title: 13970174 - IR40Gy-2h Rep2 vs Control-2h Rep2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Metabolic pathways involved in the response of plants to ionising radiation treatment.

hyb_protocol: Control-2h Repet2 Cy5 / IR40Gy-2h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,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.

organism: Arabidopsis thaliana

source_name: Control-2h Rep2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: whole plant - Media=MS medium 0,5 X ; 0,5 % sucrose ; 0,8% agar hygrometry=60% Temperature=22°C Light=16 h / day ; 6000 lux

tag: ecotype

value: columbia

tag: dev.stage (boyes et al. plant cell 2001)

tag: dose

tag: harvested time after dose

source_name: IR40Gy-2h Rep2

treatment_protocol: Name:X-Ray 40Gy 2h - time course study - abiotic stress,x-radiations:quantity 40 time 2hour . Petri dishes were irradiated (X-radiations) in a Faxitron chamber (Hewell-Packard). The doses tested were 10 and 40 Gy, which were added the corresponding control conditions (0Gy). The doses received by plants was checked with a dosimeter. The plants of three Petri dishes submitted to the same dose were harvested and pooled, 2 or 26 hours after irradiations and immediatly frozen in liquid nitrogen in safe-lock microtubes. Samples are stored at –80°C until the RNA extraction. The experimentation was repeated a second time (duplicates).

value: 40 gray of X-ray


title: Forskolin treated smooth muscle cells replicate 1

status: Public on Feb 25 2012

type: RNA

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

department: Pediatrics

country: USA

institute: University of Virginia

description: Biological replicate 1 of 3 treated

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between sample groups C and “T”. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.1) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

molecule: total RNA

organism: Mus musculus

source_name: kidney aSMCs derived from the renin cell lineage (Pentz et al, Am J Physiol Heart Circ Physiol 294: H699-H707, 2008)

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 or Cy5 dye staining.

growth_protocol: Cells were grown to ~ 80% confluence and then treated.

extract_protocol: Total RNA extracted using mirVana™ miRNA isolation kit following manufacturer's instructions.

treatment_protocol: 10µM forskolin + 100 µM IBMX for 24 hrs plus an additional treatment with 10µM forskolin for 30 min. before harvest.

tag: primary cell line

tag: passage

tag: strain

value: mixed 129Sv/C57Bl6

tag: treatment

value: Forskolin


title: Treated 3

description: treated biological replicate 3 of 3

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between sample groups C and “T”. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.10) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Kidney cortex

treatment_protocol: Mice were administered a low-sodium diet (0.05%) plus captopril in the drinking water (0.5 g/L) for 10 days.

tag: age

value: 3.5 months

tag: gender

value: Male

value: low sodium diet+captopril


title: Placebo, no lice, fish 2

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: Control, biological replicate 2 of 4

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Mixture of all samples

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Salmon post smolts were kept in tanks with sea water

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)

treatment_protocol: Salmon were injected with cortisol or placebo and infected with lice

tag: tissue

value: skin

source_name: Placebo, no lice, fish 2


title: Control smooth muscle cells replicate 1

description: Biological replicate 1 of 3 Control

treatment_protocol: untreated

value: kidney aSMCs derived from the renin cell lineage

value: Control


title: Placebo, no lice, fish 3

description: Control, biological replicate 3 of 4

source_name: Placebo, no lice, fish 3


title: Control Untreated 3

description: control biological replicate 3 of 3

value: Female

value: control - untreated


title: Placebo, no lice, fish 1

description: Control, biological replicate 1 of 4

source_name: Placebo, no lice, fish 1


title: miR-1 up-regulated group vs. control group, replicate 3

city: Beibei

first: GAO

last: Song

state: Chongqing

address: tiansheng road 2#

department: ISSB

country: China

institute: Southwest University

hyb_protocol: The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
LOWESS normalized, data obtained from processed cy3 signal intensity/ processed cy5 signal intensity.The software from CapitalBio Crop was used.
Ratio>=2.0 or Ratio<=0.5 were consideried to be up-regulated and down-regulated genes, respectively

organism: Bombyx mori

source_name: non-treated control

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

value: mixed

value: whole organism

tag: developmental stage

value: 1 day after finishing spinning

value: control

source_name: miR-1 mimics injected larvae

value: miR-1 mimics


title: Placebo, lice, fish 2

description: Lice infected, biological replicate 2 of 4

source_name: Placebo, lice, fish 2


title: Control Untreated 2

description: control biological replicate 2 of 3


title: Eu_Myc_L2 (Bioconductor lumi R)

city: Seattle

first: Russell

last: Moser

state: WA

address: 1100 Fairview Avenue N.

