title: 13602890 - Ea wt 6h set2 vs Ea dspA/E 6h set2

hyb_protocol: Ea dspA/E 6h set2 Cy5 / Ea wt 6h set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13602886 - Ea sec 6h set2 vs Ea wt 6h set2

status: Public on Jul 10 2008

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Identification of Arabidopsis genes regulated by the type three effector Dspa/E of Erwinia amylovora.

hyb_protocol: Ea wt 6h set2 Cy5 / Ea sec 6h set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Ea wt 6h set2

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - Media = soil	 hygrometry = 70%	 Temperature = 21degreeC	 Light = 8Hlight/16Hdark (900 lux)

extract_protocol: Ea wt 6h set2:15ug.

treatment_protocol: Name:Erwinia amylovora 6h - environmental treatment - pathogen infection,erwinia amylovora:quantity 108cfu/ml time 6hour . A bacterial suspension of each strain is prepared in sterile water at an optical density (600 nm) of 0,1. Arabidopsis leaves of independent plants are syringe-infiltrated with the different bacterial strains. Infected leaves are collected 6 or 24 hours post inoculation.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10

source_name: Ea sec 6h set2

extract_protocol: Ea sec 6h set2:15ug.

treatment_protocol: Name:Erwinia amylovora sec mutant 6h - environmental treatment - pathogen infection,erwinia amylovora sec mutant:quantity 108cfu/ml time 6hour . A bacterial suspension of each strain is prepared in sterile water at an optical density (600 nm) of 0,1. Arabidopsis leaves of independent plants are syringe-infiltrated with the different bacterial strains. Infected leaves are collected 6 or 24 hours post inoculation.


title: 13602882 - Ea wt 6h set1 vs Ea sec 6h set1

hyb_protocol: Ea sec 6h set1 Cy5 / Ea wt 6h set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ea sec 6h set1

extract_protocol: Ea sec 6h set1:15ug.

source_name: Ea wt 6h set1

extract_protocol: Ea wt 6h set1:15ug.


title: CDG Ic patient BO, biological replicate 2

status: Public on Jul 11 2008

city: Zurich

first: Thierry

last: Hennet

department: Institute of physiology

country: Switzerland

institute: University of Zurich

hyb_protocol: 15 mg of fragmented biotin-labeled cRNA was hybridized  to HG-U133A chips for 16 h at 45°C. Gene chips were washed and stained in the Affymetrix Fluidistic station 400.

scan_protocol: Gene Chips were scanned using the Gene-Array scanner G2500 (Agilent)

data_processing: 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 wasnormalized to a target intensity arbitrarily set to 500.

label: biotin

organism: Homo sapiens

source_name: forearm skin biopsy

label_protocol: Biotinilated cRNA was in vitro transcribed using the High Yield Transcription kit (ENZO diagnostic) from 15 mg of total RNA

growth_protocol: Primary fibroblasts from healthy control subjects and from CDG-I patients were grown in F12 Dulbecco's Modified Eagle's Medium (DMEM, Invitrogen) supplemented with 4.5 g/l glucose and 10% fetal calf serum. Cells were passaged when reached 70-80% confluence.

extract_protocol: TRIZOL extraction of Total RNA according to manufacturer's protocol followed by on column RNA clean-up (Rneasy mini Kit QIAGEN)

tag: primary skin fibroblasts


title: CDG Ic patient ME, biological replicate 1


title: SKMM1 day6 shIRF4b - repeat 2 - mAdbID:87201

status: Public on Jul 07 2008

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 87201

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization.

source_name: SKMM1 shi_2046 Untreated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: Cell line

tag: Cell type

value: myeloma

tag: Disease state

tag: genotype/variation

value: shirf4_2046 (shIRFb)

source_name: SKMM1 shi_2046 day6

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 6 days
Treatment temperature: 37c


title: SKMM1 day6 shIRF4b - repeat 1 - mAdbID:87200

description: mAdb experiment ID: 87200


title: SKMM1 day4 shIRF4b - mAdbID:87199

description: mAdb experiment ID: 87199

source_name: SKMM1 shi_2046 day4

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 4 days
Treatment temperature: 37c


title: SKMM1 day2 shIRF4b - mAdbID:87198

description: mAdb experiment ID: 87198

source_name: SKMM1 shi_2046 day2

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 2 days
Treatment temperature: 37c


title: H929 2046 - Day 4 - repeat 1 - mAdbID:74534

description: mAdb experiment ID: 74534

hyb_protocol: Lymphochip Hybridization Protocol Wash procedure: 1-2xssc 0.1%SDS 2-1xssc 1-0.5xssc 1-0.25xssc spin dry Qty. of labeled target: 50ug total RNA Time: 16-20hrs Volume: 40ul final volume Temperature: 65C Other: see Nature. 2000 Feb 3;403(6769):503-11. AND Immunity. 2000 Aug;13(2):199-212.

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 760;; 680 ScanPower: 100;; 100 LaserPower: 3.28;; 2.44 Temperature: 30.45

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: H929 shluc Day 4

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.

treatment_protocol:
Treatment type: compound
Agent: Doxycyclin
Treatment dose: 20 ng/ml
Treatment time: 4 days

value: shluc

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4ul
Label method: reverse transcription
Other: see Immunity. 2000 Aug;13(2):199-212.


title: SKMM1 2046 - Day 4 - mAdbID:74531

description: mAdb experiment ID: 74531

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 860;; 710 ScanPower: 100;; 100 LaserPower: 3.13;; 2.57 Temperature: 31.33

source_name: SKMM1 shluc Day 4

source_name: SKMM1 shi_2046 Day 4


title: KMS12 day4a shIRF4b - repeat 3 - mAdbID:87195

description: mAdb experiment ID: 87195

source_name: KMS12 shi_2046 Untreated

source_name: KMS12 shi_2046 day4


title: KMS12 day6 shIRF4b - repeat 3 - mAdbID:87197

description: mAdb experiment ID: 87197

source_name: KMS12 shi_2046 day6


title: H929 2046 - Day 4 - repeat 2 - mAdbID:73834

description: mAdb experiment ID: 73834

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 750;; 650 ScanPower: 100;; 100 LaserPower: 3.13;; 3.52 Temperature: 31.88


title: KMS12 day6 shIRF4b - repeat 2 - mAdbID:87196

description: mAdb experiment ID: 87196


title: KMS12 2046- Day 2 - mAdbID:72538

description: mAdb experiment ID: 72538

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 630 ScanPower: 100;; 100 LaserPower: 3.13;; 3.5 Temperature: 29.71

source_name: KMS12 shluc Day 2

treatment_protocol:
Treatment type: compound
Agent: Doxycyclin
Treatment dose: 20 ng/ml
Treatment time: 2 days

source_name: KMS12 shi_2046 Day 2


title: KMS12 2046 - Day 4 - mAdbID:72539

description: mAdb experiment ID: 72539

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 750;; 690 ScanPower: 100;; 100 LaserPower: 3.13;; 3.49 Temperature: 29.74

source_name: KMS12 shluc Day 4

source_name: KMS12 shi_2046 Day 4


title: KMS12 1332 - Day 7 - mAdbID:67577

description: mAdb experiment ID: 67577

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 780;; 640 ScanPower: 100;; 100 LaserPower: 3.26;; 3.42 Temperature: 31.61

source_name: KMS12 shi_1332 Day 7

treatment_protocol:
Treatment type: compound
Agent: Doxycyclin
Treatment dose: 20 ng/ml
Treatment time: 7 days

source_name: KMS12 shluc Day 7


title: KMS12 2046 - Day 0 - mAdbID:72537

description: mAdb experiment ID: 72537

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 800;; 730 ScanPower: 100;; 100 LaserPower: 3.14;; 3.47 Temperature: 29.62

source_name: KMS12 shluc Untreated


title: KMS12 1332b - Day 4 - mAdbID:71217

description: mAdb experiment ID: 71217

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 730;; 710 ScanPower: 100;; 100 LaserPower: 3.23;; 3.16 Temperature: 28.46

source_name: KMS12 shi_1332b Day 4


title: KMS12 1332b - Day 2 - mAdbID:71212

description: mAdb experiment ID: 71212

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 770;; 670 ScanPower: 100;; 100 LaserPower: 3.22;; 3.15 Temperature: 28.4

source_name: KMS12 shi_1332b Day 2


title: KMS12 1332b - Day 0 - mAdbID:71211

description: mAdb experiment ID: 71211

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 700 ScanPower: 100;; 100 LaserPower: 3.19;; 3.09 Temperature: 28.34

source_name: KMS12 shi_1332b Untreated


title: KMS12 day4b shIRF4b - repeat 2 - mAdbID:87192

description: mAdb experiment ID: 87192


title: KMS12 1332 - Day 5 - mAdbID:67576

description: mAdb experiment ID: 67576

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 790;; 640 ScanPower: 100;; 100 LaserPower: 3.25;; 3.4 Temperature: 31.58

source_name: KMS12 shi_1332 Day 5

treatment_protocol:
Treatment type: compound
Agent: Doxycyclin
Treatment dose: 20 ng/ml
Treatment time: 5 days

source_name: KMS12 shluc Day 5


title: KMS12 day2 shIRF4b - repeat 2 - mAdbID:87194

description: mAdb experiment ID: 87194

source_name: KMS12 shi_2046 day2


title: KMS12 1332 - Day 0 - mAdbID:67574

description: mAdb experiment ID: 67574

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 710;; 740 ScanPower: 100;; 100 LaserPower: 3.22;; 3.41 Temperature: 31.45

source_name: KMS12 shi_1332 Untreated


title: KMS12 day6 shIRF4b - repeat 1 - mAdbID:87193

description: mAdb experiment ID: 87193

source_name: KMS12 shi_2046 Untreated


title: KMS12 day2 shIRF4b - repeat 1 - mAdbID:87190

description: mAdb experiment ID: 87190


title: Nose35 (Never Smoker)

status: Public on Jul 03 2008

city: Gaithersburg

first: Sriram

last: Sridhar

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

description: Gene expression data from never smoker nasal epithelial sample

hyb_protocol: The biotin-labeled cRNA was purified by using the RNeasy kit (Qiagen, Valencia, CA) and fragmented into ~ 200 base pairs by alkaline treatment (200 mM Tris-acetate, pH 8.2/500 mM potassium acetate/150 mM magnesium acetate). Each verified cRNA sample was then hybridized overnight onto the Affymetrix HG-U133A_2 array.

