNA

hyb_protocol: The samples were combined with hybridization buffer (Ambion Slide hybe buffer #1) and hybridized to the microarray at  48 degrees 16-24 hours

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_570 ScanPower=100_100

data_processing: After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized LIMMA in R/Bioconductor using within-arrays print-tip-loess normaliztion,  intensity ratios were estimated and p-values calculated using the exact method adapted from the lmFit and EBayes commands.

organism: Julidochromis marlieri

source_name: Julidochromis marlieri male-JMK64m

label_protocol: Message Amp II with single round amplification

growth_protocol: Fish were grown in 30 gallon stock tanks under standard lab conditions

extract_protocol: Trizol extraction

tag: sex

tag: species

value: Julidochromis marlieri

source_name: Julidochromis marlieri female-JMK11f

value: female


title: 3T3_Mn_tech_rep1


title: 3T3_Fe_tech_rep3


title: 3T3_Mn_tech_rep4


title: 3T3_Fe_tech_rep6


title: 3T3_Fe_tech_rep4


title: p4_10s049_MES_20090328.gpr

description: Cy3= Julidochromis marlieri female aRNA Cy5= Julidochromis marlieri male aRNA

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=730_590 ScanPower=100_100

source_name: Julidochromis marlieri female-JMK53f

source_name: Julidochromis marlieri male-JMK48m


title: 3T3_Ctrl_tech_rep1


title: 3T3_Fe_tech_rep1


title: 3T3_Ctrl_tech_rep6


title: p4_10s048_MES_20090328.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=750_560 ScanPower=100_100

source_name: Julidochromis marlieri female-JMK13f


title: Sle2C1 Bs r4

city: Oklahoma City

first: Igor

middle: M

last: Dozmorov

state: OK

address: 825 NE 13th Street

department: Arthritis & Immunology

institute: OMRF

description: exp Bs replicate 4

hyb_protocol: hybridization to Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: scanned on an Affymetrix GeneChip Analysis System GC3000 7G.

data_processing:
All data analyses were based on the use of “internal standards” as presented in 1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res.
Two-step normalization procedure (1). The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”.     The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.

source_name: Bs cells from B6.Sle2c1 mice

label_protocol: cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

growth_protocol: Gene expression was compared between peritoneal cavity (Pc) B cells (B1a) and splenic B (Bs) cells from B6.Sle2c1 and C57BL/6 (B6) mice at 5 mo of age. CD43- Bs cells were isolated with the Myltenyi B cell kit, leading to a population of > 90% B220hi cells. Pc macrophages were removed by a 2 h culture at 370C in 10% FBS in PBS.  Non-adherent Pc cells were first submitted to negative selection with a cocktail of biotinylated anti-Thy1.2 and anti-CD3ε Abs, then to positive selection with biotynylated-anti-CD5 Ab. Cells bound to biotynylated Abs were removed with streptavidin-conjugated magnetic beads (Myltenyi). This protocol led to a 80% B220int CD5+ cell population.

extract_protocol: RNA was extracted with the Qiagen RNeasy Micro Kit.

value: Bs


title: p4_10s026_MES_20090220_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_560 ScanPower=100_100

value: male


title: 3T3_Ctrl_tech_rep4


title: p4_10s017_JBC_20090315.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_500 ScanPower=100_100


title: B6 Bs r4

description: control Bs replicate 4

source_name: Bs cells from B6 mice


title: p4_10s021_MES_20090215_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=800_490 ScanPower=100_100

source_name: Julidochromis marlieri female-JMK35f


title: Sle2C1 Bs r3

description: exp Bs replicate 3


title: B6 Bs r3

description: control Bs replicate 3


title: Sle2C1 Bs r2

description: exp Bs replicate 2


title: p4_10s008_20090228_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=710_550 ScanPower=100_100

source_name: Julidochromis marlieri male-JMK52m


title: B6 Bs r2

description: control Bs replicate 2


title: Sle2C1 B1a r4

description: exp B1a replicate 4

source_name: B1a cells from B6.Sle2c1 mice


title: 3T3_Ctrl_tech_rep2


title: H1_rep2

city: MAdrid

first: Gustavo

middle: J

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

country: Spain

institute: FIB Hospital NIño Jesus

description: Gene expression

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with Acetonitrile (Sigma) and 30 seconds with Stabilization and Drying Solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08  and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal was normalized to 75th percentile and baseline transformed to median of all samples.

label_protocol: 500 ng of each total RNA sample was labelled with Cy3 using the Quick-Amp Labelling kit (Agilent) according to manufacturer's instruction.

