title: C57BL/6J mice fed a low fat-diet

status: Public on Aug 27 2007

type: RNA

city: Haga-Gun, Tochigi

first: Hidehiko

last: Kondo

address: 2606 Akabane, Ichikai-Machi

department: Biological Science Laboratories

country: Japan

institute: Kao Corporation

description: Eight micrograms of total RNA were converted into double-stranded cDNA (ds-cDNA) by use of the SuperScript double-stranded cDNA synthesis kit and GeneChip T7-oligo(dT) promoter primer kit. After second-strand synthesis, the reaction mixture was purified using the GeneChip sample cleanup module. In vitro transcription was performed on the ds-cDNA with the Enzo RNA transcript labeling kit. Biotinylated cRNA was purified using the GeneChip sample cleanup module and fragmented by incubating 94°C for 35 min. The biotinylated cRNA (final 0.05 mg/ ml) was hybridized with Mouse Expression Array 430A for 16 h at 45°C. After stringent washing in a microfluidics station 400, cRNA was stained with R-phycoerythrin streptavidine and scanned after antibody amplification. Fluorescence intensities were measured with an Affymetrix Scanner. Image output files were inspected for hybridization artifacts, and based on the fluorescence intensity differences between perfect match and mismatch probes, a hybridization intensity was calculated for each transcript using Microarray Suite 5.0. Default parameters optimized by the manufacturer for this microarray chip were used for all signal analysis.

data_processing: Normalized by the value of acidic ribosomal phosphoprotein PO (1419441_at)

label: R-phycoerythrin

molecule: total RNA

organism: Mus musculus

source_name: intestinal mucosa

tag: Strain

tag: Gender

value: Male

tag: Age

value: 10 weeks

tag: Tissue

value: intestinal mucosa


title: TS-PCR  tc132_UR_618-G4-E1

status: Public on Aug 24 2007

city: Seibersdorf

first: Martin

last: Lauss

state: Lower Austria

address: Mendelstrasse 1

department: Life Sciences

country: Austria

institute: ARC Seibersdorf research

description:
Title carries following information:
Slide_RedChannel_GreenChannel-TumorSubpiece-Extract

hyb_protocol: Precipitated or dried down labeled target was resuspended in 20ul DIGeasy hybridization solution (Roche). Dissolved labeled target was heated to 99 degrees Celsius for 2 min, followed by prehybridization at 42 degrees Celsius for 10 min. The entire labeled target was applied to the prewarmed microarrays, under M-Series Lifter Slips (Erie Scientific) and incubated at 42 degrees Celsius for 16 h. Hybridized arrays were washed with 1x SSC/0.2%SDS for 5min and 0.1x SSC/0,2%SDS for 5min and then plunged repeatedly in 0.1x SSC. Slides were dried by centrifugation.

scan_protocol: Slides were scanned using an GenePix 4000A (Axon Instruments). Raw image data were extracted using GenePix 3.0 software (Axon Instruments)

data_processing: preprocessing: pmt-merging (BASE-plugin), background substraction, addition of a constant offset,  lowess normalization through calibration controls. VALUES are M-values (= log2 (R/G))

organism: Homo sapiens

label_protocol: Amplification by TS-PCR protocol with following  Klenow labelling

extract_protocol: Primary samples were dissected into smaller pieces if necessary and shock frozen in liquid nitrogen. RNA later ice (Ambion) was applied to the samples at least one day before RNA isolation and then kept at -80 degrees Celsius. Samples were disrupted in liquid nitrogen with a mortar and pestle-like device developed in our laboratory. Samples were homogenized using Qiashredder Columns (Qiagen) and total RNA was isolated by an RNeasy mini column (Qiagen). Total RNA was concentrated by ethanol precipitation and dissolved in appropriate amount of DEPC-treated distilled water (dH2O).

treatment_protocol: Tumor Subpiece 4, Extract 1

tag: Primary Thyroid Cancer, invasive

tag: PTC papillary thyroid carcinom

source_name: Universal Human Reference

extract_protocol: none, is commercially available as total RNA

tag: Universal Human Reference, Stratagene


title: TS-PCR  tc130_UR_618-G1-E2

treatment_protocol: Tumor Subpiece 1, Extract 2


title: TS-PCR  tc129_UR_618-G1-E1

treatment_protocol: Tumor Subpiece 1, Extract 1


title: Ribo-SPIA  BC91_Hpool1_Mpool3_Ov_5ng

description:
Title carries following information:
Slide_GreenChannel_RedChannel_AmplificationMethod_StartingMaterial

source_name: Hs578T, Ribo-SPIA

label_protocol: Amplification by Ribo-SPIA protocol following appropriate labelling

extract_protocol: Total RNA from human breast cancer cell lines was extracted using Trizol (Invitrogen) followed by an RNeasy mini column clean up (Qiagen) according to the manufacturers protocol

tag: breast cancer cell line established from invasive human mammacarcinoma

tag: known to be estrogen receptor negative

source_name: MCF7, Ribo-SPIA

tag: Morphology

value: Epithelial-like

tag: Human Caucasian breast adenocarcinoma


title: TS-PCR  tc112_UR_607-G7-E1

treatment_protocol: Tumor Subpiece 7, Extract 1

tag: Primary Thyroid Cancer, benign

tag: SN Stromanodosa


title: Dendrimerlabelling BC79_Hpool1_Mpool3_Dendr_2ug

source_name: Hs578T, Dendrimer

label_protocol: Dendrimerlabelling

source_name: MCF7, Dendrimer


title: TS-PCR  tc111_UR_607-G7-E3

treatment_protocol: Tumor Subpiece 7, Extract 3


title: Random-primed PEP-PCR  BC74_Mpool3_Hpool1_PEP25_100ng

source_name: MCF7, PEP

label_protocol: Amplification by random-primed PEP-PCR protocol with following  Klenow labelling

source_name: Hs578T, PEP


title: Random-primed PEP-PCR  BC51_Hpool1_Mpool3_PEP25_100ng


title: Random-primed PEP-PCR  BC40_Hpool1_Mpool3_PEP25_100ng


title: C57BL/6J mice fed a high fat-diet


title: A/J mice fed a high fat-diet

value: A/J

value: male


title: A/J mice fed a low fat-diet


title: TS-PCR  tc133_UR_618-G4-E3

treatment_protocol: Tumor Subpiece 4, Extract 3


title: Ribo-SPIA  BC29_Mpool3_Hpool1_Ov_5ng

data_processing: pmt-merging (BASE-plugin), background substraction, addition of a constant offset,  lowess normalization through calibration controls. VALUES are M-values (= log2 (R/G))

source_name: MCF7, Ribo_SPIA

extract_protocol: Total RNA from human breast cancer cell lines was extracted using Trizol (Invitrogen) followed by an RNeasy mini column clean up (Qiagen) according to the manufacturers protocol.ve


title: TS-PCR  tc131_UR_618-G1-E3

treatment_protocol: Tumor Subpiece 1, Extract 3


title: Labelled directly at reverse transcription (unamplified RNA) BC77_Mpool3_Hpool1_direkt_20ug

source_name: MCF7, direct

source_name: Hs578T, direct


title: Dendrimerlabelling BC31b_Mpool3_Hpool1_2ug_Dendr


title: TS-PCR  BC577_180_50min_Ref_TS19

description:
Title carries following information:
Slide_GreenChannel_InkubationTime_RedChannel_AmplificationMethod

growth_protocol: Inkubation for 50 min at 55 degrees Celsius after extraction

tag: invasive ductal mammacarcinom

tag: primary tissue

tag: estrogen receptor negative


title: TS-PCR  BC92_Mpool3_Hpool1_TS19Zyk_50ng

source_name: MCF7, TS-PCR

source_name: Hs578T, TS-PCR


title: TS-PCR  tc124_UR_607-G7-E2

treatment_protocol: Tumor Subpiece 7, Extract 2


title: Ribo-SPIA  BC588_254_180_Ov_50ng

source_name: 254/03, Ribo-SPIA

tag: estrogen receptor positive

source_name: 180/03, Ribo-SPIA


title: TS-PCR  BC90_Hpool1_Mpool3_TS19Zyk_50ng


title: TS-PCR  BC575_180_0min_Ref_TS19

growth_protocol: Inkubation for 0 min at 55 degrees Celsius after extraction


title: Ribo-SPIA  BC587_180_254_Ov_50ng


title: TS-PCR  BC89_Mpool3_Hpool1_TS19Zyk_50ng


title: yeast_nup84gcr1 null vs WT_glucose_rep4

status: Public on Aug 22 2007

city: Hattiesburg

first: Kellie

last: Barbara

state: MS

address: 118 College Dr. #5018

department: Biological Sciences

country: USA

institute: Univ. of Southern MS

description: labeling done with Agilent's Low RNA Input Linear Amp kit; hybridization and slide processing done according to Agilent instructions

