title: AND-TCR transgenic mouse first hybridization_MG-U74Bv2


title: C57BL/6 second hybridization_MG-U74Bv2

status: Public on Jan 31 2006

type: RNA

city: Chuo-ku

first: Tsutomu

last: Ohta

state: Tokyo

address: 5-1-1 Tsukiji

department: Medical Genomics Center

country: Japan

institute: National Cancer Center Research Institute

description: Total adult thymocytes from C57BL/6 mouse

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 4

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: thymocytes

label_protocol: 5 micro g of total RNA was processed to produce biotinylated cRNA targets.

tag: Wild type thymocytes


title: AND-TCR transgenic mouse second hybridization_MG-U74Cv2

description: Total adult thymocytes from AND-TCR transgenic mouse that were positively selected in the H-2b background

label_protocol: 5 µg of total RNA was processed to produce biotinylated cRNA targets.

tag: H-2b AND-TCR-transgenic thymocytes


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1

city: Braunschweig

first: Susanne

last: Pfoertner

address: Mascheroder Weg 1

country: Germany

institute: German Research Centre for Biotechnology (GBF)

description: CD4+CD25+ regulatory T cells from human peripheral blood

hyb_protocol: 15 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre). Samples were hybridized to individual Human TReg Chips for 16 hours at 42°C using a Lucidea Slidepro (Amersham Biosciences). After hybridisation the microarrays were washed as recommended by the manufacturer’s instructions (CodeLink Expression Bioarray System, Amersham Biosciences) and stained with Cy5-streptavidin (Amersham Biosciences).

scan_protocol: Fluorescent array images were collected for Cy5 with an arrayWorX fluorescent scanner (Applied Precision, USA) and image intensity data were extracted and analyzed with Imagene analysis software (v5.5.2, Biodiscovery).

data_processing: Spots of poor quality (flag=3) or signal intensities lower than the background intensity were excluded from further analysis. After background correction, data normalization was carried out as proposed by MWG. Briefly, signal intensities were normalized by dividing each signal by exp(median of ln[signal intensities of housekeeping genes]).

organism: Homo sapiens

label_protocol: Quality and integrity of the total RNA isolated from 1-2x10^5 CD4+CD25+ and CD4+CD25- T cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Samples were prepared by applying a double-linear amplification method according to the Eberwine protocol and modified by Affymetrix. Briefly, the first round of RNA-amplification was performed without biotinylated nucleotides using the Promega P1300 RiboMax Kit for T7 amplification (Promega, Mannheim, Germany). After clean-up of the precipitated aRNA synthesis of second round, first-strand cDNA was done using random hexamers (Pharmacia, Freiburg, Germany). Subsequent second-strand cDNA was prepared like in the first round but integrating an additional RNAse H incubation step to digest the aRNA before annealing of the T7T23V primer. The second round of RNA amplification was performed as an in vitro transcription assay in the presence of biotinylated UTP using the GeneChip® Expression 3’-Amplification Reagents Kit for IVT Labeling (Affymetrix, Santa Clara, CA). The concentration of the obtained biotin-labelled cRNA was determined by UV absorbance and its quality as means of product length distribution was again checked using the Agilent Bioanalyzer.

extract_protocol: Cells were lysed in RLT-buffer containing 1% beta-Mercaptoethanol. RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from freshly drawn blood by Ficoll density gradient centrifugation. For isolation of CD4+CD25+ regulatory and CD4+CD25- naive T cells, PBMCs were further separated using the regulatory human T cell isolation kit and an AutoMACS separation unit (Miltenyi Biotec).

tag: donor C, gender

value: female, age:27 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 1

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 1/3


title: AND-TCR transgenic mouse first hybridization_MG-U74Cv2


title: C57BL/6 first hybridization_MG-U74Cv2


title: C57BL/6 second hybridization_MG-U74Cv2


title: ES_H1_3KO2_exp2

status: Public on Jan 15 2006

city: Bronx

first: Yuhong

last: Fan

state: NY

address: 1300 Morris Park Ave., Chanin 402

department: cell biology

country: USA

institute: Albert Einstein College of Medicine

description: Total RNA extracted from exponentially growing cells.  RNA further purified with RNAeasy kit. cDNA synthesized with SuperScript cDNA synthesis kit.  IVT and cRNA labeling performed as recommended by Affymetrix.

data_processing: Affymetrix Microarray Suite 5.0 software.

source_name: H1c, H1d, H1e triple null embryonic stem cells

tag: H1c, H1d, H1e triple null ES cell line derived from littermate male blastocysts produced from matings of N7 backcrossed C57Bl6 triple heterozygous H1 mutant parents


title: ES_WT_exp1

source_name: Wild-type embryonic stem cells

tag: wild-type ES cell line derived from littermate male blastocysts produced from matings of N7 backcrossed C57Bl6 triple heterozygous H1 mutant parents


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 3

value: female, age:27 years, CD4+CD25+ TReg cells from peripheral blood, replicate 3/3


title: ES_H1_3KO1_exp2


title: C final PC3 AA 2hr

status: Public on Jan 01 2006

city: Bethesda

first: Jim

last: Boonyaratanakornkit

state: MD

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

description: PC-3 prostate cancer cells were either untreated (0hr) or incubated with 5 µg/mL arachidonic acid (AA) in RPMI media containing 0.25 mg/mL albumin for 2 hours. Albumin alone was added to untreated cells which remained inactivated.

data_processing: Data was processed in Affymetrix GeneChip Operating Software (GCOS) 1.2. Values shown are not normalized to the median of each array.

label: Phycoerythrin Streptavidin

source_name: PC-3, AA treated 2hr

tag: PC-3 human prostate cancer cell line


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, C15

tag: donor B, gender

value: female, age:57 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: ES_H1_3KO2_exp1


title: 4 PC3 2hr


title: 2 PC3 0hr

source_name: PC-3, untreated


title: 1 PC3 0hra

description: PC-3 prostate cancer cells were either untreated (0hr) or incubated with 5 µg/mL arachidonic acid (AA) in RPMI media containing 0.25 mg/mL albumin for 2 hours.  Albumin alone was added to untreated cells which remained inactivated.

data_processing: Data was processed in Affymetrix GeneChip Operating Software (GCOS) 1.2.  Values shown are not normalized to the median of each array.

label: Phycoerythrin Sreptavidin


title: 3 PC3 2hr


title: Comparison of total RRP6-delta to WT RNA (random hexamer and oligo-dT)

city: Santa Cruz

first: Carrie

middle: Anne

last: Davis

state: CA

address: 412 Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

description: Comparison of total RNA from wild-type to RRP6delta strains.

data_processing: This values represents the average log2 ratio from experiment 1 and 2

label: Cy3 or Cy5

organism: Saccharomyces cerevisiae

source_name: RRP6+ -vs- RRP6-

tag: BY4741 (wild-type) and BY4741-RRP6::KanMX (RRP6delta) from Open Biosystems

source_name: Yeast cells


title: B final PC3 ctrl


title: cDNA array +20wt/+3wt set3 (dye-swap)

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

description: Comparison of gene expression profiles of +20 DPA and +3 DPA wide-type upland cotton ovules

data_processing: All microarrays were scanned with a ScanArray Express scanner using the ScanArray 2.0 software (Packard Bioscience, Meriden, CT) and analyzed using the GenePix Pro 4.0 software (Axon Instruments, Foster City, CA). We quantified signal intensities of individual spots from the 16-bit TIFF images using GenePix Pro 4.0 (Axon Instruments). Since extensive expression pattern shift was recorded in mRNA populations of late developmental stages, such as the 10dpa/3dpa sample pair shown in Fig. 1C, we applied a linear normalization strategy (van de Peppel et al., 2003) instead of the nonlinear global-intensity-based LOWESS program used for most genome-wide microarrays (Yang et al., 2002). Expression ratios were collected only on those spots with signal intensity >800 in at least one dye channel on the microarray slides. Experimental parameters will be included in supplementary file.

organism: Gossypium hirsutum

source_name: +3 DPA wide-type cotton ovule

tag: Extracted total RNA from +3 DPA wide-type cotton ovules

source_name: +20 DPA wide-type cotton ovule

tag: Extracted total RNA from +20 DPA wide-type cotton ovules


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 3, B6

tag: donor J, gender

value: female, age:54 years, CD4+CD25- naive T cells from peripheral blood, replicate 3/3


title: cDNA array +20wt/+3wt set3


title: cDNA array +20wt/+3wt set2


title: cDNA array +20wt/+3wt set1 (dye-swap)


title: cDNA array +20wt/+3wt set2 (dye-swap)


title: cDNA array +15wt/+3wt set3

description: Comparison of gene expression profiles of +15 DPA and +3 DPA wide-type upland cotton ovules

source_name: +15 DPA wide-type cotton ovule

tag: Extracted total RNA from +15 DPA wide-type cotton ovules


title: cDNA array +15wt/+3wt set2 (dye-swap)


title: cDNA array +10wt/+3wt set3 (dye-swap)

description: Comparison of gene expression profiles of +10 DPA and +3 DPA wide-type upland cotton ovules

source_name: +10 DPA wide-type cotton ovule

tag: Extracted total RNA from +10 DPA wide-type cotton ovules


title: 1 PC3 0hr


title: D final PC3 AA 2hr


title: cDNA array +10wt/+3wt set3


title: cDNA array +15wt/+3wt set2


title: cDNA array +15wt/+3wt set1 (dye-swap)


title: cDNA array +10wt/+3wt set2 (dye-swap)


title: cDNA array +20wt/+3wt set1


title: cDNA array +10wt/+10fl set3 (dye-swap)

description: Comparison of gene expression profiles of +10 DPA wt and +10 DPA fl-mutant upland cotton ovules

source_name: +10 DPA fl-mutant cotton ovule

tag: Extracted total RNA from +10 DPA fl-mutant cotton ovules


title: cDNA array +15wt/+3wt set1


title: cDNA array +10wt/+3wt set1 (dye-swap)


title: cDNA array +3wt/+3fl set3 (dye-swap)

description: Comparison of gene expression profiles of +3 DPA wt and +3 DPA fl-mutant uplant cotton ovules.

