title: Adult Ovary biological rep3

description:
The ovaries only, excluding the spermatheca, uterus and associated tissues.
amplification: 1-round

source_name: Adult Ovary

value: Canton-S, 30 female flies, 7 days old


title: Adult Ovary biological rep2

status: Public on Jun 21 2007

type: RNA

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol)  were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G.

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Wild-type Drosophila melanogaster (Canton S strain) were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. To facilitate the collection of accurately staged adults, a laying population of around 12 males and 12 females were transferred to fresh vials daily. When adults subsequently emerged, they were transferred to fresh vials on the day of emergence, and used 7 days later. Where larvae were used, these were third instar.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Flies were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: tissue


title: Adult Ovary biological rep4


title: Adult Ovary biological rep1


title: Adult Testes biological rep1

description:
The testes only, excluding the accessory glands and associated tissues.
amplification: 1-round

source_name: Adult Testes

value: Canton-S 60 male flies, 7 days old


title: Larvae Wandering Tubules biological rep3

description:
Tubules dissected from third-instar wandering larvae as above.
amplification: 1-round

source_name: Larval Wandering Malpighian Tubule

value: Canton-S, 30 wandering third instar larvae


title: Adult Testes biological rep3


title: Larvae Wandering Tubules biological rep2


title: Adult Whole Fly biological rep1

description:
The Canton-S adult flies.
amplification: 1-round

source_name: Adult Whole Fly

value: Canton-S, 12 female and  12 male flies, 7 days old


title: Adult Head biological rep4

description:
The head capsule, including the eyes and brain.
amplification: 1-round

source_name: Adult Head

value: Canton-S, 50 female and  50 male flies, 7 days old


title: Adult Head biological rep3


title: Adult Head biological rep2


title: Larval Wandering fat body biological rep3

description:
The subcutaneous fat-body, dissected from third-instar wandering larvae.
amplification: 1-round

source_name: Larval Wandering fat body


title: Larval Wandering fat body biological rep4


title: Larval Wandering fat body biological rep1


title: Larval Wandering fat body biological rep2


title: Larvae Wandering Tubules biological rep1


title: Adult Brain biological rep4

description:
The brain, without the thoracic ganglia or eyes.
amplification: 1-round

source_name: Adult Brain

value: Canton-S, 60 female and  60 male flies, 7 days old


title: Adult Crop biological rep1

description:
The crop
amplification: 1-round

source_name: Adult Crops

value: Canton-S, 40 female and  40 male flies, 7 days old


title: Adult Head biological rep1


title: Adult Accessory gland biological rep4

description:
The accessory glands only
amplification: 1-round

source_name: Adult Accessory gland

value: Canton-S, 25 female and  25 male flies, 7 days old


title: Adult Crop biological rep2

description:
The crop
amplification: 1-round


title: Adult Brain biological rep2


title: Adult Brain biological rep3


title: Adult Crop biological rep3

description:
The crop
amplification: 1-round


title: Adult Brain biological rep1


title: Adult Mid Gut biological rep2

description:
The midgut, extending from behind the proventriculus to just in front of the insertion of the Malpighian tubules
amplification: 1-round

source_name: Adult Midgut


title: Adult Accessory gland biological rep3


title: Adult Mid Gut biological rep4


title: Adult Mid Gut biological rep3


title: Adult Hind Gut biological rep1

description:
The hindgut, from just behind the insertion of the Malpighian tubules, and including the rectum, severing at the anus
amplification: 1-round

source_name: Adult Hindgut


title: Adult Hind Gut biological rep2


title: Adult Accessory gland biological rep2


title: Adult Accessory gland biological rep1


title: Adult Hind Gut biological rep4


title: Adult Mid Gut biological rep1


title: Adult Hind Gut biological rep3


title: Adult Crop biological rep4

description:
The crop
amplification: 1-round


title: STHdhQ111/Q111-B

status: Public on Jun 20 2007

city: Boston

first: Marcy

middle: E

last: MacDonald

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Research

country: USA

institute: Mass General Hospital

description: Mutant striatal cells

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA Log

label: Biotin

organism: Mus musculus

source_name: Hdh knock-in mice striatal cells

label_protocol: Affymetrix protocol

extract_protocol: Trizol

tag: Hdh mutant (111/111-polyQ) 2


title: STHdhQ111/Q111-A

description: Mutant striatal cells

tag: Hdh mutant (111/111-polyQ) 1


title: STHdhQ7/Q7-A

description: Wild-type striatal cells

tag: Wild-type control 1


title: STHdhQ7/Q7-3NP-C

description: Wild-type striatal cells treated with 3NP

tag: Wild-type 3NP (1mM, 48hr) treated 3


title: mARF10 rep1

status: Public on Jun 17 2007

city: Corvallis

first: Hiro

last: Nonogaki

state: OR

address: 4017 ALS Bldg, Dept. of Horticulture, Oregon State University

department: Horticulture

institute: Oregon State University

description: The ARF10 gene, including the coding region (2.3 kb) and the 5’ upstream region (3 kb) (ARF10:ARF10), was amplified by PCR, and then four mutations were introduced into the miR160 target site by PCR to generate ARF10:mARF10. The ARF10 and mARF10 sequences were fused to the green fluorescent protein sequence (ARF10:ARF10-GFP or ARF10:mARF10-GFP) and plants were transformed with each construct. Independent biological replicate of Col-0_rep1, ARF10_rep1, mARF10_rep1 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.

hyb_protocol: Twenty-five μg of aRNAs were fragmented prior to hybridization in theAffymetrix GeneChip® Hybridization Oven 640, washing in the Affymetrix GeneChip® Fluidics Station 450, and then staining the arrays with biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University, Corvallis OR.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip® Scanner 3000 and the hybridization signals were quantified by Affymetrix MAS 5.0 method.

data_processing: Raw intensity values were normalized by using RMAEXPRESS (Bolstad et al., 2003)

label: biotin-11-CTP, biotin-16-UTP

organism: Arabidopsis thaliana

source_name: germinating seeds (22 hr imbibition)

label_protocol: aRNAs were labeled with biotin-11-CTP and biotin-16-UTP in vitro according to the MessageAmpTM aRNA Amplification Kit Instruction Manual (Ambion Inc., Austin, TX, USA)

extract_protocol: Total RNA was extracted from germinating seeds (22 hr imbibition) using standard phenol-SDS extraction as described before (Sambrook et al., 1989), and then checked for RNA integrity with Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). Five μg of total RNA was used to produce double-strand cDNAs which were transcribed to aRNAs (amplified RNA).

tag: mARF10 in Col-0 background, germinating seeds (22 hr imbibition), three independent seed lots


title: STHdhQ7/Q7-B

description: Wild-type control striatal

tag: Wild-type control 2


title: STHdhQ7/Q7-C

description: Wild-type control striatal cells

tag: WIld-type control 3


title: ARF10 rep2

description: The ARF10 gene, including the coding region (2.3 kb) and the 5’ upstream region (3 kb) (ARF10:ARF10), was amplified by PCR, and then four mutations were introduced into the miR160 target site by PCR to generate ARF10:mARF10. The ARF10 and mARF10 sequences were fused to the green fluorescent protein sequence (ARF10:ARF10-GFP or ARF10:mARF10-GFP) and plants were transformed with each construct. Independent biological replicate of Col-0_rep2, ARF10_rep2, mARF10_rep2 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.

extract_protocol:
Total RNA was extracted from germinating seeds (22 hr imbibition) using
standard phenol-SDS extraction as described before (Sambrook et al., 1989), and then checked for RNA integrity with Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). Five μg of total RNA was used to produce double-strand cDNAs which were transcribed to aRNAs (amplified RNA).

tag: ARF10 in Col-0 background, germinating seeds (22 hr imbibition), three independent seed lots


title: mARF10 rep2


title: ARF10 rep1


title: ARF10 rep3

description: The ARF10 gene, including the coding region (2.3 kb) and the 5’ upstream region (3 kb) (ARF10:ARF10), was amplified by PCR, and then four mutations were introduced into the miR160 target site by PCR to generate ARF10:mARF10. The ARF10 and mARF10 sequences were fused to the green fluorescent protein sequence (ARF10:ARF10-GFP or ARF10:mARF10-GFP) and plants were transformed with each construct. Independent biological replicate of Col-0_rep3, ARF10_rep3, mARF10_rep3 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.


title: Col-0 rep2

description: Independent biological replicate of Col-0_rep2, ARF10_rep2, mARF10_rep2 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.

tag: Wild-type Col-0, germinating seeds (22 hr imbibition), three independent seed lots


title: Col-0 rep3

description: Independent biological replicate of Col-0_rep3, ARF10_rep3, mARF10_rep3 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.


title: ci_NY30

city: New York

first: Elisa

last: Wurmbach

state: NY

address: 1 Gustave L. Levy Place

department: Hematology/Oncology

institute: Mount Sinai School of Medicine

description: cirrhotic liver tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix.

scan_protocol: Affymetrix standard procedure

data_processing: MAS probe set signal intensity

organism: Homo sapiens

source_name: human liver; cirrhotic liver tissue

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

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

tag: cirrhotic liver tissue


title: Col-0 rep1

description: Independent biological replicate of Col-0_rep1, ARF10_rep1, mARF10_rep1 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on two layers of filter paper (No. 2, Whatman Inc, Clifton, NJ, USA) moistened with 3 ml water and incubated at 4°C for 3 days in the dark and at 22°C for 22 hours under the light.


title: Dominant negative cJun  VZ18

status: Public on Jun 15 2007

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

description: total RNA extracted from one ApoE-/- mouse infected wtih an adenovirus expressing dominant negative cJun

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: SAM

source_name: liver

label_protocol: Affymetrix

extract_protocol: Affymetrix


title: STHdhQ7/Q7-3NP-B

tag: Wild-type 3NP (1mM, 48hr) treated 2


title: lg_NY10

description: low-grade dysplastic liver tissue

source_name: human liver; low-grade dysplastic liver tissue

tag: low-grade dysplastic liver tissue


title: Dominant negative cJun  VZ20

tag: ApoE-/- mouse infected wtih an adenovirus expressing dominant negative cJun


title: Control  VZ11

description: total RNA was extracted from liver of one ApoE-/- mouse infected with a control adenovirus expressing GFP


title: Control  VZ13

description: total RNA extracted from one ApoE-/- mouse infected wtih a control adenovirus expressing GFP


title: Dominant negative cJun  VZ17


title: Control  VZ15

tag: ApoE-/- mouse infected wtih a control adenovirus expressing GFP


title: Dominant negative cJun  VZ16


title: Dominant negative cJun  VZ19


title: Control  VZ14


title: Control  VZ12

tag: ApoE-/- mouse infected with a control adenovirus expressing GFP


title: mARF10 rep3


title: 05_0006_SepticShock_Day3_98

status: Public on Jun 14 2007

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1).

