title: F344 Sample Pool

description:
Normal mammary gland
Sample_characteristics: F344 Normal mammary gland pool
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: F344 Sample2

status: Public on Dec 30 2005

type: RNA

city: Seattle

first: Xuefeng

last: Ren

state: WA

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Normal mammary gland
Sample_characteristics: F344 Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures

molecule: total RNA

organism: Rattus norvegicus

source_name: Mammary gland


title: ACI Sample2

description:
Normal mammary gland
Sample_characteristics: ACI Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: F344 Sample3


title: F344 Sample4


title: Cop Sample2

description:
Normal mammary gland
Sample_characteristics: Cop Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: Cop Sample3


title: Neural tube, control, GD9:12, C215584

city: Houston

first: Bogdan

last: Wlodarczyk

state: TX

address: 2121 W Holcombe Blv.

department: CEGM

institute: IBT

description: The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of arsenic on embryonic development in mice during the critical phase of neural closure.  In other words, the comparison groups were the arsenic treated vs. the water injected Folbp2 nullizygous embryos, with measurements taken over time

hyb_protocol: Hybridization, coupling of Alexa Fluor 647-streptavidin (Molecular Probes), and subsequent washes were performed according to manufacturer’s protocol (Amersham Biosciences).

scan_protocol: Slides were scanned using an Agilent Microarray Scanner according to manufacturer's protocol (http://www1.amershambiosciences.com/aptrix/upp01077.nsf/Content/literature_intro).Data from image were extraxted using CodeLink Expression Analysis v.4.0 software.

data_processing: Intensities for each individual gene were determined by the median intensity of all pixels within the spot’s region. Subtraction of the median local background (computed from the subset of remaining pixels of the bounding box) yielded net intensities representing relative gene expression levels.  In order to compensate for negative (unreal) intensities, a FLOOR function with a value of 1 (range is 0-65535) was applied. For equidistant scaling, all values were logged with a base of 2 and the data was normalized using a global scaling method derived from single-channel normalization schemes used by Affymetrix analysis software.

label: Alexa Fluor 647-streptavidin

organism: Mus musculus

source_name: Anterior neural tube dissected GD9:12

label_protocol: Coupling of biotin labeled hybridized probe to dye labeled-streptavidin was performed in a 1:500 dilution of Alexa Fluor 647-streptavidin acording to the manufacturer's protocol (Molecular Probes). Excess dye was removed by washing 4 times for 5 minutes each with TNT buffer at room temperature.

extract_protocol: Total RNA was extracted with the aid of PicoPure RNA isolation kit, Arcturus.Since the limited quantities of total RNA extracted from each anterior part of the embryo neural tube did not enable us to use standard procedures for probe labeling, we utilized aRNA amplification methodologies as previously described by Eberwine (Eberwine et al. 1992) with several modifications. Briefly, total RNA was extracted (PicoPure RNA isolation kit, Arcturus). To the RNA, concentrated to a final volume of 10uL in a Speedvac (ThermoSavant), 200ng of T7 RNA polymerase primer was added and the sample was denatured at 70C and allowed to anneal slowly at 42C. First and second strand cDNA synthesis was performed using 100 units of Superscript-II (Invitrogen) and DNA Pol I (Invitrogen). The DNA was isolated by a standard PCR purification kit (Qiagen) and concentrated using a Speedvac (ThermoSavant). The cDNA was then suspended in 8uL of RNAse-free water. The aRNA amplification synthesis was performed using Megascript (Ambion) at 42C overnight in the presence of biotin-UTP. The aRNA was extracted using RNeasy kit (Qiagen) and the volume reduced to 10L using a Speedvac.

treatment_protocol:
Control sample,
Dam injected ip with water for injection (10uL/1g body weight) on GD7:12 and 8:12

tag: Folr2-/- KO,

tag: Embryo GD9:12,

tag: Anterior part of neural tube


title: Neural tube, treated, GD9:12, T215588

treatment_protocol:
Treated sample,
Dam injected ip with water solution of sodium arsenate (9.6mg of As/kg body weight) on GD7:12 and 8:12.


title: Neural tube, treated, GD9:12, T215585


title: F1(CopXF344)Hybrid Sample5

description:
Normal mammary gland
Sample_characteristics: F1(Cop X F344)Hybrid Normal mammary gland
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: Cop Sample5


title: Neural tube, treated, GD9:12, T215587


title: F1(CopXF344)Hybrid Sample2


title: Neural tube, treated, GD9:12, T215586


title: F1(CopXF344)Hybrid Sample1


title: Neural tube, control, GD9:12, C215583


title: ACI Sample3


title: Neural tube, treated, GD9:00, T215581

source_name: Anterior neural tube dissected GD9:00

tag: Embryo GD9:00,


title: Neural tube, treated, GD8:15, T216804

source_name: Anterior neural tube dissected GD8:15

tag: Embryo GD8:15,


title: Neural tube, treated, GD8:15, T216811


title: Neural tube, control, GD9:12, C214260


title: Neural tube, treated, GD8:15, T216803


title: Neural tube, control, GD9:00, C215570


title: Neural tube, control, GD8:15, C215582


title: Neural tube, control, GD9:00, C215578


title: Neural tube, treated, GD9:00, T215580


title: Neural tube, control, GD9:00, C215577


title: Neural tube, treated, GD9:00, T215571


title: Neural tube, treated, GD8:15, T216802


title: Neural tube, control, GD8:15, C211680


title: Neural tube, control, GD8:15, C216799

treatment_protocol:
Control sample,
Dam injected ip with water for injection (10uL/g body weight) on GD7:12 and 8:12.

tag: anterior part of neural tube


title: Neural tube, control, GD9:00, C215579


title: Neural tube, control, GD8:15, C216801


title: Human Hair Follicle Upper-Bulge#4

status: Public on Dec 06 2005

city: Bethesda

first: Jonathan

last: Vogel

state: MD

address: Bldg. 10 / Room 12N260

department: Dermatology

institute: National Cancer Institute; NIH

description: Affymetrix protocol

label: Biotin

organism: Homo sapiens

source_name: Human Scalp

label_protocol: T7-primer based two round linear RNA amplification protocol: "Genechip Eukaryotic Small Sample Target Labeling Assay Version II" (equivalent to the GeneChip Two-Cycle cDNA Synthesis kit, Affymetrix)

extract_protocol:
Picopure RNA isolation kit (Arcturas) and DNAse digestion (Qiagen)

Quality assessed by Agilent 2100 bioanalyzer and a RNA 6000 Pico LabChip kit (Agilent)

tag: Transverse frozen sections of human scalp were made.  After precisely defining the different anatomical locations of individual hair follicles, laser capture microdissection was used to isolate the desired hair follicle cells.