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and Affy-like background subtraction (Genes with signal/noise ratio <3 eliminated from further analysis) with Bioconductor lumi in R  (Normalized I)

label: biotin

source_name: murine lymphoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease state

value: B cell lymphoma

tag: genotype/variaton

value: Eµ-Myc


title: Myc_WRN_L2 (Bioconductor lumi R)

description: replicate 3

value: Eµ-Myc Wrn Dhel/Dhel


title: Placebo, lice, fish 1

description: Lice infected, biological replicate 1 of 4

source_name: Placebo, lice, fish 1


title: Eu_Myc_L1 (Bioconductor lumi R)

description: replicate 2


title: 13970165 - Control-2h Rep2 vs IR10Gy-2h Rep2

country: France

hyb_protocol: IR10Gy-2h Repet2 Cy5 / Control-2h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR10Gy-2h Rep2

treatment_protocol: Name:X-Ray 10Gy 2h - time course study - abiotic stress,x-radiations:quantity 10 time 2hour . Petri dishes were irradiated (X-radiations) in a Faxitron chamber (Hewell-Packard). The doses tested were 10 and 40 Gy, which were added the corresponding control conditions (0Gy). The doses received by plants was checked with a dosimeter. The plants of three Petri dishes submitted to the same dose were harvested and pooled, 2 or 26 hours after irradiations and immediatly frozen in liquid nitrogen in safe-lock microtubes. Samples are stored at –80°C until the RNA extraction. The experimentation was repeated a second time (duplicates).

value: columbia

value: 10 gray of X-ray

treatment_protocol: no treatment


title: Treated 2

description: treated biological replicate 2 of 3

value: 3.5 months

value: Male


title: Cortisol, lice, fish 4

description: Cortisol and lice, biological replicate 4 of 4

source_name: Cortisol, lice, fish 4

value: skin


title: Treated 1

description: treated biological replicate 1 of 3

value: 5 months

value: low sodium diet+captopril


title: 13970164 - IR40Gy-26h Rep1 vs Control-26h Rep1

hyb_protocol: Control-26h Repet1 Cy5 / IR40Gy-26h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Control-26h Rep1

source_name: IR40Gy-26h Rep1

treatment_protocol: Name:X-Ray 40Gy 26h - time course study - abiotic stress,x-radiations:quantity 40 time 26hour . Petri dishes were irradiated (X-radiations) in a Faxitron chamber (Hewell-Packard). The doses tested were 10 and 40 Gy, which were added the corresponding control conditions (0Gy). The doses received by plants was checked with a dosimeter. The plants of three Petri dishes submitted to the same dose were harvested and pooled, 2 or 26 hours after irradiations and immediatly frozen in liquid nitrogen in safe-lock microtubes. Samples are stored at –80°C until the RNA extraction. The experimentation was repeated a second time (duplicates).

value: 40 gray of X-ray


title: 13970162 - IR10Gy-26h Rep1 vs Control-26h Rep1

hyb_protocol: Control-26h Repet1 Cy5 / IR10Gy-26h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR10Gy-26h Rep1

treatment_protocol: Name:X-Ray 10Gy 26h - time course study - abiotic stress,x-radiations:quantity 10 time 26hour . Petri dishes were irradiated (X-radiations) in a Faxitron chamber (Hewell-Packard). The doses tested were 10 and 40 Gy, which were added the corresponding control conditions (0Gy). The doses received by plants was checked with a dosimeter. The plants of three Petri dishes submitted to the same dose were harvested and pooled, 2 or 26 hours after irradiations and immediatly frozen in liquid nitrogen in safe-lock microtubes. Samples are stored at –80°C until the RNA extraction. The experimentation was repeated a second time (duplicates).


title: Placebo, lice, fish 3

description: Lice infected, biological replicate 3 of 4

source_name: Placebo, lice, fish 3


title: 13970166 - IR10Gy-2h Rep2 vs Control-2h Rep2

hyb_protocol: Control-2h Repet2 Cy5 / IR10Gy-2h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Control-2h Rep2


title: Cortisol, lice, fish 2

description: Cortisol and lice, biological replicate 2 of 4

source_name: Cortisol, lice, fish 2


title: Control Untreated 1

description: control biological replicate 1 of 3

source_name: Kidney cortex

value: control - untreated


title: Eu_Myc_E11 (Bioconductor lumi R)

description: replicate 3


title: Placebo, lice, fish 4

description: Lice infected, biological replicate 4 of 4

source_name: Mixture of all samples

source_name: Placebo, lice, fish 4


title: 13970167 - Control-2h Rep2 vs IR40Gy-2h Rep2

hyb_protocol: IR40Gy-2h Repet2 Cy5 / Control-2h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR40Gy-2h Rep2


title: Myc_WRN_E6 (Bioconductor lumi R)

description: replicate 4


title: 13970163 - Control-26h Rep1 vs IR40Gy-26h Rep1

hyb_protocol: IR40Gy-26h Repet1 Cy5 / Control-26h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Cortisol, lice, fish 3

description: Cortisol and lice, biological replicate 3 of 4

source_name: Cortisol, lice, fish 3


title: Myc_WRN_L1 (Bioconductor lumi R)

description: replicate 1


title: Myc_WRN_E3 (Bioconductor lumi R)

description: replicate 2


title: Eu_Myc_L2 (Illumina GUI)

description: replicate 4

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R (Normalized II)