source_name: +3 DPA fl-mutant cotton ovule

tag: Extracted total RNA from +3 DPA fl-mutant cotton ovules


title: cDNA array +10wt/+10fl set1

tag: Extracted total RNA from +10DPA wide-type cotton ovules


title: cDNA array +10wt/+3wt set1


title: cDNA array +10wt/+10fl set2


title: cDNA array +10wt/+10fl set3


title: cDNA array +3wt/+3fl set2


title: cDNA array +3wt/+3fl set3


title: cDNA array +3wt/+3fl set2 (dye-swap)


title: ES_WT_exp2

tag: Wild-type ES cell line derived from littermate male blastocysts produced from matings of N7 backcrossed C57Bl6 triple heterozygous H1 mutant parents


title: Human peripheral blood, CD4+CD25+ regulatory T cells, replicate 2, 60

tag: donor H, gender

value: female, age:26 years, CD4+CD25+ TReg cells from peripheral blood, replicate 2/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 1, C7

tag: donor I, gender

value: male, age:62 years, CD4+CD25- naive T cells from peripheral blood, replicate 1/3


title: Human peripheral blood, CD4+CD25- naive T cells, replicate 2, C9

value: female, age:62 years, CD4+CD25- naive T cells from peripheral blood, replicate 2/3


title: cDNA array +3wt/+3fl set1 (dye-swap)


title: cDNA array 0wt/+3wt set3

description: Comparison of gene expression profiles of 0 DPA and +3 DPA wild-type upland cotton ovules.

source_name: 0 DPA wide-type cotton ovule

tag: Extracted total RNA from 0 DPA wide-type cotton ovules


title: cDNA array 0wt/+3wt set1 (dye-swap)


title: cDNA array +5wt/+3wt set2 (dye-swap)

description: Comparison of gene expression profiles of +5 DPA and +3 DPA wild-type upland cotton ovules.

source_name: +5 DPA wide-type cotton ovule

tag: Extracted total RNA from +5 DPA wide-type cotton ovules


title: cDNA array +10wt/+10fl set2 (dye-swap)


title: cDNA array 0wt/+3wt set2


title: cDNA array 0wt/+3wt set2 (dye-swap)


title: cDNA array +5wt/+3wt set3


title: cDNA array +3wt/+3fl set1


title: cDNA array +5wt/+3wt set2


title: cDNA array +5wt/+3wt set1 (dye-swap)


title: cDNA array +5wt/+3wt set1


title: wild type GFP positive rep 3B

city: Brookline

first: Sung

middle: Eun

last: Choe

state: MA

address: 258 Harvard St #164

institute: Wyeth Research

description: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.

data_processing: Bioconductors' affy package in conjunction with Choe et al.'s goldenspike package (Choe et al. Genome Biol. 2005).

organism: Drosophila melanogaster

source_name: mesodermal cells

label_protocol: Approximately 2.5-3 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: The embryos were dounce homogenized into a single cell suspension. These cells were then FACS sorted. The GFP-positive cells from this sort comprise this sample.


title: tolerant TCR1;CD8+, tolerant;NONE;C57/BL6,gag-specific ;29783

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: tolerant TCR1

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine

data_processing: Rosetta Resolver

label_protocol: samples were split into equal aliquots of ~50ng of total RNA, and used for three rounds of cDNA synthesis and cRNA amplification, as previously described (Scherer, A. et al. Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies. Biotechniques 34, 546-50, 552-4, 556 (2003).)

extract_protocol: Rag-/- TCR mice were immunized twice with 5x106 irradiated FBL and 10 µg anti-CD40 (Immunex, Seattle, WA) and 30 days later spleens from immunized Rag-/- TCR and non-immunized Rag-/- TCR and TCRxGag were removed.  Naïve CD44low and CD44high memory and tolerant CD8+ T cells were isolated by cell sorting on a FACSAria (Becton Dickinson, San Jose, CA).  RNA was extracted from sorted T cells using Trizol® Reagent (Invitrogen, Carlsbad, CA) and then purified further using an RNeasy cleanup kit from Qiagen (Valencia, CA) according to manufacturer’s protocol.  Total RNA was quantified using RiboGreen (Molecular Probes, Eugene, Oregon)


title: cDNA array +10wt/+10fl set1 (dye-swap)


title: wild type GFP positive rep 3C

tag: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: wild type GFP positive rep 2A


title: wild type GFP negative rep 3A

description: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-negative cells were collected using FACS.

source_name: nonmesodermal cells

extract_protocol: The embryos were dounce homogenized into a single cell suspension. These cells were then FACS sorted. The GFP-negative cells from this sort comprise this sample.


title: memory TCR2;CD8+, memory;NONE;C57/BL6,gag-specific TCR;29782

description: memory TCR2


title: wild type GFP positive rep 2B


title: wild type GFP negative rep 2C

tag: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-negative cells were collected using FACS.


title: cDNA array +5wt/+3wt set3 (dye-swap)


title: memory TCR1;CD8+, memory;NONE;C57/BL6,gag-specific TCR;29781

description: memory TCR1


title: tolerant TCR2;CD8+, tolerant;NONE;C57/BL6,gag-specific ;29784

description: tolerant TCR2


title: wild type GFP positive rep 2C


title: naive TCR2;CD8+T cells;NONE;C57/BL6,gag-specific TCR;29780

description: naive TCR2


title: wild type GFP negative rep 2A


title: wild type GFP negative rep 2B


title: FGFR gain of function rep 1A

description: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as UAS-lambda-Htl and UAS-Dof insertions that yield constitutively activated FGFR within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: naive TCR1;CD8+T cells;NONE;C57/BL6,gag-specific TCR;29779

description: naive TCR1


title: Ap_array_norm

status: Public on Dec 31 2005

city: Tucson

first: Nancy

middle: A

last: Moran

state: AZ

address: Biosciences West, Room 310, 1041 E. Lowell St.,  The University of Arizona

department: Ecology and Evolutionary Biology

institute: University of Arizona

description: two biological replicates with a dye flip for each - four slides total

data_processing: Signal intensities were measured using spot-finding software, softWoRx Tracker (version 2.20, MolecularWare Inc).  Raw median spot intensity and median background intensity data were exported; median background signal intensities were subtracted from median signal intensities.  A zero signal value was substituted for any negative signal intensities and all non-zero values were log2-transformed. We imported log2-transformed data from all four slides into SAS version 9 and used ‘PROC MIXED’ to model and remove systematic sources of variation contributed by Cy3 versus Cy5 dyes, slide and hybridization effects, slide x dye interactions and slide x treatment interactions.  Statistical residuals generated from the normalization step were subjected to mixed-model analyses of variance.

label: Heat Shock

organism:
Buchnera aphidicola
Acyrthosiphon pisum

source_name: Heat Shock

treatment_protocol: Six to ten adult A. pisum were placed on a single fava bean plant in a cup cage and allowed to reproduce at 20 ºC 16 L:8 D.  After 24 – 48 hours the adult aphids were removed from plants and flash-frozen in liquid nitrogen.  First generation aphids were then maintained for one week, the developmental period required to attain the adult stage.  Heat shock experiments were carried out 1 - 2 days following ecdysis to adulthood.  Prior to HS, 10 – 20 control aphids were removed from each plant, flash-frozen in liquid nitrogen and stored at -80 ºC until RNA extraction and microarray hybridization.  Heat shock conditions were applied by ramping from 20 ºC to 36 ºC over a two hour period at a rate of 2 ºC/15min and then maintaining aphids at 36 ºC for an additional 2 hours (4 hours in total).  At 4 hours cultures were removed from the growth chamber and aphids were quickly collected into Eppendorf tubes, flash-frozen in liquid nitrogen and stored at -80 ºC until processing.  Two biological replicates of clone TUC were exposed to heat shock in parallel.

tag: Total RNA from heat shocked aphids was hybridized in this channel

label: Control

source_name: Control

tag: Total RNA from control aphids was hybridized in this channel


title: EGFR gain of function rep 1B

description: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as a UAS-lambda-Top insertion that yields constitutively activated EGFR within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: EGFR gain of function rep 1A

tag: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as a UAS-lambda-Top insertion that yields constitutively activated EGFR within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: EGFR gain of function rep 1C


title: cDNA array 0wt/+3wt set1

tag: Extracted total RNA from +3 DPA wide-type cotton ovules


title: Control GMO8398C cell line, sample 3, A chip (GMO8398C_3_U133A.txt)

city: Boston

first: Sangeeta

last: English

address: 300 Longwood Avenue

institute: Children's Hospital

description: Primary fibroblasts were obtained from Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ, USA). The HGPS cell lines AG10750 (M, 9 years), AG11498 (M, 14 years) and AG11513 (F, 8 years) have been shown to be heterozygous for the codon 608 GGC>GGT mutation (Erikkson et al., 2003). The age indicated in parentheses refers to the age of the donor at the time of biopsy. For controls we used primary cell lines derived from age-matched, apparently normal donors: GM00038C (F, 9 years), GM00316B (M, 12 years) and GM08398C (M, 8 years). Total RNA was isolated using the TRIzol reagent (Life Technologies) and further purified on RNeasy mini columns (Qiagen).Five micrograms of total RNA was used in each labeling reaction. Hybridization was done using Affymetrix HG-U133A arrays.

data_processing: Affymetrix HG-U133A arrays were used. Intensity values were quantitated by MAS 5.0 software (Affymetrix). All the chips were scaled to the same target intensity of 500.

label: Biotin

source_name: Control primary fibroblast cell line

tag: Cell Line

value: GMO8398C, Gender:Male, Age:8 years


title: Control GM0316B cell line, sample 3, A chip (GM0316B_3_U133A.txt)

value: GM00316B, Gender:Male, Age:12 years


title: Control GMO8398C cell line, sample 2, A chip (GMO8398C_2_U133A.txt)


title: Control GM00038C cell line, sample 2, A chip (GM00038C_2_U133A.txt)

value: GM00038C, Gender:Female, Age:9 years


title: Control GMO8398C cell line, sample 1, A chip (GMO8398C_1_U133A.txt)


title: Control GM00038C cell line, sample 3, A chip (GM00038C_3_U133A.txt)


title: cDNA array +15wt/+3wt set3 (dye-swap)

tag: Extracted total RNA from +15 DPA wide-type cotton ovules


title: Control GM0316B cell line, sample 2, A chip (GM0316B_2_U133A.txt)


title: Control GM00038C cell line, sample 1, A chip (GM00038C_1_U133A.txt)


title: HGPS AG11498 cell line, sample 3, A chip (AG11498_3_U133A.txt)

source_name: Hutchinson–Gilford progeria syndrome (HGPS) primary fibroblast cell line

value: AG11498, Gender:Male, Age:14 years


title: Control GM0316B cell line, sample 1, A chip (GM0316B_1_U133A.txt)


title: HGPS AG11513 cell line, sample 2, A chip (AG11513_2_U133A.txt)

value: AG11513, Gender:Female, Age:8 years


title: HGPS AG11513 cell line, sample 1, A chip (AG11513_1_U133A.txt)


title: HGPS AG11498 cell line, sample 1, A chip (AG11498_1_U133A.txt)


title: HGPS AG11513 cell line, sample 3, A chip (AG11513_3_U133A.txt)


title: HGPS AG10750 cell line, sample 3, A chip (AG10750_3_U133A.txt)

description:
Primary fibroblasts were obtained from Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ, USA). The HGPS cell lines AG10750 (M, 9 years), AG11498 (M, 14 years) and AG11513 (F, 8 years) have been shown to be heterozygous for the codon 608 GGC>GGT mutation (Erikkson et al., 2003). The age indicated in parentheses refers to the age of the donor at the time of biopsy. For controls we used primary cell lines derived from age-matched, apparently normal donors: GM00038C (F, 9 years), GM00316B (M, 12 years) and GM08398C (M, 8 years). Total RNA was isolated using the TRIzol reagent (Life Technologies) and further purified on RNeasy mini columns (Qiagen).Five micrograms of total RNA was used in each labeling reaction. Hybridization was done using Affymetrix HG-U133A
arrays.