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
The image file was captured on an Affymetrix GeneChip Scanner 3000 and initially processed with Microarray suite 5.0 (Affymetrix).
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
Each array was normalized the same. Global scaling is used by adjusting the average intensity or signal value of each probe array to the same Target Intensity Value (TGV) of 1500. Genechip Operating Software 1v4 (Affymetrix) was then used to generate CEL files from each experiment, which were then imported into GeneSpring for all further data analysis.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

source_name: Whole blood from normal children and children with septic shock.

label_protocol: Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to manufacturer's instructions.

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene system.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were not manipulated.

tag: 05_0006_Patient, Day3


title: 04_0003_SepticShock_Day3_104

tag: 04_0003_Patient, Day3


title: 01_0030_SepticShock_Day3_109

tag: 01_0030_Patient, Day3


title: 01_0025_SepticShock_Day3_115

tag: 01_0025_Patient, Day3


title: 02_0001_SepticShock_Day3_107

tag: 02_0001_Patient, Day3


title: 06_0003_SepticShock_Day3_88

tag: 06_0003_Patient, Day3


title: 06_0006_SepticShock_Day3_84

tag: 06_0006_Patient, Day3


title: 10_0017_SepticShock_Day3_59

tag: 10_0017_Patient, Day3


title: 05_0010_SepticShock_Day3_94

tag: 05_0010_Patient, Day3


title: 01_0024_SepticShock_Day3_117

tag: 01_0024_Patient, Day3


title: 15_0007_SepticShock_Day3_14

tag: 15_0007_Patient, Day3


title: 10_0020_SepticShock_Day3_58

tag: 10_0020_Patient, Day3


title: 10_0004_SepticShock_Day3_72

tag: 10_0004_Patient, Day3


title: 10_0012_SepticShock_Day3_63

tag: 10_0012_Patient, Day3


title: 05_0008_SepticShock_Day3_96

tag: 05_0008_Patient, Day3


title: 11_0029_SepticShock_Day3_29

tag: 11_0029_Patient, Day3


title: 07_0002_SepticShock_Day3_81

tag: 07_0002_Patient, Day3


title: 11_0017_SepticShock_Day3_40

tag: 11_0017_Patient, Day3


title: 11_0001_SepticShock_Day3_55

tag: 11_0001_Patient, Day3


title: 01_0019_SepticShock_Day3_121

tag: 01_0019_Patient, Day3


title: 09_0001_SepticShock_Day3_77

tag: 09_0001_Patient, Day3


title: 09_0002_SepticShock_Day3_75

tag: 09_0002_Patient, Day3


title: 15_0004_SepticShock_Day3_17

tag: 15_0004_Patient, Day3


title: 25_70603_SepticShock_Day3_8


title: 06_0001_SepticShock_Day3_91

tag: 06_0001_Patient, Day3


title: 04_0004_SepticShock_Day3_9

tag: 04_0004_Patient, Day3


title: 01_0026_SepticShock_Day3_113

tag: 01_0026_Patient, Day3


title: 05_0007_SepticShock_Day3_2

tag: 05_0007_Patient, Day3


title: 06_0004_SepticShock_Day3_86

tag: 06_0004_Patient, Day3


title: 01_0024_SepticShock_Day1_118

tag: 01_0024_Patient, Day1


title: 01_0025_SepticShock_Day1_116

tag: 01_0025_Patient, Day1


title: 02_0001_SepticShock_Day1_108

tag: 02_0001_Patient, Day1


title: 05_0008_SepticShock_Day1_97

tag: 05_0008_Patient, Day1


title: 04_0003_SepticShock_Day1_105

tag: 04_0003_Patient, Day1


title: 01_0030_SepticShock_Day1_110

tag: 01_0030_Patient, Day1


title: 05_0006_SepticShock_Day1_99

tag: 05_0006_Patient, Day1


title: 06_0006_SepticShock_Day1_85

tag: 06_0006_Patient, Day1


title: 07_0002_SepticShock_Day1_82

tag: 07_0002_Patient, Day1


title: 01_0026_SepticShock_Day1_114

tag: 01_0026_Patient, Day1


title: 06_0003_SepticShock_Day1_89

tag: 06_0003_Patient, Day1


title: 10_0012_SepticShock_Day1_64

tag: 10_0012_Patient, Day1


title: 09_0001_SepticShock_Day1_78

tag: 09_0001_Patient, Day1


title: 06_0001_SepticShock_Day1_92

tag: 06_0001_Patient, Day1


title: 01_0019_SepticShock_Day1_120

tag: 01_0019_Patient, Day1


title: 09_0002_SepticShock_Day1_76

tag: 09_0002_Patient, Day1


title: 15_0008_SepticShock_Day3_12

tag: 15_0008_Patient, Day3


title: 06_0004_SepticShock_Day1_87

tag: 06_0004_Patient, Day1


title: 11_0017_SepticShock_Day1_41

tag: 11_0017_Patient, Day1


title: 15_0004_SepticShock_Day1_18

tag: 15_0004_Patient, Day1


title: 10_0004_SepticShock_Day1_73

tag: 10_0004_Patient, Day1


title: 11_0029_SepticShock_Day1_30

tag: 11_0029_Patient, Day1


title: 10_0017_SepticShock_Day1_60

tag: 10_0017_Patient, Day1


title: 04_0004_SepticShock_Day1_10

tag: 04_0004_Patient, Day1


title: 15_0007_SepticShock_Day1_15

tag: 15_0007_Patient, Day1


title: 15_0008_SepticShock_Day1_13

tag: 15_0008_Patient, Day1


title: 11_0001_SepticShock_Day1_56

tag: 11_0001_Patient, Day1


title: 27_70603_SepticShock_Day1_6


title: 10_0020_SepticShock_Day1_57

tag: 10_0020_Patient, Day1


title: SWR/J ACU, Rep3

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: SWR/J Acute morphine treated, striatum, biological replicate 3

hyb_protocol: Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Data was normalized by dChip 2006 (MBEI)

source_name: SWR/J Acute morphine treated, biological replicate 3

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

growth_protocol: Adult male (8 to 10 weeks of age) 129P3/J (000690), DBA/2J (000671), C57BL/6J (000664) and SWR/J (000689) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were housed 6 per cage, under a 12 h dark/light cycle, with ad libitum access to food and water. Animals weighing from 20 to 30 g were used throughout the experiments. The animal protocols used in the study were approved by the local Bioethics Commission working at the Institute of Pharmacology, Polish Academy of Sciences (Krakow, Poland).

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

treatment_protocol: Morphine (morphine hydrochloride; Polfa, Kutno, Poland) was administered subcutaneously (s.c.). Experimental groups (control, acute and chronic morphine) consisted of 9 animals from each strain. To obtain the most reliable comparison, control and acute morphine groups received injections of saline for four days in the same time schedule as the chronic group received morphine. On the fifth day, acute treated animals were injected with a single dose of morphine (20 mg/kg) and killed by decapitation after 4 h. Chronically treated animals were injected with increasing doses of morphine for five days. Mice received morphine thrice daily (09:00 h, 13:00 h and 17:00 h) for four days using a dosing schedule of 10, 20, 40 and 40 mg/kg of morphine on days 1, 2, 3 and 4, respectively. On the last day, a final morphine dose of 40 mg/kg was administered and 4 h after the last injection, the animals were sacrificed. Mice in control groups were killed 4 h after the last injection of saline. The dose scheme and time schedule were used in order to maximize strains differences in response to morphine.

tag: Striatum of 8-10 week old SWR/J mice


title: SWR/J SAL, Rep1

description: SWR/J Saline treated, striatum, biological replicate 1

source_name: SWR/J Saline treated, biological replicate 1


title: SWR/J CHR, Rep1

description: SWR/J Chronic morphine treated, striatum, biological replicate 1

source_name: SWR/J Chronic morphine treated, biological replicate 1


title: SWR/J CHR, Rep2

description: SWR/J Chronic morphine treated, striatum, biological replicate 2

source_name: SWR/J Chronic morphine treated, biological replicate 2


title: 05_0007_SepticShock_Day1_3

tag: 05_0007_Patient, Day1


title: SWR/J ACU, Rep1

description: SWR/J Acute morphine treated, striatum, biological replicate 1

source_name: SWR/J Acute morphine treated, biological replicate 1


title: SWR/J CHR, Rep3

description: SWR/J Chronic morphine treated, striatum, biological replicate 3

source_name: SWR/J Chronic morphine treated, biological replicate 3


title: DBA/2J CHR, Rep3

description: DBA/2J Chronic morphine treated, striatum, biological replicate 3

source_name: DBA/2J Chronic morphine treated, biological replicate 3

tag: Striatum of 8-10 week old DBA/2J mice


title: Substantia nigra PD rep12

city: Gaithsburg

first: Jarlath

last: ffrench-Mullen

state: MD

address: 610 Professional Drive

department: CNS Program

institute: GeneLogic, Inc.

description: Gene expression data of substantia nigra from postmortem brain of PD patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for >16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 7G Scanner.