title: Human Hair Follicle Bulge#5

description: Affymetrix protocol


title: Human Hair Follicle Upper-Bulge#5

description: Affymetrix protocol


title: Human Hair Follicle Inner-Bulge#4

description: Affymetrix protocol


title: Human Hair Follicle Suprabulbar#5

description: Affymetrix protocol


title: Human Hair Follicle Suprabulbar#4

status: Public on Dec 08 2005

description: Affymetrix protocol


title: Human Hair Follicle Bulge#3

description: Affymetrix protocol

extract_protocol:
Picopure RNA isolation kit (Arcturas) and DNAse digestion (Qiagen)
Quality assessed by Agilent 2100 bioanalyzer and a RNA 6000 Pico LabChip kit (Agilent)


title: Human Hair Follicle Bulge#2

description: Affymetrix protocol


title: Human Hair Follicle Bulge#4

description: Affymetrix protocol


title: Human Hair Follicle Inner-Bulge#5

description: Affymetrix protocol


title: Human Hair Follicle Sub-bulge#4

description: Affymetrix protocol


title: Human Hair Follicle Sub-bulge#5

description: Affymetrix protocol


title: Human Hair Follicle Sub-bulge#3

description: Affymetrix protocol


title: Human Hair Follicle Sub-bulge#2

description: Affymetrix protocol


title: Cop Sample Pool

description:
Normal mammary gland
Sample_characteristics: Cop Normal mammary gland pool
Sample_data_processing: Affymetrix Microarray Suite version 5.0
Sample_extract_protocol: The normal mammary gland tissue was disrupted with mortar and pestle in liquid nitrogen, followed by extraction of RNA using Qiagen RNAEasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA was further purified by precipitation with 4M LiCl overnight at -20, and then stored in RNase-free water at -80. The integrity of RNA was determined using an RNA 6000 Nano Assay on an Agilent Bioanalyzer 2100(Agilent, Palo Alto, CA). Only RNA with an A260/280 ratio between 1.8-2.1 and minimal or no apparent degradation was chosen for expression profiling experiments.
Sample_hyb_protocol: standard Affymetrix procedures
Sample_label: biotin
Sample_label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures


title: ILS/ISS_cerebellum_naive_470

status: Public on Dec 02 2005

city: Aurora

first: Erik

middle: James

last: MacLaren

state: CO

address: Mail Stop 8303, P.O. Box 6511

department: Pharmacology

institute: University of Colorado at Denver and Health Sciences Center

description: Baseline comparison of global gene expression in ILS and ISS cerebellum to find differences in the naive state.

hyb_protocol: After adding 10 µg of mouse COT-1 DNA (Gibco), 8 µg polyA RNA (Amersham Biosciences), 4 µg yeast tRNA (Sigma-Aldrich, St. Louis, MO), 3.1 µL 20 X SSC, and 0.5 µL 10% SDS, the probe mixture was hybridized to the arrays at 42ºC for 16 hours.

scan_protocol: The microarrays were washed using dilute SSC solution to remove debris and hybridization buffer, and then scanned with a GenePix4000A scanner (Axon Instruments, Union City, CA).

data_processing: The Cy-3 and Cy-5 fluorescence was measured for each cDNA element and any probes with a fluorescence level below background or smaller than 60% of the original spotting area was flagged as “absent” while the rest were noted as “present.

source_name: cerebella of 5 ILS mice

label_protocol: Equal amounts of total RNA from five individual mice of the same strain were pooled together and then directly labeled in a one-step reverse transcription reaction.  Twenty µg of total RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and either Cyanine 3- or Cyanine 5-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes.  The reactions were heated to 65ºC for 5 minutes (min) and then SuperScript II RNase H- Reverse Transcriptase (Gibco) was added and the mix was incubated at 42ºC for 90 min.  Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH.  The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

extract_protocol: RNeasy Midi Kit (Qiagen) was used to extract total RNA according to the manufacturer's protocol.

treatment_protocol: Mice were delivered to University of Colorado Health Sciences Center and allowed to acclimate for 14 days before sacrifice. No treatments were performed and food and water was provided ad libitum.

tag: Strain

value: Inbred Long Sleep

tag: Gender

value: Male

tag: Tissue

value: Cerebellum

tag: Condition

value: Naive

source_name: cerebella of 5 ISS mice

value: Inbred Short Sleep


title: PCP low replicate 2

status: Public on Dec 31 2005

city: Okazaki

first: Hajime

last: Watanabe

state: Aichi

address: 5-1, Higashiyama

department: Center for Integrative Bioscience

country: Japan

institute: National Institutes of Natural Sciences

description: Wild type neonate (<24h)

scan_protocol: standard GenePix procedures

data_processing: GeneSpring version7.2

organism: Daphnia magna

source_name: Daphnia magna neonate

label_protocol: Approximately 0.5ug of total RNA was processed to produce cRNA targets.

extract_protocol: Approximately 10 neonates were lysed in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

treatment_protocol: Exposed to 75 ug/l of pentachlorophenol for 24 h.

tag: Wild type, female, neonate, whole body


title: ILS/ISS_cerebellum_naive_479


title: Human Hair Follicle Bulge#1

description: per Affymetrix protocol

data_processing: MAS v5

label: biotin

source_name: Human scalp


title: Cerebellum_naive_ISS55_A

description: Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Short Sleep mouse

hyb_protocol: Hybridization is performed by incubating 200 ?L of the sample to the Affymetrix GeneChip® arrays (Affymetrix Inc., Santa Clara, California, USA).  Hybridization occurs at 45 °C for 16 hours using a GeneChip® Hybridization Oven 640 (Affymetrix). After hybridization, the hybridization solutions are removed and the arrays are washed and stained with Streptavidin-phycoerythrin using a GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays are read at a resolution of 2.5 to 3 microns using the GeneChip Scanner 3000 (Affymetrix).

data_processing: MAS5, scaled to 500

label_protocol: Total RNA (10 µg) is converted to double-stranded cDNA (ds-cDNA) by using the Superscript Choice System (Life Technologies Inc., Gaithersburg, MD, USA). An oligo-dT primer containing a T7 RNA polymerase promoter (Proligo Primers & Probes, Boulder, Colorado, USA) is utilized.  The ds-cDNA is purified and recovered by using GeneChip sample cleanup module (Affymetrix).In vitro transcription is performed to generate biotin-labeled cRNA.  In vitro transcription is performed using a RNA Transcript Labeling Kit (Enzo, Farmingdale, New York, USA) and ds-cDNA template is transcribed in the presence of a mixture of biotin-labeled ribonucleotides.  Biotin-labeled cRNA is purified using GeneChip sample cleanup module (Affymetrix) or an RNeasy affinity column (Qiagen).  To ensure optimal hybridization to the oligonucleotide array, the cRNA is fragmented.  Fragmentation is performed such that the cRNA fragments are between 50-200 bases in length by incubating the cRNA at 94 °C for 35 min in a fragmentation buffer.  The sample is then added to a hybridization solution containing 100 mM MES, 1 M Na+, and 20 mM EDTA in the presence of 0.01% Tween 20.  The final concentration of the fragmented cRNA is 0.05 µg/µL.

extract_protocol: Qiagen RNeasy Total RNA Isolation Kit

treatment_protocol: Food and water ad libitum for 14 days after transfer from IBG to UCHSC.