scan_protocol: Confocal laser scanning (Agilent) performed to detect the streptavidin-labeled fluor.

data_processing: A single weighted mean expression level for each gene was derived using MICROARRAY SUITE 5.0 (MAS 5.0) software . The MAS 5.0 software also generated a detection P value [P(detection)] using a one-sided Wilcoxon sign-ranked test, which indicated whether the transcript was reliably detected. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Nasal epithelial samples from Never Smoker

label_protocol: Eight micrograms of total RNA from bronchial epithelial cells were converted into double-stranded cDNA with the SuperScript II reverse transcriptase (Invitrogen) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, Boulder, CO). The ENZO Bioarray RNA transcript labeling kit (Affymetrix) was used for in vitro transcription of the purified double-stranded cDNA.

growth_protocol: Cells collected from human samples.

extract_protocol: Trizol extraction of buccal mucosa samples performed based on manufacturer's protocol, with RNA from serial collections from same patient pooled to obtain minimum of 8ug for hybridization to HG-U133A_2 arrays; Nasal epithelial RNA isolated via Qiagen RNeasy Mini Kits per manufacturer’s protocol, with enough RNA from one collection to hybridize to HG-U133A_2 arrays.

treatment_protocol: Buccal mucosa samples collected from cheek scrapings, stored in RNA later; Nasal epithelial samples collected by brushing inferior nasal turbinate, brushes stored in RNA later.

tag: Never Smoker


title: KMS12 1332 - Day 3 - mAdbID:67575

description: mAdb experiment ID: 67575

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 850;; 630 ScanPower: 100;; 100 LaserPower: 3.24;; 3.41 Temperature: 31.61

source_name: KMS12 shi_1332 Day 3

treatment_protocol:
Treatment type: compound
Agent: Doxycyclin
Treatment dose: 20 ng/ml
Treatment time: 3 days

source_name: KMS12 shluc Day 3


title: KMS12 day4a shIRF4b - repeat 1 - mAdbID:87191

description: mAdb experiment ID: 87191

source_name: KMS12 shi_2046 day4


title: Nose36 (Current Smoker)

description: Gene expression data from current smoker nasal epithelial sample

source_name: Nasal epithelial samples from Current Smoker

tag: Current Smoker


title: Nose37 (Current Smoker)


title: Nose34 (Current Smoker)


title: Nose33 (Never Smoker)


title: Nose14 (Current Smoker)


title: Nose15 (Current Smoker)


title: Nose31 (Never Smoker)


title: Nose13 (Never Smoker)


title: Nose32 (Never Smoker)


title: Nose16 (Never Smoker)


title: Mouth_12 (Current Smoker)

description: Gene expression data from current smoker buccal mucosa sample

hyb_protocol: The biotin-labeled cRNA was purified by using the RNeasy kit (Qiagen, Valencia, CA) and fragmented into ~ 200 base pairs by alkaline treatment (200 mM Tris-acetate, pH 8.2/500 mM potassium acetate/150 mM magnesium acetate). Each verified cRNA sample was then hybridized overnight onto the Affymetrix HG-U133A array.

source_name: Buccal mucosa sample from Current Smoker

extract_protocol: Trizol extraction of buccal mucosa samples performed based on manufacturer's protocol, with RNA from serial collections from same patient pooled to obtain minimum of 8ug for hybridization to HG-U133A arrays; Nasal epithelial RNA isolated via Qiagen RNeasy Mini Kits per manufacturer’s protocol, with enough RNA from one collection to hybridize to HG-U133A arrays.


title: Nose17 (Current Smoker)


title: Nose11 (Current Smoker)


title: Mouth_14 (Current Smoker)


title: Mouth_15 (Never Smoker)

description: Gene expression data from never smoker buccal mucosa sample

source_name: Buccal mucosa sample from Never Smoker


title: Mouth_13 (Current Smoker)


title: Nose12 (Never Smoker)


title: Nose10 (Never Smoker)


title: Mouth_3 (Never Smoker)


title: Mouth_17 (Never Smoker)


title: Kms12 with IRF4 - slide 2 - repeat 2

type: genomic

description: No additional information.

hyb_protocol: Agilent Hybridization Protocol Other: Five micrograms of each Cy5 and Cy3 labeled DNA is hybridized to array for 40 hours at 65 degrees using Agilent ACGH/ChIp-chip hybridization and wash kits.

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 244k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default normalization parameters.

molecule: genomic DNA

source_name: Kms12 with IRF4 antibody

label_protocol:
Agilent Cy5 Labeling Protocol
Other: Whole genome amplified DNA is labeled using random primed Klenow enzyme based extension protocol according to Agilent's Mammalian ChIP-on-chip protocol v9.1.

extract_protocol:
Genomic DNA Preparation Protocol
Other: Formaldehyde cross-linked, sonicated chromatin is prepared from cell lines Kms12 and Ly19 with chromatin immunoprecipitation protocol.

treatment_protocol:
Treatment type: compound
Agent: Anti-IRF4 Antibody
Treatment dose: 10 ug

value: myeloma cell line

source_name: Kms12 Control

label_protocol:
Agilent Cy3 Labeling Protocol
Other: Whole genome amplified DNA is labeled using random primed Klenow enzyme based extension protocol according to Agilent's Mammalian ChIP-on-chip protocol v9.1.

treatment_protocol:
Treatment type: compound
Agent: Normal goat serum
Treatment dose: 10 ug


title: Mouth_4 (Current Smoker)


title: Kms12 with IRF4 - slide 1 - repeat 1

description: No additional information.


title: Kms12 with IRF4 - slide 2 - repeat 1

description: No additional information.


title: Kms12 with IRF4 - slide 1 - repeat 2

description: No additional information.


title: Mouth_5 (Current Smoker)


title: Ly19 with IRF4 - slide 2 - repeat 1

description: No additional information.

source_name: Ly19 with IRF4 antibody

value: lymphoma cell line

source_name: Ly19 Control


title: Mouth_2 (Never Smoker)


title: Ly19 with IRF4 - slide 1 - repeat 2

description: No additional information.


title: Ly19 with IRF4 - slide 1 - repeat 1

description: No additional information.


title: Ly19 with IRF4 - slide 2 - repeat 2

description: No additional information.


title: Splenic Marginal Zone Lymphoma 25

status: Public on Jul 01 2008

city: Madrid

first: Mohit

last: Aggarwal

address: Melchor F. Almagro 3

country: Spain

institute: CNIO

description: Microarray expression of B-cell Non-Hodgkins Lymphoma cases

hyb_protocol: The microarray slides were denaturalized by placing in boiling water for 3 minutes. Slides were incubated in a buffer containing 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulfate for 45 minutes at 65°C followed by washing with water and filtered using a 45-µm filter. The probe was added to a solution containing 50% formamide, 20x standard saline citrate and 10% sodium dodecyl sulfate and incubated at 100°C for 3 minutes followed by 20 minutes at 42°C before applying to the microarray slide. Hybridization was performed at 42°C for 15 hours.

scan_protocol: The slides were scanned using a Scanarray 5000 XL (GSI Lumonics Kanata, Canada) The images were analyzed with the GenePix 5.1 program (Axon Instruments Inc., USA)

data_processing: To adjust for differences in the red and green labeling, Cy3/Cy5 ratios were normalized with the Diagnosis and Normalization of Microarray Data (DNMAD) tool on the basis of standard print-tip loess as implemented in the GEPAS package (http://www.gepas.org

source_name: Total RNA from human tumoral spleen specimen

label_protocol: Amplification and Labelling protocol (1):-Amplified RNA (2.5 ug) was directly labeled with Cy3-conjugated dUTP. aRNA (2.5 ug) from the Universal Human Reference RNA (Stratagene, USA) was labeled with Cy5-conjugated dUTP as reference. 4.5 µg of total RNA were converted to double-stranded cDNA using the superscript choice system (Life Technologies) using oligo-dT primer containing a T7 RNA polymerase promoter. The double-stranded cDNA was cleaned up, and T7 in vitro transcription was performed using Ampliscribe T7 in vitro transcription kit (Epicentre Technologies, Madison, WI) or Megascript T7 in vitro transcription kit (Ambion, Austin, TX) following the manufacturers’ instructions. Fluorescent first-strand cDNA was made with 4.5 µg of amplified RNA in the presence of 50 µmol/L of Cy5-dCTP or Cy3-dCTP (Amersham, Uppsala, Sweden), random hexamers (Promega), DTT, RNAsin, unlabeled dNTP (25 nmol of dCTP, dATP, and dGTP and 5 nmol of dDTP), Amp synthetic RNA (spiked cDNA synthesis control), and superscript reverse transcriptase.22 Ten µg of Cot1 human DNA (Life Technologies, Inc.) was added to the labeled probe.

extract_protocol: Total RNA was isolated in two steps using Trizol (Life Technologies Inc., USA) followed by RNeasy (Qiagen Inc., Spain) purification.

tag: Spleen

source_name: total RNA isolated from cell lines representing different human tissues.

tag: cell lines representing different human tissues; Universal Human Reference RNA (Stratagene, USA)


title: Splenic Marginal Zone Lymphoma 26


title: Mouth_1 (Never Smoker)


title: Splenic Marginal Zone Lymphoma 20


title: Splenic Marginal Zone Lymphoma 18


title: Mudanjiang8 wild type control rep2

status: Public on Jul 02 2008

city: Wuhan

first: Deyun

last: Qiu

state: Hubei

address: Luoshi Road

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

description: Microsoft Excel program was used to merge the overlapping significant genes from two transgenic generations. Annotations from Affymetrix for significant genes were checked in NCBI public database using Blastx program (Altschul et al., 1997) and in TIGR Rice Genome Annotation version 4.0 (http://rice.tigr.org, Yuan et al., 2005) and corrected if necessary.

hyb_protocol: Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.

scan_protocol: The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).