data_processing: log2 ratio after ratio-based and LOWESS normalization in Acuity 4.0

organism: Saccharomyces cerevisiae

source_name: wild type, 2% glucose

tag: wild type reporter strain (NJS2) from S288C background; grown to early-mid log in YPD at 23 degrees Celcius

source_name: nup84gcr1 null, 2% glucose

tag: nup84gcr1 null reporter strain (NJS34) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: TS-PCR  tc105_UR_604-G2-E1

treatment_protocol: Tumor Subpiece 2, Extract 1


title: Random-primed PEP-PCR  BC62_Mpool3_Hpool1_PEP25_100ng


title: Labelled directly at reverse transcription (unamplified RNA) BC54_Hpool1_Mpool3_direkt_20ug


title: yeast_nup84 null vs WT_glucose_rep4

source_name: nup84 null, 2% glucose

tag: nup84 null reporter strain (NJS10) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: TS-PCR  BC52_Hpool1_Mpool3_TS19Zyk_50ng


title: yeast_nup84 null vs WT_glucose_rep3

tag: wild type reporter strain (NJS1) from S288C background; grown to early-mid log in YPD at 23 degrees Celcius

tag: nup84 null reporter strain (NJS9) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: TS-PCR  tc104_UR_604-G2-E3

treatment_protocol: TumorSubpiece 2, Extract 3

source_name: Universal Human Reference


title: yeast_nup84 null vs WT_glucose_rep2


title: TS-PCR  BC580_254_50min_Ref_TS19


title: Ribo-SPIA  BC16_Hpool1_Mpool3_Ov_5ng

hyb_protocol: Precipitated or dried down labeled target was resuspended in 20µl DIGeasy hybridization solution (Roche). Dissolved labeled target was heated to 99°C for 2 min, followed by prehybridization at 42°C for 10 min. The entire labeled target was applied to the prewarmed microarrays, under M-Series Lifter Slips (Erie Scientific) and incubated at 42°C for 16 h. Hybridized arrays were washed with 1x SSC/0.2%SDS for 5min and 0.1x SSC/0,2%SDS for 5min and then plunged repeatedly in 0.1x SSC. Slides were dried by centrifugation.

data_processing: preprocessing: pmt-merging (BASE-plugin), background substraction, addition of a constant offset,  lowess normalization through ‘calibration controls’. ‘VALUES’ are M-values (= log2 (R/G))

source_name: Hs578T, Ribo-SPIA

extract_protocol: Total RNA from human breast cancer cell lines was extracted using Trizol (Invitrogen) followed by an RNeasy mini column clean up (Qiagen) according to the manufacturer’s protocol.

extract_protocol:
Hs578T
breast cancer cell line established from invasive human mammacarcinoma
known to be estrogen receptor negative


title: yeast_gcr1 null vs WT_glucose_rep4

source_name: gcr1 null, 2% glucose

tag: gcr1 null reporter strain (NJS4) from S288C background; grown to early-mid log in YPD at 23 degrees Celcius


title: yeast_gcr1 null vs WT_glucose_rep2


title: Ribo-SPIA  BC24_Mpool3_Hpool1_Ov_5ng

extract_protocol: Total RNA from human breast cancer cell lines was extracted using Trizol (Invitrogen) followed by an RNeasy mini column clean up (Qiagen) according to the manufacturers protocol.


title: TS-PCR  BC579_254_25min_Ref_TS19

growth_protocol: Inkubation for 25 min at 55 degrees Celsius after extraction

tag: Universal Human Reference, Stratagene


title: yeast_nutrient variation_rep1

description: labeling done with Agilent's Low RNA Input Linear Amp kit; hybridization and slide processing done according to Agilent's instructions.

source_name: yeast, 2% glucose

tag: wild type strain S288C background

tag: grown to early-mid log phase in YEP containing indicated carbon source

source_name: yeast, 3% pyruvate

tag: wild type strain, S288C background


title: E17.5 ovary replicate 3

status: Public on Aug 17 2007

city: bethesda

first: saurabh

last: joshi

state: MD

address: 9000 rockville pk

department: national institute of diabestes digestive and kidney diseases

institute: national institutes of health

description: Embryonic and newborn mouse ovaries

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software.

data_processing: Raw data was analyzed with GeneSpring (v.7) (Agilent Technologies, Inc.) using GenePix-format defaults. A Lowess curve was fit to the log-intensity versus log-ratio plot using 20.0% of the data at each point. This curve was used to adjust the control value for each measurement (if the control channel was less than 10, 10 was used). After normalization, all data were filtered to eliminate unreliable data including flagged spots, lowly expressed spots (signal less than 200), and spots with negative signal values. After filtering, the genes were chosen for further analysis on the basis of fold-change of treated samples vs. controls (? 2 up- or down-regulated) in 2 or 3 experiments with ? ? 0.05.

source_name: Wild-type E17.5 ovary replicate 3

label_protocol: Each RNA sample was amplified/labelled with Aminoallyl RNA Amplification and Labeling System (NuGen Technologies, San Carlos, CA) using ester-linked Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ).The Cy5 and Cy3 labelled cDNAs were combined and the target pairs were cleaned up over Qiaquick columns (Qiagen, 28106) and then dried to completion in a speed-vac.Dried-down targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target. The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station (BioMicro Systems, Inc., 4 chamber model).

extract_protocol: RNA isolation was accomplished with Absolutely RNA RT PCR Miniprep kit (Stratagene, La Jolla, CA) and the quality of each was validated with RNA 6000 Nano Lab-on-Chip (Agilent Technologies, Waldbronn, Germany). Each RNA sample was amplified/labelled with Aminoallyl RNA Amplification and Labeling System (NuGen Technologies, San Carlos, CA) using ester-linked Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ).

tag: Ovarian RNA from E17.5 normal/wild-type mice (CF-1)

source_name: FIGLA null E17.5 ovary replicate 3

tag: Ovarian RNA from E17.5 Figla null (129Sv/C57BL6) mice


title: TS-PCR  BC576_180_25min_Ref_TS19


title: E17.5 ovary replicate 1

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E17.5 ovary replicate 1

source_name: FIGLA null E17.5 ovary replicate 1


title: TS-PCR  BC567_254_180_TS26

description:
Title carries following information:
Slide_GreenChannel_RedChannel_AmplificationMethod

source_name: 254/03, TS-PCR 26 cycles

label_protocol: Amplification by TS-PCR protocol with following  Klenow labelling; 26 cycles

source_name: 180/03, TS-PCR 26 cycles


title: Newborn ovary dyeswap replicate 4

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null newborn ovary replicate 4

tag: Ovarian RNA from newborn Figla null (129Sv/C57BL6) mice

source_name: Wild-type newborn ovary dyeswap replicate 4

tag: Ovarian RNA from newborn normal/wild-type mice (CF-1)


title: TS-PCR  BC566_180_254_TS26

tag: invasive ductal mammacarcinom

tag: primary tissue


title: Newborn ovary dyeswap replicate 2

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null newborn ovary replicate 2

source_name: Wild-type newborn ovary dyeswap replicate 2


title: TS-PCR  BC565_254_180_TS17

source_name: 254/03, TS-PCR 17 cycles

label_protocol: Amplification by TS-PCR protocol with following  Klenow labelling; 17 cycles

tag: estrogen receptor positive

source_name: 180/03, TS-PCR 17 cycles

tag: estrogen receptor negative


title: Newborn ovary replicate 4

description: Embryonic and newborn mouse ovaries

source_name: Wild-type newborn ovary replicate 4


title: Newborn ovary replicate 3

description: Embryonic and newborn mouse ovaries

source_name: Wild-type newborn ovary replicate 3

source_name: FIGLA null newborn ovary replicate 3


title: TS-PCR  BC564_180_254_TS17

source_name: 180/03, TS-PCR 17cycles

source_name: 254/03, TS-PCR 17cycles


title: Labelled directly at reverse transcription (unamplified RNA) BC563_254_180_direct