growth_protocol: Stable well-characterized hESC lines were maintained undifferentiated in a feeder-free culture: hESCs were cultured in Matrigel (BD Biosciences)-coated T25 flasks in either human foreskin fibroblast (HFF) or mesenchymal stromal cells (MSC)-conditioned medium (HFF-CM or MSC-CM) supplemented with 8 ng/mL basic fibroblast growth factor (bFGF) (Miltenyi, Germany). Media was changed daily, and the cells were split weekly by dissociation with 200 U/mL of collagenase IV (Invitrogen, Edinburgh, Scotland). Human ESC cultures were visualized daily by phase-contrast microscopy.

extract_protocol: Human ESC samples were collected during the exponential cell growth phase and stabilized in RNA later (Ambion, Austin, TX). RNA was isolated using Agilent Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer's recommendations and was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: B6 Bs r1

description: control Bs replicate 1


title: p4_10s016_JBC_20090315.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_530 ScanPower=100_100

source_name: Julidochromis marlieri male-JMK14m


title: AND1_rep1

description: Gene expression


title: SHEF1_rep2

description: Gene expression


title: p4_10s003_MES_20090210_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=730_580 ScanPower=100_100


title: Sle2C1 B1a r3

description: exp B1a replicate 3


title: p4_10s050_MES_20090328_genepix6.gpr

description: Cy3= Julidochromis transcriptus male aRNA Cy5= Julidochromis transcriptus female aRNA

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=720_520 ScanPower=100_100

organism: Julidochromis transcriptus

source_name: Julidochromis transcriptus male-JT15m

value: Julidochromis transcriptus

source_name: Julidochromis transcriptus female-JT22f


title: H1_rep1

description: Gene expression


title: p4_10s034_MES_20090326_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=690_530 ScanPower=100_100

source_name: Julidochromis transcriptus male-JT14m


title: AND1_rep2

description: Gene expression


title: p4_10s051_MES_20090328_genepix6.gpr

description: Cy3= Julidochromis transcriptus female aRNA Cy5= Julidochromis transcriptus male aRNA

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=740_580 ScanPower=100_100

source_name: Julidochromis transcriptus female-JT20f


title: SHEF1_rep1

description: Gene expression


title: p4_10s033_MES_20090326_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=750_580 ScanPower=100_100

source_name: Julidochromis transcriptus male-JT18m

source_name: Julidochromis transcriptus female-JT21f


title: VAL3_rep2

description: Gene expression


title: Sle2C1 B1a r2

description: exp B1a replicate 2


title: B6 B1a r4

description: control B1a replicate 4

source_name: B1a cells from B6 mice


title: neurosphere P2.3

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: MPSIIIB neural stem cell

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: iPSc clones were collected as small clusters after collagenase type IV treatment. Clusters were resuspended in DMEM/F12 supplemented with 2%B27, 100ng/mL FGF2, 100ng/mL EGF and 5µg/mL Heparin and cultured as neurospheres for a minimum of 2 weeks.

extract_protocol: Total RNA was extracted using Rneasy Kit according to manufacturer recommendations.

treatment_protocol: Not applicable

tag: disease state

value: MPSIIIB

value: neural stem cells derived from MPSIIIB iPS cells and cultured as neurospheres


title: p4_10s027_MES_20090220_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=700_550 ScanPower=100_100


title: VAL3_rep1

description: Gene expression


title: p4_10s014_JBC_20090315_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=760_520 ScanPower=100_100

source_name: Julidochromis transcriptus female-JT29f


title: Sle2C1 B1a r1

description: exp B1a replicate 1


title: p4_10s015_JBC_20090315_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=750_570 ScanPower=100_100

source_name: Julidochromis transcriptus male-JT05m


title: neurosphere P1.1

description: neural stem cells derived from MPSIIIB iPS cells


title: HS181_rep1

description: Gene expression


title: HS181_rep2

description: Gene expression


title: neurosphere P1.3


title: neurosphere C3

source_name: wild-type neural stem cell

value: control

value: neural stem cells derived from unaffected iPS cells and cultured as neurospheres


title: H9_rep2

description: Gene expression


title: p4_10s013_MES_20090312_genepix 6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=810_620 ScanPower=100_100


title: B6 B1a r3

description: control B1a replicate 3

scan_protocol: scanned on an Affymetrix GeneChip Analysis System GC3000 7G.


title: neurosphere C1

description: neural stem cells derived from unaffected iPS cells


title: B6 B1a r2

description: control B1a replicate 2


title: B6 B1a r1

description: control B1a replicate 1


title: p4_10s012_MES_20090312_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=800_630 ScanPower=100_100


title: H9_rep1

description: Gene expression


title: Rabbit_WB_None_None_Repl_13

status: Public on Jul 23 2010

city: Frederick

first: Richard

middle: A

last: Lempicki

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

description: Also used for comparison to human PBMCs for validation study

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix U95A human microarray according to the manufacturer's recommended protocol.