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

source_name: Postmortem human substantia nigra

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Brain tissue was removed with a Post-Mortem Interval (PMI) of 9.03±2.2 hr for Control samples and 7.05±1.25 hr for the PD samples, subsequently sectioned and frozen.

extract_protocol: Trizol lysis extraction of total RNA was performed on an M48 BioRobot with a Quiagen Megatrack Kit.

tag: Parkinson's Disease

tag: female


title: SWR/J SAL, Rep3

description: SWR/J Saline treated, striatum, biological replicate 3

source_name: SWR/J Saline treated, biological replicate 3


title: Substantia nigra PD rep9


title: Substantia nigra PD rep14

tag: male


title: SWR/J ACU, Rep2

description: SWR/J Acute morphine treated, striatum, biological replicate 2

source_name: SWR/J Acute morphine treated, biological replicate 2


title: DBA/2J CHR, Rep2

description: DBA/2J Chronic morphine treated, striatum, biological replicate 2

source_name: DBA/2J Chronic morphine treated, biological replicate 2


title: Substantia nigra PD rep11


title: Substantia nigra PD rep10


title: Substantia nigra PD rep13


title: DBA/2J CHR, Rep1

description: DBA/2J Chronic morphine treated, striatum, biological replicate 1

source_name: DBA/2J Chronic morphine treated, biological replicate 1


title: Substantia nigra PD rep15


title: SWR/J SAL, Rep2

description: SWR/J Saline treated, striatum, biological replicate 2

source_name: SWR/J Saline treated, biological replicate 2


title: DBA/2J ACU, Rep3

description: DBA/2J Acute morphine treated, striatum, biological replicate 3

source_name: DBA/2J Acute morphine treated, biological replicate 3


title: Substantia nigra PD rep6


title: DBA/2J ACU, Rep1

description: DBA/2J Acute morphine treated, striatum, biological replicate 1

source_name: DBA/2J Acute morphine treated, biological replicate 1


title: Substantia nigra PD rep5


title: Substantia nigra PD rep8


title: DBA/2J ACU, Rep2

description: DBA/2J Acute morphine treated, striatum, biological replicate 2

source_name: DBA/2J Acute morphine treated, biological replicate 2


title: Substantia nigra PD rep7


title: DBA/2J SAL, Rep3

description: DBA/2J Saline treated, striatum, biological replicate 3

source_name: DBA/2J Saline treated, biological replicate 3


title: C57BL/6J CHR, Rep3

description: C57BL/6J Chronic morphine treated, striatum, biological replicate 3

source_name: C57BL/6J Chronic morphine treated, biological replicate 3

tag: Striatum of 8-10 week old C57BL/6J mice


title: C57BL/6J CHR, Rep2

description: C57BL/6J Chronic morphine treated, striatum, biological replicate 2

source_name: C57BL/6J Chronic morphine treated, biological replicate 2


title: Substantia nigra PD rep1


title: C57BL/6J ACU, Rep3

description: C57BL/6J Acute morphine treated, striatum, biological replicate 3

source_name: C57BL/6J Acute morphine treated, biological replicate 3


title: C57BL/6J CHR, Rep1

description: C57BL/6J Chronic morphine treated, striatum, biological replicate 1

source_name: C57BL/6J Chronic morphine treated, biological replicate 1


title: Substantia nigra PD rep3


title: C57BL/6J SAL, Rep1

description: C57BL/6J Saline treated, striatum, biological replicate 1

source_name: C57BL/6J Saline treated, biological replicate 1


title: DBA/2J SAL, Rep1

description: DBA/2J Saline treated, striatum, biological replicate 1

source_name: DBA/2J Saline treated, biological replicate 1


title: C57BL/6J ACU, Rep2

description: C57BL/6J Acute morphine treated, striatum, biological replicate 2

source_name: C57BL/6J Acute morphine treated, biological replicate 2


title: Substantia nigra normal rep5

description: Gene expression data of substantia nigra from postmortem brain of normal controls

source_name: Postmortem human substantia nigra

tag: Old Control


title: C57BL/6J SAL, Rep2

description: C57BL/6J Saline treated, striatum, biological replicate 2

source_name: C57BL/6J Saline treated, biological replicate 2


title: 129P3/J CHR, Rep1

description: 129P3/J Chronic morphine treated, striatum, biological replicate 1

source_name: 129P3/J Chronic morphine treated, biological replicate 1

tag: Striatum of 8-10 week old 129P3/J mice


title: DBA/2J SAL, Rep2

description: DBA/2J Saline treated, striatum, biological replicate 2

source_name: DBA/2J Saline treated, biological replicate 2


title: C57BL/6J SAL, Rep3

description: C57BL/6J Saline treated, striatum, biological replicate 3

source_name: C57BL/6J Saline treated, biological replicate 3


title: 129P3/J ACU, Rep3

description: 129P3/J Acute morphine treated, striatum, biological replicate 3

source_name: 129P3/J Acute morphine treated, biological replicate 3


title: Substantia nigra normal rep3


title: Substantia nigra normal rep9


title: Substantia nigra PD rep2

description: Gene expression data of substantia nigra from postmortem brain of PD patients


title: 129P3/J CHR, Rep3

description: 129P3/J Chronic morphine treated, striatum, biological replicate 3

source_name: 129P3/J Chronic morphine treated, biological replicate 3


title: C57BL/6J ACU, Rep1

description: C57BL/6J Acute morphine treated, striatum, biological replicate 1

source_name: C57BL/6J Acute morphine treated, biological replicate 1


title: Substantia nigra normal rep7


title: Substantia nigra normal rep4


title: 129P3/J CHR, Rep2

description: 129P3/J Chronic morphine treated, striatum, biological replicate 2

source_name: 129P3/J Chronic morphine treated, biological replicate 2


title: Substantia nigra PD rep16


title: Substantia nigra normal rep8


title: Substantia nigra normal rep2


title: Substantia nigra PD rep4


title: Substantia nigra normal rep6


title: 05_0010_SepticShock_Day1_95

description: 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1).

source_name: Whole blood from normal children and children with septic shock.

tag: 05_0010_Patient, Day1


title: 129P3/J ACU, Rep1

description: 129P3/J Acute morphine treated, striatum, biological replicate 1

source_name: 129P3/J Acute morphine treated, biological replicate 1


title: Substantia nigra normal rep1


title: 129P3/J SAL, Rep3

description: 129P3/J Saline treated, striatum, biological replicate 3

source_name: 129P3/J Saline treated, biological replicate 3


title: 129P3/J SAL, Rep1

description: 129P3/J Saline treated, striatum, biological replicate 1

source_name: 129P3/J Saline treated, biological replicate 1


title: 129P3/J ACU, Rep2

description: 129P3/J Acute morphine treated, striatum, biological replicate 2

source_name: 129P3/J Acute morphine treated, biological replicate 2


title: 129P3/J SAL, Rep2

description: 129P3/J Saline treated, striatum, biological replicate 2

source_name: 129P3/J Saline treated, biological replicate 2


title: Untreated, biological rep5

status: Public on Jun 13 2007

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from male mice.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scaner 3000.

data_processing: Genewise tests for significantly regulated transcripts between creatine treated and untreated mice were performed in the statistical programming language R with BioConductor using the dChip and the Robust Multichip Average (RMA) probeset summaries. Data are log-transformed and normalized with a lowess-smoother operating on MA-scale against the mean of the creatine treated group. Transcripts are called significantly regulated if the corresponding p-value of the Welch's t-test is below the 5% FDR significance level.

source_name: Mus musculus brain hemisphere

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Mice were bred and kept at the GSF animal facilities in isolated ventilated cages type II with wood shavings (Altromin, Lage, Germany) as bedding at a temperature of 20 to 24o C, humidity of 50 to 60%, 20 air exchanges per hour and a 12/12-hour light/dark cycle. They were tested for microorganisms in 12-week intervals according to the FELASA Guidelines to the level required for rederived mice

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: 6 mice were fed ad libitum on 1% creatine supplemented pellets for 6 months and 7 mice fed on equicaloric pellets without creatine (Altromin)

tag: Strain

tag: Age

value: 10-12 weeks at the beginning of the feeding regimen


title: STHdhQ7/Q7-3NP-A

description: Wild-type striatal cells treated with 3NP

source_name: Hdh knock-in mice striatal cells

tag: Wild-type 3NP (1mM, 48hr) treated 1


title: STHdhQ111/Q111-C

description: Mutant striatal cells

tag: Hdh mutant (111/111-polyQ) 3


title: Untreated, biological rep6

description: Gene expression data from male mice.


title: 1285_32d

status: Public on Jun 12 2007

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: The sample is a part of a series describing gene expression changes during postnatal development of the small intestine