value: AG10750, Gender:Male, Age:9 years


title: HGPS AG11498 cell line, sample 2, A chip (AG11498_2_U133A.txt)


title: ES_H1_3KO1_exp1

description: Total RNA extracted from exponentially growing cells.  RNA further purified with RNAeasy kit. cDNA synthesized with SuperScript cDNA synthesis kit.  IVT and cRNA labeling performed as recommended by Affymetrix.

source_name: H1c, H1d, H1e triple null embryonic stem cells

tag: ES cell lines derived from littermate male blastocysts produced from matings of N7 backcrossed C57Bl6 triple heterozygous H1 mutant parents


title: Control GM08398C cell line, sample 1, B chip (GM08398C_1_U133B.txt)

description: Primary fibroblasts were obtained from Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ, USA). The HGPS cell lines AG10750 (M, 9 years), AG11498 (M, 14 years) and AG11513 (F, 8 years) have been shown to be heterozygous for the codon 608 GGC>GGT mutation (Erikkson et al., 2003). The age indicated in parentheses refers to the age of the donor at the time of biopsy. For controls we used primary cell lines derived from age-matched, apparently normal donors: GM00038C (F, 9 years), GM00316B (M, 12 years) and GM08398C (M, 8 years). Total RNA was isolated using the TRIzol reagent (Life Technologies) and further purified on RNeasy mini columns (Qiagen).Five micrograms of total RNA was used in each labeling reaction. Hybridization was done using Affymetrix HG-U133B arrays.

data_processing: Affymetrix HG-U133B arrays were used. Intensity values were quantitated by MAS 5.0 software (Affymetrix). All the chips were scaled to the same target intensity of 500.

value: GM08398C, Gender:Male, Age:8 years


title: Control GM08398C cell line, sample 3, B chip (GM08398C_3_U133B.txt)


title: Control GM0316B cell line, sample 2, B chip (GM0316B_2_U133B.txt)

value: GM0316B, Gender:Male, Age:12 years


title: HGPS AG10750 cell line, sample 1, A chip (AG10750_1_U133A.txt)

tag: Cell line


title: Control GM0316B cell line, sample 1, B chip (GM0316B_1_U133B.txt)


title: Control GM00038C cell line, sample 2, B chip (GM00038C_2_U133B.txt)


title: Control GM08398C cell line, sample 2, B chip (GM08398C_2_U133B.txt)


title: Control GM0316B cell line, sample 3, B chip (GM0316B_3_U133B.txt)


title: HGPS AG11513 cell line, sample 3, B chip (AG11513_3_U133B.txt)


title: HGPS AG11513 cell line, sample 1, B chip (AG11513_1_U133B.txt)


title: Control GM00038C cell line, sample 1, B chip (GM00038C_1_U133B.txt)


title: HGPS AG11513 cell line, sample 2, B chip (AG11513_2_U133B.txt)


title: HGPS AG11498 cell line, sample 1, B chip (AG11498_1_U133B.txt)

tag: Line


title: HGPS AG10750 cell line, sample 3, B chip (AG10750_3_U133B.txt)


title: HGPS AG11498 cell line, sample 3, B chip (AG11498_3_U133B.txt)


title: Control GM00038C cell line, sample 3, B chip (GM00038C_3_U133B.txt)


title: HGPS AG10750 cell line, sample 2, B chip (AG10750_2_U133B.txt)


title: HGPS AG11498 cell line, sample 2, B chip (AG11498_2_U133B.txt)


title: diet_mammary_2

city: st louis

first: Yan

last: Lu

state: MO

address: 660 s. euclid ave

institute: washington univ.

description: female Spargue-Dawley rats, diet only for 7 days,  tissue: mammary gland

organism: Rattus norvegicus

source_name: normal mammary gland

value: mammary gland


title: diet_mammary_3

tag: female Spargue-Dawley rats, diet only for 7 days,  tissue


title: AtFBP7 mutant replicate 2

city: Freising

first: Claus

last: Schwechheimer

address: Emil-Ramann-Str. 4

department: Plant Systems Biology

institute: TUM

description: AtFBP7 mutant 5 day old seedlings

data_processing: Affymetrix Microarray Suite version 5.0

organism: Arabidopsis thaliana

source_name: 5 day old seedlings

label_protocol: Approximately 6 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 80 mg from 5 day old light grown AtFBP7 mutant seedlings in Nossen background  AtFBP7  were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: mutant, 5 day old seedlings, light grown


title: AtFBP7 mutant replicate 1

description: AtFBP7 mutant 5 day old seedlings


title: diet_LIVER_4

description: female Spargue-Dawley rats, diet only for 7 days,  tissue: liver

source_name: normal liver tissue

value: liver


title: diet_LIVER_3


title: AtFBP7 mutant replicate 3

description: AtFBP7 mutant 5 day old seedlings


title: VFB_mutant replicate 2

description: VFB triple mutant 10 day old seedlings

extract_protocol: Approximately 80 mg from 5 day old light grown VFB triple mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: mutant, 10 day old seedlings, light grown


title: VFB_mutant replicate 3

description: VFB triple mutant 10 day old seedlings

extract_protocol: Approximately 80 mg from 5 day old light grown No-0 wild type seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).


title: diet_Lung_3

description: female Spargue-Dawley rats, diet only for 7 days,  tissue: lung

source_name: normal lung tissue

value: lung


title: diet_mammary_4

source_name: NORMAL MAMMARY GLAND


title: AtFBP7 wild type replicate 2

description: AtFBP7 wild type 5 day old seedlings

tag: wild type, 5 day old seedlings, light grown


title: diet_mammary_1


title: diet_LIVER_1


title: 4-HPR_mammary_4

description: female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: mammary gland


title: VFB_mutant replicate 1

description: VFB triple mutant 10 day old seedlings


title: VFB wild type replicate 3

description: VFB wild type 10 day old seedlings

source_name: 10 day old seedlings

extract_protocol: Approximately 80 mg from 10 day old light grown Col-0 wild type seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: wild type, 10 day old seedlings, light grown


title: AtFBP7 wild type replicate 1

description: AtFBP7 wild type 5 day old seedlings


title: diet_LIVER_2


title: diet_Lung_2


title: 4-HPR_LIVER_4

description: female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: liver


title: 9-cis-retinoic-acid_mammary_4

description: female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: mammary gland


title: 4-HPR_LUNG_4

description: female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: lung


title: VFB wild type replicate 2

description: VFB wild type 10 day old seedlings


title: 9-cis-retinoic-acid_Lung_4

description: female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: lung


title: VFB wild type replicate 1

description: VFB wild type 10 day old seedlings


title: AtFBP7 wild type replicate 3

description: AtFBP7 wild type 5 day old seedlings


title: 9-cis-retinoic-acid_LIVER_4

description: female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: liver


title: 9-cis-retinoic-acid_mammary_3

tag: female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue


title: 9-cis-retinoic-acid_LIVER_2


title: 9-cis-retinoic-acid_Lung_1


title: 9-cis-retinoic-acid_LIVER_1


title: 9-cis-retinoic-acid_Lung_2


title: 9-cis-retinoic-acid_LIVER_3


title: 9-cis-retinoic-acid_mammary_1


title: 9-cis-retinoic-acid_mammary_2


title: 9-cis-retinoic-acid_Lung_3


title: Targretin_Lung_3

description: female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: lung


title: Targretin_LIVER_3

description: female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: liver


title: 4-HPR_LIVER_3

description: famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: liver

tag: female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue


title: Targretin_Lung_2

tag: female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue


title: Targretin_mammary_2

description: female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: mammary gland


title: 4-HPR_LUNG_3

description: famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: lung


title: Targretin_LIVER_2


title: Targretin_Lung_1


title: Targretin_mammary_3


title: Targretin_mammary_1

source_name: normal mammary tissue


title: 4-HPR_mammary_2

description: famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: mammary gland


title: 4-HPR_mammary_3


title: 4-HPR_LIVER_1

source_name: NORMAL LIVER

tag: famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue


title: Targretin_LIVER_1


title: 4-HPR_LUNG_2


title: 4-HPR_LUNG_1

source_name: NORMAL LUNG TISSUE


title: 4-HPR_LIVER_2

source_name: NORMAL LIVER TISSUE


title: rat heart - pool of 7 samples from trained rats - rep. no. 3

status: Public on Dec 28 2005

city: Bologna

first: Marina

last: Marini

address: V. Belmeloro, 8

department: Histology, Embryology and Applied Biology

country: Italy

institute: University of Bologna

description:
For each RNA pool (e.g. trained animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no. 3.

hyb_protocol: Hybridization protocol was carried out according to the manifacturer’s suggestions. Signal was developed by a chemiluminescent method (alkaline phosphatae-conjugated streptavidin and  CDP-Star®) and detected by exposing the membranes to X-ray film Kodak X-Omat AR (Sigma-Aldrich) .

scan_protocol: Flatbed scanner digitized image of developed X-ray film.

data_processing: Arrays were processed by means of GEArray software, provided by SuperArray. Minimum spot intensity was used for automatic background subtraction. Data were then normalized with respect to the housekeeping gene RPL13a, one of the positive controls in the array.

source_name: experiment "very moderate exercise training"

label_protocol: AmpoLabeling-LPR Kit (SuperArray, Bioscience Corporation, Frederick, USA).