title: Cortisol, no lice, fish 2

description: Cortisol treated, biological replicate 2 of 4

source_name: Cortisol, no lice, fish 2


title: Cortisol, no lice, fish 4

description: Cortisol treated, biological replicate 4 of 4

source_name: Cortisol, no lice, fish 4


title: 13970157 - Control-2h Rep1 vs IR40Gy-2h Rep1

hyb_protocol: IR40Gy-2h Repet1 Cy5 / Control-2h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR40Gy-2h Rep1

source_name: Control-2h Rep1


title: Myc_WRN_E6 (Illumina GUI)

description: replicate 4

source_name: murine lymphoma


title: 13970155 - IR10Gy-2h Rep1 vs Control-2h Rep1

hyb_protocol: Control-2h Repet1 Cy5 / IR10Gy-2h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR10Gy-2h Rep1


title: Cortisol, lice, fish 1

description: Cortisol and lice, biological replicate 1 of 4

source_name: Cortisol, lice, fish 1


title: Cortisol, no lice, fish 3

description: Cortisol treated, biological replicate 3 of 4

source_name: Cortisol, no lice, fish 3


title: 13970159 - Control-26h Rep1 vs IR10Gy-26h Rep1

hyb_protocol: IR10Gy-26h Repet1 Cy5 / Control-26h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR10Gy-26h Rep1

source_name: Control-26h Rep1


title: Cortisol, no lice, fish 1

description: Cortisol treated, biological replicate 1 of 4

source_name: Cortisol, no lice, fish 1


title: 13970158 - IR40Gy-2h Rep1 vs Control-2h Rep1

hyb_protocol: Control-2h Repet1 Cy5 / IR40Gy-2h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Myc_WRN_E3 (Illumina GUI)

description: replicate 2


title: Eu_Myc_E11 (Illumina GUI)

description: replicate 3


title: 13969390 - Control-26h Rep2 vs IR40Gy-26h Rep2

hyb_protocol: IR40Gy-26h Repet2 Cy5 / Control-26h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR40Gy-26h Rep2

source_name: Control-26h Rep2


title: Myc_WRN_L1 (Illumina GUI)

description: replicate 1


title: Eu_Myc_L1 (Illumina GUI)

description: replicate 2


title: Myc_WRN_L2 (Illumina GUI)

description: replicate 3


title: 13970176 - Control-26h Rep2 vs IR10Gy-26h Rep2

hyb_protocol: IR10Gy-26h Repet2 Cy5 / Control-26h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: IR10Gy-26h Rep2


title: 13969389 - IR10Gy-26h Rep2 vs Control-26h Rep2

hyb_protocol: Control-26h Repet2 Cy5 / IR10Gy-26h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13970154 - Control-2h Rep1 vs IR10Gy-2h Rep1

hyb_protocol: IR10Gy-2h Repet1 Cy5 / Control-2h Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969391 - IR40Gy-26h Rep2 vs Control-26h Rep2

hyb_protocol: Control-26h Repet2 Cy5 / IR40Gy-26h Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Eu_Myc_E8 (Illumina GUI)

description: replicate 1


title: S07-15325_2

status: Public on Feb 24 2012

city: New York

first: Jason

last: Huse

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: FFPE material/DASL processed

hyb_protocol: After the oligo hybridization, mis‐hybridized and non‐hybridized oligos are washed away. The hybridized oligos are then extended and ligated. These products form a synthetic template that is transferred to a PCR reaction containing a fluorescently labeled primer

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. Gene level data was obtained by average the probe level data for each gene.  The data were then quantile normalized in Partek

organism: Homo sapiens

source_name: FFPE block, diffuse astrocytic glioma

label_protocol: Following Illumina standard protocol, 300ng RNA  were converted to cDNA through reverse transcription reaction with biotinylated primers. The biotinylated cDNA is then annealed to assay oligonucleotides (oligos), and bound to streptavidin conjugated paramagnetic particles (SA‐PMPs)

growth_protocol: Formalin-fixed parrafin-embedded tissue blocks

extract_protocol: Samples were extracted using the miRNEASY FFPE kit from Qiagen and quality was assessed by RPL13a RT-PCR