tag: Alcohol Exposure


title: Human Hair Follicle Sub-Bulge#1

description: Affymetrix protocol


title: ILS/ISS_cerebellum_naive_436


title: Cerebellum_naive_ISS56_A


title: ILS/ISS_cerebellum_naive_474


title: Cerebellum_naive_ILS48

description: Assay of baseline expression in the cerebellum of an alcohol-naive Inbred Long Sleep mouse


title: Cerebellum_naive_ILS51


title: ILS/ISS_cerebellum_naive_437


title: ILS/ISS_cerebellum_naive_459


title: F1(CopXF344)Hybrid Sample4


title: Cerebellum_naive_ILS51_B


title: Hs 683 glioma cell lines 48hrs-2 time point

status: Public on Dec 01 2005

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description: Total RNA was isolated from candoxin-treated (n = 3 flasks for each replicate)Hs 683 glioma cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA). Replicate-2

source_name: Human Brain (Hs 683) glioma cell lines treated with 300nM of candoxin and incubated for 48 hrs


title: Hs 683 glioma cell lines 12hrs-1 time point

description: Total RNA was isolated from candoxin-treated (n = 3 flasks for each replicate)Hs 683 glioma cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA). Replicate-1

source_name: Human Brain (Hs 683) glioma cell lines treated with 300nM of candoxin and incubated for 12 hrs


title: Hs 683 Control-1

description: Total RNA was isolated from untreated control (n = 3 flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA).Replicate-1

source_name: Human Brain (Hs 683) glioma cell lines


title: Hs 683 glioma cell lines 48hrs-1 time point


title: Cerebellum_naive_ILS48_B


title: Hs 683 glioma cell lines 24hrs time point

description: Total RNA was isolated from candoxin-treated (n = 3 flasks for each replicate)Hs 683 glioma cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA). Replicate-3

source_name: Human Brain (Hs 683) glioma cell lines treated with 300nM of candoxin and incubated for 24 hrs


title: Hs 683 Control-3

description: Total RNA was isolated from untreated control (n = 3 flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA).Replicate-3


title: ISS/ILS_cerebellum_naive_417

source_name: cerebellum from 5 ISS mice

source_name: cerebellum from 5 ILS mice


title: ISS/ILS_cerebellum_naive_416

data_processing: The Cy-3 and Cy-5 fluorescence was measured for each cDNA element and any probes with a fluorescence level below background or smaller than 60% of the original spotting area was flagged as “absent” while the rest were noted as “present."  Values below 0.01 were set to 0.01.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. The data in the VALUE column is expressed as the natural log of the ch1/ch2 ratios.

tag: Strains


title: ISS/ILS_cerebellum_naive_435


title: Hs 683 glioma cell lines 12hrs time point


title: Cerebellum_naive_ISS55_B


title: Hs 683 glioma cell lines 48hrs-3 time point


title: Cerebellum_naive_ISS56_B


title: Hs 683 Control-2

description: Total RNA was isolated from untreated control (n = 3flasks) cells using RNeasy® mini kit. The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA).Replicate-2


title: LJMJDW22

city: Nashville

first: James

middle: Daryl

last: West

state: TN

address: 23rd Ave at Pierce

department: Biochemistry

institute: Vanderbilt University

description: 5 µM HNE--24h--Replicate #3

source_name: RKO human colorectal carcinoma cells


title: LJMJDW23

description: 20 µM HNE--24h--Replicate #3


title: LJMJDW19

description: 20 µM HNE--6h--Replicate #3


title: LJMJDW18

description: 5 µM HNE--6h--Replicate #3


title: LJMJDW16

description: 60 µM HNE--24h--Replicate #2


title: LJMJDW24

description: 60 µM HNE--24h--Replicate #3


title: LJMJDW14

description: 5 µM HNE--24h--Replicate #2


title: LJMJDW15

description: 20 µM HNE--24h--Replicate #2


title: 2002-08-08_Slide1_rep3

city: Fort Collins

first: Kathleen

last: Yeater

address: 2150 Centre Avenue

institute: USDA-ARS

description:
plant material grown in Metromix-200 growing media in a growth chamber (25C), material collected from top 2.5 cm of tissue on each plant,
plant material immediately placed in cryovials, frozen in liquid N, and stored at -80C until RNA extraction
day of plant material collection corresponds to differing growth rates, such that all plants used in this study were of the same growth

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were combined, and suspended in 45 µl of hybridization buffer (10X SSC and 0.2% SDS) and applied to microarray slides

scan_protocol: Fluorescent array images were collected for both Cy5 and Cy3 channels with a GenePix 4000B fluorescent scanner, image intensity data was extracted with Genepix Pro 3.0

data_processing:
MA-plots were used to assess for appropriate normalization method
Background subtracted fluorescence intensities transformed to log2 scale were used for statistical analyses
Global normalization model and gene models performed using the Mixed Procedure of SAS

organism: Vicia villosa

source_name: common hairy vetch (Vicia villosa)

label_protocol: cDNA indirectly coupled with Cy5 monoreactive fluor in 0.05 M sodium bicarbonate, pH 9.0. Labelled cDNA was purified with a QIAquick PCR purification kit and quantified.

extract_protocol: Total RNA extracted with Trizol, cleaned with RNeasy (Qiagen)

tag: collected 28 dap

organism: Vicia pannonica

source_name: Vicia pannonica PI 515988

tag: collected 42 dap


title: LJMJDW12

description: 60 µM HNE--6h--Replicate #2


title: 2002-08-08_Slide1_rep2


title: 2002-08-08_Slide2_rep1

label_protocol: cDNA indirectly coupled with Cy3 monoreactive fluor in 0.05 M sodium bicarbonate, pH 9.0. Labelled cDNA was purified with a QIAquick PCR purification kit and quantified.


title: 2002-08-08_Slide1_rep1


title: 2002-07-18_Slide2_rep3

organism: Glycine max

source_name: soybean cultivar Burlison

tag: collected 14 dap


title: 2002-07-18_Slide2_rep2


title: 2002-07-11_Slide1_rep3


title: 2002-07-11_Slide1_rep2


title: LJMJDW10

description: 5 µM HNE--6h--Replicate #2


title: 2002-07-18_Slide1_rep2


title: 2002-07-18_Slide1_rep3


title: 2002-07-18_Slide2_rep1


title: 2002-07-18_Slide1_rep1


title: LJMJDW11

description: 20 µM HNE--6h--Replicate #2


title: 2002-07-11_Slide2_rep3


title: 2002-07-11_Slide2_rep2


title: 2002-07-11_Slide2_rep1

description:
plant material grown in Metromix-200 growing media in a growth chamber (25C), material collected from top 2.5 cm of tissue on each plant, "
plant material immediately placed in cryovials, frozen in liquid N, and stored at -80C until RNA extraction"
day of plant material collection corresponds to differing growth rates, such that all plants used in this study were of the same growth"

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were combined, and suspended in 45 µl of hybridization buffer (10X SSC and 0.2% SDS) and applied to microarray slides"

scan_protocol: Fluorescent array images were collected for both Cy5 and Cy3 channels with a GenePix 4000B fluorescent scanner, image intensity data was extracted with Genepix Pro 3.0"

label_protocol: cDNA indirectly coupled with Cy5 monoreactive fluor in 0.05 M sodium bicarbonate, pH 9.0. Labelled cDNA was purified with a QIAquick PCR purification kit and quantified."