title: Newborn ovary replicate 1

description: Embryonic and newborn mouse ovaries

source_name: Wild-type newborn ovary replicate 1

source_name: FIGLA null newborn ovary replicate 1


title: Newborn ovary replicate 2

description: Embryonic and newborn mouse ovaries

source_name: Wild-type newborn ovary replicate 2


title: TS-PCR  BC561_254_180_TS19

source_name: 245/03, TS-PCR 19 cycles

label_protocol: Amplification by TS-PCR protocol with following  Klenow labelling; 19 cycles

source_name: 180/03, TS-PCR 19 cycles


title: E14.5 ovary dyeswap replicate 3

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E14.5 ovary replicate 3

tag: Ovarian RNA from E14.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E14.5 ovary dyeswap replicate 3

tag: Ovarian RNA from E14.5 normal/wild-type mice (CF-1)


title: E14.5 ovary replicate 3

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E14.5 ovary replicate 3


title: TS-PCR  BC560_180_254_TS19

source_name: 254/03, TS-PCR 19 cycles


title: yeast_nup84gcr1 null vs WT_glucose_rep3

source_name: wild type, 2% glucose

tag: wild type reporter strain (NJS1) from S288C background; grown to early-mid log in YPD at 23 degrees Celcius

source_name: nup84gcr1 null, 2% glucose

tag: nup84gcr1 null reporter strain (NJS33) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: yeast_nup84gcr1 null vs WT_glucose_rep2

tag: nup84gcr1 null reporter strain (NJS34) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius

tag: wild type reporter strain (NJS2) from S288C background; grown to early-mid log in YPD at 23 degrees Celcius


title: yeast_nup84gcr1 null vs WT_glucose_rep1


title: E14.5 ovary replicate 2

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E14.5 ovary replicate 2

source_name: FIGLA null E14.5 ovary replicate 2


title: E12.5 ovary dyeswap replicate 2

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E12.5 ovary replicate 2

tag: Ovarian RNA from E12.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E12.5 ovary dyeswap replicate 2

tag: Ovarian RNA from E12.5 normal/wild-type mice (CF-1)


title: yeast_nup84 null vs WT_glucose_rep1

source_name: nup84 null, 2% glucose

tag: nup84 null reporter strain (NJS9) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: yeast_gcr1 null vs WT_glucose_rep3

source_name: gcr1 null, 2% glucose

tag: gcr1 null reporter strain (NJS3) from S288C background; grown to early-mid log in YEPD at 23 degrees Celcius


title: E12.5 ovary replicate 2

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E12.5 ovary replicate 2


title: yeast_gcr1 null_glucose_rep1


title: Yeast_nutrient variation_rep2

source_name: yeast, 3% pyruvate

tag: wild type strain, S288C background

tag: grown to early-mid log phase in YEP containing indicated carbon-source

source_name: yeast, 2% glucose

tag: grown to early-mid log in YEP containing indicated carbon source


title: E17.5 ovary dyeswap replicate 2

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E17.5 ovary replicate 2

tag: Ovarian RNA from E17.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E17.5 ovary dyeswap replicate 2

tag: Ovarian RNA from E17.5 normal/wild-type mice (CF-1)


title: TS-PCR  BC578_254_0min_Ref_TS19

tag: invasive ductal mammacarcinom

tag: primary tissue

tag: estrogen receptor positive

source_name: Universal Human Reference

tag: Universal Human Reference, Stratagene


title: E17.5 ovary dyeswap replicate 1

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E17.5 ovary replicate 1

source_name: Wild-type E17.5 ovary dyeswap replicate 1


title: human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep1

status: Public on Aug 10 2007

city: Seattle

first: Jared

middle: C

last: Roach

state: WA

address: 1441 North 34th St

institute: Institute for Systems Biology

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductor/RMA.

label: biotin

extract_protocol: Trizol extraction of total RNA, Qiagen RNeasy.

tag: adult male


title: Newborn ovary dyeswap replicate 3

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null newborn ovary replicate 3

tag: Ovarian RNA from newborn Figla null (129Sv/C57BL6) mice

source_name: Wild-type newborn ovary dyeswap replicate 3

tag: Ovarian RNA from newborn normal/wild-type mice (CF-1)


title: E17.5 ovary replicate 2

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E17.5 ovary replicate 2


title: Newborn ovary dyeswap replicate 1

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null newborn ovary replicate 1

source_name: Wild-type newborn ovary dyeswap replicate 1


title: human peripheral blood derived monocytes, no stimulation, biological rep1


title: Dahl_Cerebral_Artery_high.salt.3

status: Public on Aug 09 2007

city: Burlington

first: Karen

middle: M.

last: Lounsbury

state: VT

address: 89 Beaumont Avenue

department: Pharmacology

institute: University of Vermont

description: Each sample consisted of RNA pooled from arteries of 3 different rats on their respective diets (i.e. 9 total rats/group).

hyb_protocol: Samples were applied to Affymetrix Gene Chip  Rat Expression Set 230A (RAE230A) at 45C for 16 hr.

scan_protocol: Biotinylated anti-streptavadin antibodies were used to amplify the signal.  Probe arrays were scanned using a Hewlett-Packard Gene Array Scanner (Agilent Technologies).

data_processing: qspline/RMA

organism: Rattus norvegicus

source_name: Dahl Rat Cerebral Artery after High Salt Diet

label_protocol: RNA samples were amplified using a Two-Cycle cDNA Synthesis Kit according to the manufacturer?s instructions (Affymetrix, Santa Clara, CA).  Following second cycle, second strand cDNA synthesis, and cleanup, biotinylated-cRNA was prepared by in vitro transcription, fragmented and labeled using a streptavadin-phycoerythrin conjugate.

growth_protocol: Rats were maintained on a 12:12 h light:dark cycle in a temperature-controlled environment. Tap-water and a low-salt chow (0.4% NaCl) were available ad libitum before initiation of the study.

extract_protocol: Total RNA was extracted from intact cerebral arteries using a modified RNeasy? protocol for isolation from animal tissues with a DNAse I digestion step (Qiagen).  To improve tissue disruption and increase RNA yield, the protocol for tissue homogenization was modified to include approximately 25 mg of 200 um silicon carbide abrasive beads from a microbial RNA Isolation kit (MoBio labs, Carlsbad, CA) and a Pellet Pestle? (Kontes, Vineland, NJ).  RNA concentrations were determined using a Nanodrop? spectrophotometer and RNA quality was assessed by an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, California).

treatment_protocol: At 7 weeks of age, Dahl rats were put on a HIGH SALT diet (8 % NaCl) diet for 12 weeks.  Animals were euthanized using pentobarbital followed by removal of the heart and brain.  Primary branch cerebral resistance arteries projecting from the Basilar/Circle of Willis were dissected (middle and posterior cerebral and posterior cerebellar) in cold HEPES buffered solution (HBS). Arteries were either snap frozen in liquid N2 and stored at -80 C or submerged in RNAlater? (Qiagen, Valencia, CA) and stored at -20 C until processed for RNA extraction.

tag: Male Dahl Rat

tag: Age high salt diet commenced

value: 7 weeks

tag: Time on diet

value: 11 weeks

tag: Tissue

value: intact cerebral artery


title: E14.5 ovary dyeswap replicate 2

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E14.5 ovary replicate 2

tag: Ovarian RNA from E14.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E14.5 ovary dyeswap replicate 2

tag: Ovarian RNA from E14.5 normal/wild-type mice (CF-1)


title: Dahl_Cerebral_Artery_high.salt.2


title: Dahl_Cerebral_Artery_high.salt.1

source_name: Dahl Rat Cerebral Artery after high salt diet


title: E14.5 ovary dyeswap replicate 1

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E14.5 ovary replicate 1

source_name: Wild-type E14.5 ovary dyeswap replicate 1


title: E14.5 ovary replicate 1

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E14.5 ovary replicate 1


title: Dahl_Cerebral_Artery_low.salt.2

source_name: Dahl Rat Cerebral Artery after low salt diet

treatment_protocol: At 7 weeks of age, Dahl rats were put on a low salt (0.4% NaCl) diet for 12 weeks.  Animals were euthanized using pentobarbital followed by removal of the heart and brain.  Primary branch cerebral resistance arteries projecting from the Basilar/Circle of Willis were dissected (middle and posterior cerebral and posterior cerebellar) in cold HEPES buffered solution (HBS). Arteries were either snap frozen in liquid N2 and stored at -80 C or submerged in RNAlater? (Qiagen, Valencia, CA) and stored at -20 C until processed for RNA extraction.

tag: Age diet commenced

value: 12 weeks


title: Testis_Taf7l knockout_rep1

city: Philadelphia

first: Jeremy

last: Wang

state: PA

address: 3800 Spruce Street

department: Animal Biology

institute: University of Pennsylvania

description: Gene expression data from Taf7l mutant testis, biological rep1.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using using the GCS3000 scanner..