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

scan_protocol: The Affymetrix system was used and the protocols supplied by Affymetrix followed.

data_processing: Log(2) transformed expression measures were calculated with the RMA procedure using the software from www.Bioconductor.org

label: Phycoerythrin

source_name: Ileum

label_protocol: First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ul reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ul RNase free water, 30 ul 5 times second strand reaction buffer (Invitrogen), 3 ul 10 mM dNTP, 1 ul Escherichia coli DNA ligase (10 U/ml), 4 ul E. coli DNA polymerase I (10 U/ml), 1 ul E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

extract_protocol: For RNA extraction, the intestinal pieces were homogenized in lysis buffer using an Ultra-Turrax T8 homonigenisator and RNA was extracted using the E.Z.N.A total RNA kit (Omega Bio-Tek). The amount and quality of the extracted RNA was evaluated using a lab-on-a-chip Bioanalyzer (Agilent Technologies, CA, USA).

value: C57BL/6, Age:32 days


title: Untreated, biological rep1

description: Gene expression data from male mice.


title: Untreated, biological rep7

description: Gene expression data from male mice.


title: Creatine-treated, biological rep1

description: Gene expression data from male mice.


title: Creatine-treated, biological rep4

description: Gene expression data from male mice.


title: Creatine-treated, biological rep2

description: Gene expression data from male mice.


title: Untreated, biological rep3

description: Gene expression data from male mice.


title: 1281_32d


title: Untreated, biological rep4

description: Gene expression data from male mice.


title: 1143_24d

value: C57BL/6, Age:24 days


title: 498_11d

value: C57BL/6, Age:11 days


title: 1279_32d

value: C57BL6, Age:32 days


title: Creatine-treated, biological rep5

description: Gene expression data from male mice.


title: 1148_24d

extract_protocol: Protocol For RNA extraction, the intestinal pieces were homogenized in lysis buffer using an Ultra-Turrax T8 homonigenisator and RNA was extracted using the E.Z.N.A total RNA kit (Omega Bio-Tek). The amount and quality of the extracted RNA was evaluated using a lab-on-a-chip Bioanalyzer (Agilent Technologies, CA, USA).

value: C57BL6, Age:24 days


title: 497_11d


title: 1146_24d


title: Untreated, biological rep2

description: Gene expression data from male mice.


title: Creatine-treated, biological rep6

description: Gene expression data from male mice.


title: 496_11d


title: Creatine-treated, biological rep3

description: Gene expression data from male mice.


title: 488_9d

value: C57BL/6, Age:9 days


title: 486_9d


title: 490_9d


title: 484_7d

value: C57BL/6, Age:7 days


title: Cnr1-/-/Cnr2-/- female number 2, DNFB-treated allergic ear (#11_Ko-Tr-5)

status: Public on Jun 11 2007

city: Bonn

first: Meliha

last: Karsak

address: Sigmund-Freud-Str. 25

department: Molecular Psychiatry

institute: University of Bonn

description: ko mouse number 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG_430 2.0 Affymetrix GeneChips . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: We used an Affymetrix GeneChip® Scanner 3000.

data_processing:
Microarry expression values were generated using GC-RMA using software ArrayAssist® 3.0 (Stratagene). The GC-RMA-obtained log2-transformed expression values were imported into searchable database using this software.. For the treatment effects, which were independent of the genotype, all control (n=6) and DNFB-treated ears (n=6) were statistically analyzed using t-test with p ≤ 0.05 after Bonferroni correction and a differential expression higher than fourfold (given as an average log 2 ratio; ALR). The genotype effects were obtained by comparison of DNFB-treated ears of Cnr1+/+/Cnr2+/+ (n=3) versus Cnr1-/-/Cnr2-/- (n=3) with p ≤ 0.001 and ALR ≥ 1. Results for treatment and genotype effects were compared using Venn diagram.
Hierarchical clustering was performed on log2 transformed values using “ArrayAssist 3.0” (Stratagene) in two dimensions (e.g. both genes and samples).

source_name: whole ear tissue, DNFB-treated allergic ear 48h after 2nd challenge

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified using RNeasy columns (Qiagen). RNA intergrity was assessed using Agilent 2100 Bioanalyzer (www.agilent.com). Five μg of total RNA was converted into double-stranded cDNA using T7-oligodT coupled primers. Ten μg of fragmented cRNA samples were hybridized to MG_430 2.0 Affymetrix GeneChips following the manufacturer´s instructions.

treatment_protocol: DNFB (1-fluoro-2,4 dinitrobenzene, Merck) was diluted in acetone/olive oil (4:1) immediately before use. Mice without any skin lesions and ear tags were sensitized by painting 50 µl of 0.2% DNFB on the shaved abdomen on two consecutive days. Controls were treated with 50 µl acetone-olive oil. For elicitation of CHS, ears of mice were painted with 10 µl of 0.3% DNFB on day 5. Ear thickness was measured 24 h, 48 h and 72 h after challenge using an engineers micrometer (Oditest, Fa. Kroeplin, Schlüchtern, Germany) and ear swelling was calculated in each mouse as the difference in ear thickness between the unchallenged control (left) and the challenged (right) ear. Experimental mice of either wildtype C57BL/6J line or CB1/CB2 double knockout mice (Cnr1-/-/Cnr2-/-) were used in the age of 8-10 weeks. Right ears of the mice were treated with DNFB, whereas left ears were untreated and used as control. All experimental animals were females. DNFB treated and control ears from three Cnr1-/-/Cnr2-/- and three Cnr1+/+/Cnr2+/+ mice were used for the gene expression analysis. Whole ear tissue was harvested 48h after the 2nd DNFB-challenge and immediately snap frozen in liquid nitrogen. Tissue was stored on –80°C until RNA isolation.

tag: Cnr1-/-/Cnr2-/- female number 2, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: 481_7d


title: 488_7d

value: C57BL/6, Age:7 dats


title: Cnr1-/-/Cnr2-/- female number 3, DNFB-treated allergic ear (#12_Ko-Tr-7)

description: ko mouse number 3

tag: Cnr1-/-/Cnr2-/- female number 3, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: Cnr1-/-/Cnr2-/- female number 3, untreated control ear (#9_Ko-C-7)

description: ko mouse number 3

source_name: whole ear tissue, untreated control ear

tag: Cnr1-/-/Cnr2-/- female number 3, 2 months old, whole ear tissue, untreated control ear


title: Cnr1-/-/Cnr2-/- female number 2, untreated control ear (#8_Ko-C-5)

description: ko mouse number 2

tag: Cnr1-/-/Cnr2-/- female number 2, 2 months old, whole ear tissue, untreated control ear


title: 478_4d

value: C57BL/6, Age:4 days


title: Cnr1-/-/Cnr2-/- female number 1, DNFB-treated allergic ear (#10_Ko-Tr-4)

description: ko mouse number 1

tag: Cnr1-/-/Cnr2-/- female number 1, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: Cnr1-/-/Cnr2-/- female number 1, untreated control ear (#7_Ko-C-4)

description: ko mouse number 1

tag: Cnr1-/-/Cnr2-/- female number 1, 2 months old, whole ear tissue, untreated control ear


title: White adipose adult rep1

status: Public on Jun 08 2007

first: Patrick

last: Seale

address: 1 Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: no additional information

hyb_protocol: The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45°C. The chip was then transferred to a fluidics instrument for washes to remove unbound cRNA. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were added using biotinylated anti-streptavidin antibody and SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values

source_name: Epididymal White Adipose Tissue

label_protocol: cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

extract_protocol: Trizol (Invitrogen) extraction, followed by purification using Qiagen RNeasy column

treatment_protocol: Untreated, ambient temperature

tag: strain

tag: Sex

value: male

tag: age

value: 10-12 week old

tag: tissue

value: Epididymal White Adipose Tissue


title: 476_4d

description: The sample is a part of a time-course study of small intestinal gene expression from the pre-weaning to the post weaning stage.


title: Brown adipose adult rep3

description: no additional information

source_name: Interscapular Brown Adipose Tissue

value: Interscapular Brown Adipose Tissue


title: 480_4d


title: White adipose adult rep2

description: no additional information


title: White adipose adult rep3

description: no additional information


title: C57BL/6J female number 3, DNFB-treated allergic ear (#6_Wt-Tr-7)

description: wt mouse number 3

tag: C57BL/6J female number 3, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: C57BL/6J female number 2, untreated control ear (#2_Wt-C-4)

description: wt mouse number 2

tag: C57BL/6J female number 2, 2 months old, whole ear tissue, untreated control ear


title: C57BL/6J female number 1, DNFB-treated allergic ear (#4_Wt-Tr-3)

description: wt mouse number 1

tag: C57BL/6J female number 1, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: Brown adipose adult rep2

description: no additional information


title: RCC110-tumor tissue_rep 1

status: Public on Jun 07 2007

city: Tuebingen

first: Andreas

middle: Oliver

last: Weinzierl

address: Auf der Morgenstelle 15

department: Department of Immunology

institute: University of Tuebingen

description: HLA-typing: A*02, B*18, B*27

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. Incubation, washing, and staining were carried out according to the GeneChip Mapping Assay Manual, using standard protocols on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene-Chip Scanner 3000.

data_processing: Data were analyzed with the GCOS software (Affymetrix), using default settings for all parameters. Pairwise comparisons were calculated using the respective normal kidney array as baseline. For normalization, 100 housekeeping genes provided by Affymetrix were used (http://www.affymetrix.com/support/technical/mask_files.affx). Relative expression values were calculated from the signal log ratios given by the software.