extract_protocol: Frozen cardiac tissue was reduced to powder by means of a sterilized ceramic mortar and pestle. RNA isolation was obtained by TRIZOL  (Invitrogen s.r.l., Milan, Italy), as suggested by the manufacturer (Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987; 162: 156-9). The absence of RNA degradation was assessed by evaluation of 28S and 18S band sharpness after denaturing electrophoresis. The absence of contaminating genomic DNA was confirmed by PCR analysis with tubulin promoter-specific primers. An equivalent mass of total RNA from each subject in the group was pooled to generate the total RNA sample for probe generation.

treatment_protocol: Rats were placed in individual cages and fed standard diet without limitations; room temperature was kept at 21 ± 2°C; 12 hours of light were automatically alternated to 12 hours of dark. The exercise was produced on a specific treadmill for rats, with four lanes. The training protocol was aimed at providing a gradually increasing effort to reach 50 % VO2max in 11 weeks; such workload was sustained for a further 3 wks. Animals were trained 1hr three times a week.

tag: strain

value: albino Sprague-Dowley

tag: gender

value: male

tag: age

value: 23 weeks at the time of sacrifice

tag: tissue

value: left ventricula of 7 trained animals. Pool of RNAs.


title: Seasonal variation in leafy spurge crown bud gene expression (Sep. 01)

status: Public on Dec 29 2005

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Horvath DP, Soto-Suárez M, Chao WS, Jia Y, Anderson JV. Transcriptome Analysis of Paradormancy Release in Root Buds of Leafy Spurge (Euphorbia esula L.). Weed Sci. 53: 793-801. 2005.

scan_protocol: Microarrays were scanned on an Affy428 scanner and spots were selected and quantified using the Jaguar 2.0 software package.

data_processing: Intensity data was fed into the LIMMA software package. Data was trimmed to remove all non-plant controls, blank spots, and poorly hybridizing spots (those with A-values <8.0. The remaining data points were subjected to print-tip loess normalization.

organism: Euphorbia esula

source_name: Cy 5 control sample- paradormant root buds from greenhouse-grown leafy spurge

extract_protocol:
Pine tree RNA exctraction protocol:
Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113 116.

tag: Paradormant root buds

tag: 3.5 month old greenhouse-grown plants

tag: Biotype 1984-ND001

tag: 16 hr photoperiod

tag: Collected between 8:00 and 10:00 AM

source_name: CY3 paradormant crown buds of garden-grown leafy spurge

growth_protocol: Plants were grown in 4 liter plastic pots that were buried to soil level in the ground.

tag: Paradormant crown buds

tag: 1.5 year old garden-grown plants

tag: Natural lighting, supplemental watering as needed.

tag: Collected on Sep. 15, 2001


title: Seasonal variation in leafy spurge crown bud gene expression (Aug. 03)

source_name: CY5 paradormant crown buds of garden-grown leafy spurge

label_protocol: Horvath DP, Soto-Suárez M, Chao WS, Jia Y, Anderson JV. Transcriptome Analysis of Paradormancy Release in Root Buds of Leafy Spurge (Euphorbia esula L.). Weed Sci. 53: 793-801. 2005.

tag: Collected on Aug. 11, 2003

source_name: CY3 control sample- paradormant root buds from greenhouse-grown leafy spurge


title: Seasonal variation in leafy spurge crown bud gene expression (Sep. 03)

tag: Collected on Sep. 12, 2003


title: rat heart - pool of 7 samples from trained rats - rep. no. 1

description:
For each RNA pool (e.g. trained animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no. 1.

treatment_protocol:
Rats were placed in individual cages and fed standard diet without limitations; room temperature was kept at 21 ± 2°C; 12 hours of light were automatically alternated to 12 hours of dark. The exercise was produced on a specific treadmill for rats, with four lanes. The training protocol was aimed at providing a gradually increasing effort to reach 50 % VO2max in 11 weeks; such workload was sustained for a further 3 wks. Animals were trained 1hr three times a week.
Animals were sacrificed 48 hrs after the last training session.
Rats were anesthetized (100 mg/kg ip heparinized sodium thiopental); hearts were removed and imediately frozen in liquid nitrogen and stored at -80°C.


title: rat heart - pool of 7 samples from trained rats - rep. no. 2

description:
For each RNA pool (e.g. trained animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no. 2.


title: Seasonal variation in leafy spurge crown bud gene expression (Dec 03)

hyb_protocol: Horvath DP, Soto-Suárez M, ChaoWS, JiaY, Anderson JV. Transcriptome Analysis of Paradormancy Release in Root Buds of Leafy Spurge (Euphorbia esula L.). Weed Sci. 53: 793-801. 2005.

source_name: CY5 ecodormant crown buds of garden-grown leafy spurge

tag: Ecodormant crown buds

tag: Collected on Dec. 7, 2003


title: rat heart - pool of 8 control samples - rep. no. 3

description:
For each RNA pool (e.g. control animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no. 3

source_name: control of experiment "very moderate exercise training"

treatment_protocol: Rats were placed in individual cages and fed standard diet without limitations; room temperature was kept at 21 ± 2°C; 12 hours of light were automatically alternated to 12 hours of dark. Control animals were placed on a non-moving treadmill during the training sessions.

tag: strain

value: left ventricula of 8 control (sedentary, untrained) animals. Pool of RNA.


title: Seasonal variation in leafy spurge crown bud gene expression (Nov. 03)

tag: Collected on Nov. 1, 2003

source_name: Cy 3 control sample- paradormant root buds from greenhouse-grown leafy spurge


title: Seasonal variation in leafy spurge crown bud gene expression (Oct. 03)

source_name: CY5 endodormant crown buds of garden-grown leafy spurge

tag: Endodormant crown buds

tag: Collected on Oct. 12, 2003


title: Seasonal variation in leafy spurge crown bud gene expression (Dec 01)

label_protocol: Horvath DP, Soto-Suárez M, ChaoWS, JiaY, Anderson JV. Transcriptome Analysis of Paradormancy Release in Root Buds of Leafy Spurge (Euphorbia esula L.). Weed Sci. 53: 793-801. 2005.

tag: Paradormant root buds

source_name: CY3 ecodormant crown buds of garden-grown leafy spurge

tag: Collected on Dec. 4, 2001


title: rat heart - pool of 8 control samples - rep. no. 1

description:
For each RNA pool (e.g. control animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no.1

scan_protocol: Flatbed scanner digitized image of developed X-ray film. The image was processed by means opf the freely available software ScanAlyze provided by eisen@genome.stanford.edu

treatment_protocol:
Rats were placed in individual cages and fed standard diet without limitations; room temperature was kept at 21 ± 2°C; 12 hours of light were automatically alternated to 12 hours of dark. Control animals were placed on a non-moving treadmill during the training sessions.
Rats were anesthetized (100 mg/kg ip heparinized sodium thiopental); hearts were removed and imediately frozen in liquid nitrogen and stored at -80°C.

tag: gender

value: males

tag: age

tag: tissue

value: left ventricula of 8 control (sedentary, untrained) animals; pooled RNA samples.


title: Seasonal variation in leafy spurge crown bud gene expression (Oct. 01)

tag: 3.5 month old greenhouse-grown plants

tag: Biotype 1984-ND001

tag: 16 hr photoperiod

tag: Collected between 8:00 and 10:00 AM

source_name: CY3 endodormant crown buds of garden-grown leafy spurge

tag: Collected on Oct. 15, 2001


title: Dactyl 2.4

status: Public on Dec 26 2005

city: Lexington

first: Timothy

last: McClintock

state: KY

address: 800 Rose Street

department: Department of Physiology

institute: University of Kentucky

description: Raw intensity data for each experiment was normalized by first calculating the average intensity for each individua

hyb_protocol: Hybridization was done at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001). Washing wash done twice in 2x SSC and 0.1% SDS for 10 min and twice in 1x SSC and 0.1%SDS for 15 min at room temperature.

scan_protocol: Signals from hybridized arrays were quantified using a STORM phosphorimaging device running ImageQuant software (Molecular Dynamics, Sunnyvale, CA). ImageQuant,was used to segment each spot and calculate the volume signal intensity for each.

data_processing: Global Normalization (Cheadle et al., 2003) was used to normalize raw intensity data.

molecule: polyA RNA

organism: Homarus americanus

source_name: Leg dactyl

label_protocol: 33P-labeled cDNA were produced by oligo-dT priming of reverse transcription using the RadPrime DNA labeling kit (Invitrogen)

extract_protocol: TriReagent was added to the frozen tissue samples, the mixture was immediately homogenized with a polytron, total RNA was isolated and then poly A+ RNA was purified on oligo-dT cellulose columns (Molecular Resource Center, Cincinnati, OH).

tag: Live lobsters were maintained in Instant Ocean, Aquarium Systems, at 6˚C for no more than 2 weeks prior to use for tissue harvest.


title: rat heart - pool of 8 control samples - rep. no. 2

description:
For each RNA pool (e.g. control animals), three independent labeling procedures were carried out and three arrays were hybridized.
This is replica no. 2

value: left ventricula of 8 control (sedentary, untrained) animals; pool of RNA from 8 subjects


title: Dactyl 2.3


title: Mature zone 2.3

source_name: Mature zone of olfactory organ.


title: Dactyl 2.2


title: Mature zone 2.4


title: Mature zone 2.2


title: Mature zone 2.1

description: Raw intensity data for each experiment was normalized by first calculating the average intensity for each individual

hyb_protocol: Hybridization was done at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001).  Washing wash done twice in 2x SSC and 0.1% SDS for 10 min and twice in 1x SSC and 0.1%SDS for 15 min at room temperature.

scan_protocol: Signals from hybridized arrays were quantified using a STORM phosphorimaging device running ImageQuant software (Molecular Dynamics, Sunnyvale, CA).  ImageQuant,was used to segment each spot and calculate the volume signal intensity for each.

data_processing: Global Normalization (Cheadle et al., 2003)  was used to normalize raw intensity data.


title: Seasonal variation in leafy spurge crown bud gene expression (Nov 01)

tag: Ecodormant crown buds

tag: 1.5 year old garden-grown plants

tag: Natural lighting, supplemental watering as needed.

tag: Collected on Nov. 3, 2001


title: Dactyl 1.4


title: Mature zone 1.3


title: Dactyl 2.1

source_name: Leg Dactyl


title: Dactyl 1.2


title: Mature zone 1.2

description:
Raw intensity data for each experiment was normalized by first calculating the average intensity for each individual
dataset, and then calculating the average of the averages. This grand average was used as the basis for the computation of normalization factors that were subsequently applied to each experiment. The average of all normalized data thereafter equaled the grand average (Cheadle et al., 2003).