data_processing: The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix, Inc.).The genes with probe set signal lower than 100 on the repeated six arrays were considered as non-expression and filtered out (Hu and Ma, 2006), resulting in 24283 expressed genes in rice line D11UM1-1 and 24293 expressed genes in D11UM7-2 for further analysis. The Significance Analysis of Microarrays (SAM) Excel Add-in (Tusher et al., 2001) was used to identify significantly differentially expressed genes between the control and OsWRKY13-overexpressing plants. The number of permutation for SAM analysis was 100. The delta value in the SAM was adjusted so that the estimated false discovery rate (FDR) was < 5% for significant genes. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency (Hu and Ma, 2006).

organism: Oryza sativa

source_name: Mudanjiang8 wild type control plant

label_protocol: Biotin labeled cRNA was produced with MessageAmp II-Biotin Kit (Ambion Inc., Texas) with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: Leaves of a 20 different plants pool were harvested from the 4-week old wild-type Mudanjiang 8 (Oryza sativa ssp. japonica) and OsWRKY13-overexpressing independent transgenic lines (D11UM1-1 and D11UM7-2) growing in the greenhouse at 26°C with 12 hours daylight. The experiment was repeated three times.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD) and was further purified with Nucleospin RNA Clean-up Kit (Macherey-Nagel, Germany) according to the manufacture’s instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and concentration was quantitated by spectrophotometric analysis.

tag: Mudanjiang8 wild type control


title: Splenic Marginal Zone Lymphoma 19


title: Splenic Marginal Zone Lymphoma 17


title: Splenic Marginal Zone Lymphoma 23


title: Splenic Marginal Zone Lymphoma 24


title: Splenic Marginal Zone Lymphoma 21


title: Splenic Marginal Zone Lymphoma 22


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM7-2 rep1

source_name: Mudanjiang8 OsWRKY13 Overexpressing tansgenic plant D11UM7-2

tag: OsWRKY13-overexpressing independent transgenic line T3 D11UM7-2


title: Mudanjiang8 wild type control rep3


title: Splenic Marginal Zone Lymphoma 16


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM7-2 rep2


title: Splenic Marginal Zone Lymphoma 12


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM1-1 rep1

description: The results were quantified and normalized using MicroArray Suite 5.0 (GCOS1.4) software (Affymetrix, Inc.).

hyb_protocol: Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual). Subsequently, 10 g of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.

data_processing: The genes with probe set signal lower than 100 on the repeated six arrays were considered as non-expression and filtered out (Hu and Ma, 2006), resulting in 24283 expressed genes in rice line D11UM1-1 and 24293 expressed genes in D11UM7-2 for further analysis. The Significance Analysis of Microarrays (SAM) Excel Add-in (Tusher et al., 2001) was used to identify significantly differentially expressed genes between the control and OsWRKY13-overexpressing plants. The number of permutation for SAM analysis was 100. The delta value in the SAM was adjusted so that the estimated false discovery rate (FDR) was < 5% for significant genes. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency (Hu and Ma, 2006). Microsoft Excel program was used to merge the overlapping significant genes from two transgenic generations. Annotations from Affymetrix for significant genes were checked in NCBI public database using Blastx program (Altschul et al., 1997) and in TIGR Rice Genome Annotation version 4.0 (Yuan et al., 2005) and corrected if necessary.

source_name: Mudanjiang8 OsWRKY13_Overexpressing transgenic plant D11UM1-1

tag: OsWRKY13-overexpressing independent transgenic line D11UM1-1 T3


title: Splenic Marginal Zone Lymphoma 11


title: Splenic Marginal Zone Lymphoma 15


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM1-1 rep3

source_name: Mudanjiang8 OsWRKY13 Overexpressing tansgenic plant D11UM1-1

tag: OsWRKY13-overexpressing independent transgenic line T3 D11UM1-1


title: Splenic Marginal Zone Lymphoma 13


title: Mudanjiang8 wild type control rep1


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM1-1 rep2


title: Splenic Marginal Zone Lymphoma 14


title: Splenic Marginal Zone Lymphoma 27


title: Splenic Marginal Zone Lymphoma 6


title: Splenic Marginal Zone Lymphoma 9


title: Nodal Marginal Zone Lymphoma 5

source_name: Total RNA from human Lymph node specimen

tag: Lymph node


title: Splenic Marginal Zone Lymphoma 8


title: Splenic Marginal Zone Lymphoma 3


title: Splenic Marginal Zone Lymphoma 10


title: Splenic Marginal Zone Lymphoma 7


title: Nodal Marginal Zone Lymphoma 4


title: Nodal Marginal Zone Lymphoma 6


title: Splenic Marginal Zone Lymphoma 1


title: Splenic Marginal Zone Lymphoma 5


title: Splenic Marginal Zone Lymphoma 4


title: Nodal Marginal Zone Lymphoma 1


title: Follicular Lymphoma 27


title: Follicular Lymphoma 32


title: Splenic Marginal Zone Lymphoma 2


title: Follicular Lymphoma 31


title: Follicular Lymphoma 28


title: Nodal Marginal Zone Lymphoma 2


title: Follicular Lymphoma 30


title: Follicular Lymphoma 26


title: Nodal Marginal Zone Lymphoma 3


title: Follicular Lymphoma 29


title: Follicular Lymphoma 33


title: Follicular Lymphoma 25


title: Follicular Lymphoma 24


title: Follicular Lymphoma 23


title: Follicular Lymphoma 22


title: Follicular Lymphoma 17


title: Follicular Lymphoma 19


title: Follicular Lymphoma 16


title: Follicular Lymphoma 20


title: Follicular Lymphoma 21


title: Follicular Lymphoma 18


title: Follicular Lymphoma 14


title: Follicular Lymphoma 15


title: Follicular Lymphoma 10


title: Follicular Lymphoma 11


title: Follicular Lymphoma 13


title: Follicular Lymphoma 12


title: Follicular Lymphoma 1


title: Follicular Lymphoma 9


title: Chronic Lymphocytic Lymphoma 38


title: Chronic Lymphocytic Lymphoma 37


title: Follicular Lymphoma 6


title: Follicular Lymphoma 7


title: Follicular Lymphoma 2


title: Chronic Lymphocytic Lymphoma 36


title: Follicular Lymphoma 3


title: Follicular Lymphoma 5


title: Follicular Lymphoma 4


title: Follicular Lymphoma 8


title: Chronic Lymphocytic Lymphoma 35


title: Chronic Lymphocytic Lymphoma 32


title: Chronic Lymphocytic Lymphoma 29


title: Chronic Lymphocytic Lymphoma 34


title: Chronic Lymphocytic Lymphoma 28


title: Chronic Lymphocytic Lymphoma 31


title: Chronic Lymphocytic Lymphoma 30


title: Chronic Lymphocytic Lymphoma 19


title: Chronic Lymphocytic Lymphoma 26


title: Chronic Lymphocytic Lymphoma 23


title: Chronic Lymphocytic Lymphoma 21


title: Chronic Lymphocytic Lymphoma 25


title: Chronic Lymphocytic Lymphoma 22


title: Chronic Lymphocytic Lymphoma 20


title: Chronic Lymphocytic Lymphoma 33


title: Chronic Lymphocytic Lymphoma 24


title: Chronic Lymphocytic Lymphoma 27


title: Chronic Lymphocytic Lymphoma 15


title: Chronic Lymphocytic Lymphoma 13


title: Chronic Lymphocytic Lymphoma 12


title: Chronic Lymphocytic Lymphoma 14


title: Chronic Lymphocytic Lymphoma 16


title: Chronic Lymphocytic Lymphoma 10


title: Chronic Lymphocytic Lymphoma 9


title: Chronic Lymphocytic Lymphoma 7


title: Chronic Lymphocytic Lymphoma 8


title: Chronic Lymphocytic Lymphoma 17


title: Chronic Lymphocytic Lymphoma 6


title: Chronic Lymphocytic Lymphoma 18


title: Chronic Lymphocytic Lymphoma 5


title: Chronic Lymphocytic Lymphoma 4


title: Chronic Lymphocytic Lymphoma 2


title: Chronic Lymphocytic Lymphoma 11


title: Diffuse Large Bcell Lymphoma 27


title: Diffuse Large Bcell Lymphoma 30


title: Diffuse Large Bcell Lymphoma 36


title: Diffuse Large Bcell Lymphoma 26


title: Diffuse Large Bcell Lymphoma 32


title: Diffuse Large Bcell Lymphoma 29


title: Chronic Lymphocytic Lymphoma 1


title: Diffuse Large Bcell Lymphoma 28


title: Diffuse Large Bcell Lymphoma 35


title: Diffuse Large Bcell Lymphoma 23


title: Diffuse Large Bcell Lymphoma 21


title: Diffuse Large Bcell Lymphoma 20


title: Diffuse Large Bcell Lymphoma 19


title: Diffuse Large Bcell Lymphoma 22


title: Diffuse Large Bcell Lymphoma 25


title: Diffuse Large Bcell Lymphoma 31


title: Diffuse Large Bcell Lymphoma 18


title: Diffuse Large Bcell Lymphoma 33


title: Chronic Lymphocytic Lymphoma 3


title: Diffuse Large Bcell Lymphoma 34


title: Diffuse Large Bcell Lymphoma 15


title: Diffuse Large Bcell Lymphoma 16


title: Diffuse Large Bcell Lymphoma 24


title: Diffuse Large Bcell Lymphoma 17


title: Diffuse Large Bcell Lymphoma 12


title: Diffuse Large Bcell Lymphoma 13


title: Diffuse Large Bcell Lymphoma 14


title: Diffuse Large Bcell Lymphoma 10


title: Diffuse Large Bcell Lymphoma 11


title: Diffuse Large Bcell Lymphoma 8


title: Diffuse Large Bcell Lymphoma 2


title: Diffuse Large Bcell Lymphoma 4


title: Diffuse Large Bcell Lymphoma 7


title: Diffuse Large Bcell Lymphoma 1


title: Diffuse Large Bcell Lymphoma 3


title: Diffuse Large Bcell Lymphoma 9


title: Diffuse Large Bcell Lymphoma 5


title: Mantle Cell Lymphoma 38


title: Mantle Cell Lymphoma 32


title: Mantle Cell Lymphoma 34


title: Mantle Cell Lymphoma 30


title: Mudanjiang8 OsWRKY13 Overexpressing D11UM7-2 rep3


title: Mantle Cell Lymphoma 36


title: Mantle Cell Lymphoma 27


title: Mantle Cell Lymphoma 33


title: Mantle Cell Lymphoma 31


title: Mantle Cell Lymphoma 28


title: Diffuse Large Bcell Lymphoma 6


title: Mantle Cell Lymphoma 25


title: Mantle Cell Lymphoma 26


title: Mantle Cell Lymphoma 29


title: Mantle Cell Lymphoma 24


title: Mantle Cell Lymphoma 23


title: Mantle Cell Lymphoma 21


title: LNCaP HOXC6 overexpression, biological rep 2

city: Atlanta

first: Colleen

middle: D

last: McCabe

state: GA

address: 615 Michael St

institute: Emory University

description: Gene expression data from LNCaP cells with HOXC6 overexpression

hyb_protocol: cRNA probes were hybridized overnight to the Human Genome U133 GeneChip set. GeneChips were washed in the Affymetrix GeneChip Fluidics WorkStation.

scan_protocol: GeneChips were scanned according to manufacturer's protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) to filter genes that were called present in fewer that 50% of samples.

source_name: LNCaP cells, 48 hours post transient overexpression of HOXC6 transfection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-3 ug total RNA.

growth_protocol: LNCaP cells grown in T-medium containing 10% FBS at 37C and 5% CO2.