tag: tumor type

value: diffuse astrocytic glioma

tag: who grade

value: II

tag: subclass

value: NB

tag: idh mut status

value: mut

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

value: wt

tag: pten del

value: No

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp

value: Yes


title: S03_15163

description: FFPE material/DASL processed

value: M

value: U


title: S10-36549

description: FFPE material/DASL processed

value: III

value: PG


title: S03_21672

description: FFPE material/DASL processed

value: EPL


title: S03_42092

description: FFPE material/DASL processed


title: S10-1503

description: FFPE material/DASL processed


title: 04_28949

description: FFPE material/DASL processed


title: S11-11395

description: FFPE material/DASL processed


title: S05_30874

description: FFPE material/DASL processed


title: 04_17506

description: FFPE material/DASL processed


title: S05_48279

description: FFPE material/DASL processed


title: S02_38678

description: FFPE material/DASL processed


title: S10-33581

description: FFPE material/DASL processed


title: S05-21206

description: FFPE material/DASL processed


title: 05_3472

description: FFPE material/DASL processed


title: 03_8728

description: FFPE material/DASL processed


title: 04_32467

description: FFPE material/DASL processed


title: Harvard Sib CHB1000006603

type: genomic

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: Harvard.Sib

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

molecule: genomic DNA

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: group

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

tag: cell type

value: leukocyte


title: Harvard Sib CHB1000006599

description: Harvard.Sib

hyb_protocol: Followed the manufacturer's (Illumina) specifications


title: Harvard Sib CHB1000006565

description: Harvard.Sib


title: Harvard Sib CHB1000005858

description: Harvard.Sib

value: White


title: Harvard Sib CHB1000006587

description: Harvard.Sib


title: 02_7622_2

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status


title: 00_37982

description: FFPE material/DASL processed

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del


title: Harvard Sib CHB1000006579

description: Harvard.Sib


title: Harvard Sib CHB1000005878

description: Harvard.Sib


title: Harvard Sib CHB1000005892

description: Harvard.Sib


title: S02_39806

description: FFPE material/DASL processed

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: S01_31501

description: FFPE material/DASL processed


title: Harvard Sib CHB1000006591

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id

tag: sentrix position


title: Harvard Sib CHB1000006613

description: Harvard.Sib

tag: experiment

tag: age at collection months

tag: ethnicity

tag: cell type


title: Harvard Sib CHB1000005664

description: Harvard.Sib


title: 02_32089_2

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status


title: Harvard Sib CHB1000005832

description: Harvard.Sib


title: S08_44027

description: FFPE material/DASL processed

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del


title: S08_20810

description: FFPE material/DASL processed

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: S08_52763

description: FFPE material/DASL processed


title: S03_15078

description: FFPE material/DASL processed


title: 01_31149_4

description: FFPE material/DASL processed


title: S09_45027

description: FFPE material/DASL processed


title: Eu_Myc_E8 (Bioconductor lumi R)

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

tag: strain

tag: disease state

value: B cell lymphoma

tag: genotype/variaton

value: Eµ-Myc


title: S09_26735

description: FFPE material/DASL processed

value: diffuse astrocytic glioma


title: S03_17795

description: FFPE material/DASL processed

value: II


title: Harvard Sib CHB1000007293

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity


title: S07_24733

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation


title: S08_26312

description: FFPE material/DASL processed

tag: tp53 seq

tag: pten del

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: Spleen_infected day 14_Alabama_replicate 1

city: Moulis

first: Camille

last: Bonneaud

address: Station d'Ecologie Experimentale

institute: Centre National de la Recherche Scientifique (CNRS)

hyb_protocol: Immediately prior to hybridisation, we added 0.45 µl 10% SDS to the probe, heated it for 2 min at 100ºC and allowed it to cool down at room temperature for 10 min.  The arrays were placed in Corning Microarray hybridisation chambers and a clean Lifterslip (Eerie Scientific) was placed over each array.  After injecting the probes under the lifterslips, we added 50 µl 3 SSC to the hybridisation chambers and placed them in a 62ºC water bath for 12-16h.  Following hybridisation, the slides were washed in 0.2 SSC with 2% SDS and then in 0.2 SSC.  We spun the slides dry by centrifuging them at 1000 rpm for 2 min and scanned using an Axon 4000A microarray scanner (Axon Instruments).

scan_protocol: Slides were scanned using an Axon 4000A microarray scanner (Axon Instruments). We used the software package GenePix to yield log base-2 (log2) measurements for mean fluorescence intensities for each dye channel in each spot on the array and to flag low quality spots.

data_processing: Normalisation of the raw fluorescence intensities was performed in 3 steps using bioconductor package marray and limma(12) implemented in R language (http://www.r-project.org).  First, background adjustment was performed using the normexp method.  Second, spatial and print-tip loess normalisation (two dimensional method) were performed to remove spatial and dye biases for each slide.  Third, we performed a scale normalisation to control for variation between slides.

organism: Haemorhous mexicanus

source_name: Spleen_infected day 14_Alabama

label_protocol: Each pooled House finch RNA sample was prepared for cDNA microarray hybridisation by reverse-transcribing 15µg of total pooled RNA in 30.8 µl reaction volumes containing 1 µl of a mix of oligo dT (dT12-, 13-, 14-, 15-, 16-, 17- and 18-mer; final concentration 5 µg/µl), 6 µl of 5 First Strand Buffer (Invitrogen), 3 µl of 0.1M DTT, 0.8 µl 50 aminoallyl-dUTP/dNTP mix (20mM dATP, 20mM dCTP, 20mM dGTP, 12mM dTTP, 8mM aminoallyl-dUTP), 2.5 µl (500U) of Superscript II Reverse Transcriptase (Invitrogen).  Reactions were incubated at 42ºC for 3h. cDNA samples were subsequently hydrolyzed by adding 10 µl of 1M NaOH, 10 µl of 0.5M EDTA and incubated at 65ºC for 15 min.  Neutralization was performed by addition of 25 µl 1M HEPES pH 7.5. All samples were labelled using Cy5 dye and the common reference was labelled with Cy3.