title: Dactyl 1.1


title: Dactyl 1.3

hyb_protocol: Hybridization was at 50˚C in 50 ml tubes in a hybridization oven as described in Barrett et al. (2001). Washing wash done twice in 2x SSC and 0.1% SDS for 10 min and twice in 1x SSC and 0.1%SDS for 15 min at room temperature.


title: Mature zone 1.1


title: Mature zone 1.4


title: PB_healthyControl_III

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of three healthy volunteers

data_processing: MAS 5.0 scaled to 150

label: Streptavidin-PE

source_name: CD3+ T cells, peripheral blood derived, healthy volunteers

tag: Pool of three samples (n=3);

tag: cells

value: CD3+ T cells, peripheral blood;

tag: healthy volunteers; gender

value: two females, one male; age:25 and 37 years old


title: BM_healthyControl_III

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of two healthy volunteers

source_name: CD3+ T cells, bone marrow derived, healthy volunteers

tag: Pool of two samples (n=2);

value: CD3+ T cells, bone marrow;

value: one male, one female; age:58 and 42 years old


title: PB_preTherapy_I

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of all SAA patients..

source_name: CD3+ T cells, peripheral blood derived, SAA patients

tag: Pool of four samples (n=4);

tag: gender

value: three female/one male;

tag: disease

value: (severe) aplastic anemia (SAA)


title: diet_Lung_4

description: female Spargue-Dawley rats, diet only for 7 days,  tissue: lung

source_name: normal lung tissue


title: CGH3_36, APC_T_D1.26

status: Public on Dec 25 2005

type: genomic

city: Lisbon

first: Joana

last: Cardoso

address: Av. Prof Egaz Moniz

country: Portugal

institute: Faculty of Medicine

description: Phi-29 amplified microdissected dysplatic colon mucosa DNA sample from an individual affected by Familial Adenomatous Polyposis with a known APC mutation.Details of the sample are available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.

data_processing: Log2 ratios of vsn normalized intensities defined as ch1 divided by ch2.

molecule: genomic DNA

tag: Phi-29 amplified genomic DNA from 1000 microdissected low grade dysplastic tumor colon mucosa cells

source_name: non-amplified commercial male (46, XY) genomic DNA


title: CGH3_38, APC_T_D5.11

tag: non-amplified commercial male (46, XY) genomic DNA


title: CGH3_40, APC_N_D5.14


title: CGH11_27, MYH_T_UK2.6

description: Phi-29 amplified microdissected dysplatic colon mucosa DNA sample from an individual affected by MYH Associated Polyposis with a known MYH mutation.Details of the sample are available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.


title: CGH3_23, APC_T_D5.1


title: CGH3_44, APC_T_D1.39D


title: CGH3_34, APC_N_D5.8H


title: CGH3_24, APC_T_D5.2


title: CGH3_25, APC_T_D5.4


title: CGH3_30, APC_N_D5.6


title: CGH3_32, APC_T_D5.8D


title: BM_preTherapy_IIa

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of both SAA patients..

source_name: CD3+ T cells, bone marrow derived, SAA patients

value: one female/one male;

tag: age

value: 70/64 years old;


title: PB_preTherapy_IIa

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of both SAA patients.


title: BM_preTherapy_I

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bonemarrow of all SAA patients..


title: CGH11_25, MYH_T_UK2.5


title: CGH11_24, MYH_N_UK2.4N


title: PB_postTherapy_IIb

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of both SAA patients in remission. Sample was compared to the same two patients prior therapy (PB_preTherapy_IIa).

source_name: CD3+ T cells, peripheral blood, SAA patients post therapy / in hematological remission

value: (severe) aplastic anemia (SAA) post therapy / in hematological remission


title: BM_postTherapy_IIb

description: Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of both SAA patients in remission. Sample was compared to the same two patients prior therapy (BM_preTherapy_IIb).

source_name: CD3+ T cells, bone marrow, SAA patients post therapy / in hematological remission


title: CGH11_26, MYH_N_UK2.5N


title: CGH11_23, MYH_T_UK2.4


title: cDNA array 0wt/+3wt set3 (dye-swap)

description: Comparison of gene expression profiles of 0 DPA and +3 DPA wild-type upland cotton ovules.

source_name: +3 DPA wide-type cotton ovule

tag: Extracted total RNA from +3 DPA wide-type cotton ovules

source_name: 0 DPA wide-type cotton ovule

tag: Extracted total RNA from 0 DPA wide-type cotton ovules


title: CGH11_20a, MYH_T_UK1.1


title: CGH11_21, MYH_T_UK1.2


title: CGH11_19, MYH_N_RE1.4


title: CGH11_22, MYH_T_UK2.3


title: CGH11_18, MYH_T_RE1.2


title: CGH11_17, MYH_T_RE1.1


title: CGH11_16, MYH_T_D8.6D


title: CGH11_15, MYH_N_D8.1N


title: CGH11_10, MYH_T_D8.3


title: CGH11_12, MYH_N_D8.6H


title: CGH11_11, MYH_T_D8.5.


title: CGH11_05, APC_T_D18.10


title: CGH11_04, APC_N_D18.4


title: CGH11_06, APC_N_D18.10N


title: CGH11_08, MYH_T_D8.2D


title: CGH11_09, MYH_N_D8.2N


title: CGH11_07, MYH_T_D8.1D


title: CGH11_03, APC_T_D18.2


title: CGH3_15, APC_N_D2.8


title: CGH3_3, 46XX

description: 3ng of a commercially available normal genomic DNA were amplified with Phi-29 enzyme (GenomiPhi kit-Amersham) in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.

source_name: 3ng of Phi-29 amplified commercial female (46, XX) genomic DNA

tag: Phi-29 amplified female (46, XX) genomic DNA


title: CGH3_14, APC_T_D2.7


title: CGH3_13, APC_T_D2.4


title: CGH11_32, MYH_T_UK3.2


title: CGH3_4, 46XX

source_name: 3ng of Phi-29 amplified commercial male (46, XY) genomic DNA

tag: Phi-29 amplified male (46, XY) genomic DNA


title: CGH3_1, 46XX

description: 2ng of a commercially available normal genomic DNA were amplified with Phi-29 enzyme (GenomiPhi kit-Amersham) in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.

source_name: 2ng of Phi-29 amplified commercial female (46, XX) genomic DNA


title: CGH3_2, 46XX

source_name: 2ng of Phi-29 amplified commercial male (46, XY) genomic DNA


title: CGH11_3, MYH_T_UK2.2


title: CGH11_31, MYH_T_UK3.1


title: CGH5_26, CON_N_XY+XX_XX

description: 2ng of a a commercially available normal genomic male (XY) DNA amplified with Phi-29 enzyme (GenomiPhi kit-Amersham), in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.

source_name: non-amplified commercial female (46, XX) genomic DNA


title: CGH5_27, CON_N_XY_XX

tag: non-amplified commercial female (46, XX) genomic DNA


title: CGH11_33, MYH_T_UK3.2H


title: CGH11_02, APC_T_D18.1l


title: CGH11_28, MYH_N_UK1.3


title: CGH3_12, APC_T_D2.2


title: CGH11_29, MYH_T_UK2.1


title: CGH4_74, CON_N_X+XX

description: 2ng of a a lymphoblastoid cell line genomic DNA containing a known X trisomy (XXX), in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.


title: CGH4_73, CON_N_5cl20XY

description: 2ng of a patient genomic DNA containing a known trisomy over 5 clones on chromosome 20, in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.


title: CGH4_75, CON_N_XXX+XX

description: 2ng of a 1 to 1 mixture of a lymphoblastoid cell line genomic DNA containing a known X trisomy (XXX)  with a commercial normal female (XX) genomic DNA, in order to simulate the amounts of a microdissected sample. Details of the sample can be found in the publications Cardoso J. et al., Nucleic Acids Res, 32: e146, 2004. Details of the experiment is available in the publication Cardoso J. et al., “Chromosomal instability in MYH- and APC-mutant adenomatous polyps”, Cancer Research, accepted for publication.


title: CGH4_54, APC_T_L2.7


title: CGH4_60, CON_N_N2


title: CGH4_58, APC_T_L2.13


title: CGH4_56, APC_N_L2.11


title: CGH4_57, APC_N_L2.12


title: CGH4_55, APC_T_L2.10


title: CGH4_61, CON_N_N3


title: CGH4_53, APC_T_L2.4


title: CGH4_23, APC_T_D12.19


title: CGH4_59, CON_N_N1


title: CGH4_51, APC_T_L2.2


title: CGH4_22, APC_T_D12.13


title: CGH4_16, APC_T_D9.44D


title: CGH4_17, APC_N_D9.44N


title: CGH4_21, APC_T_D12.5


title: CGH4_18, APC_T_D12.2


title: CGH4_24, APC_T_D12.29


title: CGH4_20, APC_T_D12.3.


title: _CGH4_1, APC_N_D1.56


title: CGH4_10, APC_T_D9.16


title: CGH4_25, APC_T_D12.45


title: CGH4_15, APC_T_D9.38


title: CGH4_52, APC_T_L2.3


title: CGH4_11, APC_N_D9.25


title: CGH4_12, APC_T_D9.26


title: CGH4_14, APC_T_D9.35


title: CGH4_13, APC_T_D9.32


title: CGH3_48, APC_T_D1.46


title: CGH3_50, APC_T_D1.55


title: CGH4_19, APC_N_D12.2N


title: CGH3_46, APC_N_D1.39N


title: Brn3a Knockout TG e13.5 U74Bv2 1

status: Public on Dec 24 2005

city: La Jolla

first: Eric

last: Turner

address: 9500 Gilman Dr., BSB 2077

department: Psychiatry

institute: University of California San Diego

description: Trigeminal ganglia were dissected, placed in RNAse inhibitor solution (RNAlater, Ambion) and frozen until enough tissue was harvested to be pooled by genotype. Approximately 10-12 ganglia were pooled for a single analysis, which was extracted using the RNeasy system (Qiagen).

data_processing: MAS 5.0

label: Affymetrix

source_name: e13.5 Trigeminal Ganglion

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


title: Brn3a Knockout TG e13.5 U74Bv2 2


title: Brn3a Heterozygote TG e13.5 U74Bv2 2

label: Affymetrix Protocol

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


title: Brn3a Wildtype TG e13.5 U74Av2 2

tag: Brn3a wildtype trigeminal ganglia pooled from e13.5 mouse embryos.


title: Brn3a Wildtype TG e13.5 U74Av2 1


title: Heterozygote TG e13.5 U74Bv21


title: 65

city: Ithaca

first: Ruairidh

middle: J

last: Sawers

address: Tower Rd

institute: Boyce Thompson Institute

description: A number of taxa utilize C4 photosynthesis, to limit the impact of photorespiration upon photosynthetic performance. In order to achieve a local elevation of CO2 concentration, maize plants possess two photosynthetic cell types. Rubisco accumulation is restricted to bundle sheath (BS) cells that surround the leaf veins. Carbon fixation occurs initially in adjacent mesophyll (ME) cells. C4 compounds are transported into the BS cells where they are subsequently decarboxylated, releasing CO2. Although the major components of the C4 pathway have been well characterized, less is known about further metabolic partitioning in the maize leaf. Microarray hybridizations have been performed in order to further investigate metabolic differences between BS and ME cell types. BS strands and ME protoplasts were isolated from the leaves of 10 day old maize seedlings by mechanical disruption and enzymatic digestion respectively. To control for differences arising from these different protocols, total leaf (TO) and total leaf stress (ST) samples were also isolated. The ST sample was subjected to the same treatments as the ME sample, with the omission of cell-wall degrading enzymes. Leaves for the TO sample were harvested as for the BS strand sample. An interwoven loop design was used to compare the four treatment groups. A biological group consisted of a growth of plants from which pooled individuals were taken for the four treatments. Six biological replicates (groups) were used. Labeling was performed using the Genisphere Array 900-MPX kit according to the manufacturer's protocol. Post hybridization washes were performed according to the recommendations of the Maize Oligo Array Project. Scan settings were used for detection of moderate to high expression signals (gain ~ 60%. power 90%). Following hybridization with TO cDNA, ~1/3 of features provided signal above twice background and below saturation.