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

treatment_protocol: Cells were transiently transfected with 100nM siRNA or 4ug vector DNA.

tag: LNCaP cells after transient overexpression of HOXC6 transfection


title: Mantle Cell Lymphoma 20


title: Mantle Cell Lymphoma 18


title: LNCaP HOXC6 overexpression, biological rep 1


title: Mantle Cell Lymphoma 19


title: Mantle Cell Lymphoma 13


title: Mantle Cell Lymphoma 15


title: LNCaP HOXC6 siRNA, biological rep 2

description: Gene expression data from LNCaP cells with HOXC6 siRNA knockdown

source_name: LNCaP cells, 48 hours post siRNA knockdown of HOXC6 transfection

tag: LNCaP cells after siRNA knockdown of HOXC6 transfection


title: Mantle Cell Lymphoma 14


title: LNCaP HOXC6 siRNA, biological rep 1


title: LNCAp control, biological rep 2

description: Gene expression data from LNCaP cells with control transfection

source_name: LNCaP cells, 48 hours post control transfection

tag: LNCap cells


title: Mantle Cell Lymphoma 9


title: Mantle Cell Lymphoma 12


title: Mantle Cell Lymphoma 8


title: Mantle Cell Lymphoma 10


title: Mantle Cell Lymphoma 6


title: Mantle Cell Lymphoma 7


title: LNCaP control, biological rep 1

tag: LNCaP cells


title: Mantle Cell Lymphoma 17


title: Mantle Cell Lymphoma 4


title: Mantle Cell Lymphoma 3


title: Mantle Cell Lymphoma 1


title: Mantle Cell Lymphoma 16


title: Mantle Cell Lymphoma 5


title: Mantle Cell Lymphoma 2


title: Mantle Cell Lymphoma 11


title: Burkitt Lymphoma 9


title: Burkitt Lymphoma 5


title: Burkitt Lymphoma 7


title: Burkitt Lymphoma 6


title: Spleen Control 5


title: Burkitt Lymphoma 3


title: Burkitt Lymphoma 4


title: Burkitt Lymphoma 1


title: Spleen Control 2


title: Reactive Lymph Node 7

tag: Reactive Lymph node


title: Spleen Control 1


title: Reactive Lymph Node 8


title: Reactive Lymph Node 6


title: Spleen Control 3


title: Burkitt Lymphoma 8


title: Reactive Lymph Node 5


title: Reactive Lymph Node 4


title: ReactiveLymph Node 1


title: Reactive Lymph Node 3


title: Spleen Control 4


title: Burkitt Lymphoma 2


title: Reactive Lymph Node 2


title: Mantle Cell Lymphoma 37


title: Large Congenital Melanocytic Naevi (CMN) : NCG23_1

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Hybridization were replicated with dye swap (see NCG23_2)

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of human cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2

source_name: Medium Congenital Melanocytic Naevi (CMN) : NCG23_1

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Label source :GE Healthcare Bio-Sciences, New Jersey, USA).

growth_protocol: Cell cultures were performed with Ham-F10 basal medium supplemented with 9% FCS (Invitrogen, Carlsbad, CA, USA), L-Glutamine 1mM (Sigma-Aldrich, Saint-Louis, Missouri, USA), Penicilline G 100U/ml (Sigma-Aldrich, Saint-Louis, Missouri, USA), Kanamycine Sulfate 100µg/ml (Invitrogen, Carlsbad, CA, USA), Streptomycine Sulfate 100µg/ml (Invitrogen, Carlsbad, CA, USA), Choleratoxin 1nM (Sigma-Aldrich, Saint-Louis, Missouri, USA), BPE 40µg/ml, TPA 30nM (Sigma-Aldrich, Saint-Louis, Missouri, USA), IBMX 50µM (Sigma-Aldrich, Saint-Louis, Missouri, USA), Phosphoéthanolamine 100µM (Sigma-Aldrich, Saint-Louis, Missouri, USA), Hydrocortisone 0.5µM (Sigma-Aldrich, Saint-Louis, Missouri, USA), Ethanolamine 100µM (Sigma-Aldrich, Saint-Louis, Missouri, USA), all of these from the same batch. In order to prevent fibroblastic contamination, Geneticine (200 µg/ml, Carlsbad, CA, USA) was added at passage 1 and during 24 hours.

extract_protocol: RNA from melanocytic cells was extracted by ultracentrifugation in a guanidine isothiocyanate-cesium chloride gradient, followed by phenol-chloroform RNA extraction.

treatment_protocol: Cells from Large Congenital Melanocytic Naevi samples were isolated using a collagenase/dispase preparation (Morandini R., personal communication).

tag: Cells from medium Congenital Melanocytic Naevi. BRAF V600E mutated sample.

source_name: Reference RNA : pool of 13 different foreskins

treatment_protocol: Cells from normal melanocytes obtained from 13 different foreskins were isolated using a collagenase/dispase preparation (Morandini R., personal communication).

tag: Pool of normal melanocytes cells from 13 different foreskins


title: Wild_type_37_degrees_vs_Wild_type_25_degrees

city: Ramat Gan

first: Don

middle: Jay

last: Katcoff

address: Ramat Gan

department: Life Sciences

country: Israel

institute: Bar Ilan University

description: Wild type strain was grown at 37 degrees C, wild type strain was grown at 25 degrees C.

hyb_protocol: For each hybridization, 750 ng of cyanine 3- and 750 ng of cyanine 5-labeled cRNA were fragmented and hybridized to an Agilent Technologies Yeast (V2) Gene Expression Microarray (part number G4140B), using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the manual.

scan_protocol: All microarrays were scanned using Agilent's dual laser DNA microarray scanner G2505B. The data were then extracted from images by using Feature Extraction 9.1 software (Agilent Technologies).

data_processing: The R 2.4 software and the LIMMA package from the Bioconductor project (http://www.bioconductor.org ) were used to normalize the microarray data using VSN normalization. VALUES presented as log 2 of ratio (wt37/wt25).

organism: Saccharomyces cerevisiae

source_name: Wild type grown at 37 degrees C.

label_protocol: Total RNA was amplified and fluorescently labeled using the Agilent Technologies Low Input Linear Amplification Kit (part number 5184-3523) following the protocol described in the kit manual.

growth_protocol: Cells were grown at 37 degrees C in YPAD medium to 0D600 0.5 with agitation.

extract_protocol: Hot phenol

treatment_protocol: Wild type cells were grown in YAPD medium to OD600 0.5, then rapidly heated to 37 degrees C for 15 minutes

tag: Euroscarf strain BY4741 (Mat alpha, his3 delta 1, leu2 delta 0, met15 delta 0, ura3 delta 0)

source_name: Wild type grown at 25 degrees C.

growth_protocol: Cells were grown at 25 degrees C in YPAD medium to 0D600 0.5 with agitation.


title: Large Congenital Melanocytic Naevi (CMN) : NCG24_1

description: Hybridization were replicated with dye swap (see NCG24_2)

tag: Cells from Large Congenital Melanocytic Naevi. BRAF translocation.

tag: Karyotype

extract_protocol: RNA from melanocytic cells was extracted by ultracentrifugation in a guanidine isothiocyanate-cesium chloride gradient, followed by phenol-chloroform RNA extraction


title: HHO1_delta_25_degrees_vs_Wild_type_25_degrees

description: Yeast were grown at 25 degrees C.

data_processing: The R 2.4 software and the LIMMA package from the Bioconductor project (http://www.bioconductor.org ) were used to normalize the microarray data using VSN normalization. VALUES presented as log 2 ratio (mu25/wt25).

source_name: HHO1 delta grown at 25 degrees C.

tag: Euroscarf strain Y02125 (Mat alpha, his3 delta 1, leu2 delta 0, met15 delta 0, ura3 delta 0, YPL127C::kanMx4)


title: Large Congenital Melanocytic Naevi (CMN) : NCG26_1

description: Hybridization were replicated with dye swap (see NCG26_2)

tag: Cells from Large Congenital Melanocytic Naevi. BRAF V600E mutated sample.


title: HHO1_delta_37_degrees_vs_Wild_type_25_degrees

description: HHO1 delta strain was grown at 37 degrees C, wild type strain was grown at 25 degrees C.

data_processing: The R 2.4 software and the LIMMA package from the Bioconductor project (http://www.bioconductor.org ) were used to normalize the microarray data using VSN normalization. VALUES presented as log 2 of ratio (mu37/wt25).

source_name: HHO1 delta grown at 37 degrees C.