extract_protocol: Total RNA extracted from approximately 17 mg of spleen tissue using Qiagen RNeasy miniprep spin columns and followed by DNase digestion of genomic DNA according to the manufacturers’ protocols.

tag: tissue

value: spleen

tag: treatment

value: infected day 14

tag: population

value: Alabama

tag: replicate


title: Spleen_infected day 14_Alabama_replicate 2


title: S09_41280

description: FFPE material/DASL processed

value: mut

value: No


title: S07_20178

description: FFPE material/DASL processed


title: Harvard Sib CHB1000006595

description: Harvard.Sib

tag: group

tag: gender

value: M

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

tag: cell type


title: S09_33710

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

value: U

tag: tp53 seq

value: wt

tag: pten del


title: S09_53440

description: FFPE material/DASL processed

value: PG

value: Yes

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: Spleen_infected day 3_Alabama_replicate 2

source_name: Spleen_infected day 3_Alabama

tag: tissue

tag: treatment

value: infected day 3

tag: population

tag: replicate


title: SO5_21626

description: FFPE material/DASL processed


title: S08_43365

description: FFPE material/DASL processed

value: III

value: EPL


title: Harvard Sib CHB1000005872

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

tag: cell type

value: leukocyte


title: Harvard Sib CHB1000006583

description: Harvard.Sib


title: Harvard Sib CHB1000006563

description: Harvard.Sib


title: Harvard Sib CHB1000005830

description: Harvard.Sib


title: S06_32427

description: FFPE material/DASL processed

tag: tumor type

value: diffuse astrocytic glioma

tag: who grade

tag: subclass

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del


title: Harvard Sib CHB1000005946

description: Harvard.Sib

value: White


title: S08_28134

description: FFPE material/DASL processed

value: II

value: NB

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: S09_7746

description: FFPE material/DASL processed


title: Spleen_control_Alabama_replicate 2

tag: tissue

value: spleen

tag: treatment

value: control

tag: population

value: Alabama

tag: replicate


title: S09_426

description: FFPE material/DASL processed

value: mut

value: No


title: S06_7988

description: FFPE material/DASL processed

value: wt


title: Harvard Sib CHB1000005874

description: Harvard.Sib

tag: group

tag: gender

value: M

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

tag: cell type


title: Harvard Sib CHB1000006575

description: Harvard.Sib


title: Spleen_infected day 3_Alabama_replicate 1


title: S09_55284

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

value: U

tag: tp53 seq

tag: pten del


title: Harvard Sib CHB1000014521

description: Harvard.Sib


title: 10_12740

description: FFPE material/DASL processed

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: 09_14995

description: FFPE material/DASL processed


title: S01_27901

description: FFPE material/DASL processed


title: Spleen_control_Alabama_replicate 1

tag: tissue

tag: treatment

tag: population

tag: replicate


title: Spleen_control_Arizona_replicate 1

label_protocol:
Samples were labelled using Cy5 dye and were then hybridised against a common reference, made by pooling an aliquot of all the individual samples and labelled with Cy3.  We made a calibration curve of hybridisation efficiency by diluting the E. coli external PCR products at known concentrations.  Each hybridisation was performed on one half-slide.  Each pooled House finch RNA sample was prepared for cDNA microarray hybridisation by reverse-transcribing 15µg of total pooled RNA in 30.8 µl reaction volumes containing 1 µl of a mix of oligo dT (dT12-, 13-, 14-, 15-, 16-, 17- and 18-mer; final concentration 5 µg/µl), 6 µl of 5 First Strand Buffer (Invitrogen), 3 µl of 0.1M DTT, 0.8 µl 50 aminoallyl-dUTP/dNTP mix (20mM dATP, 20mM dCTP, 20mM dGTP, 12mM dTTP, 8mM aminoallyl-dUTP), 2.5 µl (500U) of Superscript II Reverse Transcriptase (Invitrogen).  Reactions were incubated at 42ºC for 3h. cDNA samples were subsequently hydrolyzed by adding 10 µl of 1M NaOH, 10 µl of 0.5M EDTA and incubated at 65ºC for 15 min.  Neutralization was performed by addition of 25 µl 1M HEPES pH 7.5.