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Zea mays

growth_protocol: 10 days, 16h Light:8h Dark, 500umol m-2 s-1 light, 28C

treatment_protocol: Mesophyll prep

tag: Zea mays, Leaf, Development


title: 59


title: 48

treatment_protocol: Stress

treatment_protocol: Bundle sheath prep


title: Brn3a Heterozygote TG e13.5 U74Av2 2


title: Brn3a Knockout TG e13.5 U74Av2 2

tag: Brn3a knockout trigeminal ganglia pooled from e13.5 mouse embryos.


title: 50


title: 67


title: Brn3a Wildtype TG e13.5 U74Bv2 1


title: 61


title: Brn3a Knockout TG e13.5 U74Av2 1


title: 70


title: 55


title: 54


title: 69


title: 63


title: 47


title: 53


title: 57


title: 66


title: 60


title: 62


title: 68


title: 49


title: 56


title: Brn3a Heterozygote TG e13.5 U74Av2 1


title: 58


title: 51


title: 520right

status: Public on Dec 22 2005

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

description: sulfur mustard exposed mouse ear

hyb_protocol: Spiked controls were added to 15 µg of fragmented cRNA before overnight hybridization using 10 µg of cRNA.

scan_protocol: Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Agilent GeneArray Scanner driven by Microarray Suite 5.0 software (Affymetrix).  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface.

data_processing: Arrays were then washed and stained with streptavidin-phycoerythrin before being scanned on an Agilent GeneArray Scanner.  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface.  All arrays were scaled to a target intensity of 150 (using Affymetrix Microarray Suite 5.0 array analysis software), and internal controls were assessed to determine array quality.

label: biotin and streptavidin/phycoerythrin

source_name: ear tissue

label_protocol: 10 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated nucleotides (Enzo Kits from Affymetrix), resulting in approximately 100-fold amplification of cRNA.  The target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/ manual/expression_manual.affx).

growth_protocol: A single 5 microL application of SM (0.08 mg dose, 0.5 micromoles) in methylene chloride was applied topically to the inner surface of the right ear.  The left ear (vehicle control) was exposed to 5 microL of methylene chloride only.  For drug treatment, animals were administered 10 microL of dimercaprol (6.25 mg dose, 50.3 micromoles), 30 microL of OHV (0.585 mg dose, 1.995 micromoles), or 20 microL of indomethacin (1.34 mg dose, 3.74 micromoles) in ethanol 15 minutes prior to SM challenge.  A group of animals received only drug on the right ear and ethanol (drug vehicle) on the left ear.  A group of untreated, unexposed animals served as naïve controls.  At 24 hr post-exposure, animals were euthanized and an 8 mm diameter skin biopsy was obtained.  The skin biopsy was weighed and immediately frozen in liquid nitrogen.

extract_protocol: RNA was isolated from frozen mouse ear biopsies using the RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  The quality and amount of RNA was monitored throughout processing with an Agilent Bioanalyzer (Agilent, Palo Alto, CA) and a NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, DE).

treatment_protocol:
0.6 mg Octylhomovanillamide
24 hr

tag: CD1 male mice 25-35 g


title: 52


title: Liver_KnockOut_3

city: Los Angeles

first: Nicole

middle: Kim

last: MacLennan

address: 10833 LeConte Ave

department: Pediatrics

institute: University of California, Los Angeles

description: GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values) was used to generate the data.

data_processing: GCOS data analyzed with dChip.

treatment_protocol: Glycerol kinase knockout mice.

tag: Strain

value: Inbred C57BL/6J;

tag: Gender

value: male;

tag: Age

value: day of life 3;

tag: Tissue

value: liver


title: Liver_KnockOut_1


title: 64


title: Liver_WildType_2

description:
GeneChip Operating Software (GCOS) 1.2
software (Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values) was used to generate the data.

treatment_protocol: Age-matched wildtype littermates of glycerol kinase knockout mice.


title: 520left

description: sulfur mustard exposed mouse ear

treatment_protocol:
Ethanol
24 hr


title: 519right

description: sulfur mustard exposed mouse ear


title: 518right

description: sulfur mustard exposed mouse ear


title: Liver_WildType_4


title: Liver_WildType_3


title: 515right

description: sulfur mustard exposed mouse ear

treatment_protocol:
1.34 mg Indomethacin
24 hr


title: 517right

description: sulfur mustard exposed mouse ear


title: Liver_KnockOut_4


title: Liver_WildType_1


title: 514right

description: sulfur mustard exposed mouse ear


title: 512right

description: sulfur mustard exposed mouse ear


title: Liver_KnockOut_2


title: 516right

description: sulfur mustard exposed mouse ear


title: 511right

description: sulfur mustard exposed mouse ear


title: 515left

description: sulfur mustard exposed mouse ear


title: 506right

description: sulfur mustard exposed mouse ear

treatment_protocol:
6.25 mg Dimercaprol
24 hr


title: 507right

description: sulfur mustard exposed mouse ear


title: 502right

description: sulfur mustard exposed mouse ear

treatment_protocol:
Naïve
24 hr


title: 503right

description: sulfur mustard exposed mouse ear


title: 510right

description: sulfur mustard exposed mouse ear


title: 503left

description: sulfur mustard exposed mouse ear


title: 502left

description: sulfur mustard exposed mouse ear


title: 508right

description: sulfur mustard exposed mouse ear


title: 501left

description: sulfur mustard exposed mouse ear


title: 507left

description: sulfur mustard exposed mouse ear


title: 36left

description: sulfur mustard exposed mouse ear

treatment_protocol:
Methylene Chloride
24 hr


title: 37right

description: sulfur mustard exposed mouse ear

treatment_protocol:
0.08 mg Sulfur Mustard
24 hr


title: 38left

description: sulfur mustard exposed mouse ear


title: 30left

description: sulfur mustard exposed mouse ear


title: 33right

description: sulfur mustard exposed mouse ear

treatment_protocol:
0.6 mg Octylhomovanillamide 15 min before 0.08 mg Sulfur Mustard
24 hr


title: 33left

description: sulfur mustard exposed mouse ear


title: 36right

description: sulfur mustard exposed mouse ear


title: 29right

description: sulfur mustard exposed mouse ear


title: 19right

description: sulfur mustard exposed mouse ear

treatment_protocol:
1.34 mg Indomethacin 15 min before 0.08 mg Sulfur Mustard
24 hr


title: 22right

description: sulfur mustard exposed mouse ear


title: 37left

description: sulfur mustard exposed mouse ear


title: 27left

description: sulfur mustard exposed mouse ear


title: 28right

description: sulfur mustard exposed mouse ear


title: 18right

description: sulfur mustard exposed mouse ear


title: 27right

description: sulfur mustard exposed mouse ear


title: 17left

description: sulfur mustard exposed mouse ear


title: 17right

description: sulfur mustard exposed mouse ear


title: 22left

description: sulfur mustard exposed mouse ear


title: 26left

description: sulfur mustard exposed mouse ear


title: 29left

description: sulfur mustard exposed mouse ear


title: 19left

description: sulfur mustard exposed mouse ear


title: 16right

description: sulfur mustard exposed mouse ear


title: 28left

description: sulfur mustard exposed mouse ear


title: 12right

description: sulfur mustard exposed mouse ear

treatment_protocol:
6.25 mg Dimercaprol 15 min before 0.08 mg Sulfur Mustard
24 hr