treatment_protocol: HHO1 delta cells were grown in YAPD medium to OD600 0.5, then rapidly heated to 37 degrees C for 15 minutes

tag: Euroscarf strain Y02125 (Mat alpha, his3 delta 1, leu2 delta 0, met15 delta 0, ura3 delta 0, YPL127C::kanMX4)


title: Large Congenital Melanocytic Naevi (CMN) : NCG27_1

description: Hybridization were replicated with dye swap (see NCG27_2)


title: Large Congenital Melanocytic Naevi (CMN) : NCG26_2

description: Hybridization were replicated with dye swap (see NCG26_1)


title: Large Congenital Melanocytic Naevi (CMN) : NCG27_2

description: Hybridization were replicated with dye swap (see NCG27_1)


title: Large Congenital Melanocytic Naevi (CMN) : NCG23_2

description: Hybridization were replicated with dye swap (see NCG23_1)

tag: Cells from Medium Congenital Melanocytic Naevi. BRAF V600E mutated sample.


title: Large Congenital Melanocytic Naevi (CMN) : NCG24_2

description: Hybridization were replicated with dye swap (see NCG24_1)


title: Mantle Cell Lymphoma 35

tag: cell lines representing different human tissues; Universal Human Reference RNA (Stratagene, USA)


title: 1 day differentiated C2C12

status: Public on Jun 30 2008

city: St Lucia

first: Chung Fai

last: Wong

state: Q

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

description: the 1 day differentiated sample has 4 biological replicates - 2 labelled cy3 and 2 labelled Cy5

hyb_protocol: Hybridised by the Adelaide microarray facility

scan_protocol: Scanned and data extracted using Spot

data_processing: Samples were analysed in Genespring.

organism: Mus musculus

source_name: reference_prol C2C12

label_protocol: labelled by the Adelaide Microarray Facility

growth_protocol: Cells were grown when proliferating, at about 70 - 80% confluence.

extract_protocol: Trizol extracted

tag: reference, proliferating C2C12, pool of 4 biological replicates

source_name: 1 day differentiated C2C12

growth_protocol: harvested 1 day post-differentiation induction

extract_protocol: Trizol

treatment_protocol: cells were grown in 2% horse serum at confluence and harvested 1 day later

tag: 1 day differentiated C2C12, 4 biological replicates


title: 2 day differentiated C2C12

description: the 2 day differentiated sample has 4 biological replicates - 2 labelled cy3 and 2 labelled Cy5

source_name: reference_proliferating C2C12

tag: reference pool of 4 proliferating C2C12 samples

source_name: 2 day differentiated C2C12

growth_protocol: harvested 2 day post-differentiation induction

treatment_protocol: cells were grown in 2% horse serum at confluence and harvested 2 days later

tag: 4 biological replicates, 2 day post-differentiation induction


title: 4 days differentiated C2C12

description: the 4 day differentiated sample has 4 biological replicates - 2 labelled cy3 and 2 labelled Cy5

tag: reference, pool of 4 proliferating C2C12 samples

source_name: 4 days post-differentiation induction

growth_protocol: harvested 4 day post-differentiation induction

treatment_protocol: cells were grown in 2% horse serum at confluence and harvested 4 days later

tag: 4 days post-differentiation induction, 4 biological replicates


description: Hybridization were replicated with dye swap (NCG21_1)

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is Log (base 2) of the ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm)

source_name: Large Congenital Melanocytic Naevi (CMN) : NCG21_2 (dye-swap)


title: Large Congenital Melanocytic Naevi (CMN) : NCG21_1

description: Hybrization were replicated with dye swap (NCG21_2)


title: Large Congenital Melanocytic Naevi (CMN) : NCG22_2

description: Hybridization were replicated with dye swap (see NCG22_1)

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 (532 nm) to Channel 2 (635 nm)


title: Large Congenital Melanocytic Naevi (CMN) : NCG22_1

description: Hybridization were replicated with dye swap (see NCG22_2)

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm)


title: miRNA_proliferating C2C12

description: the proliferating sample has 4 biological replicates - 2 labelled cy3 and 2 labelled Cy5

source_name: reference C2C12

tag: reference sample, proliferating C2C12, pool of four biological replicates

source_name: proliferating C2C12

growth_protocol: harvested at 70 -  80% confluence

tag: proliferating C2C12 samples, nromalised data from 4 biological replicates


title: miRNA_confluent C2C12

description: the confluent sample has 4 biological replicates - 2 labelled cy3 and 2 labelled Cy5

source_name: reference

growth_protocol: harvested at 100% confluence

tag: 100% confluent C2C12, 4 biological replicates


title: C10 congenic_Sentrix_P0.5 whole brain_rep 5

city: Dallas

first: Sanghyeon

last: Kim

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern medical center

hyb_protocol: The labeled probe was hybridized to Illumina's Sentrix mouse-6 Expression BeadChips (Illumina, San Diego, CA).

scan_protocol: Illumina's BeadStation 500GX Genetic Analysis System

data_processing: The raw image data of Illumina BeadChip arrays were analyzed and normalized using the cubic spline method via the BeadStudio software (Illumina, San Diego, CA).

source_name: whole brain

label_protocol: Total RNA was reverse transcribed, then in vitro transcribed to cRNA and labeled with biotin-16-UTP.

growth_protocol: All mice of the same strain and gender were raised in groups of four with food (Teklad 7002; 6%fat; Harlan Teklad, Madison, Wi.) and water freely available. All experiments followed the NIH Guide for the Care and Use of Laboratory Animals and received Institutional Animal Care and Use approval.

extract_protocol: total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s manual. RNA was treated with DNA-freeTM (Ambion, Austin, Tx.) to remove residual contaminating DNA.

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 5


title: B6_Sentrix_P0.5 whole brain_rep2

description: B6_Sentrix_P0.5 whole brain_rep2

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate 2


title: C10 congenic_430B_hippocamous_pool1

description: C10 congenic_430B_hippocamous_pool1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The raw image files of Affymetrix microarrays were analyzed and normalized using the Probe Logarithmic Intensity Error estimation (PLIER) algorithm in the ArrayAssist Expression software package (Stratagene, La Jolla, Ca). The software performed a two-step analysis: one for present/absent calls by MAS5, and the other for data generation by PLIER.

source_name: Adult hippocampus

label_protocol: Standard Affymetrix protocol

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , adult hippocampus, 3 hippocampi /pool


title: B6_Sentrix_P0.5 whole brain_rep 5

description: B6_Sentrix_P0.5 whole brain_rep 5

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate 5


title: C10 congenic_Sentrix_P0.5 whole brain_rep 4

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 4


title: C10 congenic_Sentrix_P0.5 whole brain_rep 2

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 2


title: C10 congenic_430B_hippocamous_pool3

description: C10 congenic_430B_hippocamous_pool3


title: Mantle Cell Lymphoma 22

description: Microarray expression of B-cell Non-Hodgkins Lymphoma cases

source_name: Total RNA from human Lymph node specimen

tag: Lymph node

source_name: total RNA isolated from cell lines representing different human tissues.


title: AJ_Sentrix_P0.5 whole brain_rep2

description: AJ_Sentrix_P0.5 whole brain_rep2

source_name: Whole brain

tag: Male AJ mice, P0.5 whole brain, biological replicate2


title: C10 congenic_Sentrix_P0.5 whole brain_rep 6

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 6


title: AJ_Sentrix_P0.5 whole brain_rep3

description: AJ_Sentrix_P0.5 whole brain_rep3

tag: Male AJ mice, P0.5 whole brain, biological replicate3


title: AJ_Sentrix_P0.5 whole brain_rep4

description: AJ_Sentrix_P0.5 whole brain_rep4

tag: Male AJ mice, P0.5 whole brain, biological replicate4


title: C10 congenic_430B_hippocamous_pool2

description: C10 congenic_430B_hippocamous_pool2


title: B6_Sentrix_P0.5 whole brain_rep 6

description: B6_Sentrix_P0.5 whole brain_rep 6

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate 6


title: C10 congenic_Sentrix_P0.5 whole brain_rep 3

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 3


title: B6_430B_hippocamous_pool3

source_name: adult hippocampus

tag: Male C57BL/6J mice, adult hippocampus, 3 hippocampi /pool


title: B6_430B_hippocamous_pool1


title: B6_430B_hippocamous_pool2


title: AJ_Sentrix_P0.5 whole brain_rep5

description: AJ_Sentrix_P0.5 whole brain_rep5

tag: Male AJ mice, P0.5 whole brain, biological replicate5


title: AJ_430B_hippocamous_pool4

tag: Male A/J mice, adult hippocampus, 3 hippocampi /pool


title: AJ_Sentrix_P0.5 whole brain_rep6

description: AJ_Sentrix_P0.5 whole brain_rep6

tag: Male AJ mice, P0.5 whole brain, biological replicate6


title: AJ_Sentrix_P0.5 whole brain_rep1

description: AJ_Sentrix_P0.5 whole brain_rep1

tag: Male AJ mice, P0.5 whole brain, biological replicate1


title: B6_Sentrix_P0.5 whole brain_rep1

description: B6_Sentrix_P0.5 whole brain_rep1

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate1


title: B6_Sentrix_P0.5 whole brain_rep3

description: B6_Sentrix_P0.5 whole brain_rep3

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate 3


title: C10 congenic_Sentrix_P0.5 whole brain_rep 1

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , P0.5 whole brain, biological replicate 1


title: C10 congenic_430A_hippocamous_pool3

description: C10 congenic_430A_hippocamous_pool3

tag: Interval-specific congenic strain of Chromosome 10 (C10 congenic) mice were generated and maintained on the A/J background after at least 10 backcrosses as heterozygotes (B6/A) for the chr. 10 region, male , adult hippocampus, 3 hippocampi /pool


title: AJ_430B_hippocamous_pool3


title: AJ_430B_hippocamous_pool2


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 4 (NeuroDev v2.2)

type: other

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

description: Biological replicate one of four.

hyb_protocol: cDNA microarrays were pre-hybridized during 1 hour at 42¡C in 5x SSC, 0.1% SDS, 1% BSA, washed with distilled water and dried. They were hybridized overnight at 42¡C in 25% formamide, 5x SSC, 0.1%SDS with Cy5- and Cy3-labelled cDNA, washed in 1x SSC, 0.2% SDS at 42¡C, in 0.1x SSC, 0.2% SDS and two times in 0.1x SSC at room temperature and finally were spin-dried.

scan_protocol: The hybridized microarrays were scanned using Genepix 4000B (Axon) and the resulting image files analyzed by GenePix Pro 5.0 software (Axon).