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

source_name: testis

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

growth_protocol: male mice were sacrificed at 8 weeks old

extract_protocol: Trizol extraction followed by Qiagen RNEasy clean-up.

treatment_protocol: Testis was snap-frozen and stored at -80°C.

tag: Genotype

value: Taf7l knockout

tag: Strain

tag: Age


title: E12.5 ovary dyeswap replicate 3

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E12.5 ovary replicate 3

tag: Ovarian RNA from E12.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E12.5 ovary dyeswap replicate 3

tag: Ovarian RNA from E12.5 normal/wild-type mice (CF-1)


title: E12.5 ovary dyeswap replicate 1

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E12.5 ovary replicate 1

source_name: Wild-type E12.5 ovary dyeswap replicate 1


title: E12.5 ovary replicate 1

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E12.5 ovary replicate 1


title: E12.5 ovary replicate 3

description: Embryonic and newborn mouse ovaries

source_name: Wild-type E12.5 ovary replicate 3


title: human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep1


title: human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep2


title: human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep2


title: TSA 7.5h Replicate 2

status: Public on Aug 02 2007

city: Giessen

first: Hamid

last: Hossain

address: Gaffky Str. 20

department: University of Giessen

country: Germany

institute: Institute for Medical Microbiology

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94gr.C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37gr.C / 300 rpm. cRNA of each group was hybridized in duplicate (technical replicates). In total, 10 bioarrays (2 arrays per group) were processed in parallel using the CodeLink Shaker Kit and CodeLink Parallel Processing Kit (Amersham Biosciences).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: Spot signals of the CodeLink bioarrays were quantified using CodeLink Expression Software 1.21 based on ImaGene 5.5 (BioDiscovery, Marina Del Ray, CA). The image segmentation and quantification process is outlined in the ImaGene 5.5 user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds (0.062 to 0.211) for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Data of 10 arrays (two replicates per group) were subjected to data analysis. Genes with missing values >= 50% in all arrays were excluded from the analysis. The remaining missing values were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). Microarray data containing 9897 genes were normalized using quantiles normalization in R (Bolstad et al. 2003).

label_protocol: Total RNA were subjected to cDNA synthesis using a poly-A binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with the NanoDrop (NanoDrop Technologies) and quality was assesed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

growth_protocol: Animals were kept under controlled conditions of light, temperature and humidity receiving water and standard food ad libitum.

extract_protocol: Total RNA was extracted from frozen tissue of 3 animals per group using the RNeasy Mini Kit (Qiagen, Germany). The material from each group was pooled. Both quality and quantity of RNA was checked by Agilent 2100 Bioanalyzer and UV spectrophotometer.

treatment_protocol: TSA was resolved in dimethylsulfoxide and PBS. 15 animals were divided into 5 groups each containing 3 mice. Group 1 received only the carrier and were sacrificed after 10h (control). Groups 2 - 5 received 60ug/day/mouse TSA applied by one subcutaneous injection and were sacrificed after 2.5h (group 2), 5h (group 3), 7.5h (group 4) and 10h (group 5).

tag: Balb-c mice, age

value: 9 week, gender:male, tissue:testis


title: TSA 5h Replicate 2


title: TSA 5h Replicate 1


title: E17.5 ovary dyeswap replicate 3

description: Embryonic and newborn mouse ovaries

source_name: FIGLA null E17.5 ovary replicate 3

tag: Ovarian RNA from E17.5 Figla null (129Sv/C57BL6) mice

source_name: Wild-type E17.5 ovary dyeswap replicate 3

tag: Ovarian RNA from E17.5 normal/wild-type mice (CF-1)


title: human peripheral blood derived monocytes, 4 hour LPS stimulation, biological rep2

tag: adult male


title: human peripheral blood derived monocytes, 4 hour LPS stimulation, biological rep1


title: human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep2


title: human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep3


title: human peripheral blood derived monocytes, no stimulation, biological rep2


title: Unknown 5 - mAdbID:77930

status: Public on Aug 01 2007

city: Bethesda

first: Stuart Yuspa

last: Adam Glick

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: mAdb experiment ID: 77930

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Mouse Universal Reference Total RNA -Cy5

label_protocol:
Cy5 Labeling
Label amount: 40000 pmol dye
Label method: Aminoallyl Method
Other: Protocol Similar to that found at the J. David Gladstone Institutes Genomic Core Laboratory (SOP #P004). Used CyeDye Post-Labelling Reactive Dye Pack.

tag: Other

value: whole tissues

source_name: Unknown 5

label_protocol:
Cy3 Labeling
Label amount: 40000 pmol dye
Label method: Aminoallyl Coupling Method
Other: Protocol Similar to that found at the J. David Gladstone Institutes Genomic Core Laboratory (SOP #P004). Used CyeDye Post-Labelling Reactive Dye Pack.

extract_protocol:
RNA Extraction
Extraction method: Trizol-QIAgen RNeasy Kit
Other: Tumors were Homogenized in TRIzol, and RNA purified with the Quiagen RNeasy clean up kit.

treatment_protocol:
Treatment type: compound
Agent: DMBA/TPA

value: Sencar

tag: Gender

value: female

value: 7-8 Weeks Initiated

value: chemically-derived skin tumor

tag: Developmental stage

value: adult

tag: Disease state

value: Papilloma


title: Dahl_Cerebral_Artery_low.salt.3

tag: Male Dahl Rat

tag: Time on diet

tag: Tissue


title: Dahl_Cerebral_Artery_low.salt.1

source_name: Dahl rat intact cerebral artery, low salt diet

label_protocol: RNA samples were amplified using a Two-Cycle cDNA Synthesis Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).  Following second cycle, second strand cDNA synthesis, and cleanup, biotinylated-cRNA was prepared by in vitro transcription, fragmented and labeled using a streptavadin-phycoerythrin conjugate.

extract_protocol: Total RNA was extracted from intact cerebral arteries using a modified RNeasy® protocol for isolation from animal tissues with a DNAse I digestion step (Qiagen).  To improve tissue disruption and increase RNA yield, the protocol for tissue homogenization was modified to include approximately 25 mg of 200 um silicon carbide abrasive beads from a microbial RNA Isolation kit (MoBio labs, Carlsbad, CA) and a Pellet Pestle® (Kontes, Vineland, NJ).  RNA concentrations were determined using a Nanodrop® spectrophotometer and RNA quality was assessed by an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, California).

treatment_protocol: At 7 weeks of age, Dahl rats were put on a low salt (0.4% NaCl) diet for 12 weeks.  Animals were euthanized using pentobarbital followed by removal of the heart and brain.  Primary branch cerebral resistance arteries projecting from the Basilar/Circle of Willis were dissected (middle and posterior cerebral and posterior cerebellar) in cold HEPES buffered solution (HBS). Arteries were either snap frozen in liquid N2 and stored at -80 C or submerged in RNAlater® (Qiagen, Valencia, CA) and stored at -20 C until processed for RNA extraction.

tag: Age put on diet


title: Testis_wild type_rep2

description: Gene expression data from wild type testis, biological rep2.

tag: Genotype

value: wild type


title: Testis_Taf7l knockout_rep2

tag: Strain


title: TSA 10h Replicate 2


title: Testis_wild type_rep1

description: Gene expression data from wild type testis, biological rep1.