source_name: clear cell renal cell carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: tissues were shock frozen in liquid nitrogen directly after surgery.

tag: birthday 29/04/1931; female


title: RCC110-normal tissue_rep 1

description: HLA-typing: A*02, B*18, B*27

source_name: normal kidney tissue


title: C57BL/6J female number 2, DNFB-treated allergic ear (#5_Wt-Tr-4)

description: wt mouse number 2

tag: C57BL/6J female number 2, 2 months old, whole ear tissue, DNFB-treated allergic ear


title: C57BL/6J female number 1, untreated control ear (#1_Wt-C-3)

description: wt mouse number 1

tag: C57BL/6J female number 1, 2 months old , whole ear tissue, untreated control ear


title: C57BL/6J female number 3, untreated control ear (#3_Wt-C-7)

description: wt mouse number 3

tag: C57BL/6J female number 3, 2 months old, whole ear tissue, untreated control ear


title: RCC099_tumor tissue_rep 1

description: HLA-typing: A*02, B*27, B*57

tag: birthday 30/11/1930; male; tumor mass 7.7g


title: HCT116 cells with empty vector, technical replicate 2

city: Baltimore

first: Joshua

middle: T

last: Mendell

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

description:
Gene expression data from HCT116 cells infected with empty vector.  Described in:
Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. (2007).  Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis.  Mol Cell, 26: 745-752.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a Hewlett-Packard GeneArray Scanner G2500.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy's 5A media plus 10% fetal bovine serum plus antibiotics.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Cells were infected with retoviral vectors (empty or miR-34a) and selected for 2 weeks in 1 ug/mL puromycin.

tag: colon cancer cells


title: RCC099_normal tissue_rep 1

description: HLA-typing: A*02, B*27, B*57

tag: birthday 30/11/1930; male; normal tissue mass 12.4g


title: HCT116 cells with empty vector, technical replicate 1


title: Brown adipose adult rep1

description: no additional information


title: HCT116 cells with enforced miR-34a expression, technical replicate 2

description:
Gene expression data from HCT116 cells with enforced expression of miR-34a.  Described in:
Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. (2007).  Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis.  Mol Cell, 26: 745-752.


title: Microarray analysis of NL and PCOS oocytes (P3)

status: Public on Jun 05 2007

city: Lincoln

first: Jennifer

last: Wood

state: NE

address: 3800 Fair St.

department: Animal Science

institute: University of Nebraska

description: Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles.  PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity.  Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence.  To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips.

source_name: MII arrested oocyte

tag: MII-arrested oocyte collected from a PCOS woman undergoing gonadotropin-releasing hormone (GnRH) analog/ recombinant human (rh) follicle stimulating hormone (FSH) therapy for IVF.  A MII oocyte was defined by one polar body in the perivitelline space and no visible nuclear structure in the cytoplasm


title: Microarray analysis of NL and PCOS oocytes (P5)


title: Microarray analysis of NL and PCOS oocytes (P2)


title: HCT116 cells with enforced miR-34a expression, technical replicate 1


title: Microarray analysis of NL and PCOS oocytes (NL6)

tag: MII-arrested oocyte collected from a normal ovulatory woman undergoing gonadotropin-releasing hormone (GnRH) analog/ recombinant human (rh) follicle stimulating hormone (FSH) therapy for IVF due to tubal or male factor infertility.  A MII oocyte was defined by one polar body in the perivitelline space and no visible nuclear structure in the cytoplasm


title: Microarray analysis of NL and PCOS oocytes (NL4)


title: Microarray analysis of NL and PCOS oocytes (P4)


title: Microarray analysis of NL and PCOS oocytes (NL5)


title: Microarray analysis of NL and PCOS oocytes (P1)


title: embryo_released_at_day3.5_rep2

status: Public on Jun 04 2007

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from embryos released from the U0126-induced arrest at day 3.5.

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

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GCRMA algorithm

source_name: Mouse preimplnatation embryos released from the U0126-induced arrest at day 3.5.

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (Two-Cycle Target Labeling Assays) from 0.1 ug total RNA.

extract_protocol: Total RNA was isolated by following the manual of ISOGEN (NIPPON GENE CO., LTD).

tag: Strain

value: ICR


title: Microarray analysis of NL and PCOS oocytes (P6)


title: embryo_released_at_day4.5_rep2

description: Gene expression data from embryos released from the U0126-induced arrest at day 4.5.

source_name: Mouse preimplnatation embryos released from the U0126-induced arrest at day 4.5.


title: Microarray analysis of NL and PCOS oocytes (NL1)

description: Previous microarray analyses have demonstrated that whole ovaries and isolated theca cells from normal and PCOS women have unique gene expression profiles.  PCOS follicles have elevated androgen levels before and after GnRH analog/rhFSH therapy for IVF and contain excess amounts of insulin that are positively correlated with adiposity.  Taken together, these studies suggest that the altered PCOS hormonal milieu and/or intrinsic abnormalities might alter gene expression in the PCOS oocyte which could impact oocyte developmental competence.  To this end, we compared the gene expression profiles of normal and PCOS oocytes using Affymetrix microarray chips


title: embryo_at_day3.5_rep2

description: Gene expression data from embryos at day 3.5.

source_name: Mouse preimplnatation embryos at day 3.5.


title: embryo_at_day3.5_rep1


title: embryo_released_at_day4.5_rep1


title: embryo_at_day1.5_rep2

description: Gene expression data from embryos at day 1.5.

source_name: Mouse preimplnatation embryos at day 1.5.


title: embryo_released_at_day3.5_rep1


title: embryo_at_day1.5_rep1


title: embryo_U0126-treated_at_day2.5_rep1

description: Gene expression data from U0126 (20uM)-treated embryos at day 2.5.

source_name: Mouse preimplnatation U0126 (20uM)-treated embryos at day 2.5.


title: Microarray analysis of NL and PCOS oocytes (NL3)


title: embryo_U0126-treated_at_day2.5_rep2


title: Microarray analysis of NL and PCOS oocytes (NL2)


title: embryo_at_day2.5_rep1

description: Gene expression data from embryos at day 2.5.

source_name: Mouse preimplnatation embryos at day 2.5.


title: embryo_at_day2.5_rep2


title: SKBR3 PR 2

status: Public on Jun 01 2007

city: Los Angeles

first: Igor

last: Vivanco

state: CA

address: 700 Westwood plaza

department: Mol. & Md. Pharmacology

institute: UCLA

description: PTEN RNAi

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: GCOS 1.3 was used to convert intensities using Expression Analysis settings :Parameters -default, Baseline - default, Probemask - default, Normalization - all probe sets, Scaling - all probe sets, Target Signal: 2500

source_name: breast adenocarcinoma, cell line

label_protocol: see Affymetrix expression manual, section 2

growth_protocol: Cell were grown to log phase prior to RNA extraction in DMEM media containing 10% fetal bovine serum, L-glutamine and penicillin/streptomycin

extract_protocol: QIAGEN Rneasy

tag: ATCC HTB-30


title: SKBR3 WT 2

description: control


title: SKBR3 PR 1

description: PTEN RNAi


title: HCC827 PR 1

description: PTEN RNAi

source_name: lung adenocarcinoma, cell line

tag: ATCC CRL-2868


title: HCC827 WT 1

description: control


title: A431 PR 2

description: PTEN RNAi

source_name: epidermoid carcinoma, cell line

tag: ATCC CRL-1555


title: SKBR3 WT 1

description: control


title: A431 PR 1

description: PTEN RNAi


title: HCC827 WT 2

description: control


title: A431 WT 2

description: control


title: A431 WT 1

description: control


title: HCC827 PR 2

description: PTEN RNAi


title: WT-E2-4hr-3

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

description: 4 hr estrogen treated ovariectomized wild type mouse

hyb_protocol: For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing:
Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling:All Probe Sets, Target Signal=500
Normalization value:1
Parameters: defalut settings

source_name: the left femurs from ovariectomized wild type mouse

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

extract_protocol: The distal 5 mm of the left femurs were harvested after sacrificing by cervical dislocation. Samples were then homogenized in ISOGEN(Nippon gene, Japan) and total RNA extracted according to the manufacturer’s instructions. The extracted total RNA was cleaned up and concentrated using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) for GeneChip analysis (Proc Natl Acad Sci U S A. 2006;103(1):224-9.).

tag: Gender

value: female

tag: Tissue

value: the left femurs


title: WT-E2-4hr-2


title: WT-E2-4hr-4


title: WT-OVX-4

description: Vehicle control ovariectomized wild type mouse


title: ERaKO-E2-4hr-1

description: Osteoclast-specific estrogen receptor alpha knock-out mice that were ovariectomized and estrogen treated for four hours

source_name: the left femurs from ovariectomized osteoclast specific ERaKO mouse


title: WT-E2-4hr-1


title: ERaKO-E2-4hr-3


title: WT-OVX-2


title: ERaKO-OVX-2

description: Osteoclast-specific estrogen receptor alpha knock-out mice that were ovariectomized


title: ERaKO-E2-4hr-4


title: WT-OVX-3


title: ERaKO-OVX-3


title: GMPwt_430_2

city: Berlin-Steglitz

first: Dirk

last: Carstanjen

state: Berlin

address: Krahmer Strasse 6

department: Molecular Genetics

institute: Institute for Molecular Pharmacology

description: GMP from Icsbp wild type mice were isolated by flow cytometry.