title: 18left

description: sulfur mustard exposed mouse ear


title: 30right

description: sulfur mustard exposed mouse ear


title: 11left

description: sulfur mustard exposed mouse ear


title: 10left

description: sulfur mustard exposed mouse ear


title: 11right

description: sulfur mustard exposed mouse ear


title: 21right

description: sulfur mustard exposed mouse ear


title: 8right

description: sulfur mustard exposed mouse ear


title: 3right

description: sulfur mustard exposed mouse ear


title: 7left

description: sulfur mustard exposed mouse ear


title: 6right

description: sulfur mustard exposed mouse ear


title: 2left

description: sulfur mustard exposed mouse ear


title: 9left

description: sulfur mustard exposed mouse ear


title: 5right

description: sulfur mustard exposed mouse ear


title: 38leftB

description: sulfur mustard exposed mouse ear


title: 1right

description: sulfur mustard exposed mouse ear


title: 36leftB

description: sulfur mustard exposed mouse ear


title: 9right

description: sulfur mustard exposed mouse ear


title: 36rightB

description: sulfur mustard exposed mouse ear


title: 37leftB

description: sulfur mustard exposed mouse ear


title: 1left

description: sulfur mustard exposed mouse ear


title: 30rightB

description: sulfur mustard exposed mouse ear


title: 10right

description: sulfur mustard exposed mouse ear


title: 8left

description: sulfur mustard exposed mouse ear


title: 28leftB

description: sulfur mustard exposed mouse ear


title: 27leftB

description: sulfur mustard exposed mouse ear


title: 33rightB

description: sulfur mustard exposed mouse ear


title: 28rightB

description: sulfur mustard exposed mouse ear


title: 29leftB

description: sulfur mustard exposed mouse ear


title: 29rightB

description: sulfur mustard exposed mouse ear


title: 3left

description: sulfur mustard exposed mouse ear


title: 37rightB

description: sulfur mustard exposed mouse ear


title: 27rightB

description: sulfur mustard exposed mouse ear


title: 30leftB

description: sulfur mustard exposed mouse ear


title: 33leftB

description: sulfur mustard exposed mouse ear


title: 21rightB

description: sulfur mustard exposed mouse ear


title: 26leftB

description: sulfur mustard exposed mouse ear


title: 22rightB

description: sulfur mustard exposed mouse ear


title: 22leftB

description: sulfur mustard exposed mouse ear


title: 19rightB

description: sulfur mustard exposed mouse ear


title: 18rightB

description: sulfur mustard exposed mouse ear


title: 17leftB

description: sulfur mustard exposed mouse ear


title: 16rightB

description: sulfur mustard exposed mouse ear


title: 19leftB

description: sulfur mustard exposed mouse ear


title: 11leftB

description: sulfur mustard exposed mouse ear


title: 17rightB

description: sulfur mustard exposed mouse ear


title: 10rightB

description: sulfur mustard exposed mouse ear


title: 11rightB

description: sulfur mustard exposed mouse ear


title: 18leftB

description: sulfur mustard exposed mouse ear


title: 10leftB

description: sulfur mustard exposed mouse ear


title: 12rightB

description: sulfur mustard exposed mouse ear


title: 9rightB

description: sulfur mustard exposed mouse ear


title: 9leftB

description: sulfur mustard exposed mouse ear


title: 8leftB

description: sulfur mustard exposed mouse ear


title: 6rightB

description: sulfur mustard exposed mouse ear


title: 5rightB

description: sulfur mustard exposed mouse ear


title: 7leftB

description: sulfur mustard exposed mouse ear


title: 3leftB

description: sulfur mustard exposed mouse ear


title: colon normal vs carcinoma 2

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

department: Pathology

country: South Korea

institute: University of Ulsan College of Medicine

description: colon cancer, adenoma, microdissected using LCM, amplification

hyb_protocol: Hybridization was done with formamide hybridization buffer overnight in a 42 ℃ .

scan_protocol: The arrays were scanned with a GenePix 4000B scanner

data_processing: The resulting images were analyzed using the ImaGeneTM 4.0 software.

source_name: microdissected colon normal cell

label_protocol: The probe labeling was done using the amine-modified random primer aminoallyl method

extract_protocol: Deparaffinized sections are incubated at 70 ℃ for 1 hr, treated Proteinase K and extracted with TRIzol. The first strand are synthesized using T7dT primers and the second strand are  treated RNaseH and are synthesized using T3N6 primers.  Then the double stranded DNA was applied PCR with T3 and T7 promoter primer. Following the PCR amplification, aRNA synthesis (in vitro transcription) was performed using an T7 transcription kit.

treatment_protocol: microdissected normal colonic mucosa cells from formalin-fixed, paraffin-embedded sections.

tag: human normal colon byopsies

source_name: microdissected colon carcinoma cell

treatment_protocol: microdissected carcinoma colonic mucosa cells from formalin-fixed, paraffin-embedded sections.

tag: human carcinoma colon byopsies


title: 3rightB

description: sulfur mustard exposed mouse ear


title: colon normal vs carcinoma 4

source_name: microdissedted colon carcinoma cell


title: colon normal vs carcinoma 3


title: 8rightB

description: sulfur mustard exposed mouse ear


title: colon normal vs adenoma 2

label_protocol: The probe labeling was done using the amine-modified random primer aminoallyl method.

source_name: microdissedted colon adenoma cell

treatment_protocol: microdissected adenoma colonic mucosa cells from formalin-fixed, paraffin-embedded sections.

tag: human adenoma colon byopsies


title: colon normal vs adenoma 4

source_name: microdissected colon adenoma cell

treatment_protocol: microdissected adenoma colonic mucosaadenoma cells from formalin-fixed, paraffin-embedded sections.


title: colon normal vs carcinoma 1


title: C57BL/6 H.pylori vs. C57BL/6 Cholesterol H.pylori

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: Total RNA was prepared using the RNeasy protocol with on-column DNAse digestion (Qiagen, Hilden, Germany) and confirmed to be intact and free of contaminating DNA using an Agilent 2100 bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA). A custom tailored 'in situ' synthesized 60-mer oligonucleotide microarray (Agilent) comprising 8014 murine genes with immunological focus was used for expression profiling. RNA was amplified and labeled using a reverse-transcriptase/T7 polymerase linear amplification labeling kit (Agilent), and 1.5 mg of respective cRNAs labeled either with Cy3 or Cy5 were hybridized for 16 h at 65°C. Slides were used and processed according to the manufacturer's manuals.

data_processing: Features were extracted with an Image Analysis software (Version A.7.5.1, Agilent). Intensities were normalized by local background correction and by rank consistency filtering with a combination of linear and LOWESS normalization. Data analysis was performed with Rosetta Resolver Biosoftware (Build 5.1.0.0.163, Rosetta Biosoftware, Seattle, WA).

source_name: C57BL/6 H.pylori

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were infected with a single oral dose of 9.5 × 10e8 Hp76 cells suspended in PBS and 0.2 M NaHCO3. The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.

source_name: C57Bl/6 Cholesterol H.pylori

tag: Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were treated with 2% or 0% cholesterol diet (custom product (Altromin, Lage, Germany), initiated 14 days before infection. Mice were infected with a single oral dose of 9.5 × 10e8 Hp76 cells suspended in PBS and 0.2 M NaHCO3. The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.


title: 2leftB

description: sulfur mustard exposed mouse ear


title: 1rightB

description: sulfur mustard exposed mouse ear


title: colon normal vs adenoma 1


title: colon normal vs adenoma 3


title: 1leftB

description: sulfur mustard exposed mouse ear


title: C57BL/6 Cholesterol H.pylori vs. C57BL/6 H.pylori


title: nmd treated 1

status: Public on Dec 21 2005

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

institute: University of Milan

description: We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age.

data_processing: MicroArray Suite 5.0 (Affymetrix)

source_name: lumbar spinal cord

tag: B6.BKS Ighmbp2nmd-2J mouse

tag: 6 weeks of age

tag: male

tag: Intratechally transplanted with Spinal cord derived Neural Stem Cells


title: Mouse embryonic fibroblasts 15.5E wild type vs Wrn-PARP1 double mutant (duplicate)

city: Quebec

first: Michel

last: Lebel

state: Qc

address: 2705 Laurier Blvd, Local T-2-04

department: Centre Hospitalier de l’Université Laval (CHUL)

country: Canada

institute: Centre de Recherche du CHU de Québec

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufactures instructions.

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent). The data was then extracted from images by the Feature Extraction software 6.1 (Agilent).

data_processing: The GeneSpring software (Agilent) was used to generate lists of selected genes and for different statistical methods. An Intensity-Dependent Normalization (known as Lowess normalization) was applied to correct for artifacts caused by nonlinear rates of dye incorporation as well as inconsistencies of the relative fluorescence intensity between some red and green dyes.

molecule: cytoplasmic RNA

source_name: Mouse embryonic fibroblasts, 15.5 days embryos, wild type

label_protocol: Protocol from Agilent

growth_protocol: Mouse embryonic cells were maintained in DMEM, 10% calf serum, 1% pen/strep. Cytoplasmic RNA was extracted at the second passage in culture.

extract_protocol: Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

value: 129/Sv-Black Swiss wild type

tag: Pool of three healthy embryos

tag: mouse embryonic fibroblasts derived from embryonic tissues

source_name: Mouse embryonic fibroblasts, 15.5 days embryos, Wrn-PARP1 double mutant


title: nmd treated 2


title: nmd untreated 3

description:
We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age.
Frozen tissue was stored at -80°C. Total RNA was purified from tissue, using the EUROZol Kit (EuroClone Ltd., United Kingdom) following the manufacturer’s instructions. Total RNA (5 ug) was reverse-transcribed with a cDNA synthesis kit in the presence of SuperScript II RT (Invitrogen-Life Technologies, Inc.) and an oligo dT-T7 primer (Affymetrix Inc., Santa Clara, CA). After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air-dried and re-suspended in 12 uL of diethyl pyrocarbonate-treated water and quantified by spectrophotometer measurement. An aliquot of each sample was conserved for gel electrophoresis and for inspection of RNA quality (i.e., 28S:18S RNA ratio). 10 ul was used for the IVT (In Vitro Transcription) amplification reaction, in the presence of biotinylated nucleotides (Enzo Biochem Inc.). Labeled cRNA (15 ug) was fragmented by incubation at 94°C for 35 minutes in fragmentation buffer (GeneChip Sample Cleanup, Qiagen) and the fragmented cRNA was then hybridized competitively against the Affymetrix 430 2.0 Array oligonucleotide array. Hybridization occurred at 47°C overnight. The arrays were scanned using a GeneArray 2500 Scanner (Affymetrix) and analyzed using MicroArray Suite 5.0 (Affymetrix). All experiments were validated after direct measures of cRNA quality: 5':3' ratios for beta-actin and for GAPDH (determined from Affymetrix chip hybridization analysis) are indirect indicators of overall RNA preservation. The default parameters were used for the statistical algorithm and for probe set scaling. The target intensity was set to 1,000 to normalize expression levels across all samples.


title: Mouse embryonic fibroblasts 15.5E wild type vs PARP-1 null (duplicate)

source_name: Mouse embryonic fibroblasts, 15.5 days embryos, PARP-1 null

value: 129/Sv-Black Swiss PARP-1 null


title: Mouse embryonic fibroblasts 15.5E wild type vs Wrn helicase mutant (duplicate)

source_name: Mouse embryonic fibroblasts, 15.5 days embryos, Wrn helicase in-frame deletion

value: 129/Sv-Black Swiss Wrn helicase in-frame deletion mutant


title: Mouse embryonic fibroblasts 15.5E wild type vs Wrn helicase mutant

source_name: mouse embryonic fibroblasts, 15.5 days embryos, wild type

source_name: mouse embryonic fibroblasts, 15.5 days embryos, Wrn helicase in-frame deletion


title: CGH_Mouse54_26G

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Mouse colon tumor 26G gemcitabine resistant.

source_name: Mouse liver DNA

source_name: Mouse tumor 26G DNA


title: CGH_Mouse53_26G


title: nmd untreated 2


title: nmd untreated 1


title: nmd treated 3


title: wild-type mouse 2

tag: wild-type littermate of B6.BKS Ighmbp2nmd-2J mice


title: wild-type mouse 3


title: CGH_Mouse52_26A

description: Mouse colon tumor 26A gemcitabine sensitive.