tag: Age


title: TSA 10h Replicate 1


title: Unknown 3 - mAdbID:76031

description: mAdb experiment ID: 76031

source_name: Unknown 3

treatment_protocol:
Treatment type: compound
Agent: DMBA/TPA
Treatment time: Many weeks


title: Unknown 1 - mAdbID:76030

description: mAdb experiment ID: 76030

source_name: Unknown 1


title: SCC-4 - mAdbID:51607

description: mAdb experiment ID: 51607

value: Squamous Cell Carcinoma


title: Unknown 10 - mAdbID:75429

description: mAdb experiment ID: 75429

source_name: Unknown 10


title: Unknown 8 - mAdbID:75061

description: mAdb experiment ID: 75061

source_name: Unknown 8


title: Normal Skin-2 - mAdbID:51437

description: mAdb experiment ID: 51437

source_name: N3 Normal Skin

treatment_protocol: Treatment type: No treatment

value: normal skin


title: TSA 7.5h Replicate 1

source_name: testis


title: TSA 2.5h Replicate 1


title: TSA 2.5h Replicate 2


title: TSA 0 Control 1

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94gr.C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37gr.C, 300 rpm. cRNA of each group was hybridized in duplicate (technical replicates). In total, 10 bioarrays (2 arrays per group) were processed in parallel using the CodeLink Shaker Kit and CodeLink Parallel Processing Kit (Amersham Biosciences).


title: Unknown 2 - mAdbID:78458

description: mAdb experiment ID: 78458

source_name: Unknown 2


title: High Risk-10 - mAdbID:51462

description: mAdb experiment ID: 51462

source_name: 1B-50C-High Risk 10


title: High Risk-1 - mAdbID:51398

description: mAdb experiment ID: 51398

source_name: 1B-51A -High Risk 1


title: Unknown 9 - mAdbID:75428

description: mAdb experiment ID: 75428

source_name: Unknown 9


title: Unknown 7 - mAdbID:75060

description: mAdb experiment ID: 75060

source_name: Unknown 7


title: SCC-1 - mAdbID:51433

description: mAdb experiment ID: 51433


title: High Risk-3 - mAdbID:51394

description: mAdb experiment ID: 51394

source_name: 1B-29A -High Risk 3


title: High Risk-2 - mAdbID:51396

description: mAdb experiment ID: 51396

source_name: 1B-51B -High Risk 2


title: Low Risk-4 - mAdbID:51439

description: mAdb experiment ID: 51439

source_name: 2-53D Low Risk-4


title: Unknown 4 - mAdbID:77928

description: mAdb experiment ID: 77928

source_name: Mouse Universal Reference Total RNA -Cy5

source_name: Unknown 4


title: High Risk-4 - mAdbID:51393

description: mAdb experiment ID: 51393

source_name: 1B-38 -High Risk 4


title: Unknown 6 - mAdbID:77929

description: mAdb experiment ID: 77929

source_name: Unknown 6


title: Low Risk-7 - mAdbID:51434

description: mAdb experiment ID: 51434

source_name: 2-125A Low Risk-7


title: SCC-3 - mAdbID:51399

description: mAdb experiment ID: 51399


title: SCC-2 - mAdbID:51400

description: mAdb experiment ID: 51400


title: Low Risk-5 - mAdbID:51436

description: mAdb experiment ID: 51436

source_name: 2-55A Low Risk-5


title: Low Risk-8 - mAdbID:51106

description: mAdb experiment ID: 51106

source_name: 2-127E Low Risk-8


title: High Risk-5 - mAdbID:51392

description: mAdb experiment ID: 51392

source_name: 1B-29B-High Risk 5


title: High Risk-7 - mAdbID:79156

description: mAdb experiment ID: 79156

source_name: 1B-39-High Risk 7


title: High Risk-8 - mAdbID:51389

description: mAdb experiment ID: 51389

source_name: 1B-22-High Risk 8


title: High Risk-6 - mAdbID:51391

description: mAdb experiment ID: 51391

source_name: 1B-50B-High Risk 6


title: Low Risk-3 - mAdbID:47785

description: mAdb experiment ID: 47785

source_name: Mouse Universal Reference Total RNA -Cy3

source_name: 2-52A Low Risk-1 rev


title: SCC-5 - mAdbID:51385

description: mAdb experiment ID: 51385


title: Normal Skin-5 - mAdbID:46053

description: mAdb experiment ID: 46053

source_name: N1 Normal Skin


title: High Risk-9 - mAdbID:51384

description: mAdb experiment ID: 51384

source_name: 1B-18-High Risk 9


title: Normal Skin-1 - mAdbID:51371

description: mAdb experiment ID: 51371

source_name: 21 Normal Skin


title: Y YOKE D059

status: Public on Jul 31 2007

city: Gainesville

first: Corinna

last: Burger

state: FL

address: 1600 SW Archer Red

institute: University of Florida

description:
Y YOKE D059
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

data_processing: Affymetrix Microarray Suite version 5.0

source_name: dentate gyrus hippocampus

label_protocol: two rounds of RNA  amplification were performed following the Affymetrix Small Sample Target Labeling version II protocol, which consists of two cycles of cDNA synthesis.  (The detailed protocol can be obtained at the Affymetrix website: http://www.affymetrix.com/index.affx).

growth_protocol: Fisher-344 male rats, 3 and 24 month old, were housed (2 per cage) in a 12:12 light-dark cycle with ad libitum access to food and water.  Behavioral testing occurred during the light phase of the cycle.

extract_protocol: Animals were sacrificed 24 hours after the last behavioral trial by decapitation, following a lethal dose of pentobarbital (100 mg/kg), and the brains were extracted from the skull and washed with ice-cold PBS.  The brains were sectioned into 1 mm slices and placed in RNAlater (Ambion).  The brain slices were stored at -20°C until ready for further dissection and RNA isolation.  The RNAlater gave the tissue a “fixed” consistency and allowed for clear visualization of the hippocampal cellular layers.  Three main anatomical areas of the hippocampus were dissected.  Using a 300 µm micro punch (Electron Microscopy Sciences), the main cell layer of the CA1 region from each animal was dissected out and placed in tubes containing 50 µl of RNAlater.  RNA was isolated using the Qiagen RNeasy protocol (Qiagen).  The tissue was homogenized in 400 µl of RLT buffer and 1% mercaptoethanol, and treated with 200 µg/ml proteinase K for 10 minutes at 55ºC.  After RNA isolation with the Qiagen RNeasy kit we assessed the quality of the RNA using an Agilent 2100 bioanalyzer using the RNA 6000 Nanochips assay kit (Agilent Technologies).  The RNA was stored at -80°C until further use.

treatment_protocol: animals were trained in the water maze. C = control rats stayed in cages, Y=swam with no platform, V= were trained with visible platform, H= animals were trained in the hidden version of the paradigm

tag: Y YOKE D059


title: Low Risk-6 - mAdbID:51292

description: mAdb experiment ID: 51292

source_name: Mouse Universal Reference Total RNA -Cy5

source_name: 2-126B Low Risk-6


title: Low Risk-10 - mAdbID:51291

description: mAdb experiment ID: 51291

source_name: 2-123B Low Risk-3


title: SCC-6 - mAdbID:51232

description: mAdb experiment ID: 51232


title: Y YOKE D058

description:
Y YOKE D058
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y YOKE D058


title: Normal Skin-6 - mAdbID:46054

description: mAdb experiment ID: 46054

source_name: 121 Normal Skin


title: Y YOKE D060

description:
Y YOKE D060
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y YOKE D060


title: Low Risk-2 - mAdbID:46619

description: mAdb experiment ID: 46619

source_name: 2-127B Low Risk-2


title: Y YOKE D024

description:
Y YOKE D024
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y YOKE D024


title: Low Risk-9 - mAdbID:46617

description: mAdb experiment ID: 46617

source_name: 2-54C Low Risk-9


title: Normal Skin-4 - mAdbID:46052

description: mAdb experiment ID: 46052

source_name: 122 Normal Skin


title: Y VIS  D066

description:
Y VIS  D066
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y VIS  D066


title: Y YOKE D023

description:
Y YOKE D023
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y YOKE D023


title: Low Risk-1 - mAdbID:46618

description: mAdb experiment ID: 46618

tag: Other

source_name: 2-52A Low Risk-1


title: Normal Skin-3 - mAdbID:46051

description: mAdb experiment ID: 46051

source_name: 71 Normal Skin


title: Y VIS  D065

description:
Y VIS  D065
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y VIS  D065


title: Y VIS  D064

description:
Y VIS  D064
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y VIS  D064


title: Y SIT D076

description:
Y SIT D076
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D076


title: Y VIS  D029

description:
Y VIS  D029
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y VIS  D029


title: Y VIS  D030

description:
Y VIS  D030
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y VIS  D030


title: Y SIT D075

description:
Y SIT D075
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D075


title: Y HID D039

description:
Y HID D039
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D039


title: Y HID D003

description:
Y HID D003
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D003


title: Y HID D002

description:
Y HID D002
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D002


title: Y SIT D073

description:
Y SIT D073
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D073