hyb_protocol: 15 µg cRNA was hybridized to Affymetrix mouse expression 430 2.0 arrays at 45 °C for 16 h.

scan_protocol: Scanned according to the manufacturer's protocol (GA3000).

data_processing: Scanned GeneChip DAT files were analyzed by the GCOS Software (Affymetrix) with global scaling to 500.

source_name: GMP from Icsbp wt mice

label_protocol: Total RNA (1-2 μg) was reverse transcribed into cDNA with the one cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA). cRNA was generated with the one-cycle target labeling kit (Affymetrix, Santa Clara).

extract_protocol: Total RNA was isolated from purified progenitor cell populations from 10 –16 week old mice using the RNeasy Kit including DNase digestion (Qiagen, Hilden, Germany).


title: WT-OVX-1

hyb_protocol: For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol(Fluidics Protocol: EuKGE-WS2v4).


title: ERaKO-OVX-4


title: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_1

status: Public on May 31 2007

city: Cambridge

first: Todd

middle: A

last: Sangster

address: Nine Cambridge Center

institute: Whitehead Institute

description: See Sangster et al. "Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels" for experimental rationale.

hyb_protocol: Standard Affymetrix Eukaryotic Target Hybridization Protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Standard Affymetrix GeneChip Scanner 3000 Protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

data_processing: MAS5 transformed

source_name: 14 day old seedling grown in long days on GM medium, aerial tissue only

label_protocol: Standard Affymetrix One-Cycle Eukaryotic Target Labeling Assay (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

extract_protocol: Total RNA was isolated using the SV Total RNA Isolation kit (Promega) protocol on the ground tissue, omitting the DNase treatment in the manufacturer’s protocol.  Eluted total RNA was treated with RQ1 Rnase-free DNase (Promega).  A 65°C, 15 min incubation step inactivated the enzyme, instead of the kit’s Stop Solution.  Multiple identical RNA isolations were pooled and concentrated with the RNeasy (Qiagen) cleanup protocol.

tag: Accession

tag: Age

value: 14 days

value: All aerial tissue

tag: Transgenic

value: HSP90 reduced


title: ERaKO-OVX-1


title: ERaKO-E2-4hr-2


title: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_2


title: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_2


title: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_2


title: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_1

extract_protocol: Total RNA was isolated using the SV Total RNA Isolation kit (Promega) protocol on the ground tissue, omitting the DNase treatment in the manufacturer’s protocol.  Eluted total RNA was treated with RQ1 Rnase-free DNase (Promega).  A 65°C, 15 min incubation step inactivated the enzyme, instead of the kit’s Stop Solution.  Multiple identical RNA isolations were pooled and concentrated with the (Qiagen) RNeasy  (Qiagen) cleanup protocol.


title: HSP90_Reduced_Salk_hsp90.3_Biological_Replicate_3


title: HSP90_Reduced_hsp90.2-3_Biological_Replicate_3

description:
See Sangster et al. "Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels" for experimental rationale.
The hsp90.2-3 mutant is described in Hubert DA, Tornero P, Belkhadir Y, Krishna P, Takahashi A, et al. (2003) "Cytosolic HSP90 associates with and modulates the Arabidopsis RPM1 disease resistance protein." Embo J 22: 5679-5689.


title: HSP90_Reduced_Salk_hsp90.1_Biological_Replicate_3


title: HSP90_Reduced_hsp90.2-3_Biological_Replicate_2


title: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_3


title: HSP90_Reduced_Salk_hsp90.2_Biological_Replicate_1


title: GMPho_430_2

description: GMP from Icsbp-deficient mice were isolated by flow cytometry.

source_name: Icsbp (Irf-8) deficient mice


title: HSP90_Reduced_Control-3_Biological_Replicate_3

description: See Sangster et al. "Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels" for experimental rationale

value: Control for HSP90 reduced


title: HSP90_Reduced_hsp90.2-3_Biological_Replicate_1

description:
See Sangster et al. "Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels" for experimental rationale
The hsp90.2-3 mutant is described in Hubert DA, Tornero P, Belkhadir Y, Krishna P, Takahashi A, et al. (2003) "Cytosolic HSP90 associates with and modulates the Arabidopsis RPM1 disease resistance protein." Embo J 22: 5679-5689.


title: HSP90_Reduced_Control-1_Biological_Replicate_3


title: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_1


title: HSP90_Reduced_Control-1_Biological_Replicate_1


title: HSP90_Reduced_Control-3_Biological_Replicate_2


title: HSP90_Reduced_Control-1_Biological_Replicate_2


title: HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1


title: HSP90_Reduced_Control-2_Biological_Replicate_2_Technical_Replicate_2


title: HSP90_Reduced_RNAi-A1_Biological_Replicate_2_Technical_Replicate_2


title: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_2


title: HSP90_Reduced_RNAi-A3_Biological_Replicate_1


title: HSP90_Reduced_RNAi-A1_Biological_Replicate_1


title: HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_2


title: HSP90_Reduced_Col-0_CS60000_Biological_Replicate_3


title: HSP90_Reduced_Control-2_Biological_Replicate_2_Technical_Replicate_1


title: HSP90_Reduced_Control-3_Biological_Replicate_1


title: HSP90_Reduced_RNAi-B1_Biological_Replicate_3


title: HSP90_Reduced_RNAi-A2_Biological_Replicate_1


title: HSP90_Reduced_RNAi-C1_Biological_Replicate_1


title: HSP90_Reduced_RNAi-A2_Biological_Replicate_2


title: HSP90_Reduced_RNAi-C1_Biological_Replicate_2


title: HSP90_Reduced_RNAi-C1_Biological_Replicate_3


title: HSP90_Reduced_Control-2_Biological_Replicate_1


title: HSP90_Reduced_RNAi-A1_Biological_Replicate_2_Technical_Replicate_1


title: HSP90_Reduced_RNAi-B1_Biological_Replicate_2


title: Normal organelle (NE9)

status: Public on May 30 2007

city: Boston

first: Andrea

last: Richardson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description:
no additional info
none

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with dchip with default normalization settings.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-71

extract_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-73

treatment_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-72

tag: NO


title: Normal organelle (NE4)

description:
no additional info
none


title: Normal organelle (NE1)

description:
no additional info
none


title: Normal organelle (NE8)

description:
no additional info
none


title: HSP90_Reduced_RNAi-B1_Biological_Replicate_1


title: Normal organelle (NE10)

description:
no additional info
none


title: Normal organelle (NE6)

description:
no additional info
none


title: Normal organelle (NE768)

description:
no additional info
none


title: Normal organelle (NE5)

description:
no additional info
none


title: Normal organelle (NE817)

description:
no additional info
none


title: Normal organelle (NE2)

description:
no additional info
none


title: Normal organelle (NE3)

description:
no additional info
none


title: Normal organelle (NE7)

description:
no additional info
none


title: 636-1

status: Public on May 26 2007

first: James

middle: Dirk

last: Iglehart

address: 44 Binney St.

institute: Dana Farber Cancer Institute

description: Gene expression data from breast cancer tumor tissue.

hyb_protocol: standard Affymetrix protocol.

scan_protocol: standard Affymetrix protocol.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the DNA-Chip Analyzer (dChip).

source_name: breast cancer tumor tissue

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

extract_protocol: Total RNA extracted from frozen tissue was used to generate biotinylated cRNA target.

treatment_protocol: The frozen bulk tumor samples were confirmed to contain at least 70% viable tumor by area on histologic thin sections.

tag: ER

value: neg

tag: B-R grade

value: III

tag: node status

value: pos

tag: LVI

tag: tumor type

value: Ductal

tag: tumor size


title: C184

value: II

value: Mixed


title: 911-1


title: C181

value: I

value: Lobular


title: C183


title: C169


title: C172


title: C165


title: B68


title: C158


title: B61


title: B98


title: B80


title: B66


title: B70


title: B51


title: B28


title: B20


title: B19


title: B40


title: GT1

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7981

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10 ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: genital tubercle

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Genital tubercle region micro-dissected based on SMAA/EYFP expression.
Female FVB/N mice were time-mated to SMAA/EYFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80ºC until RNA was extracted for gene expression analysis.

tag: gene reported

value: SMAA/EYFP transgenic

tag: strain

value: FVB/N

tag: Sex

value: male

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark

value: Distal borders of anterior and posterior footplates indented; digit widths and locations discernable.


title: 271_ureter

status: Public on May 25 2007

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7980

source_name: ureter

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Ureter was micro-dissected between the kidney and bladder based on the presence of SMGA/EGFP.
Female FVB/N mice were mated to SMGA/EGFP transgenic males and allowed to deliver.  The SMGA/EGFP mice were euthanized by standard carbon dioxide asphyxiation at adulthood.  Tissue samples were dissected, rapidly frozen and stored at -80 °C until RNA was extracted for gene expression analysis.

value: SMGA/EGFP transgenic / PMID:14713859

tag: sex

value: Adult

value: N/A-Adult


title: GT3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7983

value: Individual fingers visible in the anterior footplate with indentations between the toes which are not separated.


title: GT2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7982

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Genital tubercle region micro-dissected based on SMAA/EYFP expressio.
Female FVB/N mice were time-mated to SMAA/EYFP transgenic males.  Pregnant FVB/N mice were euthanized by standard carbon dioxide asphyxiation at 14 days post-coitus.  Embryonic samples were euthanized by decapitation and tissues were micro-dissected, rapidly frozen and stored at -80ºC until RNA was extracted for gene expression analysis.