scan_protocol: Hybridized Affymetrix U95A human microarrays were scanned according to the manufacturer's recommended protocol.

data_processing: Non-normalized MAS5 signals were used to compare raw probeset intensity values between human and rabbit samples. Final rabbit study analyses were conducted with expression values summarized using dChip, log2 transformed and Loess normalized using an R package (http://www.elwood9.net/spike). Genes with maximum expression values less than 7 for all samples were eliminated from analysis. Multi-way ANOVA along with specific contrasts, K-means clustering and gene expression visualizations were performed using Partek Genomics Suite (St. Louis, MO). Genes were identified as significantly modulated if the ANOVA contrast p-value was <0.05 and the absolute log2 fold change was >1.0.

label: Biotin

organism: Oryctolagus cuniculus

source_name: Rabbit, Whole Blood, Backbone=None, Peptide=None

label_protocol: The cRNA probes were prepared from mRNA using the Affymetrix gene chip eukaryotic small sample target labeling protocol assay version II (Affymetrix, Santa Clara, CA) using 2 cycles of cDNA synthesis and in vitro transcription (IVT) reactions. In the first round, cDNA was synthesized from 100 ng RNA (Superscript, Invitrogen) using a T7- Oligo (dT) promoter primer.  Resulting cDNA was used in IVT reactions (T7 Megascript Ambion, Austin, Texas) to generate first cycle cRNA and cDNA synthesized from this cRNA was subsequently used in the second IVT cycle for obtaining biotinylated cRNA using CTP and UTP (EnzoBioarray, Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Rabbits from the NIAID colony were pedigreed, non-inbred, and allotype-defined.  The animal studies described here were reviewed and approved by the animal care and use committees of NIAID/National Institutes of Health, Bethesda, MD (animal study protocol LI-6) and of the Spring Valley Laboratories (Woodbine, MD), where the NIAID allotype-defined rabbit colony was bred and housed. When introduced into a study group, the rabbits were housed in a room separate from the main colony and monitored with video cameras. We describe here four groups of one to two-year old rabbits totaling 47 (26 males, 21 females) that were selectively bred. Rabbits in sequential Groups 2, 3 or 4 were related to Group 1 or 2 animals and/or their siblings.  Fourteen normal unimmunized rabbits including some that were subsequently immunized were also used for RNA extraction.

extract_protocol: For RNA extraction from PWBC, heparinized blood diluted 2:1 with warm 3% gelatin in PBS was incubated for 50 min at 37°C in 5% CO2. The upper layer was then removed and centrifuged at RT, 400 g for 12 min to pellet leukocytes.  After discarding supernatants, leukocyte pellets were washed twice with PBS and centrifuged again for 15 min. The washed pellet was then lysed with TRIzol (Invitrogen, Carlsbad, CA) and total RNA was extracted using RNAeasy Mini columns following manufacturer's instructions (Qiagen, Valencia, CA).

treatment_protocol: Rabbits were immunized as described in with one of two peptide immunogens synthesized on MAP-4 (Group 2 rabbits) or MAP-8 (Groups 1, 3, and 4) backbones (AnaSpec Inc., San Jose, CA).  Peptide ‘SM’ is derived from a major antigenic region of the nuclear protein Sm B/B' while peptide ‘GR’ corresponds to the known rabbit sequence of an extracellular epitope of the 2b subunit of neuronal postsynaptic N-methyl-D-aspartate (NMDA) receptors. Control rabbits were immunized with MAP-4 or MAP-8 backbone (BB) in identical adjuvants. Three rabbits (PB-45 through 47) that were identically handled and injected with PBS only and 14 unimmunized rabbits were also included in the microarray analysis. Rabbits were first injected s.c. with 0.5 mg MAP-peptide/0.5 ml BBS (pH8.0) + 0.5 ml CFA and then boosted at 3 week intervals with the same antigen in IFA.