data_processing: For each GenePix output files, two filters were applied, one to clear out spots and another one to discard saturating spots, where the median foreground intensity was greater than 60,000 in one of the two channels. The resulting median foreground intensities were normalised, without background signal subtraction, for dye bias using a global Lowess correction.

molecule: other

source_name: Four r4 samples of the same genotype (Phox2b LacZ/LacZ) were pooled together.

label_protocol: Two µg of amplified RNA were retrotranscribed and labelled with dUTP-Cy3 (Amersham) using Superscript III Reverse Transcriptase (Invitrogene) in the presence of 5µg random primers (Invitrogene) and appropriate buffer (Invitrogene). RNA was degraded by alkaline lysis and cDNA was purified using QIAquick purification kit (Qiagen).

extract_protocol: RNA was extracted and amplified using the RNAqueous-Micro Kit (Ambion) and the Message Amp aRNA amplification kit (Ambion) according to the instructions of the manufacturer.

tag: Phox2bLacZ/+ mice were intercrossed and the hindbrains of E10.5 embryos were dissected out and incubated for 2 min at 37¡C with 1µg/µL fluorescein di-(alpha -D-galactopyranoside) (Sigma, St. Louis, MO). The left and right beta-galactosidase expressing domains of ventral r4 with the floorplate in between were excised under a fluorescent binocular and stored at -20¡C in RNALater solution (Ambion).

source_name: Four r4 samples of the same genotype (Phox2b LacZ/+) were pooled together.

label_protocol: Two µg of amplified RNA were retrotranscribed and labelled with dUTP-Cy5 (Amersham) using Superscript III Reverse Transcriptase (Invitrogene) in the presence of 5µg random primers (Invitrogene) and appropriate buffer (Invitrogene). RNA was degraded by alkaline lysis and cDNA was purified using QIAquick purification kit (Qiagen).


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 1 dye swap (NeuroDev v2.2)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 3 (NeuroDev v2.2)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 1 (NeuroDev v2.2)

description: Biological replicate one of four.


title: C10 congenic_430A_hippocamous_pool1

description: C10 congenic_430A_hippocamous_pool1


title: AJ_430A_hippocamous_pool4


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 2 (NeuroDev v2.2)

description: Biological replicate one of four.


title: B6_430A_hippocamous_pool2


title: AJ_430A_hippocamous_pool2


title: B6_430A_hippocamous_pool3


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 3 dye swap (NeuroDev v2.2)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 4 dye swap (NeuroDev v2.2)

description: Biological replicate one of four.


title: C10 congenic_430A_hippocamous_pool2

description: C10 congenic_430A_hippocamous_pool2


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 2 dye swap (NeuroDev v2.2)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 3 dye swap (NIA 15k)

description: Biological replicate one of four.


title: AJ_430A_hippocamous_pool3


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 3 (NIA 15k)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 4 (NIA 15k)

description: Biological replicate one of four.


title: B6_430A_hippocamous_pool1

tag: Male C47BL/6J mice, adult hippocampus, 3 hippocampi /pool


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 1 dye swap (NIA 15k)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 4 dye swap (NIA 15k)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 2 dye swap (NIA 15k)

description: Biological replicate one of four.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 2 (NIA 15k)

description: Biological replicate one of four.


title: pseudoblastema, N1 transgenic 2

city: Dunedin

first: Caroline

last: Beck

address: 340 Great King Street

department: Zoology

country: New Zealand

institute: University of Otago

description: Xenopus hind limb pseudoblastema, N1 transgenic 2

hyb_protocol: Affymetrix recommended protocol; undertaken by Liam Williams at Centre for Genomics and Proteomics at the University of Auckland

scan_protocol: Affymetrix GCOS; undertaken by Liam Williams at Centre for Genomics and Proteomics at the University of Auckland

data_processing: Data were normalised to other samples in this series using MAS5.0 algorithm in GCOS; undertaken by Liam Williams at Centre for Genomics and Proteomics at the University of Auckland

organism: Xenopus laevis

source_name: 3 day post amputation pseudoblastema from transgenic N1 Xenopus laevis hind limb

label_protocol: Affymetrix 2-cycle labelling kit; undertaken by Liam Williams at Centre for Genomics and Proteomics at the University of Auckland

extract_protocol: TRIzol extracted and purified with Qiagen RNeasy mini kit.

tag: Tissue taken from distal stump 3 days following hind limb partial amputation at the level of the future ankle of a tadpole at Nieuwkoop and Faber stage 52 of development. The tissue includes the forming pseudoblastema mesenchyme and overlying wound epithelium and does not have the potential to regenerate. 10 pseudoblastemas were pooled before extraction of total RNA.


title: Phox2b LacZ+/- vs Phox2b LacZ-/- dissection 1 (NIA 15k)

description: Biological replicate one of four.


title: blastema, wild type 1

description: Xenopus hind limb blastema, wild type 1

source_name: 3 day post amputation blastema from wild type Xenopus laevis hind limb

tag: Tissue taken from distal stump 3 days following hind limb partial amputation at the level of the future ankle of a tadpole at Nieuwkoop and Faber stage 52 of development. The tissue includes the forming regeneration blastema mesenchyme and overlying apical ectodermal cap which forms from the wound epithelium. Tissue from 20 hind limbs blastemas was pooled before extraction of total RNA.


title: Rat Adrenal Zona Glomerulosa Cells-Control-Exp2

status: Public on Jun 29 2008

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

description: Cells were incubated in DMEM:F12 (1:1) media containing 0.5 % fatty acid free bovine serum albumin under basal conditions at 37 C in a 5 % CO2 incubator for 2 h.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Standard Affymetrix GCOS

organism: Rattus norvegicus

source_name: zona glomerulosa adrenal cells

label_protocol: Standard Affymetrix

extract_protocol: Total RNA was extracted with the RNeasy Midi kit (Qiagen, Valencia, CA), on-column deoxyribonuclease digested

treatment_protocol: Cells obtained by a combination of enzymatic and mechanical dispersion

tag: Male Sprague Dawley rats (3 month old)


title: Rat Adrenal Zona Glomerulosa Cells-Ang II-Exp2

description: Cells were incubated in DMEM:F12 (1:1) media containing 0.5 % fatty acid free bovine serum albumin under Ang II (100 nM) stimulatory conditions at 37 C in a 5 % CO2 incubator for 2 h.


title: blastema, wild type 2

description: Xenopus hind limb blastema, wild type 2


title: Lower pulvinus 15 min polysomal RNA biorep 2

status: Public on Jun 27 2008

city: Raleigh

first: Henrietta

last: Myburg

state: NC

address: 42218 Gardner Hall

department: Botany

institute: NC State University

description: no additional info

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc.

scan_protocol: Scanning of the Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc.

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

molecule: polyA RNA

organism: Zea mays

source_name: lower pulvinus_15min_Polysomal RNA_biorep 2

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic one-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual.

growth_protocol: Maize (Zea mays strain B73) plants were cultivated in soil using 20cm diameter pots (two plants per pot, 6 plants per time point).  Greenhouse conditions were as follow: natural light, 30ºC day and 26ºC night temperatures.  Plants were grown to an age of ~6 weeks.

extract_protocol: Pulvini tissue was immediately frozen in liquid nitrogen after harvesting in the greenhouse.  The harvested pulvini samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  This frozen powder was separated into aliquots, one used for extraction of total RNA, the other for isolation of polysomes and subsequent extraction of polysomal RNA.  Polyribosomes were harvested as described in Davies, E. and S. Abe (1995). (Methods for isolation and analysis of polyribosomes. Methods Cell Biol 50: 209-22). Total RNA and polysome associated RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Plants were gravity stimulated by turning the pots horizontally (90º reorientation).  Harvesting of the most gravity competent pulvinus (second pulvinus above soil level) was done at the following time points: 2 min, 5 min, 15 min, 30 min and 60 min.  The upper (slow elongation) and lower (fast elongation) halves of six pulvini were harvested per time point.  Control plants were kept vertical (no gravity stimulation).  Pulvini from the control plants were separated into left and right halves (simulating upper and lower harvesting of pulvini in the gravity stimulated plants).

tag: Polysomal RNA extracted from lower pulvinus

tag: Gravity stimulation for 15min


title: Lower pulvinus 5 min polysomal RNA biorep 2

description: no additional info

source_name: lower pulvinus_5min_Polysomal RNA_biorep 2

tag: Gravity stimulation for 5min


title: Rat Adrenal Zona Glomerulosa Cells-Potassium-Exp2

description: Cells were incubated in DMEM:F12 (1:1) media containing 0.5 % fatty acid free bovine serum albumin under potassium (16 mM) stimulatory conditions at 37 C in a 5 % CO2 incubator for 2 h.


title: Lower pulvinus 30 min polysomal RNA biorep 2

description: no additional info

source_name: lower pulvinus_30min_Polysomal RNA_biorep 2

tag: Gravity stimulation for 30min


title: B6_Sentrix_P0.5 whole brain_rep 4

description: B6_Sentrix_P0.5 whole brain_rep 4

tag: Male C57BL/6J  mice, P0.5 whole brain, biological replicate 4


title: Lower pulvinus 2 min polysomal RNA biorep 2

description: no additional info

source_name: lower pulvinus_2min_Polysomal RNA_biorep 2

tag: Gravity stimulation for 2min


title: Rat Adrenal Zona Glomerulosa Cells-Potassium-Exp1

description: Cells were incubated in DMEM:F12 (1:1) media containing 0.5 % fatty acid free bovine serum albumin under Potassium (16 mM) stimulatory conditions at 37 C in a 5 % CO2 incubator for 2 h.