source_name: Mouse tumor 26A DNA


title: Bl6_WAP_IFNy_3

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

institute: Institute for medical microbiology

description: BALB/c BMDM naive

data_processing: Affymetrix Microarray Suite version 5.0, dchip PM-MM Difference Model

source_name: Macrophages

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

extract_protocol: Standard TRIzol

tag: C57BL/6 BMDM stimulated overnight with 50 IU/ml IFNg and infected with WA(pYV)


title: Bl6_WAP_IFNy_2

description: BALB/c BMDM naive


title: Bl6_WAP_1

description: BALB/c BMDM naive

tag: C57BL/6 BMDM infected with WA(pYV)


title: Bl6_WAP_IFNy_1

description: BALB/c BMDM naive


title: Bl6_p60_IFNy_2

description: BALB/c BMDM naive

tag: C57BL/6 BMDM stimulated overnight with 50 IU/ml IFN-g and infected with WA(pTTS,pP60)


title: Bl6_WAP_3

description: BALB/c BMDM naive


title: Bl6_WAP_2

description: BALB/c BMDM naive


title: Mouse embryonic fibroblasts 15.5E wild type vs PARP-1 null

tag: Strain


title: Bl6_p60_IFNy_3

description: BALB/c BMDM naive


title: Mouse embryonic fibroblasts 15.5E wild type vs Wrn-PARP1 double mutant

value: 129/Sv-Black Swiss Wrn-PARP1 double mutant


title: Bl6_p60_3

description: BALB/c BMDM naive

tag: C57BL/6 BMDM infected with WA(pTTS,pP60)


title: Bl6_Mock_IFNy_2

description: BALB/c BMDM naive

tag: C57BL/6 BMDM stimulated overnight with 50 IU/ml IFN-g


title: Bl6_Mock_3

description: BALB/c BMDM naive

tag: C57BL/6 BMDM naive


title: wild-type mouse 1


title: Bl6_p60_1

description: BALB/c BMDM naive


title: Bl6_Mock_IFNy_3

description: BALB/c BMDM naive


title: Bl6_Mock_1

description: BALB/c BMDM naive


title: Bc_WAP_IFNy_3

description: BALB/c BMDM naive

tag: BALB/c BMDM stimulated overnight with 50 IU/ml IFN-g and infected with WA(pYV)


title: Bl6_Mock_2

description: BALB/c BMDM naive


title: Bl6_p60_2

description: BALB/c BMDM naive


title: Bl6_p60_IFNy_1

description: BALB/c BMDM naive


title: Bl6_Mock_IFNy_1

description: BALB/c BMDM naive


title: Bc_WAP_IFNy_1

description: BALB/c BMDM naive


title: NG014_b

city: Beerse

first: Pieter

middle: Johan

last: Peeters

address: Turnhoutseweg 30

department: Internal Medicine

country: Belgium

institute: J&J Pharmaceutical R&D

description: Laser captured visceral sensory neurons.

source_name: nodose ganglion

label_protocol: Approximately 12 microgram of amplified RNA was processed to produce biotinylated cRNA targets.

extract_protocol: approximately 150 Laser Capture Microdissected neurons were collected in RLT buffer.

treatment_protocol: normal standard housing conditions

tag: BALB/c


title: Bc_WAP_1

description: BALB/c BMDM naive

tag: BALB/c BMDM infected with WA(pYV)


title: Bc_WAP_2

description: BALB/c BMDM naive


title: Bc_WAP_IFNy_2

description: BALB/c BMDM naive


title: Bc_p60_IFNy_3

description: BALB/c BMDM naive

tag: BALB/c BMDM stimulated overnight with 50 IU/ml IFN-g ans infected with WA(pTTS,pP60)


title: Bc_p60_1

description: BALB/c BMDM naive

tag: BALB/c BMDM infected with WA(pTTS, pP60)


title: Bc_p60_3

description: BALB/c BMDM naive


title: Bc_p60_IFNy_2

description: BALB/c BMDM naive


title: Bc_p60_IFNy_1

description: BALB/c BMDM naive


title: Bc_WAP_3

description: BALB/c BMDM naive


title: Bc_p60_2

description: BALB/c BMDM naive


title: NG007_b


title: Bc_Mock_IFNy_2

description: BALB/c BMDM naive

tag: BALB/c BMDM stimulated with 50 IU/ml IFN-g overnight


title: NG003_b


title: Bc_MOCK_IFNy_4

description: BALB/c BMDM naive


title: Bc_Mock_4

description: BALB/c BMDM naive

tag: BALB/c BMDM naive


title: Bc_Mock_IFNy_1

description: BALB/c BMDM naive


title: cardiomyocyte SRF-null 2

city: Milwaukee

first: Ravi

middle: P.

last: Misra

state: WI

address: 8701 Watertown Plank Road

department: Biochemistry

institute: Medical College of Wisconsin

description: To investigate the role of Serum Response Factor (SRF) in the heart, we utilized the Cre-loxP system to generate SRF-null neonatal mouse cardiomyocytes.

data_processing: Values normalized using dChip v1.3

source_name: explanted neonatal cardiomyocyte


title: NG008_b

data_processing: Affymetrix Microarray Suite version 5.0


title: Bc_Mock_2

description: BALB/c BMDM naive


title: cardiomyocyte control 3


title: cardiomyocyte SRF-null 1


title: Cardiomyocyte control 2

source_name: Explanted neonatal cardiomyocyte


title: cardiomyocyte control 1


title: Bc_Mock_1

description: BALB/c BMDM naive


title: S1_d3PDa2

city: BORDEAUX

first: Helene

last: BOEUF

country: France

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM PD169316. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.

source_name: Embryonic stem cell line


title: NG008_c

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

extract_protocol: approximately 150 Laser Capture Microdissected neurons were put in RLT buffer.


title: 3D7 Sir2 knockout asexual blood stage 24hr

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

country: Australia

institute: The Walter and Eliza Hall Institute

description: SIR2 knockout on 3D7 background at 24 hours

data_processing: GCRMA, RMA and MOID

organism: Plasmodium falciparum

source_name: SIR2 knockout parasites


title: 3D7 PfRh2b knockout asexual blood stage 48hr_rep2

description: PfRh2b knockout on 3D7 background, replicate 2

source_name: PfRh2b knockout parasites


title: NG014_c


title: D10 wildtype asexual blood stage 48hr_rep1

description: D10 wildtype at 48 hours, replicate 1

source_name: D10 wildtype

tag: D10 wildtype at 48 hours, replicate 1


title: cardiomyocyte SRF-null 3


title: 3D7 wildtype asexual blood stage 48hr_rep2

description: 3D7 wildtype at 48 hours, replicate 2

source_name: 3D7 wildtype

tag: 3D7 wildtype at 48 hours, replicate 2


title: NG007_c


title: NG005_c


title: Bc_MOCK_IFNy_3

description: BALB/c BMDM naive


title: 3D7 EBA175 knockout asexual blood stage 48hr

description: 3D7 parasites with EBA175 disrupted

source_name: EBA175 knockout

tag: 3D7 parasites with EBA175 disrupted


title: D4_d3PD

description: D4 ES cell line, feeder-dependent, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells, cultured twice without feeders, were diluted at 10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM PD169316. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.


title: S1_d3PDa1


title: S1_d3a2

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000cells/ml in ES cell medium without LIF. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.


title: NG015_c


title: NG001_c


title: D4_d3

description: D4 ES cell line, feeder-dependent, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells, cultured twice without feeders, were diluted at 10 000 cells/ml in ES cell medium without LIF. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.


title: NG010_b


title: NG003_c


title: NG010_c


title: D10 wildtype asexual blood stage 48hr_rep2

description: D10 wildtype at 48 hours, replicate 2

tag: D10 wildtype at 48 hours, replicate 2


title: DRG014_b

source_name: dorsal root ganglion


title: NG012_c


title: DRG006_c


title: 3D7 EBA140 knockout asexual blood stage 48hr

description: 3D7 parasites with EBA140 disrupted

source_name: EBA140 knockout

tag: 3D7 parasites with EBA140 disrupted


title: DRG010_b


title: DRG011_c


title: S1_d3a1

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of the array was arbitrarily set to 300.


title: 3D7 PfRh2b knockout asexual blood stage 48h_rep1

description: PfRh2b knockout on a 3D7 background, replicate 1

source_name: PfRh2b knockout parasite


title: DRG014_c


title: NG013_c


title: DRG003_b


title: 3D7 wildtype asexual blood stage 48hr_rep1

description: 3D7 wildtype at 48 hours, replicate 1

source_name: wildtype 3D7 parasites

tag: 3D7 wildtype at 48 hours, replicate 1


title: DRG008_b


title: 3D7 wildtype asexual blood stage 24hr

description: 3D7 wildtype at 24 hours

tag: 3D7 wildtype at 24 hours


title: DRG003_c


title: DRG010_c


title: DRG008_c


title: DRG037_a

extract_protocol: Whole ganglia were put in RLT buffer.


title: DRG002_c


title: Gemcitabine resistant tumor (26G-1) x Gemcitabine resistant tumor (26G-1)

description: One solid tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G".

source_name: Colon tumor 26G-1


title: NG023_a


title: DRG026_a


title: NG039_a


title: DRG084_a


title: DRG070_a


title: Non resistant tumor x Gemcitabine resistant tumor

source_name: Colon tumor 26A-5

source_name: Colon tumor 26G-6


title: DRG005_c


title: NG073_a


title: Atm-/- 120 min post IR, B

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: Atm-/- murine lymph node, 120 min post-IR, replicate B

source_name: murine lymph node


title: DRG015_c


title: NG002_c

source_name: nodose ganglion


title: DRG006_b


title: NG046_a


title: Atm-/- 30 min post IR, A

description: Atm-/- murine lymph node, 30 minpost-IR, replicate A


title: Atm-/- untreated, C

description: Atm-/- murine lymph node, untreated, replicate C


title: NG036_a


title: Cell line cA8 x Cell line cG7

description: One solid tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G". Afterwards two cell lines were mantained from the two tumor types, the resistant and the non resistant.

source_name: Cell line cA8 (non gemcitabine resistant)

source_name: Cell line cG7 (gemcitabine resistant)


title: Atm-/- untreated, B

description: Atm-/- murine lymph node, untreated, replicate B


title: Atm+/+ 120 min post IR, B

description: Atm+/+ murine lymph node, 120 min post IR, replicate B