tag: backbone

tag: peptide

tag: rabbit group

tag: number of immunization boost

value: F

tag: rabbit id

value: Whole Blood

tag: alias

value: K


title: p4_10s009_MES_20090228_genepix6.gpr

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0. PMTGain=770_590 ScanPower=100_100


title: Rabbit_WB_None_None_Repl_5

value: M


title: Rabbit_WB_None_None_Repl_14

value: L


title: Rabbit_WB_None_None_Repl_6


title: Rabbit_WB_None_None_Repl_9


title: Rabbit_WB_None_None_Repl_7


title: Rabbit_WB_None_None_Repl_8


title: Rabbit_WB_None_None_Repl_11


title: Rabbit_WB_None_None_Repl_12


title: Rabbit_WB_None_None_Repl_1


title: Rabbit_WB_None_None_Repl_10


title: Rabbit_WB_MAP8_SM_Repl_9

source_name: Rabbit, Whole Blood, Backbone=MAP8, Peptide=SM

value: SM

value: E


title: Rabbit_WB_None_None_Repl_2


title: Rabbit_WB_MAP8_SM_Repl_6


title: Rabbit_WB_MAP8_SM_Repl_7


title: Rabbit_WB_None_None_Repl_4


title: Rabbit_WB_MAP8_SM_Repl_5


title: Rabbit_WB_MAP8_SM_Repl_1

value: A


title: Rabbit_WB_MAP8_SM_Repl_8

value: D


title: Rabbit_WB_MAP8_SM_Repl_2

value: B


title: Rabbit_WB_MAP8_None_Repl_5

source_name: Rabbit, Whole Blood, Backbone=MAP8, Peptide=None


title: Rabbit_WB_MAP8_PBS_Repl_3

source_name: Rabbit, Whole Blood, Backbone=MAP8, Peptide=PBS

value: PBS


title: Rabbit_WB_MAP8_SM_Repl_3

value: C


title: Rabbit_WB_None_None_Repl_3


title: Rabbit_WB_MAP8_SM_Repl_4


title: Rabbit_WB_MAP8_PBS_Repl_1


title: Rabbit_WB_MAP8_None_Repl_4


title: Rabbit_WB_MAP8_None_Repl_1

value: J


title: Rabbit_WB_MAP8_None_Repl_3


title: Rabbit_WB_MAP8_None_Repl_2


title: Rabbit_WB_MAP8_PBS_Repl_2


title: Rabbit_WB_MAP8_GR_Repl_12

source_name: Rabbit, Whole Blood, Backbone=MAP8, Peptide=GR

value: GR

value: G


title: Rabbit_WB_MAP8_GR_Repl_10


title: CD26pos_30066 vs. Reference

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

description: ovine lymphatic CD26 positive, dentritic cells

hyb_protocol: Cy3 labeled cDNA was co-hybridized with the cy5 reference probe

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Quantile normalized using median signal of the Red and Green signal. Agilent software was used. Data in column LogRatio in the raw .txt files are in log10 and correspond to the ratio Cy5/Cy3 (reference/test).

organism: Ovis aries

source_name: skin lymph dendritic cell subsets CD26+

label_protocol: Bioprime Array CGH Genomic Labelling System Kit. Total RNAs (200 ng) were amplified by linear PCR and labelled with Cy3 using Bioprime Array CGH Genomic Labelling System Kit (Invitrogen, Carlsbad, CA). Total RNA from one culture of LP-1cl1 cells was similarly amplified, labelled with Cy5 and used as a reference probe for hybridization.

extract_protocol: total RNA was extracted usingQiagen Rneasy Micro Kit

treatment_protocol: cell sorting of CD1b+CD26+ and CD1b+CD26- lymph DC

tag: animal

value: sheep 30066

value: dendritic cell

tag: dendritic cell subset

source_name: reference, total enriched lymph DC

tag: sample type

value: reference (from sheep distinct from 10081&30066)


title: Rabbit_WB_MAP8_GR_Repl_11

tag: tissue

value: Whole Blood

value: F


title: CD26neg_10081 vs. Reference

description: ovine lymphatic CD26 negative, dentritic cells

source_name: skin lymph dendritic cell subsets CD26-

value: sheep 10081

tag: cell type


title: Rabbit_WB_MAP8_GR_Repl_9


title: CD26neg_30066 vs. Reference


title: CD26pos_10081 vs. Reference


title: Rabbit_WB_MAP8_GR_Repl_8

value: M


title: Rabbit_WB_MAP8_GR_Repl_7


title: Sle2C1 Bs r1

description: exp Bs replicate 1

source_name: Bs cells from B6.Sle2c1 mice

value: Bs


title: Dmagna_Zn(-/-)F2_rep3

city: Gent

first: Michiel

last: Vandegehuchte

address: Jozef Plateaustraat 22

department: Applied ecology and environmental biology

country: Belgium

institute: Ghent University (UGent)

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F2 day 22 Zn(-/-) versus Reference pool

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 4.1 (Axon Instruments).