extract_protocol: Total RNA extracted with Trizol, cleaned with RNeasy (Qiagen)"


title: LJMJDW7

description: 20 µM HNE--24 h--Replicate #1


title: LJMJDW3

description: 20 µM HNE--6h--Replicate #1


title: LJMJDW20

description: 60 µM HNE--6h--Replicate #3


title: 2002-07-11_Slide1_rep1


title: LJMJDW6

description: 5 µM HNE--24 h--Replicate #1


title: LJMJDW8

description: 60 µM HNE--24 h--Replicate #1


title: LJMJDW4

description: 60 µM HNE--6h--Replicate 1


title: LJMJDW2

description: 5 µM HNE--6h--Replicate #1


title: 2002-10-11_Slide2_rep3

source_name: Vicia pannonica PI 170008


title: 2002-10-09_Slide2_rep3


title: 2002-10-11_Slide1_rep2


title: 2002-10-11_Slide2_rep2


title: 2002-10-11_Slide2_rep1


title: 2002-10-09_Slide2_rep1


title: 2002-10-11_Slide1_rep3


title: 2002-08-08_Slide2_rep3


title: 2002-10-09_Slide1_rep3


title: 2002-10-02_Slide2_rep2


title: 2002-10-11_Slide1_rep1


title: 2002-08-08_Slide2_rep2


title: 2002-10-09_Slide1_rep2


title: 2002-10-02_Slide2_rep3


title: 2002-10-09_Slide2_rep2


title: 2002-08-16_Slide1_rep1


title: 2002-08-16_Slide2_rep2


title: 2002-08-16_Slide2_rep1


title: 2002-08-16_Slide1_rep2


title: 2002-10-02_Slide1_rep3


title: 2002-10-02_Slide2_rep1


title: 2002-10-09_Slide1_rep1


title: 2002-10-02_Slide1_rep1


title: 2002-10-02_Slide1_rep2


title: 2002-08-16_Slide2_rep3


title: Catfish_spleen_LPS injection, 24h sampling post-injection_replicate2

city: Stoneville

first: Geoffrey

middle: C.

last: Waldbieser

state: MS

address: 141 Experiment Station Road

department: Agricultural Research Service

institute: U.S. Dept of Agriculture

description: USDA103 strain catfish spleen

hyb_protocol: Microarrays were pre-hybridized with 1X MES hybridization buffer (100mM MES, 1.0M Na+, 20mM EDTA, 0.01% Tween20) plus 40 µg of herring sperm DNA and 200 µg of acetylated BSA at 45°C for 15 min, followed by hybridization in the same buffer with 10µg of denatured and fragmented cRNA per microarray at 45°C for 16 – 20h with constant rotation. After hybridization, the microarrays were immediately washed extensively with non-stringent wash buffer (6x SSPE, 0.01% Tween20) at RT, and stringent wash buffer (100mM MES salt and free acid solution, 0.1M Na+, 0.01% Tween20) at 45°C. After final rinsing with non-stringent wash buffer, the microarrays were stained with 1x Stain buffer (100mM MES, 1M Na+, 0.05% Tween20, 50mg/ml of BSA, and 1mg/ml of Cy3-streptavidin) at room temp. for 25min. After the stain buffer was removed, the microarrays were rinsed with non-stringent wash buffer and immediately dried under argon gas.

scan_protocol: The microarrays were scanned with an Axon GenePix 4000B scanner (Molecular Devices Corp., Union City, CA) at 5 µM resolution.

data_processing: The data was extracted from the raw images with NimbleScan software (Nimblegen, Inc.).  Relative signal intensities for each feature were generated using the Robust Multi-Array Average algorithm and log2 transformed.  Transformed data were then processed using quantile normalization, and the average and std. error for each gene were calculated from the 10 perfectly matched oligos.  After detransformation, the ratio (fold change) was calculated using PBS treated samples (control) as the baseline against LPS-treated samples.

organism: Ictalurus punctatus

source_name: Spleen, 24h post-LPS injection

label_protocol: The 1st strand cDNA was synthesized from 2.5ug total RNA using SuperScript II reverse transcriptase and 100 pmoles T7 promoter-oligo dT primer.  Complementary RNA was then synthesized with a MEGAscript in vitro Transcription kit (Ambion) containing biotin-16 UTP and biotin-11 CTP.  The biotinylated cRNA products were fragmented to 50-200 bp prior to hybridization.

growth_protocol: Fish fed commercial diet to apparent satiation until 24h prior to LPS injection.  Fish were killed by anesthesia overdose at 24h post-injection, spleen was dissected and transferred to Trizol reagent

extract_protocol: Total RNA was purified according to Invitrogen protocol for Trizol reagent, treated with DNase1 and further purified using an RNease Mini kit (Qiagen).

treatment_protocol: LPS from E. coli 0127:B8 (Sigma Aldrich) was resuspended in PBS (ph7.0).  Fish were anesthetized with tricaine methanesulfonate and injected intraperitoneally with LPS at 2.5 mg/kg body weight.

tag: USDA103 strain, average weight ~200g, spleen tissue


title: Catfish_spleen_LPS injection, 24h sampling post-injection_replicate1

description: USDA103 strain catfish spleen


title: Catfish_spleen_PBS injection, samples pooled from 2 fish each at 2 to 24 h post-injection_hyb1

description: USDA103 strain catfish spleen

source_name: Spleen, PBS injection

growth_protocol: Fish fed commercial diet to apparent satiation until 24h prior to injection.  Fish were killed by anesthesia overdose at 2, 4, 8, and 24h post-injection, spleen was dissected and transferred to Trizol reagent

treatment_protocol: Fish were anesthetized with tricaine methanesulfonate and injected intraperitoneally with 0.5ml PBS.


title: Catfish_spleen_LPS injection, 4h sampling post-injection_replicate2

description: USDA103 strain catfish spleen

source_name: Spleen, 4h post-LPS injection

growth_protocol: Fish fed commercial diet to apparent satiation until 24h prior to LPS injection.  Fish were killed by anesthesia overdose at 4h post-injection, spleen was dissected and transferred to Trizol reagent


title: Catfish_spleen_LPS injection, 2h sampling post-injection_replicate2

description: USDA103 strain catfish spleen

source_name: Spleen, 2h post-LPS injection

growth_protocol: Fish fed commercial diet to apparent satiation until 24h prior to LPS injection.  Fish were killed by anesthesia overdose at 2h post-injection, spleen was dissected and transferred to Trizol reagent


title: Catfish_spleen_LPS injection, 8h sampling post-injection_replicate2

description: USDA103 strain catfish spleen

source_name: Spleen, 8h post-LPS injection

growth_protocol: Fish fed commercial diet to apparent satiation until 24h prior to LPS injection.  Fish were killed by anesthesia overdose at 8h post-injection, spleen was dissected and transferred to Trizol reagent


title: Catfish_spleen_LPS injection, 2h sampling post-injection_replicate1

description: USDA103 strain catfish spleen


title: Catfish_spleen_LPS injection, 8h sampling post-injection_replicate1

description: USDA103 strain catfish spleen


title: Catfish_spleen_PBS injection, samples pooled from 2 fish each at 2 to 24 h post-injection_hyb2

description: USDA103 strain catfish spleen


title: Catfish_spleen_LPS injection, 4h sampling post-injection_replicate1

description: USDA103 strain catfish spleen


title: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep2

city: Glasgow

first: Gareth

last: Jenkins

address: Bower Building

department: Institute of Biomedical and Life Sciences

country: United Kingdom

institute: University of Glasgow

description: Arabidopsis (Landsberg erecta) leafs of plants with hy5-1 mutation grown for 3 weeks in continuous white light and subsequently exposed to to 4hours of UV-B light

hyb_protocol: Biotinylated cRNA was hybridised to Affymetrix Arabidopsis ATH1 GeneChips using the standard Affymetrix procedure (45oC, 60 revs min-1, 16 hrs). Washing and staining were performed in a Fluidics Station 400 (Affymetrics) using Affymetrix protocol EukGE-WS2v4; the chips were stained with Streptavidin Phycoerythrin (SAPE) followed by biotinylated antibody followed by SAPE again.