title: Y SIT D070

description:
Y SIT D070
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D070


title: Y HID D080

description:
Y HID D080
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D080


title: Y SIT D071

description:
Y SIT D071
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D071


title: Y HID D078

description:
Y HID D078
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D078


title: Y SIT D074

description:
Y SIT D074
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D074


title: Y SIT D034

description:
Y SIT D034
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y SIT D034


title: Y HID D040

description:
Y HID D040
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D040


title: Y HID D077

description:
Y HID D077
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D077


title: Y HID D037

description:
Y HID D037
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D037


title: A YOKE D095

description:
A YOKE D095
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D095


title: Y HID D038

description:
Y HID D038
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: Y HID D038


title: A YOKE D093

description:
A YOKE D093
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D093


title: A YOKE D094

description:
A YOKE D094
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D094


title: A YOKE D063

description:
A YOKE D063
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D063


title: A YOKE D027

description:
A YOKE D027
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D027


title: A YOKE D061

description:
A YOKE D061
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D061


title: A VIS  D067

description:
A VIS  D067
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A VIS  D067


title: A VIS  D033

description:
A VIS  D033
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A VIS  D033


title: A VIS  D096

description:
A VIS  D096
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A VIS  D096


title: A YOKE D025

description:
A YOKE D025
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A YOKE D025


title: A SIT D098

description:
A SIT D098
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A SIT D098


title: A HID U D054

description:
A HID U D054
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D054


title: A VIS  D031

description:
A VIS  D031
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A VIS  D031


title: A HID U D049

description:
A HID U D049
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D049


title: A HID U D042

description:
A HID U D042
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D042


title: A HID U D020

description:
A HID U D020
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D020


title: A HID U D016

description:
A HID U D016
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D016


title: A HID U D018

description:
A HID U D018
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D018


title: A HID U D007

description:
A HID U D007
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D007


title: A SIT D099

description:
A SIT D099
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A SIT D099


title: A HID U D089

description:
A HID U D089
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D089


title: A SIT D100

description:
A SIT D100
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A SIT D100


title: A HID U D045

description:
A HID U D045
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D045


title: A HID U D019

description:
A HID U D019
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D019


title: A HID B D011

description:
A HID B D011
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D011


title: A HID I D051

description:
A HID I D051
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D051


title: A HID I D050

description:
A HID I D050
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D050


title: A HID U D004

description:
A HID U D004
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D004


title: A HID U D005

description:
A HID U D005
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D005


title: A HID I D083

description:
A HID I D083
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D083


title: A HID I D055

description:
A HID I D055
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D055


title: A HID I D052

description:
A HID I D052
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D052


title: A HID I D044

description:
A HID I D044
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D044


title: A HID I D047

description:
A HID I D047
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D047


title: A HID B D092

description:
A HID B D092
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D092


title: A HID I D048

description:
A HID I D048
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D048


title: A HID B D091

description:
A HID B D091
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D091


title: A HID B D090

description:
A HID B D090
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D090


title: A HID B D086

description:
A HID B D086
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D086


title: A HID I D056

description:
A HID I D056
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D056


title: A HID U D053

description:
A HID U D053
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D053


title: A HID U D084

description:
A HID U D084
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID U D084


title: A HID I D008

description:
A HID I D008
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID I D008


title: A HID B D088

description:
A HID B D088
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D088


title: A HID B D057

description:
A HID B D057
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D057


title: A HID B D021

description:
A HID B D021
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D021


title: A HID B D082

description:
A HID B D082
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D082


title: A HID B D014

description:
A HID B D014
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D014


title: A HID B D006

description:
A HID B D006
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D006


title: Gene expression of stria vascularis of newborn rats_cultivation_hypoxia_repeat 2 inner ear

status: Public on May 31 2007

city: Berlin

first: Johann

last: Gross

address: Spandauer Damm 130

department: Otorhinolaryngology

institute: Charité

description: Total RNA from cultured stria vascularis, pool from 12 cochleas.

hyb_protocol: Commercial Affymetrix

scan_protocol: Scanning was carried out by  Agilent G2500A GeneArrayScanner (Konfocal argon laser). Software of Affymetrix MAS (MicroArraySuite).

data_processing: Normalization method, data selection procedures, transformation algorithm.

label: Commercial Affymetrix

source_name: Inner ear of newborn rats following 24 h cultivation including 5 h hypoxia

label_protocol: Commercial Affymetrix

growth_protocol: Storing of the tissue at -80 °C.

extract_protocol: RNA easy (Quiagen)

treatment_protocol:
Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. For culturing, the fragments were incubated in 4 well culture dishes (4 times 1.9 cm2, Nunc, Wiesbaden, Germany) in 500 Âµl DulbeccoÂ´s Modified Eagle Medium/F12 Nutrient (1:1) Mixtures (DMEM/F12, Gibco, Karlsruhe, Germany) medium with 10% fetal calf serum (FCS, Biochrom AG, Berlin, Germany), 10 mM hepes, 20 mM NaHCO3, 5 mM l-glutamine, 10 Âµg/ml ciprofloxacin, 25 Âµg/ml insulin, 100 Âµg/ml transferrin, 60 Âµg/ml putrescine, 0.6% glucose at 37 Â°C [Lowenheim H, Kil J, Gultig K and Zenner H P (1999) Determination of Hair Cell Degeneration and Hair Cell Death in Neomycin Treated Cultures of the Neonatal Rat Cochlea. Hear Res 128: pp 16-26]. 24 hrs after onset of cultivation, regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at -80 °C.
Hypoxia: Three hours after plating, the cultures were exposed to hypoxia in the medium for 5 h in an incubation chamber at 37°C (Billups-Rothenburg, Del Mar, CA, USA). The chamber with the plates was perfused with a calibrated gas mixture of 5% CO2, 95% N2  for 15 min. The oxygen pressure inside the culture medium was 15-20 mm Hg after 10 min exposure time and reached a steady state level of 10-20 mm Hg after 25 min up to the end of hypoxia. At the end of the hypoxia period, the cultures were kept under normoxic conditions for another 16 hours. Thus, both normoxic and hypoxic explant cultures were washed and lysed for RNA preparation 24 h after onset of cultivation. All studies were performed in accordance with the German Prevention of Cruelty to Animals Act and permission was obtained from the Berlin Senate Office for Health (T0234/00).

tag: Wistar rats, Strain Crl:WI, 3 - 5 days old, inner ear, cultivation 24 h including 5 h exposure to hypoxia, gender not analyzed


title: A HID  B D017

description:
A HID  B D017
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID  B D017


title: A HID B D010

description:
A HID B D010
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D010


title: Gene expression of stria vascularis of newborn rats_cultivation_hypoxia_repeat 1 inner ear

growth_protocol: Storing of the tissue at -80°C.


title: Gene expression of modiolus of newborn rats_cultivation_hypoxia_repeat 2 inner ear

description: Total RNA from cultured modiolus, pool from 12 cochleas.


title: Gene expression of organ of Corti of newborn rats_cultivation_hypoxia_repeat 2 inner ear

description: Total RNA from cultured organ of Corti, pool from 12 cochleas.

treatment_protocol:
Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. For culturing, the fragments were incubated in 4 well culture dishes (4 times 1.9 cm2, Nunc, Wiesbaden, Germany) in 500 µl Dulbecco´s Modified Eagle Medium/F12 Nutrient (1:1) Mixtures (DMEM/F12, Gibco, Karlsruhe, Germany) medium with 10% fetal calf serum (FCS, Biochrom AG, Berlin, Germany), 10 mM hepes, 20 mM NaHCO3, 5 mM l-glutamine, 10 µg/ml ciprofloxacin, 25 µg/ml insulin, 100 µg/ml transferrin, 60 µg/ml putrescine, 0.6% glucose at 37 °C [Lowenheim H, Kil J, Gultig K and Zenner H P (1999) Determination of Hair Cell Degeneration and Hair Cell Death in Neomycin Treated Cultures of the Neonatal Rat Cochlea. Hear Res 128: pp 16-26]. 24 hrs after onset of cultivation, regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at –80 °C.
Hypoxia: Three hours after plating, the cultures were exposed to hypoxia in the medium for 5 h in an incubation chamber at 37°C (Billups-Rothenburg, Del Mar, CA, USA). The chamber with the plates was perfused with a calibrated gas mixture of 5% CO2, 95% N2  for 15 min. The oxygen pressure inside the culture medium was 15-20 mm Hg after 10 min exposure time and reached a steady state level of 10-20 mm Hg after 25 min up to the end of hypoxia. At the end of the hypoxia period, the cultures were kept under normoxic conditions for another 16 hours. Thus, both normoxic and hypoxic explant cultures were washed and lysed for RNA preparation 24 h after onset of cultivation. All studies were performed in accordance with the German Prevention of Cruelty to Animals Act and permission was obtained from the Berlin Senate Office for Health (T0234/00).