data_processing: Prior to the actual statistical analysis, the quality of the microarray spots was assessed. Over-saturated spots and bad quality spots identified during the feature identification process (visual inspection of the slides) were excluded from further analysis. Hereafter, a local background correction was performed on these datasets using the Bioarray Software Environment (BASE) version 1.2.17, developed by the  Intelligent Systems Laboratory, University of Antwerp (http://www.islab.ua.ac.be/base/). Those spots with foreground levels lower than the background levels for both channels were excluded from the analysis. Spots for which the foreground was smaller than the mean (local) background ±2 standard deviations for both channels were given a ‘weight’ of 0.1. All other included spots are given a weight of 1. Subsequently, microarray datasets were normalized using the variance stabilizing normalization (VSN) (Huber 2002) in BASE. The significantly differentially expressed genes (between control and treatment) were statistically determined using LIMMA (LInear Model for Microarray Analysis) (Smyth 2004) in BASE. Results were corrected for multiple testing using the false discovery rate (FDR) and differential gene expression was detected in probes with p<0.05. An additional threshold which was taken into account is the fold induction cut-off (Log2) of (-)0.75. In conclusion, genes with fold inductions outside these thresholds and p-values below 0.05 were selected as differentially expressed.

organism: Daphnia magna

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 5µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin column protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 50 pmol labelled target was vacuum dried.

extract_protocol:
Ten Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

tag: clone

value: whole body extracts

tag: composition

value: 10 organisms

tag: generation

tag: age

value: 22 days

tag: zinc exposure

source_name: Reference pool

extract_protocol:
Ten (21-day old) to twenty (6-day old or 13-day old) Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

value: subsample of pooled RNA from 60 6-day-old, 60 13-day-old and 60 21-day-old daphnids

value: reference


title: Dmagna_Zn(+)F2_rep2

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F2 day 21 Zn(+) versus Reference pool

value: 21 days


title: Rabbit_WB_MAP8_GR_Repl_2

tag: gender


title: Rabbit_WB_MAP8_GR_Repl_4

tag: backbone


title: Rabbit_WB_MAP8_GR_Repl_5

tag: peptide


title: Rabbit_WB_MAP8_GR_Repl_6

tag: rabbit group


title: Rabbit_WB_MAP8_GR_Repl_3

tag: number of immunization boost


title: Dmagna_Zn(-/-)F2_rep1

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F2 day 22 Zn(-/-)


title: Dmagna_Zn(+/-)F2_rep1

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F2 day 22 Zn(+/-) versus Reference pool


title: Dmagna_Zn(-/-)F2_rep2


title: Dmagna_Zn(+/-)F2_rep3

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F2 day 22 Zn(+/-)


title: Dmagna_Zn(+)F2_rep3

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F2 day 21 Zn(+)


title: Rabbit_WB_MAP4_SM_Repl_5

source_name: Rabbit, Whole Blood, Backbone=MAP4, Peptide=SM

value: SM

tag: rabbit id


title: Reference vs. Reference (self-hybridization)

description: ovine dentritic cells


title: Dmagna_Zn(+/-)F2_rep2


title: p4_10s036_MES_20090326.gpr

source_name: Julidochromis marlieri male-JMK52m

tag: sex

value: male

tag: species

value: Julidochromis marlieri

source_name: Julidochromis marlieri female-JMK53f

value: female


title: Rabbit_WB_MAP4_SM_Repl_3

tag: alias


title: Rabbit_WB_MAP4_SM_Repl_2


title: Rabbit_WB_MAP8_GR_Repl_1

value: GR

value: I


title: Rabbit_WB_MAP4_SM_Repl_4

value: Whole Blood


title: Rabbit_WB_MAP4_None_Repl_4

source_name: Rabbit, Whole Blood, Backbone=MAP4, Peptide=None

value: F


title: Dmagna_CtrlF2_rep2

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F2 day 20 Ctrl

tag: sample type

value: 20 days

value: control


title: Dmagna_Zn(-)F1_rep2

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F1 day 21 Zn(-)

tag: tissue


title: Dmagna_Zn(+)F2_rep1


title: Rabbit_WB_MAP4_SM_Repl_1

value: M


title: Rabbit_WB_MAP8_GR_Repl_13

value: H


title: Dmagna_Zn(-)F1_rep1

value: whole body extracts

value: 10 organisms


title: Dmagna_CtrlF2_rep3

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F2 day 20 Ctrl versus Reference pool

value: subsample of pooled RNA from 60 6-day-old, 60 13-day-old and 60 21-day-old daphnids


title: Dmagna_CtrlF2_rep1

value: reference


title: Rabbit_WB_MAP4_None_Repl_3


title: Rabbit_WB_MAP4_None_Repl_2


title: Dmagna_Zn(+)F1_rep1

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: Reference pool versus F1 day 21 Zn(+)