scan_protocol: scanned on the Gene Array Scanner 2500 using standard Affymetrix procedures

data_processing: Robust Multichip Average (RMA, module Affy 1.4.32 of Bioconductor)

organism: Arabidopsis thaliana

source_name: leaf, hy5-1 mutant, UV-B light

label_protocol: RNA was reverse transcribed using the SuperScript II system (Invitrogen). The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3', as recommended by Affymetrix. dscDNA was in vitro transcribed to produce biotinylated cRNA using the Affymetrix GeneChip labelling kit.

growth_protocol: Plants were grown in compost for 3 weeks in 25 micromol m-2 s-1 continuous white light (warm white fluorescent tubes) at 21 oC

extract_protocol: RNA was isolated from leaf tissue using the Purescript kit (Flowgen) according to the manufacturer instructions.

treatment_protocol: Plants exposed to 3 micromol m-2 s-1 UV-B (UV-B 313 tubes; Q-Panel, USA) for 4 hours

tag: leafs of plants with hy5-1 mutation exposed to 4hours of UV-B light


title: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep3

description: Arabidopsis (Landsberg erecta) leafs of plants with uvr8-1 mutation grown for 3 weeks in continuous white light

source_name: leaf, uvr8-1 mutant, white light

treatment_protocol: no futher treatment

tag: leafs of plants with uvr8-1 mutation exposed to continuous white light


title: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep3


title: Arabidopsis_leaf_hy5-1_mutant_in_UV-B_light_rep1

scan_protocol: scanned on the Gene Array Scanner 2500 using standard Affymetrix procedure


title: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep1


title: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep2

description: Arabidopsis (Landsberg erecta) leafs of plants with uvr8-1 mutation grown for 3 weeks in continuous white light and subsequently exposed to to 4hours of UV-B light

source_name: leaf, uvr8-1 mutant, UV-B light

tag: leafs of plants with uvr8-1 mutation exposed to 4hours of UV-B light


title: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep3


title: Arabidopsis_leaf_wildtype_in_UV-B_light_rep1

description: Arabidopsis (Landsberg erecta) leafs of wild type plants grown for 3 weeks in continuous white light and subsequently exposed to to 4hours of UV-B light

source_name: leaf, wildtype, UV-B light

tag: leafs of wild type plants exposed to 4hours of UV-B light


title: Arabidopsis_leaf_uvr8-1_mutant_in_UV-B_light_rep1


title: Arabidopsis_leaf_uvr8-1_mutant_in_white_light_rep2


title: Arabidopsis_leaf_wildtype_in_UV-B_light_rep3

growth_protocol:
Plants were grown in compost for 3 weeks in 25 micromol m-2 s-1 continuous white light (warm white fluorescent tubes) at 21 oC
Plants were grown in compost for 3 weeks in 25 micromol m-2 s-1 continuous white light (warm white fluorescent tubes) at 21 oC


title: Arabidopsis_leaf_wildtype_in_white_light_rep1

description: Arabidopsis (Landsberg erecta) leafs of wild type plants grown for 3 weeks in continuous white light

source_name: leaf, wildtype, white light

tag: leafs of wild type plants exposed to continuous white light


title: MicMa709_AB_REP2

status: Public on Nov 30 2005

city: Foster City

first: Yulei

last: Wang

state: CA

address: 850 Lincoln Centre Dr

institute: Applied Biosystems

description: biopsy of breast carcinoma

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC.  Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

label: DIG-UTP

source_name: biopsy of breast carcinoma

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 ?g of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).

extract_protocol: biopsy samples were fresh frozen immediately after surgery and stored at -80oC. All specimens analyzed contained more than 40% tumor cells (of the total number of cells counted). The majority of tumors were invasive ductal carcinomas, tumor status T1-T2 and histological grade 2 and 3 (Table S1). Total RNA was isolated by phenol-chloroform extraction (TRIzol reagent, Invitrogen), the quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: early stage, breast carcinoma


title: Arabidopsis_leaf_wildtype_in_white_light_rep2


title: MicMa709_AB_REP1

description: biopsy of breast carcinoma

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).


title: MicMa632_AB_REP1

description: biopsy of breast carcinoma


title: MicMa267_AB_REP1

description: biopsy of breast carcinoma


title: MicMa185_AB_REP1

description: biopsy of breast carcinoma


title: MicMa263_AB_REP1

description: biopsy of breast carcinoma


title: MicMa185_AB_REP2

description: biopsy of breast carcinoma


title: icMa267_AB_REP2

description: biopsy of breast carcinoma


title: Arabidopsis_leaf_wildtype_in_UV-B_light_rep2


title: MicMa148_AB_REP1

description: biopsy of breast carcinoma


title: MicMa632_AB_REP2

description: biopsy of breast carcinoma


title: MicMa263_AB_REP2

description: biopsy of breast carcinoma


title: MicMa146_AB_REP1

description: biopsy of breast carcinoma


title: MicMa148_AB_REP2

description: biopsy of breast carcinoma


title: MicMa146_AB_REP2

description: biopsy of breast carcinoma


title: MicMa132_AB_REP2

description: biopsy of breast carcinoma


title: MicMa122_AB_REP2

description: biopsy of breast carcinoma


title: MicMa101_AB_REP2

description: biopsy of breast carcinoma


title: MicMa091_AB_REP2

description: biopy of breast carcinoma

source_name: biopy of breast carcinoma

extract_protocol: Biopy samples were fresh frozen immediately after surgery and stored at -80oC. All specimens analyzed contained more than 40% tumor cells (of the total number of cells counted). The majority of tumors were invasive ductal carcinomas, tumor status T1-T2 and histological grade 2 and 3 (Table S1). Total RNA was isolated by phenol-chloroform extraction (TRIzol reagent, Invitrogen), the quality and integrity of the total RNA was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).