title: Rat Adrenal Zona Glomerulosa Cells-Potassium-Exp3


title: pseudoblastema, N1 transgenic 1

description: Xenopus hind limb pseudoblastema, N1 transgenic


title: Rat Adrenal Zona Glomerulosa Cells-Ang II-Exp1


title: Rat Adrenal Zona Glomerulosa Cells-Control-Exp3


title: Upper pulvinus 60 min polysomal RNA biorep 2

description: no additional info

source_name: upper pulvinus_60min_Polysomal RNA_biorep 2

tag: Polysomal RNA extracted from upper pulvinus

tag: Gravity stimulation for 60min


title: Lower pulvinus 60 min polysomal RNA biorep 2

description: no additional info

source_name: lower pulvinus_60min_Polysomal RNA_biorep 2


title: Upper pulvinus 15 min polysomal RNA biorep 2

description: no additional info

source_name: upper pulvinus_15min_Polysomal RNA_biorep 2


title: Right pulvinus control polysomal RNA biorep 2

description: no additional info

source_name: right pulvinus_control_Polysomal RNA_biorep 2

tag: Polysomal RNA extracted from right pulvinus

tag: No gravity stimulation


title: Left pulvinus control polysomal RNA biorep 2

description: no additional info

source_name: left pulvinus_control_Polysomal RNA_biorep 2

tag: Polysomal RNA extracted from left pulvinus


title: Upper pulvinus 5 min polysomal RNA biorep 2

description: no additional info

source_name: upper pulvinus_5min_Polysomal RNA_biorep 2


title: Rat Adrenal Zona Glomerulosa Cells-Ang II-Exp3


title: Upper pulvinus 30 min polysomal RNA biorep 2

description: no additional info

source_name: upper pulvinus_30min_Polysomal RNA_biorep 2


title: Upper pulvinus 2 min polysomal RNA biorep 2

description: no additional info

source_name: upper pulvinus_2min_Polysomal RNA_biorep 2


title: Lower pulvinus 60 min total RNA biorep 2

description: no additional info

source_name: lower pulvinus_60min_Total RNA_biorep 2

tag: Total RNA extracted from lower pulvinus


title: Lower pulvinus 15 min total RNA biorep 2

description: no additional info

source_name: lower pulvinus_15min_Total RNA_biorep 2


title: Rat Adrenal Zona Glomerulosa Cells-Control-Exp1


title: Lower pulvinus 5 min total RNA biorep 2

description: no additional info

source_name: lower pulvinus_5min_Total RNA_biorep 2


title: Lower pulvinus 30 min total RNA biorep 2

description: no additional info

source_name: lower pulvinus_30min_Total RNA_biorep 2


title: Lower pulvinus 2 min total RNA biorep 2

description: no additional info

source_name: lower pulvinus_2min_Total RNA_biorep 2


title: Upper pulvinus 5 min total RNA biorep 2

description: no additional info

source_name: upper pulvinus_5min_Total RNA_biorep 2

tag: Total RNA extracted from upper pulvinus


title: Upper pulvinus 2 min total RNA biorep 2

description: no additional info

source_name: upper pulvinus_2min_Total RNA_biorep 2


title: Upper pulvinus 15 min total RNA biorep 2

description: no additional info

source_name: upper pulvinus_15min_Total RNA_biorep 2


title: Upper pulvinus 15 min polysomal RNA biorep 1

description: no additional info

source_name: upper pulvinus_15min_Polysomal RNA_biorep 1


title: Right pulvinus control total RNA biorep 2

description: no additional info

source_name: right pulvinus_control_Total RNA_biorep 2

tag: Total RNA extracted from right pulvinus


title: Lower pulvinus 2 min polysomal RNA biorep 1

description: no additional info

source_name: lower pulvinus_2min_Polysomal RNA_biorep 1


title: Lower pulvinus 60 min polysomal RNA biorep 1

description: no additional info

source_name: lower pulvinus_60min_Polysomal RNA_biorep 1


title: Upper pulvinus 60 min total RNA biorep 2

description: no additional info

source_name: upper pulvinus_60min_Total RNA_biorep 2


title: Upper pulvinus 5 min polysomal RNA biorep 1

description: no additional info

source_name: upper pulvinus_5min_Polysomal RNA_biorep 1


title: Right pulvinus control polysomal RNA biorep 1

description: no additional info

source_name: right pulvinus_control_Polysomal RNA_biorep 1


title: Upper pulvinus 30 min polysomal RNA biorep 1

description: no additional info

source_name: upper pulvinus_30min_Polysomal RNA_biorep 1


title: Upper pulvinus 2 min polysomal RNA biorep 1

description: no additional info

source_name: upper pulvinus_2min_Polysomal RNA_biorep 1


title: Lower pulvinus 30 min polysomal RNA biorep 1

description: no additional info

source_name: lower pulvinus_30min_Polysomal RNA_biorep 1


title: Upper pulvinus 30 min total RNA biorep 2

description: no additional info

source_name: upper pulvinus_30min_Total RNA_biorep 2


title: Upper pulvinus 60 min polysomal RNA biorep 1

description: no additional info

source_name: upper pulvinus_60min_Polysomal RNA_biorep 1


title: Lower pulvinus 60 min total RNA biorep 1

description: no additional info

source_name: lower pulvinus_60min_Total RNA_biorep 1


title: Stomach, Male (MoSt.Male)

type: MPSS

city: Hayward

first: Daixing

last: Zhou

state: CA

address: 25861 Industrial Blvd

department: Bioinformatics

institute: Solexa

description:
Cells/tissue:
Library lib_name
Cell type Stomach, Male (MoSt.Male)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

data_processing: raw count

source_name: Stomach, Male (MoSt.Male)

extract_protocol: RNA isolation Illumina mRNA QC passed

tag: Strain

tag: Stomach, Male (MoSt.Male) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)

value: 1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6):630-634).  Briefly, the mRNA was reverse transcribed and the cDNA was digested with Dpn II. The 20 bases adjacent to the 3? most Dpn II site was cloned into a Megaclone vector.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.


title: Left pulvinus control total RNA biorep 2

description: no additional info

source_name: left pulvinus_control_Total RNA_biorep 2

tag: Total RNA extracted from left pulvinus


title: Lower pulvinus 30 min total RNA biorep 1

description: no additional info

source_name: lower pulvinus_30min_Total RNA_biorep 1


title: Lower pulvinus 5 min total RNA biorep 1

description: no additional info

source_name: lower pulvinus_5min_Total RNA_biorep 1


title: Lower pulvinus 15 min polysomal RNA biorep 1

description: no additional info

source_name: lower pulvinus_15min_Polysomal RNA_biorep 1

tag: Polysomal RNA extracted from lower pulvinus


title: Spinal cord entire, Male (MoSC.MaEn)

description:
Cells/tissue:
Library lib_name
Cell type Spinal cord entire, Male (MoSC.MaEn)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Spinal cord entire, Male (MoSC.MaEn)

tag: Spinal cord entire, Male (MoSC.MaEn) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Lower pulvinus 5 min polysomal RNA biorep 1

description: no additional info

source_name: lower pulvinus_5min_Polysomal RNA_biorep 1

tag: Gravity stimulation for 5min


title: Left pulvinus control polysomal RNA biorep 1

description: no additional info

source_name: left pulvinus_control_Polysomal RNA_biorep 1


title: Stomach, Female (MoSt.Feml)

description:
Cells/tissue:
Library lib_name
Cell type Stomach, Female (MoSt.Feml)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Stomach, Female (MoSt.Feml)

tag: Stomach, Female (MoSt.Feml) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Parotid Gland, Female (MoPt.Feml)

description:
Cells/tissue:
Library lib_name
Cell type Parotid Gland, Female (MoPt.Feml)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Parotid Gland, Female (MoPt.Feml)

tag: Parotid Gland, Female (MoPt.Feml) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Parotid Gland, Male (MoPt.Male)

description:
Cells/tissue:
Library lib_name
Cell type Parotid Gland, Male (MoPt.Male)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Parotid Gland, Male (MoPt.Male)

tag: Parotid Gland, Male (MoPt.Male) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Lower pulvinus 2 min total RNA biorep 1

description: no additional info

source_name: lower pulvinus_2min_Total RNA_biorep 1

tag: Gravity stimulation for 2min


title: Spinal cord entire, Female (MoSC.FeEn)

description:
Cells/tissue:
Library lib_name
Cell type Spinal cord entire, Female (MoSC.FeEn)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Spinal cord entire, Female (MoSC.FeEn)

tag: Spinal cord entire, Female (MoSC.FeEn) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Lower pulvinus 15 min total RNA biorep 1

description: no additional info

source_name: lower pulvinus_15min_Total RNA_biorep 1

tag: Gravity stimulation for 15min


title: Right pulvinus control total RNA biorep 1

description: no additional info

source_name: right pulvinus_control_Total RNA_biorep 1

tag: No gravity stimulation


title: Left pulvinus control total RNA biorep 1

description: no additional info

source_name: left pulvinus_control_Total RNA_biorep 1


title: Upper pulvinus 15 min total RNA biorep 1

description: no additional info

source_name: upper pulvinus_15min_Total RNA_biorep 1


title: Upper pulvinus 5 min total RNA biorep 1

description: no additional info

source_name: upper pulvinus_5min_Total RNA_biorep 1


title: Brain Hippocampus, Female (MoBr.FeHi)

description:
Cells/tissue:
Library lib_name
Cell type Brain Hippocampus, Female (MoBr.FeHi)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Brain Hippocampus, Female (MoBr.FeHi)

tag: Brain Hippocampus, Female (MoBr.FeHi) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Upper pulvinus 2 min total RNA biorep 1

description: no additional info

source_name: upper pulvinus_2min_Total RNA_biorep 1


title: Pancreas, Female (MoPn.Feml)

description:
Cells/tissue:
Library lib_name
Cell type Pancreas, Female (MoPn.Feml)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Pancreas, Female (MoPn.Feml)

tag: Pancreas, Female (MoPn.Feml) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Liver right lobe, Female (MoLi.FeLL)

description:
Cells/tissue:
Library lib_name
Cell type Liver right lobe, Female (MoLi.FeLL)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Liver right lobe, Female (MoLi.FeLL)

tag: Liver right lobe, Female (MoLi.FeLL) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Upper pulvinus 30 min total RNA biorep 1

description: no additional info

source_name: upper pulvinus_30min_Total RNA_biorep 1

tag: Total RNA extracted from upper pulvinus

tag: Gravity stimulation for 30min


title: Bone marrow, Female (MoBM.Feml)

description:
Cells/tissue:
Library lib_name
Cell type Bone marrow, Female (MoBM.Feml)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Bone marrow, Female (MoBM.Feml)

tag: Strain

tag: Bone marrow, Female (MoBM.Feml) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Brain Hippocampus, Male (MoBr.MaHi)