title: 238_ureter

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7978


title: B16


title: 205_ureter

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7977

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 10 ug


title: Sheff 4 hesc  grown upon Matrigel replicate 2

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Gene expression data from hesc grown upon Matrigel, untreated

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human U133 plus 2 GeneChips in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45?C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: human embryonic stem cell line Sheff 4 (CSCB)

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: cells had been cultured under standard conditions (37'C in media) prior to RNA extraction

extract_protocol: Qiagen Rneasy kit was used for RNA extraction according to manufacturers' instructions

treatment_protocol: cells had been cultured under standard conditions (37'C in media) upon MEFs prior to RNA extraction. One group were treated with S1P.

tag: Male embryonic stem cell line grown upon Matrigel


title: 244_ureter

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7979


title: C126


title: Sheff 4 hesc S1P treated replicate 2

description: Gene expression data from hesc grown upon MEFs, treated with 20um S1P

tag: Male embryonic stem cell line grown upon MEFs. Treated with S1P


title: Sheff 4 hesc S1P treated replicate1


title: Sheff 4 hesc replicate 3

description: Gene expression data from hesc grown upon MEFs, untreated

tag: Male embryonic stem cell line grown upon MEFs


title: Sheff 4 hesc replicate 2


title: Sheff 4 hesc  grown upon Matrigel replicate 3


title: CF knockout HMCF CHN310

status: Public on May 21 2007

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

country: Canada

institute: McGill University

description: Gene expression data from B6xBALB F2 mouse lung

data_processing: affyPLM in bioconductor

source_name: whole right lung


title: CF knockout LFCF CHN309


title: CF knockout HFCF CHN308


title: Sheff 4 hesc S1P treated replicate 3


title: CF knockout HMCF CHN537


title: Normoxic SV129 array 1

status: Public on May 18 2007

city: Nashville

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

institute: Vanderbilt University

description: Whole lung homogenate from SV129 mice kept at Denver altitude (85 kPa) for 4 weeks.

hyb_protocol: following Affymetrix GeneChip Expression Analysis Manual

data_processing: Affymetrix chp and cel files

source_name: Whole lung homogenate

extract_protocol: right lung was removed immediately after sacrifice, snap frozen, and later converted to RNA using Qiagen rnEasy columns.


title: Hypoxic SV129 array 2

description: Whole lung homogenate from SV129 mice exposed to 4 weeks hypobaric hypoxia (50 kPa)

scan_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: CF knockout HMCF CHN539


title: Human_airway_control

status: Public on May 22 2007

city: Portland

first: John

last: Wong

address: 3181 SW Sam Jackson Park Rd. (L215)

department: Cell & Developmental Biology

institute: Oregon Health & Science University

description: Gene expression data

hyb_protocol: The biotinylated cRNA target is fragmented and assembled into a hybridization cocktail that contains biotinylated control RNA spikes for hybridization.  The individual hybridization cocktails are loaded onto the prescribed GeneChip and incubated overnight (16 hrs.) in a hybridization oven.  The arrays are stained to detect biotinylated cRNA distribution during a 3 step process using R-Phycoerythrin Streptavidin.

scan_protocol: The chips are scanned using an Agilent Gene Array Scanner.

data_processing: Image processing and expression analysis were performed using Affymetrix GCOS v1.2 software.

source_name: Human airway cells, untreated, 24 h

label_protocol: 1st strand cDNA synthesis from RNA, 2nd strand cDNA synthesis, synthesis of cRNA from cDNA using biotin-conjugated rNTP's

extract_protocol: TRIzol

tag: Normal human tracheal airway cells


title: Sheff 4 hesc replicate 1


title: Human_airway_ricin

description: Gene expression data

source_name: Human airway cells, 1 ng/mL ricin, 24 h


title: Hypoxic FVB/N array 2

description: Whole lung homogenate from FVB/N mice exposed to 4 weeks hypobaric hypoxia (50 kPa)

label_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: CF control DFW CHN312


title: CF knockout HMCF CHN538


title: CF knockout LFCF CHN532


title: CF knockout LMCF CHN531


title: Hypoxic SV129 array 5

tag: Whole lung homogenate from SV129 mice exposed to 4 weeks hypobaric hypoxia (50 kPa)


title: MNR 8-2 KO Treated 3

first: Narsa

middle: Reddy

last: Machireddy

address: 615, N Wolfe St

department: Environmental Health Sciences

institute: Bloomberg School of Public Health

description: Mouse Lung Type II cell gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

source_name: Type II cells from Nrf2-/- mouse supplemented with GSH.

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: Type II cells were isolated by instilling and incubating lung with Dispase II for 45 munutes.lungs were teased and cells were incubated on IgG coated plates for an hour to remove lung macrophases. The non adherent cells were further incubated on petridishes for two hours for fibroblast adherence.  The non adherent cells were cultured on fibronectin/collagen coated plates in the presense of keratinocyte growth factor for five days.

extract_protocol: Trizol extraction of total RNA was performed followed by RNA clean up using Qiagen Rneasy kit according to the manufacturers' instructions.

treatment_protocol: no treatment

tag: ICR10 mouse strain (Nrf2-/-)  gender- female, age- 2 months, n = 1, # of tissue = 1, tissue

value: Lung, Cell:Type II, Supplementation:GSH.


title: Hypoxic FVB/N array 6

tag: Whole lung homogenate from FVB/N mice exposed to 4 weeks hypobaric hypoxia (50 kPa)


title: Hypoxic BL6 array 2

description: Whole lung homogenate from C57/BL6 mice exposed to 4 weeks hypobaric hypoxia (50 kPa)


title: MNR 5-2 KO 2

description: Mouse Lung Type II cell gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

source_name: Type II cells from Nrf2-/- mouse.

value: Lung, Cell:Type II.


title: Normoxic BL6 array 1

description: Whole lung homogenate from BL6 mice kept at Denver altitude (85 kPa) for 4 weeks.


title: MNR 6-2 KO 3

description: Mouse Lung Type II cell gene expression


title: Normoxic FVB/N array 1

description: Whole lung homogenate from FVB/N mice kept at Denver altitude (85 kPa) for 4 weeks.


title: MNR 7-2 KO Treated 2

description: Mouse Lung Type II cell gene expression


title: Hypoxic BL6 array 5

tag: Whole lung homogenate from C57/BL6 mice exposed to 4 weeks hypobaric hypoxia (50 kPa)


title: MNR 2-2 WT 4

description: Mouse Lung Type II cell gene expression

source_name: Type II cells from Nrf2+/+ mouse.

tag: ICR10 mouse strain (WT,)  gender- female, age- 2 months, n = 1, # of tissue = 1, tissue


title: C182

description: Gene expression data from breast cancer tumor tissue.

tag: ER

value: neg

tag: B-R grade

tag: node status

tag: LVI

tag: tumor type

tag: tumor size


title: MNR 1-2 WT 3

description: Mouse Lung Type II cell gene expression


title: GFP- CD25+ CD4+ cells from Foxp3(gfp/gfp) mice

city: Seattle

first: Alexander

last: Rudensky

state: WA

address: 1959 Pacific St

department: Immunology

institute: University of Washington

description: Foxp3(gfp/gfp) homozygous female mice bear a GFP-Foxp3 fusion protein knockin allele, allowing for the visualization of regulatory T cells due to GFP-Foxp3 protein fluorescence.

hyb_protocol: Standard hybridization to Affymetrix 430_2.0 arrays.

scan_protocol: Standard scanning of Affymetrix 430_2.0 arrays.

data_processing: GCMRA, Bioconductor

source_name: pooled lymph node and spleen

label_protocol: RNA was converted to biotinylated cRNA (2 rounds of amplification) using commercially available reagent kits (MessageAmp II, Ambion, Austin, TX) and were hybridized to Affymetrix mouse 430 2.0 microarrays.

extract_protocol: TelTest Stat-60 RNA extraction.

treatment_protocol: Cells were isolated by magnetic bead sorting followed by fluorescence activated cell sorting.

tag: Strain

value: C57BL/6 backcross 8-10 from 129/Sv Gender:Female Age:6-8 weeks


title: GFP+ CD4+ cells from Foxp3(gfp/gfp) mice

value: C57BL/6 backcross 8-10 from 129/Sv

tag: Gender

value: Female Age:6-8 weeks


title: GFP- CD25+ CD4+ cells from Foxp3(gfp/gfp) mice treated with IL-2

treatment_protocol: Mice were injected with 50 ng/g IL-2 or vehicle (PBS) four times within 24 hrs.  30 min following the last treatment, cells were isolated by magnetic bead sorting followed by fluorescence activated cell sorting.


title: GFP- CD25- CD4+ cells from Foxp3(gfp/gfp) mice

value: Female

tag: Age

value: 6-8 weeks


title: GITR+ CD4+ cells from C57BL/6 mice transduced with MigR1-PDE3B

description: GITR expression and Foxp3 expression correlated well in these experiments.  Transduced cells were dectected by the MigR1 marker gene, GFP.  GFP+ GITR+ CD4+ Ly5.1- cells were sorted from recipient mice for RNA.