title: MicMa132_AB_REP1

description: biopsy of breast carcinoma


title: MicMa101_AB_REP1

description: biopsy of breast carcinoma


title: MicMa091_AB_REP1

description: biopy of breast carcinoma


title: MicMa088_AB_REP2

description: biopy of breast carcinoma


title: MicMa085_AB_REP2

description: biopy of breast carcinoma


title: MicMa088_AB_REP1

description: biopy of breast carcinoma


title: MicMa079_AB_REP2

description: biopy of breast carcinoma


title: MicMa122_AB_REP1

description: biopsy of breast carcinoma


title: MicMa085_AB_REP1

description: biopy of breast carcinoma


title: MicMa067_AB_REP2

description: biopy of breast carcinoma


title: MicMa053_AB_REP1

description: biopy of breast carcinoma


title: MicMa031_AB_REP1

description: biopy of breast carcinoma


title: MicMa079_AB_REP1

description: biopy of breast carcinoma


title: MicMa053_AB_REP2

description: biopy of breast carcinoma


title: MicMa020_AB_REP1

description: biopy of breast carcinoma


title: MicMa067_AB_REP1

description: biopy of breast carcinoma


title: MicMa042_AB_REP2

description: biopy of breast carcinoma


title: MicMa031_AB_REP2

description: biopy of breast carcinoma


title: MicMa065_AB_REP1

description: biopy of breast carcinoma


title: 2M22 Cy3

type: genomic

city: Heidelberg

first: Frank

last: Mendrzyk

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Comparison of normal versus tumor DNA (medulloblastoma). Whole-genome screening of DNA-copy number changes by array-based or matrix comparative genomic hybridization (matrix-CGH). Every experiment was performed as dye-swap.

molecule: genomic DNA

source_name: Pooled reference DNA from either 4 healthy males or females of the opposite sex compared to the sample.

source_name: Isolated tumor DNA, derived from cerebellar medulloblastoma.


title: Arabidopsis_leaf_wildtype_in_white_light_rep3


title: MicMa042_AB_REP1

description: biopy of breast carcinoma


title: 2M21 Cy5


title: MicMa020_AB_REP2

description: biopy of breast carcinoma


title: 2M21 Cy3


title: 2M20 Cy3


title: 2M22 Cy5


title: 2M20 Cy5


title: 2M19 Cy3


title: 2M19 Cy5


title: 2M18 Cy5


title: 2M18 Cy3


title: 2M17 Cy3


title: 2M17 Cy5


title: 2M9 Cy5


title: 2M15 Cy5


title: 2M13 Cy3


title: 2M16 Cy3


title: 2M15 Cy3


title: 2M10 Cy5


title: 2M11 Cy5


title: 2M13 Cy5


title: 2M16 Cy5


title: 2M7 Cy3


title: 2M12 Cy3


title: 2M9 Cy3


title: 2M4 Cy5


title: 2M8 Cy5


title: 2M3 Cy5


title: 2M12 Cy5


title: 2M6 Cy5


title: 2M5 Cy5


title: 2M11 Cy3


title: 2M4 Cy3


title: 2M10 Cy3


title: MicMa065_AB_REP2

description: biopy of breast carcinoma


title: 2M3 Cy3


title: 2M8 Cy3


title: 2M5 Cy3


title: 2M6 Cy3


title: 2M2 Cy5


title: 2M7 Cy5


title: M26 Cy5


title: M28 Cy5


title: M24 Cy3


title: M29 Cy5


title: M29 Cy3


title: M20 Cy5


title: M28 Cy3


title: M25 Cy5


title: M17 Cy3


title: M18 Cy3


title: M23 Cy3


title: M21 Cy3


title: M17 Cy5


title: M32 Cy5


title: M18 Cy5


title: M24 Cy5


title: M26 Cy3


title: M23 Cy5


title: M20 Cy3


title: M19 Cy5


title: M22 Cy5


title: M32 Cy3


title: M19 Cy3


title: M13 Cy5


title: M16 Cy3


title: M13 Cy3


title: M16 Cy5


title: M15 Cy3


title: M15 Cy5


title: M11 Cy5


title: M9 Cy5


title: M12 Cy5


title: M9 Cy3


title: M12 Cy3


title: M10 Cy3


title: M10 Cy5


title: M8 Cy5


title: M8 Cy3


title: M11 Cy3


title: M5 Cy3


title: M5 Cy5


title: M4 Cy3


title: M2 Cy3


title: M3 Cy5


title: M4 Cy5


title: M2 Cy5


title: M3 Cy3


title: 2M2 Cy3


title: M1 Cy3


title: M1 Cy5


title: M25 Cy3


title: Mouse Models Muscular Dystrophy 25

status: Public on Nov 24 2005

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Comparative analysis of mouse models for muscular dystrophy using gene expression profiling


title: Mouse Models Muscular Dystrophy 21


title: Mouse Models Muscular Dystrophy 23


title: Mouse Models Muscular Dystrophy 20


title: 2M1 Cy5


title: Mouse Models Muscular Dystrophy 22


title: Mouse Models Muscular Dystrophy 24


title: Mouse Models Muscular Dystrophy 26


title: Mouse Models Muscular Dystrophy 12


title: M22 Cy3


title: Mouse Models Muscular Dystrophy 17


title: Mouse Models Muscular Dystrophy 19


title: Mouse Models Muscular Dystrophy 15


title: Mouse Models Muscular Dystrophy 07


title: Mouse Models Muscular Dystrophy 08


title: Mouse Models Muscular Dystrophy 13


title: 2M1 Cy3


title: Mouse Models Muscular Dystrophy 14


title: Mouse Models Muscular Dystrophy 11


title: Mouse Models Muscular Dystrophy 09


title: Mouse Models Muscular Dystrophy 16


title: Mouse Models Muscular Dystrophy 10


title: Mouse Models Muscular Dystrophy 06


title: Mouse Models Muscular Dystrophy 18


title: M21 Cy5


title: Mouse Models Muscular Dystrophy 05


title: Mouse Models Muscular Dystrophy 01


title: 5-7cm/0-2cm - rep4

status: Public on Nov 18 2005

city: Vancouver

first: Carl

middle: J

last: Douglas

state: BC

department: Department of Botany

country: Canada

institute: University of British Columbia

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 63 (channel 1) and 60 (channel 2).
This file describes results for replicate 4 of 4 comparing 5-7 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 019

source_name: 0-2 cm from the tip of inflorescence stems totalling 5 cm in length (reference, Cy3)

source_name: 5-7 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy5)


title: 7-9cm/0-2cm - rep3

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and 63 (channel 2).
This file describes results for replicate 3 of 4 comparing 7-9 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 020

source_name: 0-2 cm from the tip of inflorescence stems totalling 5 cm in length (reference, Cy5)

source_name: 7-9 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy3)


title: Mouse Models Muscular Dystrophy 03


title: 7-9cm/0-2cm - rep4

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 63 (channel 1) and 60 (channel 2).
This file describes results for replicate 4 of 4 comparing 7-9 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 021

source_name: 7-9 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy5)


title: 5-7cm/0-2cm - rep3

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and 63 (channel 2).
This file describes results for replicate 1 of 4 comparing 5-7 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 018

source_name: 5-7 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy3)


title: 5-7cm/0-2cm - rep1

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and 62 (channel 2).
This file describes results for replicate 1 of 4 comparing 5-7 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 014


title: 3-5cm/0-2cm - rep4

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 61 (channel 1) and 62 (channel 2).
This file describes results for replicate 4 of 4 comparing 3-5 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 013

source_name: 3-5 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy3)


title: 3-5cm/0-2cm - rep3

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 61 (channel 1) and 62 (channel 2).
This file describes results for replicate 3 of 4 comparing 3-5 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 012