description:
Cells/tissue:
Library lib_name
Cell type Brain Hippocampus, Male (MoBr.MaHi)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Brain Hippocampus, Male (MoBr.MaHi)

tag: Brain Hippocampus, Male (MoBr.MaHi) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Liver left lobe, Male (MoLi.MaLL)

description:
Cells/tissue:
Library lib_name
Cell type Liver left lobe, Male (MoLi.MaLL)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Liver left lobe, Male (MoLi.MaLL)

tag: Liver left lobe, Male (MoLi.MaLL) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Pancreas, Male (MoPn.Male)

description:
Cells/tissue:
Library lib_name
Cell type Pancreas, Male (MoPn.Male)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Pancreas, Male (MoPn.Male)

tag: Pancreas, Male (MoPn.Male) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: Upper pulvinus 60 min total RNA biorep 1

description: no additional info

source_name: upper pulvinus_60min_Total RNA_biorep 1

tag: Gravity stimulation for 60min


title: spontaneously hypertensive rat diesel exposure rep 1

status: Public on Jun 23 2008

city: Research Triangle Park

first: Urmila

middle: P

last: Kodavanti

address: 109 TW Alexander Drive

department: NHEERL, ETD

institute: USEPA

description: Diesel emision particle exposure is linked to increases in cardiovascular effects. This effect is enhanced in individuals with pre-existing disease. Animal models of cardiovascular disease are used to study this susceptibility. The heart is rich in mitochondria, which produce high levels of free radicals, leading to inactivation of tricarboxylic acid cycle enzymes. We hypothesized that a 4-wk DEP inhalation would result in strain-related structural impairment of cardiac mitochondria and changes in these enzyme activities in WKY and SHR. Male rats (12-14 wks age) were exposed whole body to air or 0.5 or 2.0 mg/m3 DEP for 6h/d, 5 d/wk for 4 wks.

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix GCOS scanning protocol

data_processing: MAS 5.0

source_name: left ventricular heart

label_protocol: Affymetrix labeling protocol

extract_protocol: Qiagen RNeasy columns

tag: strain

value: spontaneously hypertensive

tag: stress

value: diesel

tag: protocol

value: Spontaneously hypertensive male rats (12-14 wks age) exposed whole body to 2.0 mg/m3 diesel emission particles for 6h/d, 5 d/wk for 4 wks.

tag: tissue

value: left ventricular heart


title: Wistar Kyoto (WKY) rat air exposure rep 4

value: Wistar Kyoto (WKY)

value: air

value: Wistar Kyoto (WKY) male rats (12-14 wks age) exposed whole body to air for 6h/d, 5 d/wk for 4 wks.


title: spontaneously hypertensive rat diesel exposure rep 3


title: Wistar Kyoto (WKY) rat diesel exposure rep 3

value: Wistar Kyoto (WKY) male rats (12-14 wks age) exposed whole body to 2.0 mg/m3 diesel emission particles for 6h/d, 5 d/wk for 4 wks.


title: Wistar Kyoto (WKY) rat air exposure rep 2


title: Wistar Kyoto (WKY) rat diesel exposure rep 1


title: spontaneously hypertensive rat air exposure rep 4

value: Spontaneously hypertensive male rats (12-14 wks age) exposed whole body to air for 6h/d, 5 d/wk for 4 wks.


title: spontaneously hypertensive rat diesel exposure rep 2


title: spontaneously hypertensive rat diesel exposure rep 4


title: Wistar Kyoto (WKY) rat diesel exposure rep 2


title: Wistar Kyoto (WKY) rat air exposure rep 1

value: Wistar Kyoto (WKY) rat male rats (12-14 wks age) exposed whole body to air for 6h/d, 5 d/wk for 4 wks.


title: Wistar Kyoto (WKY) rat air exposure rep 3


title: Wistar Kyoto (WKY) rat diesel exposure rep 4


title: spontaneously hypertensive rat air exposure rep 2


title: Bone marrow, Male (MoBM.Male)

description:
Cells/tissue:
Library lib_name
Cell type Bone marrow, Male (MoBM.Male)
Source NHGRI
cDNA library:
Library 	DpnII restriction - (signature captured by MmeI)
Sequence length	20 bp
CSMA
Run
Lane
Clusters
Total clusters successfully sequenced - 3309760
Processed Signatures - xxxxxxx

source_name: Bone marrow, Male (MoBM.Male)

tag: Bone marrow, Male (MoBM.Male) total RNA  received from National Human Genome Research Institute was analyzed through Bioanalyzer and passed our quality control test.  The mRNA was processed according to the MPSS protocol as outlined in the previous publications (Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4)


title: spontaneously hypertensive rat air exposure rep 3


title: spontaneously hypertensive rat air exposure rep1


title: Xenograft_Non infected_rep1

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

institute: Pasteur Institute

description: Quality were checked with Agilent Bioanalyseur

hyb_protocol: Following Affymetrix protocole: PE-streptavidin

scan_protocol: Scanner GCS 3000 with GCOS software

data_processing: RMA normalization

source_name: Non infected intestinal xenograft tissue

label_protocol: Following Affymetrix protocole, using 5 microgrammes of total RNA

extract_protocol: Qiagen RNeasy mini kit

tag: Scid mice engrafted with human intestinal tissue


title: Xenograft_infected with MxiE mutant strain_rep1

source_name: infected intestinal xenograft tissue

tag: Scid mice engrafted with human intestinal tissue infected with MxiE mutant strain


title: Xenograft_infected with non-invasive strain_rep2

tag: Scid mice engrafted with human intestinal tissue infected with non-invasive Shigella strain


title: Xenograft_infected with MxiE mutant strain_rep2


title: Xenograft_infected with invasive strain_rep2

tag: Scid mice engrafted with human intestinal tissue infected with wild type shigella strain


title: NY85

status: Public on Jun 22 2008

city: Chapel Hill

first: Derek

last: Chiang

address: UNC Lineberger Cancer Center, 450 West Drive, CB #7295

department: Department of Genetics

institute: University of North Carolina

description: 103 hepatocellular carcinomas and 95 adjacent cirrhotic, non-tumoral liver tissue were obtained at the time of surgical resection of orthotopic transplantation.

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: Copy numbers were estimated by the GenePattern SNPFileCreator module

source_name: non-tumoral cirrhotic liver

label_protocol: Affymetrix standard procedure

growth_protocol: Tumors obtained at time of surgical resection or transplantation, according to institutional review board approved protocols

extract_protocol: Genomic DNA was extracted with the ChargeSwitch gDNA mini kit (Invitrogen) according to manufacturer's instructions, followed by phenol-chloroform extraction

tag: non-tumoral cirrhotic liver


title: Xenograft_infected with non-invasive strain_rep1

first: Thierry


title: Xenograft_Non infected_rep2


title: NY83


title: NY92


title: Xenograft_infected with invasive strain_rep1

tag: Scid mice engrafted with human intestinal tissue infected with wild type Shigella strain


title: NY67


title: NY80


title: NY98


title: NY71


title: NY8


title: NY90


title: NY37


title: NY324


title: NY231


title: NY306


title: NY316


title: NY310


title: NY301


title: NY35


title: NY332


title: NY3


title: NY225


title: NY328


title: NY330


title: NY320


title: NY38


title: NY308


title: NY30


title: NY43


title: NY322


title: NY223


title: NY217


title: NY19


title: NY326


title: NY312


title: NY227


title: NY207


title: NY17


title: NY201


title: NY318


title: NY203


title: M99


title: M97


title: M72


title: M93


title: M95


title: M80


title: M91


title: M50


title: M107


title: M54


title: M89


title: M103


title: M16


title: M82


title: M36


title: M44


title: M101


title: B97


title: B87


title: M105


title: B85


title: M60


title: M68


title: B93


title: M32


title: M18


title: NY205


title: B95


title: B91


title: B89


title: B77


title: B79


title: B83


title: B81


title: B92


title: B73


title: B75


title: B71


title: M14


title: B69


title: B67


title: NY94

source_name: hepatocellular carcinoma

value: transplant

tag: TP53 mutation

tag: CTNNB1 mutation

tag: Immunocytochemistry

value: pAkt :1


title: NY99

value: C

tag: Age

tag: Sex

value: F

value: resection

tag: Class

value: Proliferation

tag: AFP

value: pRPS6 :1

value: pIGFR1 :0

value: CTNNB1 :0


title: B32


title: NY70

value: pRPS6 :0

value: pAkt :0


title: B38


title: NY82

value: CTNNB1 :1


title: NY79


title: B36


title: B14


title: B26


title: B40


title: B24


title: B42


title: NY84


title: B22


title: B28


title: NY77


title: B65


title: B16


title: NY96

value: M


title: B18


title: NY41

value: Inflammation


title: NY45


title: NY65

value: A


title: NY7


title: NY6


title: B30


title: NY88


title: NY39


title: NY36


title: NY34


title: NY331


title: NY333


title: NY319

value: Polysomy chr7


title: NY329

value: pIGFR1 :1


title: NY317


title: NY232


title: NY26

value: transplant


title: NY327


title: NY321


title: NY307


title: NY311


title: NY302


title: NY323

value: pAkt :1


title: NY309

value: B


title: NY224

value: C


title: NY325

value: resection


title: NY228

value: F


title: NY44


title: NY222

source_name: Hepatocellular carcinoma

value: pRPS6 :1


title: NY18

value: pIGFR1 :0


title: NY204


title: NY208


title: NY218


title: NY226


title: NY202


title: M90

value: CTNNB1 :0


title: M92

value: Unannotated


title: M98

value: pRPS6 :0


title: NY16

value: pAkt :0


title: NY313


title: NY206

value: M

value: CTNNB1 :1


title: NY2


title: M94

value: A


title: M79

value: Proliferation


title: M81


title: M73

value: Inflammation


title: M59


title: M69

value: pIGFR1 :1


title: M71


title: M67

value: pAkt :1


title: M35


title: M31


title: M43


title: M88


title: M104


title: M17


title: M11


title: M15


title: M53

value: B


title: M102


title: B88


title: B90


title: M13


title: M96


title: M49


title: M100


title: B86


title: M106


title: B96

value: Polysomy chr7