We purified the mixtures using microcon-30 filters.  We added 1 µl of NaHCO3 to 10 µl purified probe.  We resuspended the cyanine dyes (Cy3 and Cy5) with the probe and incubated the mixture in the dark at room temperature for 2h to allow coupling of the cDNA to the N-hydroxy succinamide ester of the dyes.  All samples were labelled using Cy5 dye and the common reference was labelled with Cy3.  The mixtures were then purified using QIAGEN QIAquick PCR purification kit.  The eluted Cy-3 and Cy-5 labelled probes were combined and added into a microcon-30 filer, spun for 3 min at 10000 g and the filter was then inverted and spun at 4500 g for 5 min.  We prepared the concentrated probes for hybridisation by adding 3 µl of 20 SSC, 1.5 µl poly(A) (7 µg/µl), 0.48 µl 1M HEPES pH 7.0, and we applied the mixture to pre-humidified Millipore 0.45 µm filters, spun them at 10000 g for 1 min and stored the flow-through at 4ºC until further use.

extract_protocol: We extracted total RNA from approximately 17 mg of sonicated spleen tissue using Qiagen RNeasy miniprep spin columns and followed by DNase digestion of genomic DNA according to the manufacturers’ protocols.

value: Arizona


title: 07_37234

description: FFPE material/DASL processed

value: III


title: Spleen_infected day 14_Arizona_replicate 2

source_name: Spleen_infected day 14_Arizona

value: infected day 14


title: S07_39881

description: FFPE material/DASL processed


title: 07_32398

description: FFPE material/DASL processed

value: EPL


title: Spleen_infected day 14_Arizona_replicate 1


title: aerial structures, rep2

city: Utrecht

first: R

last: Bleichrodt

address: Padualaan 8

country: Netherlands

institute: Utrecht University

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1.1 software. Normalization was done using the MAS5.0 algorithm using a baseline correction of the median.

organism: Aspergillus niger

source_name: aerial structures

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger strain N402 was grown for 7 days on minimal medium containing 25 mM maltose as sandwich colony (Wosten et al., 1991, Journal of General Microbiology 137: 2017–2023). The last 24 h it was allowed to sporulate.

extract_protocol: Trizol extraction was performed using manufacturers instructions for vegetative mycelium. Aerial structures were first submersed in RNA later ICE (Ambion; www.ambion.com) and RNA was isolated using the MasterPure Yeast RNA Purification Kit (Epicentre Biotechnologies; www.epibio.com) according to Bleichrodt et al. (Studies in Mycology, 2012).

treatment_protocol: Vegetative mycelium and aerial structures were harvested from 3 and 5 separate cultures, respectively.

tag: strain

tag: tissue source

value: maltose-grown sporulating sandwich cultures

tag: culture age

value: 7 day-old

value: Aerial structures


title: S09_13073

description: FFPE material/DASL processed

tag: tumor type

value: diffuse astrocytic glioma

tag: who grade

value: II

tag: subclass


title: Harvard Sib CHB1000005910

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: White

tag: cell type

value: leukocyte


title: S10_10938

description: FFPE material/DASL processed

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del

value: Yes

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: S07_15159

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

value: NB


title: Spleen_infected day 3_Arizona_replicate 1

tag: tissue

value: spleen

tag: treatment

value: infected day 3

tag: population


title: WAT_P2X7-/-_HFD_repl3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on high fat diet, replicate 3

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 13 arrays that were used in this experiment were provided as subset of a 1x 16 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Wild type C57/BL6 (CD45.2+, #000664) and B6.129P2-P2rx7tm1Gab/J (P2X7-/-, #005576) were purchased from the Jackson Laboratory and bred in our facility. The P2X7-/- mice have been backcrossed to the B6 background for 7 generations.

extract_protocol: Total RNA was prepared from adipose tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Six week-old mice were placed on a low fat diet (chow, Harlan Teklad #2914) or high fat diet  (D12492, Research Diets Inc.) for 12 weeks, containing 13 energy% or 60 energy% fat, respectively. After this intervention period, the animals were killed and epididymal white adipose tissue was removed.

tag: background strain

tag: genotype/variation

value: P2X7 knoutout

tag: gender

value: male

tag: age

value: 18 weeks

value: epididymal adipose tissue


title: 10_15877

description: FFPE material/DASL processed

value: III

tag: idh mut status

value: mut

tag: pten methylation

value: M

tag: cdkn2a methylation

value: U

value: No


title: WAT_P2X7-/-_HFD_repl2

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on high fat diet, replicate 2


title: aerial structures, rep1

tag: strain

tag: tissue source

value: maltose-grown sporulating sandwich cultures

tag: culture age

value: 7 day-old

value: Aerial structures


title: 05_36346

description: FFPE material/DASL processed

value: diffuse astrocytic glioma

value: EPL

tag: tp53 seq

tag: pten del

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: vegetative mycelium, rep1

source_name: vegetative mycelium

tag: tissue

value: Vegetative mycelium


title: Harvard Sib CHB1000005932

description: Harvard.Sib

tag: group

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

tag: cell type

value: leukocyte


title: Spleen_control_Arizona_replicate 2

source_name: Spleen_control_Arizona_replicate 2

value: spleen

tag: treatment

value: control

tag: population

value: Arizona

tag: replicate


title: 04_39898

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

value: wt


title: 08_28808

description: FFPE material/DASL processed

value: III

value: PG

tag: pten del

value: Yes

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: 05_10007

description: FFPE material/DASL processed

value: M


title: WAT_WT_HFD_rpl2

description: epididymal adipose tissue, wild type mouse, after 12 weeks on high fat diet, replicate 2