title: 0-3cm/0-2cm - rep3

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and  62 (channel 2).
This file describes results for replicate 3 of 4 comparing 0-3cm sections (Channel 2, Cy3) with 0-2cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 008

source_name: 0-2cm from the tip of inflorescence stems totalling 5cm in length (reference, Cy5)

source_name: 0-3cm from the tip of inflorescence stems totalling 10cm in length (sample, Cy3)


title: 0-3cm/0-2cm - rep4

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and  62 (channel 2).
This file describes results for replicate 4 of 4 comparing 0-3cm sections (Channel 2, Cy3) with 0-2cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 009


title: 0-3cm/0-2cm - rep2

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 95% and photo-multiplier-tube set to 62 (channel 1) and  60 (channel 2).
This file describes results for replicate 2 of 4 comparing 0-3cm sections (Channel 2, Cy5) with 0-2cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 007

source_name: 0-2cm from the tip of inflorescence stems totalling 5cm in length (reference, Cy3)

source_name: 0-3cm from the tip of inflorescence stems totalling 10cm in length (sample, Cy5)


title: 7-9cm/0-2cm - rep1

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 60 (channel 1) and 62 (channel 2).
This file describes results for replicate 1 of 4 comparing 7-9 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 016


title: 3-5cm/0-2cm - rep2

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 61 (channel 2).
This file describes results for replicate 2 of 4 comparing 3-5 cm sections (Channel 2, Cy5) with 0-2 cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 011

source_name: 3-5 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy5)


title: 2-4cm/0-2cm - rep1

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 59 (channel 2).
This file describes results for replicate 1 of 4 comparing 2-4cm sections (Channel 2, Cy5) with 0-2cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 002

source_name: 2-4 cm from the tip of inflorescence stems totalling 5 cm in length (sample, Cy5)


title: Mouse Models Muscular Dystrophy 02


title: 3-5cm/0-2cm - rep1

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 61 (channel 2).
This file describes results for replicate 1 of 4 comparing 3-5 cm sections (Channel 2, Cy5) with 0-2 cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 010

source_name: 3-5 cm from the tip of inflorescence stems totalling 5 cm in length (sample, Cy5)


title: Mouse Models Muscular Dystrophy 04


title: 2-4cm/0-2cm - rep4

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 59 (channel 1) and 62 (channel 2).
This file describes results for replicate 4 of 4 comparing 2-4 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 005

source_name: 2-4 cm from the tip of inflorescence stems totalling 5 cm in length (sample, Cy3)


title: 2-4cm/0-2cm - rep2

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 59 (channel 2).
This file describes results for replicate 2 of 4 comparing 2-4cm sections (Channel 2, Cy5) with 0-2cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 003


title: 5-7cm/0-2cm - rep2

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 60 (channel 2).
This file describes results for replicate 1 of 4 comparing 5-7 cm sections (Channel 2, Cy5) with 0-2 cm sections (Channel 1, Cy3)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 015


title: DL50685_t6

status: Public on Nov 15 2005

first: Ellen

last: Sterrenburg

description:
Time course experiment
Myogenesis
DMD primairy human cells

source_name: Reference sample


title: 2-4cm/0-2cm - rep3

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 59 (channel 1) and 62 (channel 2).
This file describes results for replicate 3 of 4 comparing 2-4cm sections (Channel 2, Cy3) with 0-2cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-000-DE001, array 004


title: DL50685_t10


title: DL50685_t4


title: DL470_t14


title: DL470_t4

source_name: DL470_t=4 DMD


title: DL50685_t0


title: 0-3cm/0-2cm - rep1

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 60 (channel 2).
This file describes results for replicate 1 of 4 comparing 0-3 cm sections (Channel 2, Cy5) with 0-2 cm sections (Channel 1, Cy3)

Lot batch = FOAR03-S1-0001-DE001, array 006


title: DL50685_t14


title: DL470_t6

source_name: DL470_t=6 DMD


title: DL589_t2

source_name: DL589_t=2 DMD


title: DL589_t14


title: DL470_t2

source_name: DL470_t=2 DMD


title: DL470_t10


title: DL589_t10


title: DL470_t0

source_name: DL470_t=0 DMD


title: DL50685_t2


title: DL589_t0

source_name: DL589_t=0 DMD


title: DL589_t1

source_name: DL589_t=1 DMD


title: DL589_t6

source_name: DL589_t=6 DMD


title: DL589_t4

source_name: DL589_t=4 DMD


title: HPP4_t0

description:
Timecourse experiment
Healthy vs DMD
myoblasts/myotubes

source_name: HPP4_t=0 Healthy


title: HPP4_t4

source_name: HPP4_t=4 Healthy


title: KM109_t14

source_name: KM109_t=14 Healthy


title: HPP4_t14

source_name: HPP4_t=14 Healthy


title: HPP4_t1

source_name: HPP4_t=1 Healthy


title: HPP4_t2

source_name: HPP4_t=2 Healthy


title: HPP4_t10

source_name: HPP4_t=10 Healthy


title: KM109_t2

source_name: Reference sample

source_name: KM109_t=2 Healthy


title: HPP4_t6

source_name: HPP4_t=6 Healthy


title: KM109_t10

source_name: KM109_t=10 Healthy


title: KM109_t6

source_name: KM109_t=6 Healthy


title: KM108_t6

source_name: KM108_t=6 Healthy


title: KM108_t2

source_name: KM108_t=2 Healthy


title: KM108_t4

source_name: KM108_t=4 Healthy


title: KM108_t14

source_name: KM108_t=14 Healthy


title: KM108_t0

source_name: KM108_t=0 Healthy


title: KM109_t1

source_name: KM109_t=1 Healthy


title: KM109_t4

source_name: KM109_t=4 Healthy


title: KM109_t0

source_name: KM109_t=0 Healthy


title: KM108_t10

source_name: KM108_t=10 Healthy


title: KM108_t1

source_name: KM108_t=1 Healthy


title: DL50685_t1


title: Ws wild-type, 1µM ABA treatment, replicate 3

status: Public on Nov 14 2005

city: Bronx

first: Zhi-Liang

last: Zheng

state: NY

address: 250 Bedford Park Blvd W

department: Biological Sciences

institute: Lehman College of City University of New York

description: Wild type (Ws), seedlings treated by 1µM ABA (dissolved in DMSO) for 4 hours in liquid medium (MS) after 7 days of growth liquid medium (MS + 3% sucrose) at 150rpm shaking.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.1.1 software

source_name: Ws, 1µM ABA treatment

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 100 mg of 7-day old seedlings were frozen and ground in liquid nitrogen. Total RNA was extracted using an TRIzol kit (Invitrogen) and purified by RNeasy kit (Qiagen).

tag: Wild type ecotype Wassilewskija (Ws), young seedlings


title: rop10-1 mutant, 1µM ABA treatment, replicate 2

description: rop10-1 seedlings treated by 1µM ABA (dissolved in DMSO) for 4 hours in liquid medium (MS) after 7 days of growth liquid medium (MS + 3% sucrose) at 150rpm shaking.