title: Gene expression of modiolus of newborn rats_cultivation_hypoxia_repeat 1 inner ear


title: Gene expression of modiolus of newborn rats_cultivation_normoxia_repeat 1 inner ear

description: Total RNA from cultured modiolus, pool from 12 cochleas; used as control for hypoxia.

source_name: Inner ear of newborn rats following 24 h cultivation

treatment_protocol: Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. For culturing, the fragments were incubated in 4 well culture dishes (4 times 1.9 cm2, Nunc, Wiesbaden, Germany) in 500 Âµl DulbeccoÂ´s Modified Eagle Medium/F12 Nutrient (1:1) Mixtures (DMEM/F12, Gibco, Karlsruhe, Germany) medium with 10% fetal calf serum (FCS, Biochrom AG, Berlin, Germany), 10 mM hepes, 20 mM NaHCO3, 5 mM l-glutamine, 10 Âµg/ml ciprofloxacin, 25 Âµg/ml insulin, 100 Âµg/ml transferrin, 60 Âµg/ml putrescine, 0.6% glucose at 37 Â°C [Lowenheim H, Kil J, Gultig K and Zenner H P (1999) Determination of Hair Cell Degeneration and Hair Cell Death in Neomycin Treated Cultures of the Neonatal Rat Cochlea. Hear Res 128: pp 16-26]. 24 hrs after onset of cultivation, regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at -80 °C.

tag: Wistar rats, Strain Crl:WI, 3 - 5 days old, inner ear, cultivation 24 h under normoxia, gender not analyzed


title: Gene expression of modiolus of newborn rats inner ear

description: Total RNA from fresh prepared modiolus, pool from 12 cochleas (=6 animals); used as control.

source_name: Inner ear of newborn rats

treatment_protocol: Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. 24 hrs after onset of cultivation, regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at -80 °C.

tag: Wistar rats, Strain Crl:WI, 3 - 5 days old, inner ear, gender not analyzed


title: Gene expression of stria vascularis of newborn rats_cultivation_normoxia_repeat 1 inner ear

description: Total RNA from cultured stria vascularis, pool from 12 cochleas; used as control for hypoxia.

data_processing: Normalization method, data selection procedures, transformation algorithm


title: Gene expression of stria vascularis of newborn rats_cultivation_normoxia_repeat 2 inner ear


title: A HID B D012

description:
A HID B D012
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

tag: A HID B D012


title: Gene expression of stria vascularis of newborn rats inner ear

description: Total RNA from fresh prepared stria vascularis, pool from 12 cochleas (=6 animals); used as control


title: Gene expression of modiolus of newborn rats_cultivation_normoxia_repeat 2 inner ear


title: Gene expression of organ of Corti of newborn rats_repeat 2 inner ear

description: Total RNA from fresh prepared organ of Corti, pool from 12 cochleas (=6 animals); used as control

hyb_protocol: commercial Affymetrix

label: commercial Affymetrix

label_protocol: commercial Affymetrix

growth_protocol: Storing of the tissue at -80°C

treatment_protocol: Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. Regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at -80 °C.


title: Gene expression of organ of Corti of newborn rats_repeat 1 inner ear

description: Total RNA from fresh prepared OC, pool from 12 cochleas (=6 animals); used as control.

growth_protocol: Storing of the tissue at -80 °C

tag: Wistar rats, Strain Crl:WI,  3 - 5 days old, inner ear, gender not analyzed


title: Sh-Mt-Gi vs Mt-shoot, rep6

status: Public on Mar 08 2007

city: Ithaca

first: Maria

middle: J.

last: Harrison

state: NY

address: Tower Road, Cornell Campus

institute: Boyce Thompson Institute for Plant Research

description: Gene expression data of Sh-Mt-Gi vs Mt shoot samples

data_processing: Normalization and analysis of microarray data were performed using Genespring software (version 6.2, Silicon Genetics, CA, USA). For each experiment, data from six slides were imported into Genespring software and values for all spots on the arrays were normalized with per spot and per chip intensity dependent (Lowess) normalization, using 20% of the data to calculate the Lowess fit at each point.

organism: Medicago truncatula

source_name: Sh-Mt-Gi, Cy3

tag: Shoot tissues from Glomus intraradices inoculated Medicago truncatula plants

source_name: Mt-shoot, Cy5

tag: Shoot tissues from Glomus intraradices mock-inoculated Medicago truncatula plants


title: Sh-Mt-Gi vs Mt-shoot, rep3

data_processing: Normalization and analysis of microarray data were performed using Genespring? software (version 6.2, Silicon Genetics, CA, USA). For each experiment, data from six slides were imported into Genespring? software and values for all spots on the arrays were normalized with per spot and per chip intensity dependent (Lowess) normalization, using 20% of the data to calculate the Lowess fit at each point.

source_name: Mt-shoot, Cy3

source_name: Sh-Mt-Gi, Cy5


title: Mt-Gigi vs Mt-root, rep6

description: Gene expression data of Mt/Gigi vs Mt root samples

organism:
Medicago truncatula
Gigaspora gigantea

source_name: Mt/Gigi-root, Cy3

tag: Gigaspora gigantea inoculated Medicago root tissues

source_name: Mt-root, Cy5

tag: Gigaspora gigantea mock-inoculated M. truncatula root tissues


title: Mt-Gigi vs Mt-root, rep5


title: Mt-Gigi vs Mt-root, rep2

source_name: Mt-root, Cy3

source_name: Mt/Gigi-root, Cy5


title: A VIS  D032

description:
A VIS  D032
The first letter of the title refers to the age of the animal:
3 months (Y)
24 months (A)
The second word in the title refers to the treatment:
hidden platform (HID)
visible platform (VIS)
yoke control, no platform (YOKE)
cage control (SIT)
The next letter, if present, corresponds to:
learning unimpaired (U)
learning impaired (I)
learning intermediate (B)

source_name: dentate gyrus hippocampus

tag: A VIS  D032


title: Mt-Gi vs Mt-root, rep4

description: Gene expression data of Mt/Gi vs Mt root samples

tag: G. intraradices mock-inoculated M. truncatula root tissues

organism:
Medicago truncatula
Rhizophagus intraradices

source_name: Mt/Gi-root, Cy5

tag: G. intraradices inoculated M. truncatula root tissues


title: Mt-Gi vs Mt-root, rep3

source_name: Mt/Gi-root, Cy3


title: Gene expression of organ of Corti of newborn rats_cultivation_normoxia_repeat 2 inner ear

description: Total RNA from cultured organ of Corti, pool from 12 cochleas; used as control for hypoxia.

growth_protocol: Storing of the tissue at -80 C

treatment_protocol: Newborn rats were decapitated and the organ of Corti, modiolus and stria vascularis were prepared according to the protocol of Sobkovic [Sobkowicz HM, Loftus J M and Slapnick S M (1993) Tissue Culture of the Organ of Corti. Acta Otolaryngol Suppl Stockh 502: pp 3-36]. Preparation was carried out in buffered saline glucose solution on cooling boxes using a stereomicroscop. For culturing, the fragments were incubated in 4 well culture dishes (4 times 1.9 cm2, Nunc, Wiesbaden, Germany) in 500 ?l Dulbecco?s Modified Eagle Medium/F12 Nutrient (1:1) Mixtures (DMEM/F12, Gibco, Karlsruhe, Germany) medium with 10% fetal calf serum (FCS, Biochrom AG, Berlin, Germany), 10 mM hepes, 20 mM NaHCO3, 5 mM l-glutamine, 10 ?g/ml ciprofloxacin, 25 ?g/ml insulin, 100 ?g/ml transferrin, 60 ?g/ml putrescine, 0.6% glucose at 37 ?C [Lowenheim H, Kil J, Gultig K and Zenner H P (1999) Determination of Hair Cell Degeneration and Hair Cell Death in Neomycin Treated Cultures of the Neonatal Rat Cochlea. Hear Res 128: pp 16-26]. 24 hrs after onset of cultivation, regions of 3 cochleae were collected in a tube and stored in lysis buffer (Quiagen) at -80 C.