tag: background strain

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 18 weeks

tag: tissue

value: epididymal adipose tissue


title: 09_14429

description: FFPE material/DASL processed

tag: tumor type

value: diffuse astrocytic glioma

value: U


title: WAT_WT_HFD_rpl1

description: epididymal adipose tissue, wild type mouse, after 12 weeks on high fat diet, replicate 1


title: WAT_WT_HFD_rpl3

description: epididymal adipose tissue, wild type mouse, after 12 weeks on high fat diet, replicate 3


title: 05_14601

description: FFPE material/DASL processed

tag: who grade

value: NB

value: mut

value: No


title: 07_38868

description: FFPE material/DASL processed

tag: subclass

value: EPL


title: Harvard Sib CHB1000005682

description: Harvard.Sib

tag: group

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

tag: cell type

value: leukocyte


title: WAT_WT_LFD_repl3

description: epididymal adipose tissue, wild type mouse, after 12 weeks on low fat diet (chow), replicate 3


title: WAT_P2X7-/-_HFD_repl4

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on high fat diet, replicate 4

value: P2X7 knoutout


title: aerial structures, rep3

tag: strain

tag: tissue source

value: maltose-grown sporulating sandwich cultures

tag: culture age

value: 7 day-old

value: Aerial structures


title: mouse colon3

city: Boston

first: Janghee

last: Woo

address: 44 Binney st.

institute: Dana-Farber Cancer Institute

description: Gene expression data from colonic SEMFs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOUSE Genome 430 2.0 Arrays or HUMAN Genome U133 plus2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AFFYMETRIX GENE CHIP SCANNER 3000.

data_processing: Microarray expression: RMA (bioconductor) with custom CDFs for background elimination and normalization in adddition to array normalization using Cluster

source_name: colonic SEMFs

label_protocol: Biotinylated cRNA were prepared according to the standard 3' IVT EXPRESS Affymetrix protocol from 0.1 ug total RNA (GENE CHIP 3' IVT EXPRESS User Manual, P/N702646 REV8, Affymetrix)

growth_protocol: Intestinal SEMFs were cultured under published conditions. Human cancer cells were grafted subcutaneousely in combination with murine ISEMFs and grown in immunodeficient NOD/SCID mice.

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

value: subepithelial myofibroblasts


title: 05_12017

description: FFPE material/DASL processed

value: III

tag: idh mut status

value: wt

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc

tag: egfr amp


title: vegetative mycelium, rep3

tag: tissue

value: Vegetative mycelium


title: 07_10751

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

value: M


title: Harvard Sib CHB1000005696

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

tag: cell type


title: vegetative mycelium, rep2

tag: strain

tag: tissue source

tag: culture age


title: Harvard Sib CHB1000006589

description: Harvard.Sib

value: White


title: 08_45333

description: FFPE material/DASL processed

value: diffuse astrocytic glioma

value: PG

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

value: U

tag: tp53 seq

tag: pten del

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc


title: WAT_P2X7-/-_LFD_repl3

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on low fat diet (chow), replicate 3

tag: background strain

tag: genotype/variation

tag: gender

value: male

tag: age

value: 18 weeks

tag: tissue

value: epididymal adipose tissue


title: WAT_P2X7-/-_LFD_repl1

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on low fat diet (chow), replicate 1


title: WAT_P2X7-/-_HFD_repl1

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on high fat diet, replicate 1


title: WAT_P2X7-/-_LFD_repl2

description: epididymal adipose tissue, P2X7 knockout, after 12 weeks on low fat diet (chow), replicate 2


title: 05_11139

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

value: NB

value: No

tag: egfr amp


title: Harvard Sib CHB1000005882

description: Harvard.Sib

tag: group

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

value: Other

tag: cell type

value: leukocyte


title: Harvard Sib CHB1000006569

description: Harvard.Sib


title: 07_50669

description: FFPE material/DASL processed

tag: idh mut status

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del

value: Yes

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc


title: 09_35837

description: FFPE material/DASL processed

tag: tumor type

tag: who grade

tag: subclass

value: EPL

value: mut


title: Harvard Sib CHB1000005852

description: Harvard.Sib

tag: group

tag: gender

tag: sentrix id


title: 03_40450

description: FFPE material/DASL processed

value: III

value: wt

tag: egfr amp


title: 07_43472

description: FFPE material/DASL processed

value: M


title: Expt. #8.4-Baboon

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Simple annotation: Comparative genomics, DNA