source_name: rop10-1, 1µM ABA treatment

tag: rop10-1 in Ws background, young seedlings


title: rop10-1 mutant, 1µM ABA treatment, replicate 3


title: Ws wild-type, 1µM ABA treatment, replicate 2

description: Wild type (Ws) seedlings treated by 1µM ABA (dissolved in DMSO) for 4 hours in liquid medium (MS) after 7 days of growth liquid medium (MS + 3% sucrose) at 150rpm shaking.


title: rop10-1 mutant, 1µM ABA treatment, replicate 1


title: rop10-1 mutant, no ABA control, replicate 2

description: rop10-1 seedlings mock-treated by DMSO for 4 hours in liquid medium (MS) after 7 days of growth in liquid medium (MS + 3% sucrose) at 150rpm shaking.

source_name: rop10-1, no ABA control


title: Ws wild-type, 1µM ABA treatment, replicate 1

description: Wild type (Ws) seedlings treated by 1µM ABA (dissolved in DMSO) for 4 hours in liquid medium (MS) after 7 days of growth in liquid medium (MS + 3% sucrose) at 150rpm shaking.


title: rop10-1 mutant, no ABA control, replicate 3


title: Ws wild-type, no ABA control, replicate 3

description: Wild type (Ws) seedlings mock-treated by DMSO for 4 hours in liquid medium (MS) after 7 days of growth liquid medium (MS + 3% sucrose) at 150rpm shaking.

source_name: Ws, no ABA control


title: Ws wild-type, no ABA control, replicate 2


title: rop10-1 mutant, no ABA control, replicate 1


title: Ws wild-type, no ABA control, replicate 1


title: DL470_t1

source_name: Reference sample

source_name: DL470_t=1 DMD


title: germ cell tumors (GCT) and normal controls Norm1B3 1

status: Public on Nov 10 2005

city: New York

last: Korkola

address: 1275 York Ave

department: Cell Biology

institute: Memorial Sloan-Kettering

description: Normal Testis Specimen

data_processing: RMA (robust multi-array)

source_name: normal testis control

label_protocol: Approximately 12 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Frozen tissue from normal testis was minced and homogenized in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: normal testis


title: germ cell tumors (GCT) and normal controls 600A 1

description: Adult Male Germ Cell Tumor

source_name: germ cell tumor

extract_protocol: Frozen tissue from a germ cell tumor was minced and homogenized in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: pure GCT (Teratoma)


title: germ cell tumors (GCT) and normal controls 596A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls NormPool 1

description: pooled testis specimen (consists of equal amounts of norm1B1, norm1B2, norm1B3, norm1B4, and norm1C10)

source_name: pooled normal testis control


title: germ cell tumors (GCT) and normal controls Norm1B2 1

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 594A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 595A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls Norm1B1 1

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls Norm1C10 1

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 603A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 602A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 593A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls Norm1B4 1

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 587A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Seminoma)


title: germ cell tumors (GCT) and normal controls 590A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 601A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Choriocarcinoma)


title: germ cell tumors (GCT) and normal controls 585A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Seminoma)


title: germ cell tumors (GCT) and normal controls 586A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, Embryonal Carcinoma)


title: 7-9cm/0-2cm - rep2

description:
Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA).  Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 60 (channel 2).
This file describes results for replicate 2 of 4 comparing 7-9 cm sections (Channel 2, Cy3) with 0-2 cm sections (Channel 1, Cy5)

Keywords = fiber
Keywords = lignin
Keywords = stem development
Lot batch = FOAR03-S1-0001-DE001, array 017

source_name: 0-2 cm from the tip of inflorescence stems totalling 5 cm in length (reference, Cy3)

source_name: 7-9 cm from the tip of inflorescence stems totalling 10 cm in length (sample, Cy5)


title: germ cell tumors (GCT) and normal controls 583A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 584A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 570A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Teratoma with secondary somatic malignancy)


title: germ cell tumors (GCT) and normal controls 582A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 580A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 562A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 581A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 573A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 564A 1

description: Adult Male Germ Cell Tumor

tag: mixed non-seminomatous GCT


title: germ cell tumors (GCT) and normal controls 539A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 520A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma, syncytiotrophoblast)


title: germ cell tumors (GCT) and normal controls NormPool 2


title: germ cell tumors (GCT) and normal controls 513A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 526A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 532B 1

description: Adult Male Germ Cell Tumor from lung metastasis (same patient as 532A)

tag: mixed GCT (Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls 479A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls Norm1C10 2

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls Norm1B2 2

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 493A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls Norm1B3 2

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 602A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 500A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac, Teratoma)


title: germ cell tumors (GCT) and normal controls 497A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 521A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 473A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Choriocarcinoma, Embryonal Carcinoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 601A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 465A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls Norm1B1 2

description: Normal Testis Specimen


title: germ cell tumors (GCT) and normal controls 532A 1

description: Adult Male Germ Cell Tumor from mediastinum (same patient as 532B)


title: germ cell tumors (GCT) and normal controls 595A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 596A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 503A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, syncytiotrophoblasts)


title: germ cell tumors (GCT) and normal controls 472A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 460A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 593A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 594A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 600A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 430A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 429A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 590A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 425A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 582A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 585A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 413A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 403A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 414A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 586A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 583A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 584A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 570A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 587A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 603A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 428A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 573A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 391A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Choriocarcinoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 401A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 411A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 581A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 385A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Teratoma)


title: germ cell tumors (GCT) and normal controls 396A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Teratoma)


title: germ cell tumors (GCT) and normal controls 564A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 580A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 399A 1

description: Adult Male Germ Cell Tumor

tag: pure GCT (Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 562A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 373A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac)


title: germ cell tumors (GCT) and normal controls 532A 2


title: germ cell tumors (GCT) and normal controls 532B 2


title: germ cell tumors (GCT) and normal controls 372B 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac Tumor, syncytiotrophoblasts)


title: germ cell tumors (GCT) and normal controls 539A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Seminoma)


title: germ cell tumors (GCT) and normal controls 354B 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 526A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 318D 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 310A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, Yolk Sac Tumor, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 513A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 362A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 503A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 520A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 305A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Yolk Sac)


title: germ cell tumors (GCT) and normal controls 521A 2

description: Adult Male Germ Cell Tumor

tag: pure GCT (Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 512A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Yolk Sac, Teratoma)


title: germ cell tumors (GCT) and normal controls 497A 2

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 288A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 303B 1

description: Adult Male Germ Cell Tumor from adrenal gland metastasis (same patient as 303B)

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor)


title: germ cell tumors (GCT) and normal controls 371A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 299A 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Teratoma, Yolk Sac, Embryonal Carcinoma)


title: germ cell tumors (GCT) and normal controls 479A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac Tumor, Teratoma)


title: germ cell tumors (GCT) and normal controls 289A 1

description: Adult Male Germ Cell Tumor


title: germ cell tumors (GCT) and normal controls 303A 1

description: Adult Male Germ Cell Tumor from retroperitoneal lymph node metastasis (same patient as 303A)


title: germ cell tumors (GCT) and normal controls 500A 2

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Embryonal Carcinoma, Yolk Sac, Teratoma)


title: germ cell tumors (GCT) and normal controls 287B 1

description: Adult Male Germ Cell Tumor

tag: mixed GCT (Seminoma, Teratoma, Yolk Sac)