title: Gene expression of organ of Corti of newborn rats_cultivation_hypoxia_repeat 1 inner ear


title: Gene expression of organ of Corti of newborn rats_cultivation_normoxia_repeat 1 inner ear


title: Donor 2 GSE

status: Public on Feb 17 2007

city: LONDON

first: Roger

last: Corder

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary, University of London

description: cultured cell experiment

data_processing: normalized with affymetrix software

source_name: GSE treated endothelial cells

tag: cultured cells


title: Donor 2 CRE

description: cultured cell experiment

source_name: cranberry extract treated endothelial cells


title: Donor 1 RWE

description: cultured cell experiment

source_name: RWE treated cultured endothelial cells


title: Donor 3 control

description: cultured cell experiment

source_name: control endothelial cell


title: Donor 1 CRE

description: cultured cell experiment

source_name: CRE treated cultured endothelial cells

tag: cell culture experiment


title: Sh-Mt-Gi vs Mt-shoot, rep4


title: Sh-Mt-Gi vs Mt-shoot, rep5


title: Sh-Mt-Gi vs Mt-shoot, rep2

hyb_protocol: Equivalent quantity of Cy3 labeled cDNA and Cy5 labeled cDNA probes were combined and evaporated to dryness in a speedvac at darkness. The combined dried cDNA targets were then suspended in 58 μl of hybridization solution containing 46 μl of 1.25x formamide based HybIt2? hybridization solution (Telechem international, USA: catalog no. HHS2), 1 μl Poly (dA) (Invitrogen: catalog no. POLYA.GF) and 11 μl of H2O. The re-suspended cDNA probes were then incubated at 95?C for 5min and applied to a pre-warmed (50?C) slide, and covered with a clean glass LifterSlip (Erie Scientific company, USA: catalog no. 22X50I-2-4711). The slides were then sealed in Corning hybridization chambers (Corning Inc., USA: catalog no. 2551) and maintained at 43?C H2O bath with gentle shaking at 40 rpm for 16-20 hrs in the dark.

scan_protocol: Slides were scanned using a two-channel confocal microarray scanner (ScanArray5000, GSI Lumonics, MA, USA) and the associated ScanArray software (version3.1, Packard BioChip Technologies, MA, USA).

label_protocol: 25ug total RNA was used to generate fluorescently labeled cDNA probes using SuperScriptTM Indirect cDNA Labeling System (Invitrogen: catalog no. L1014-02).

growth_protocol: Medicago truncatula cv Jemalong, line A17 plants were grown in growth rooms under a 16-h-light (25 ?C ) / 8-h-dark (22 ?C ) regime.

extract_protocol: Total RNA was isolated with Trizol Reagent? (Invitrogen) with an extra phenol-chloroform purification step, treated with RNase-free DNase (Promega) at 37?C for 20 minutes, and then purified using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer?s instructions.

treatment_protocol: 2-week old M. truncatula seedlings were transplanted to 11-cm pot containing sterile Turface (eight plants per pot) and were mock-inoculated with the final distilled-water wash from the spore purification procedure. The plants were fertilized with half-strength Hoagland?s solution containing 0.02mM KH2PO4 twice weekly and harvested at 30 days post inoculation (dpi).

treatment_protocol: 2-week old M. truncatula seedlings were transplanted to 11-cm pot containing sterile Turface (eight plants per pot) and about 8,000 G. intraradices spores were evenly inoculated onto the root of the seedlings. The plants were fertilized with half-strength Hoagland?s solution containing 0.02mM KH2PO4 twice weekly and harvested at 30 days post inoculation (dpi).


title: Donor-1 control

description: cultured cell experiment

source_name: enothelial cells

tag: cultured cell


title: Mt-Gigi vs Mt-root, rep4


title: Mt-Gi vs Mt-root, rep6


title: Mt-Gigi vs Mt-root, rep3


title: Donor 3 RWE

description: cultured cell experiment

source_name: RWE treated endothelial cell


title: Mt-Gi vs Mt-root, rep5

source_name: Mt/Gi root, Cy5


title: Conjunctiva Sample 2

status: Public on Feb 10 2007

city: New York

first: Jose

middle: Mario

last: Wolosin

address: 1 Gustave L. Levy Place

department: Ophthalmology

institute: Mount Sinai School of Medicine

description: Standard Affymetrix protocols performed

hyb_protocol: Hybridization cocktail made according to Affymetrix protocols. Heated to 99C and then heat block for 5 mins at 45oC. Incubate probe array with 1X hybridization buffer (MES, 1M [Na], 20mM EDTA, 0.01% Tween) for 10 mins 45oC. Hybridize for 16 h 45oC using final volume of 200ul. For washing use GeneChip Fluidics Station 450 using fluidics protocol EukGE-WS2v4. Hybridized microarrays were stained with a strepavidin-phycoerythrin (SAPE) reagent.

scan_protocol: Hybridized microarrays were stained with a strepavidin-phycoerythrin (SAPE) reagent and fluorescence images were captured using an Agilent G2500A laser scanner.

data_processing: Microarray Analysis Suite, version 5.0 (MAS 5.0; Affymetrix)

label: Biotin-labled cRNA

source_name: Fresh Human Conjunctiva

label_protocol: Biotin labeled cRNA using the ENZO RNA transcript labeling Kit 9 (BioArray High Yeald Labeling Kit, P/N 900182). IVT cRNA cleanup and quantitation, cRNA fragmentation, control targets performed according to Affymetrix protocols. Synthesis of cDNA using T7-(dT)24 Primer (Genset Corp) and Superscript Choice System (Gibco BRL Life technologies).

growth_protocol: N/A Fresh tissue

extract_protocol: Epithelial sheets were manually transferred from the Dispase solution directly into lysis buffer, total RNA was isolated using the RNeasy minikit (Qiagen Inc., Valencia, CA) and was further purified using RNeasy (Qiagen) spin columns. RNA was suspended in RNase-Free water at a concentration of 1.5 ug/ul

treatment_protocol: None. Fresh tissue from donor, post mortem

tag: This sample comprises of RNA isolated from human conjunctivae pooled from a mixed population of (age, sex and cause of death identified). Only Tissue was send to us by the National Disease Resource Center (NDRI).


title: Cornea Sample 1

description: Standard Affymetrix protocols performed

source_name: Fresh human cornea

tag: This sample comprises of RNA isolated from human cornea pooled from a mixed population of (age, sex and cause of death identified). Tissue was send to us by the National Disease Resource Center (NDRI); http://www.ndriresource.org/


title: Brn3a Heterozygote DRG e13.5 430A v2.0 replicate

status: Public on Jan 28 2007

city: La Jolla

first: Eric

last: Turner

state: CA

address: 9500 Gilman Dr., BSB 2077

department: Psychiatry

institute: University of California San Diego

description: Approximately 10 pairs of the most anterior dorsal root ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until sufficient tissue was harvested to be pooled by genotype. Ganglia from 5 embryos were pooled for a single analysis and RNA extracted using the RNeasy system (Qiagen).

data_processing: Gene Chip Operating Software

label: Affymetrix

source_name: e13.5 Dorsal Root Ganglia

tag: Brn3a heterozygote dorsal root ganglia pooled from e13.5 mouse embryos.


title: Donor 3 GSE

description: cultured cell experiment


title: Donor 3 CRE

description: cultured cell experiment

source_name: CRE treated endothelial cells


title: Donor 2 RWE

description: cultured cell experiment

source_name: RWE treated endothelial cells


title: Mt-Gi vs Mt-root, rep2

data_processing: Normalization and analysis of microarray data were performed using Genespring® software (version 6.2, Silicon Genetics, CA, USA). For each experiment, data from six slides were imported into Genespring® software and values for all spots on the arrays were normalized with per spot and per chip intensity dependent (Lowess) normalization, using 20% of the data to calculate the Lowess fit at each point.

source_name: Mt-root, Cy5

tag: G. intraradices inoculated root tissues


title: Brn3a Knockout DRG e13.5 430A v2.0

tag: Brn3a mutant dorsal root ganglia pooled from e13.5 mouse embryos.


title: Donor 1 GSE

description: cultured cell experiment

source_name: GSE treated cultured endothelial cells


title: Donor 2 control

description: cultured cell experiment

source_name: control endothelial cells