value: 21 days


title: Dmagna_Zn(-)F1_rep3


title: Rabbit_WB_MAP4_None_Repl_1


title: Dmagna_Zn(+)F1_rep2


title: Dmagna_CtrlF1_rep1

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F1 day 22 Ctrl versus Reference pool

value: 22 days


title: Rabbit_WB_MAP4_GR_Repl_1

source_name: Rabbit, Whole Blood, Backbone=MAP4, Peptide=GR


title: Dmagna_ZnF0_rep3

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F0 day 23 Zn versus Reference pool

value: 23 days

value: Zn


title: Human_PBMC_NA_NA_Repl_9

source_name: Human, PBMC, Backbone=NA, Peptide=NA

value: Unknown

tag: cell type

value: PBMC


title: Rabbit_WB_MAP4_GR_Repl_3

value: GR


title: Rabbit_WB_MAP4_GR_Repl_4

value: Whole Blood


title: Dmagna_CtrlF1_rep3

tag: clone


title: Human_PBMC_NA_NA_Repl_8


title: Dmagna_CtrlF1_rep2

tag: composition


title: Human_PBMC_NA_NA_Repl_7


title: Human_PBMC_NA_NA_Repl_6


title: mutant M245 L Replicate 2

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

country: Australia

institute: University of Adelaide

hyb_protocol: Hybridization and image extraction were performed by Agilent Technologies

scan_protocol: Agilent Technologies FE 9.1 software was used for feature extraction.

data_processing: The data was normalization to the 59 housekeeping genes present on the array without prior background subtraction. Prior to normalization, signal intensity values of less than 1.0 were set to zero, while all other values were log2 transformed.

organism: Hordeum vulgare

source_name: stem lower zone

label_protocol: One color (Cy3)  labelling was performed by Agilents Technologies using standard protocols

growth_protocol: Mutant and wildtype barley seeds were sown in Horsham mix in pots and vernalized at 4°C for six weeks, transferred to the glasshouse and grown under standard conditions as described in Burton et al. (2004) Plant Physiol. 134, 224-236.  At Zadocks developmental stage 49 (Tottman, 1987; Annals of Applied Biology 110, 441-454) upper and lower zones from the 4th internodes of stems were collected for RNA isolation.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and then treated with DNaseI using the DNA-free kit (Ambion, Austin, TX).  Total RNA quality was assessed on an Agilent BioAnalyzer 2100 before polyA(+)-RNA was isolated and used for the synthesis of cDNA for hybridization against the array.

tag: phenotype

value: brittle stem mutant


title: Human_PBMC_NA_NA_Repl_1


title: Shiroseto (line J156) L Replicate 3

value: wildtype


title: mutant M245 L Replicate 1


title: Rabbit_WB_MAP4_GR_Repl_2

value: F


title: Dmagna_ZnF1_rep3

tag: generation

tag: age


title: Ohichi (line J755) U Replicate 1

source_name: stem upper zone


title: Ohichi (line J755) U Replicate 2


title: Dmagna_CtrlF0_rep3

description:
Daphnia magna clone K6 originates from a pond in Kiel, Antwerp, Belgium. It has been cultured for more than 20 years at the laboratory of environmental toxicology and aquatic ecology, Ghent University.

Hybridization: F0 day 20 control versus Reference pool

value: 20 days

value: control


title: Shiroseto (line J156) L Replicate 2


title: Dmagna_ZnF0_rep2

value: whole body extracts

tag: zinc exposure


title: Human_PBMC_NA_NA_Repl_5

tag: backbone

tag: gender


title: Dmagna_CtrlF0_rep2

value: 10 organisms


title: Shiroseto (line J156) L Replicate 1


title: Human_PBMC_NA_NA_Repl_2

tag: peptide


title: anaerobic at time 0

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene Expression data from anaerobic at time 0

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: Data was processed using BioConductor suite for background correction (GCRMA), qspline (normalization). The chip also contains probes for S. pombe, which were masked out to obtain only the expression values for S. cerevisiae.

organism: Saccharomyces cerevisiae

source_name: anaerobic at time 0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were grown on mineral salts medium with glucose as the limiting nutrient. At the commencement of the experiment, the concentration of glucose was increased linearly as ammonia became the limiting nutrient. The experiment was conducted under aerobic or anaerobic conditions.

extract_protocol: Total RNA was extracted using RNeasy kits from Qiagen. Any DNA contamination was removed by treating it with DNase on column.

treatment_protocol: Biomass was quenched on ice and separated from the growth medium by centrifuging at 4C for 2 min and was frozen in liquid nitrogen.