treatment_protocol: CD25+CD4+ from B6 mice or CD25–CD4+ cells from B6.SJL mice (Ly5.1+), isolated by magnetic bead sorting, were stimulated with 100 ng/ml anti-CD3 and 100 ng/ml anti-CD28 in goat-anti-hamster IgG (Jackson ImmunoResearch) coated 12-well plates.  IL-2 (100 U/ml) was added to CD25+CD4+ cells on day 0 and to CD25–CD4+ cells on day 1 of culture.  On days 1 and 2 following stimulation, cells were “spinfected” (90 min, 2500 rpm, 37°C) with retroviral supernatants, supplemented with 5 ug/ml polybrene, 10 mM HEPES and IL-2, from transfected phoenix-E cells transfected with MigR1, MigR1-PDE3B or MigR1-PDE3B-H801A.  On day 5 of culture, aliquots of cells were stained for Foxp3.  Cultures of CD25+CD4+ cells routinely contained >70% Foxp3+ cells, >55% of which were transduced (GFP+), while cultures of CD25–CD4+ cells contained >35% transduced cells.  CD25–CD4+ cells were spinfected only on day 1 because retroviral transduction of these cells was more efficient than for TR.  Cells transduced with the same vectors were mixed and transferred into TCRalpha-deficient recipients.  Three weeks after transfer cells were analyzed by flow cytometry and isolated by FACS sorting for gene expression analysis.


title: GFP+ CD4+ CD8- thymocytes from Foxp3(gfp/gfp) mice

source_name: thymocytes

label_protocol: RNA was converted to biotinylated cRNA (2 rounds of amplification) using commercially available reagent kits (Affymetrix, Santa Clara, CA) and were hybridized to Affymetrix mouse 430 2.0 microarrays.

extract_protocol: Qiagen RNeasy

value: C57BL/6 backcross 4-6 from 129/Sv Gender:Female Age:6-8 weeks


title: GFP+ CD4+ cells from Foxp3(gfpko/wt) mice

description: Foxp3(gfpko/wt) hemizygous female mice express GFP in place of Foxp3 from the gfpko allele, allowing for the visualization of cells transcribing a mutant Foxp3 locus.  Foxp3 is X-linked, thus cells have inactivated either the Foxp3(wt) or the Foxp3(gfpko) locus.

value: C57BL/6 backcross 5 from 129/Sv


title: GFP+ CD4+ CD8- thymocytes from Foxp3(gfpko/wt) mice

value: C57BL/6 backcross 2 from 129/Sv


title: GITR+ CD4+ cells from C57BL/6 mice transduced with MigR1-PDE3B(H801A)


title: Cochlea_D257A_9mo_3

city: Madison

first: Shinichi

last: Someya

state: WI

address: 425 Henry Mall Dr

department: Medical Genetics

institute: University of Wisconsin-Madison

hyb_protocol: Hybridization (hybridization oven 640) (Affymetrix), and washing and staining (fluidics station 400) (Affymetrix) were accomplished according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix).

data_processing: GCOS 1.3 (Affymetrix), scaled to 1500

source_name: RNA

label_protocol: cDNA synthesis from total RNA (Invitrogen), cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplished according to the manufacturer’s instructions.

growth_protocol: All mice were raised under 12:12 dark/light conditions, and housed in the specific pathogen-free facility at University of Wisconsin-Madison, and provided a nonpurified diet and acidified water ad libitum.

extract_protocol: Total RNA was isolated from cochlea tissues using the TriZol Reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: To identify and analyze mtDNA mutation-responsive genes, a comparison of cochlea tissues from WT (control) and D257A mice was conducted. We examined changes in gene expression in the cochleae induced by age-related accumulation of mtDNA mutations.

value: PolgD257A/D257A mice

value: male

value: 9 month-old

tag: Tissue

value: cochlea

tag: For additional details about the strain used please refer to the following reference:

tag: Kujoth, G.C. et al. (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-4.


title: GFP+ CD4+ cells from Foxp3(gfpko/wt) mice treated with IL-2

description: Foxp3(gfpko/wt) hemizygous female mice express GFP in place of Foxp3 from the gfpko allele, allowing for the visualization of cells transcribing a mutant Foxp3 locus. Foxp3 is X-linked, thus cells have inactivated either the Foxp3(wt) or the Foxp3(gfpko) locus.


title: Cochlea_D257A_9mo_1


title: Cochlea_D257A_9mo_2


title: Cochlea_WT_9mo_1

hyb_protocol: Hybridization (hybridization oven 640) (Affymetrix), washing, and staining (fluidics station 400) (Affymetrix) were accomplished according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed using GCOS 1.3 (Affymetrix).

label_protocol: cDNA synthesis from total RNA (Invitrogen), cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplised according to the manufacture's instructions (Affymetrix).

value: Wild-type Polg+/+

value: 9 months old


title: Cochlea_WT_9mo_5

value: Polg+/+ mice


title: Cochlea_D257A_9mo_4


title: Cochlea_WT_9mo_2


title: GFP+ CD4+ cells from Foxp3(gfp/gfp) mice treated with IL-2


title: Cochlea_D257A_9mo_5


title: GFP- CD25- CD4+ CD8- thymocytes from Foxp3(gfp/gfp) mice

value: C57BL/6 backcross 4-6 from 129/Sv


title: Cochlea_WT_9mo_3

tag: For additional details about the strain used please refer to the following r


title: Cochlea_WT_9mo_4


title: CF control DMW CHN313


title: Polyamide 3

status: Public on May 17 2007

city: Pasadena

first: Peter

last: Dervan

address: 1200 East California Blvd

institute: California Institute of Technology

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 3

hyb_protocol: Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

data_processing: Resolver (Rosetta Biosoftware, Seattle); Affymetrix GeneChip Operating Software (GCOS) integrated into the Rosetta Resolver gene expression data analysis system

source_name: Polyamide treated U251 cells stimulated with DFO, biological replicate 3

growth_protocol: U251 cells seeded in 12-well plates in 10% FBS RPMI for 1 day.

extract_protocol: Cells were harvested for RNA using the Qiagen RNEasy kit and protocol.  Control cells that were not treated with DFO were also harvested.

treatment_protocol: After the 1-day growth, media was changed and at this time 1 microM of polyamide targeted to the HRE or siRNA against HIF-1a (invitrogen, as per the invitrogen protocol) was added to appropriate wells.  Cells were grown for 48 hours more.  Echinomycin (100 nM) was added to the appropriate cells, incubataed for 2 hours.  DFO was added (300 microM) for 16 hours prior to harvest.

tag: cultured U251 cells

tag: refer to ATTC


title: Polyamide 1

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 1

scan_protocol: Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

source_name: Polyamide treated U251 cells stimulated with DFO, biological replicate 1


title: Polyamide 2

description: Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 2

source_name: Polyamide treated U251 cells stimulated with DFO, biological replicate 2

label_protocol: Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)


title: Ech 3

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 3

source_name: Echinomycin treated U251 cells stimulated with DFO, biological replicate 3


title: Control 1

description: Untreated LNCaP cells stimulated with DHT, biological replicate 1

source_name: Untreated U251 cells stimulated with DFO, biological replicate 1


title: thymocytes_DN4_2

city: Bunkyo-ku

first: Masahito

last: Kawazu

address: Hongo 7-3-1

department: Department of Hematology and Oncology

institute: University of Tokyo Hospital

description:
Cell source of DN2_1, DN3_1, and DN4_1 are identical.
Cell source of DN2_2, DN3_2, and DN4_2 are identical.
Cell source of DN2_3, DN3_3, and DN4_3 are identical.
Cell source of DN2_4, DN3_4, and DN4_4 are identical.
Each cell sorce was derived from four mice.

hyb_protocol: Following fragmentation, Biotin-labeled cRNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

scan_protocol: The array was scanned with GeneChip Scanner 3000 7G.

data_processing: Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).

source_name: double negative thymocytes subset DN4

label_protocol: Biotin-labeled cRNA probes were prepared using Two-Cycle cDNA synthesis kit® (Affymetrix®, Santa Clara, CA), according to Affymetrix protocol.

extract_protocol: RNA was extracted from sorted cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol:
FACS sorting
All antibodies used for cell sorting were purchased from BD Pharmingen (San Diego, CA). Thymocytes were harvested from 5- to 6-week-old female C57BL/6 mice. Four independent cell sortings were performed and four mice were sacrificed for each experiment. Before cell sorting, CD4+ cells and CD8+ cells were depleted using the MACS LD system (Miltenyi Biotec, Bergisch Gladbach, Germany). The remaining fraction was stained with anti-CD44 and anti-CD25 antibodies conjugated to FITC or PerCP-Cy5.5, respectively, and also with PE-conjugated antibodies to CD4, CD8, CD3, NK1.1, and TCRgamma-delta and sorted using a FACSAria cell sorter (BD Bioscience). DN2, DN3, and DN4 subsets were identified as FITC+PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5- populations, respectively.

tag: Strain:C57BL/6, Gender:female, Age:5-6 weeks,


title: No_DFO_control 2

description: Untreated LNCaP cells not stimulated with DHT, biological replicate 1

source_name: Untreated U251 cells not stimulated with DFO, biological replicate 3


title: GITR+ CD4+ cells from C57BL/6 mice transduced with empty MigR1 vector


title: thymocytes_DN2_2

source_name: double negative thymocytes subset DN2


title: thymocytes_DN4_4


title: Ech 2

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 2

source_name: Echinomycin treated U251 cells stimulated with DFO, biological replicate 2


title: thymocytes_DN2_3


title: No_DFO_control 1

source_name: Untreated U251 cells not stimulated with DFO, biological replicate 1


title: siRNA 3

description: Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 3

source_name: siRNA treated U251 cells stimulated with DFO, biological replicate 3


title: Ech 1

description: Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 1

source_name: Echinomycin treated U251 cells stimulated with DFO, biological replicate 1


title: No_DFO_control 3

description: Untreated LNCaP cells not stimulated with DHT, biological replicate 2