tag: strain

tag: glucose concentration

value: 1 g/L

tag: condition

value: anaerobic

tag: time

value: 0 h


title: mutant M245 U Replicate 3


title: aerobic at time 9.6 h

description: Gene Expression data from aerobic at time 9.6 h

source_name: aerobic at time 9.6 h

value: aerobic


title: anaerobic at time 42.85 h

description: Gene Expression data from anaerobic at time 42.85 h

source_name: anaerobic at time 42.85 h


title: Human_PBMC_NA_NA_Repl_4

tag: number of immunization boost

tag: alias


title: aerobic at time 14.5 h

description: Gene Expression data from aerobic at time 14.5 h

source_name: aerobic at time 14.5 h


title: anaerobic at time 50.85 h

description: Gene Expression data from anaerobic at time 50.85 h

source_name: anaerobic at time 50.85 h


title: anaerobic at time 4.35 h

description: Gene Expression data from anaerobic at time 4.35 h

source_name: anaerobic at time 4.35 h


title: Dmagna_ZnF0_rep1

tag: tissue

value: 23 days

value: subsample of pooled RNA from 60 6-day-old, 60 13-day-old and 60 21-day-old daphnids

tag: sample type

value: reference


title: Human_PBMC_NA_NA_Repl_3

value: Unknown

tag: cell type

value: PBMC


title: anaerobic at time 10.38 h

description: Gene Expression data from anaerobic at time 10.38 h

source_name: anaerobic at time 10.38 h


title: aerobic at time 6.85 h

description: Gene Expression data from aerobic at time 6.85 h

source_name: aerobic at time 6.85 h


title: aerobic at time 0

description: Gene Expression data from aerobic at time 0

source_name: aerobic at time 0


title: mutant M245 U Replicate 1


title: mutant M245 U Replicate 2


title: Shiroseto (line J156) U Replicate 3


title: Shiroseto (line J156) U Replicate 1


title: Shiroseto (line J156) U Replicate 2


title: anaerobic at time 35.67 h

description: Gene Expression data from anaerobic at time 35.67 h

source_name: anaerobic at time 35.67 h


title: mutant X054 L Replicate 3


title: anaerobic at time 16.88 h

description: Gene Expression data from anaerobic at time 16.88 h

source_name: anaerobic at time 16.88 h


title: aerobic at time 4.1 h

description: Gene Expression data from aerobic at time 4.1 h

source_name: aerobic at time 4.1 h


title: anaerobic at time 26.52 h

description: Gene Expression data from anaerobic at time 26.52 h

source_name: anaerobic at time 26.52 h


title: Dmagna_CtrlF0_rep1

tag: clone

tag: composition

source_name: Reference pool


title: aerobic at time 53.95 h

description: Gene Expression data from aerobic at time 53.95 h

source_name: aerobic at time 53.95 h


title: mutant X054 L Replicate 1

source_name: stem lower zone

tag: phenotype


title: Ex3aERKO Uterus_estradiol_24h_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression in Ex3aERKO (ERa null) ovariectomized E2 24 hour treated uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The default setting for the protocol we used is polynomial data fit.

source_name: Ex3aERKO uterus, E2 treated 24 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

treatment_protocol: ovariectomized mice were allowed to rest for 10-14 days, then injected with 100 ul saline or 250 ng estradiol in 100 ul saline ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

tag: esr1 genotype

value: Ex3aERKO (Esr1 null)

tag: agent

tag: time point

tag: age

value: adult (10+ weeks)

value: ovariectomized female

value: uterus


title: Ohichi (line J755) L Replicate2

value: wildtype


title: mutant X054 L Replicate 2

value: brittle stem mutant


title: aerobic at time 42.65 h

description: Gene Expression data from aerobic at time 42.65 h

source_name: aerobic at time 42.65 h


title: Ex3aERKO Uterus_estradiol_24h_rep1

tag: gender


title: mutant X054 U Replicate 1

source_name: stem upper zone


title: Ex3aERKO Uterus_saline_24h_rep3

description: gene expression in Ex3aERKO (ERa null) ovariectomized saline vehicle treated uterus

source_name: Ex3aERKO uterus, saline control

value: saline control

tag: strain


title: mutant X054 U Replicate 2


title: Ex3aERKO Uterus_estradiol_24h_rep2


title: mutant X054 U Replicate 3


title: Ohichi (line J755) L Replicate1


title: WT Uterus_estradiol_24h_rep2

description: gene expression in WT ovariectomized E2 24 hour treated uterus

source_name: WT uterus, E2 treated 24 hours

value: WT


title: Ohichi (line J755) U Replicate 3


title: Ex3aERKO Uterus_estradiol_2h_rep1

description: gene expression in Ex3aERKO (ERa null) ovariectomized E2 2 hour treated uterus

source_name: Ex3aERKO uterus, E2 treated 2 hours


title: Ex3aERKO Uterus_estradiol_2h_rep3


title: WT Uterus_estradiol_24h_rep3


title: aerobic at time 27.25 h

description: Gene Expression data from aerobic at time 27.25 h

source_name: aerobic at time 27.25 h

tag: glucose concentration


title: Ex3aERKO Uterus_saline_24h_rep1


title: WT Uterus_estradiol_2h_rep2

description: gene expression in WT ovariectomized E2 2 hour treated uterus

source_name: WT uterus, E2 treated 2 hours


title: Ex3aERKO Uterus_estradiol_2h_rep2


title: Low pH, female sample 3

status: Public on Jul 22 2010

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

institute: National Institute of Advanced Industrial Science and Technology

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH4.0 by slowly flowing of 0.1N HCl.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

hyb_protocol: Hybridization, washing and scanning were carried out following standard procedures (NimbleGen Systems, Inc.).

scan_protocol: Scanning were performed by GenePix4000B.

data_processing: Data extraction and processing were performed by NimbleScan (NimbleGen Systems, Inc.). The expression level of each target was calculated by averaging the intensities of signals from seven different probes. The signals between each array were normalized using RMA (Robust Multi-chip Analysis) normalization.

label: biotin (Cy3-SA)

organism: Oryzias latipes

source_name: ACID F3, whole frozen medaka

label_protocol: Total RNA from whole frozen medaka was first converted to double-stranded cDNA, followed by the synthesis of biotin-labeled cRNA using in vitro transcription. cRNA was then purified and fragmented to an average size of 50 to 200 bp.

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH4.0 by slowly flowing of 0.1N HCl.

extract_protocol: For microarray analysis, female and male fish (body wt ∼400 mg; total length ∼3 cm) were flash-frozen in liquid nitrogen, and stored at −80°C for RNA extraction.  Total RNA from whole frozen medaka was isolated using the EASYPrep RNA (TaKaRa Bio Inc., Shiga, Japan) following procedures recommended by the manufacturer.

value: female

tag: stress

value: low pH


title: WT Uterus_estradiol_24h_rep1


title: WT Uterus_estradiol_2h_rep3


title: High pH, male sample 1

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH10.8 by slowly flowing of 0.1N NaOH  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ALK M1, whole frozen medaka

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH10.8 by slowly flowing of 0.1N NaOH

value: male

value: high pH


title: WT Uterus_saline_24h_rep2

description: gene expression in WT ovariectomized saline vehicle treated uterus

source_name: WT uterus, saline control


title: WT Uterus_estradiol_2h_rep1


title: Ex3aERKO Uterus_saline_24h_rep2


title: WT Uterus_saline_24h_rep3


title: High pH, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH10.8 by slowly flowing of 0.1N NaOH  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ALK F3, whole frozen medaka


title: Low pH, female sample 2

source_name: ACID F2, whole frozen medaka


title: Low pH, female sample 1

source_name: ACID F1, whole frozen medaka


title: Low oxygen, female sample 1

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except dissolved oxygen conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h in well closed bottle. Dring 96 h test piriod, concentration of dissolved oxygen (DO) were monitored continuouly and kept 10% by slowly flowing of air-satulated water.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: DO F1, whole frozen medaka

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except dissolved oxygen conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h in well closed bottle. Dring 96 h test piriod, concentration of dissolved oxygen (DO) were monitored continuouly and kept 10% by slowly flowing of air-satulated water.

value: low oxygen


title: High pH, male sample 2

source_name: ALK M2, whole frozen medaka


title: Dual species array test for human RNA_Channel-2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: GenePix 4000B axon scanner Images were quantified using Agilent Feature Extraction Software version9

data_processing: Background correction: local background subtracted mean expression values from FE software.

source_name: 0.75µg human RNA and 0.75µg mouse RNA

label_protocol: 1.5µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: N/A, Total RNA purchased from ArrayIt (Sunnyvale, CA)

value: 0.75µg human RNA and 0.75µg mouse RNA


title: Low pH, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH4.0 by slowly flowing of 0.1N HCl.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ACID M3, whole frozen medaka


title: Low oxygen, female sample 3

source_name: DO F3, whole frozen medaka


title: High pH, female sample 2

source_name: ALK F2, whole frozen medaka


title: Low pH, male sample 2

source_name: ACID M2, whole frozen medaka


title: High pH, female sample 1

source_name: ALK F1, whole frozen medaka