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Reference

label_protocol: not provided

extract_protocol: not provided

tag: Reference

organism: Papio hamadryas

source_name: Test

tag: Test


title: 09_26795

description: FFPE material/DASL processed

tag: idh mut status


title: 09_34892

description: FFPE material/DASL processed

tag: pten methylation


title: 07_3664

description: FFPE material/DASL processed

tag: cdkn2a methylation


title: mouse ileum4

description: Gene expression data from ileal SEMFs

source_name: ileal SEMFs

tag: cell type

value: subepithelial myofibroblasts

tag: strain


title: 08_13920

description: FFPE material/DASL processed

value: diffuse astrocytic glioma

tag: tp53 seq

tag: pten del

tag: pdgfra ihc


title: 06_47205

description: FFPE material/DASL processed

tag: tumor type

tag: p53 ihc

tag: p-pras40 ihc


title: mouse colon4

description: Gene expression data from colonic SEMFs


title: WAT_WT_LFD_repl1

description: epididymal adipose tissue, wild type mouse, after 12 weeks on low fat diet (chow), replicate 1

tag: background strain

tag: genotype/variation

value: wild type

tag: age

tag: tissue


title: WAT_WT_LFD_repl2

description: epididymal adipose tissue, wild type mouse, after 12 weeks on low fat diet (chow), replicate 2

tag: gender


title: mouse ileum3

description: Gene expression data from ileal SEMFs


title: mouse colon2

description: Gene expression data from colonic SEMFs


title: human cancer_Caco2_colon1

description: Gene expression data from cancer cells

value: cancer cells

tag: cell line


title: mouse colon1

description: Gene expression data from colonic SEMFs


title: 06_31479

description: FFPE material/DASL processed

tag: who grade

tag: subclass

tag: idh mut status

value: U

tag: egfr amp


title: Harvard Sib CHB1000005850

description: Harvard.Sib

tag: group

tag: sentrix id

tag: sentrix position

tag: experiment

tag: age at collection months

tag: ethnicity

tag: cell type


title: human cancer_T84_colon2

description: Gene expression data from cancer cells


title: human cancer_Caco2_ileum1

description: Gene expression data from cancer cells


title: Harvard Sib CHB1000005930

description: Harvard.Sib


title: human cancer_T84_ileum2

description: Gene expression data from cancer cells


title: mouse ileum2

description: Gene expression data from ileal SEMFs

tag: strain


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 6 SD rats, biological replicate 2

city: Adelaide

first: Melinda

middle: N

last: Tea

state: South Australia

address: Flinders Medical Centre, Carpark Building

department: Ophthalmology

country: Australia

institute: Flinders University

hyb_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Hybridization, Wash and Stain Kit (P/N 900720)

scan_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Scanner 3000 7G

data_processing: CEL files generated from DAT files automatically by Affymetrix AGCC software.  CEL files processed using Partek Genomics Suite v 6.4 using RMA background correction and Partek GC content correction.

label: Biotin

organism: Rattus norvegicus

source_name: Retinae, exposed to cyclic hyperoxia to post-natal day 6

label_protocol: As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix WT cDNA Synthesis and Amplification Kit (Part# 900673) and  Affymetrix WT Terminal Labeling and Control Regents (Part# 901524). The rRNA reduction step is not recommended by Affymetrix for the Genearrays and was not performed.

extract_protocol: Total RNA was extracted from the retinae of individual rats using TRIzol according to the manufacturer's method. Total RNA was further purified using a Qiagen Rneasy Micro column purification kit according to the manufacturer's protocol.

treatment_protocol: Within 12 hours of birth, female rats and their litters were placed in a humidified oxygen chamber and exposed to alternating 24 hour cycles of hyperoxia (80% oxygen in air) and normoxia (21% oxygen in air) until the rats were euthansed at post-natal days 5 and 6. Age-matched room air-exposed rats were used as controls.

value: Sprague Dawley

value: retina

tag: treatment

value: cyclic hyperoxia-exposed


title: 02_7685_2

description: FFPE material/DASL processed

tag: tumor type

value: PG

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

tag: pten del

value: No

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc


title: mouse ileum1

description: Gene expression data from ileal SEMFs


title: RNA: LAMA-84

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44573.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 8360; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 00:49:35; Parameter PMT Volts = 640; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 113298; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.66; Parameter Scan Time = 00:49:35; Parameter PMT Volts = 660; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 332290; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger

source_name: CRH

tag: reference

value: CRH

tag: cell line


title: Expt. #8.4-Baboon2

tag: Reference

tag: Test


title: Macaque #487

organism: Macaca sp.


title: RNA: HEL

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44572.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 8440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.54; Parameter Scan Time = 00:36:40; Parameter PMT Volts = 620; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 113284; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.54; Parameter Scan Time = 00:36:40; Parameter PMT Volts = 660; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 332277; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger

source_name: HEL

value: HEL


title: 02_33905_2

description: FFPE material/DASL processed

tag: who grade

tag: subclass

value: NB

tag: idh mut status

tag: egfr amp


title: Pooled retinal RNA from room air-exposed post-natal day 6 F344 rats, biological replicate 2

source_name: Retinae, exposed to room air to post-natal day 6

tag: strain

value: Fischer 344

tag: tissue

tag: treatment

value: room air-exposed

tag: age


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 6 F344 rats, biological replicate 2


title: 06_21226

description: FFPE material/DASL processed

tag: tumor type

value: III

value: wt

tag: pten methylation

tag: cdkn2a methylation

tag: tp53 seq

value: Yes


title: RNA: MV4-11

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44571.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2000, 8440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 00:18:48; Parameter PMT Volts = 620; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 113266; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 00:18:48; Parameter PMT Volts = 680; Parameter Scan Date = 2003-08-27; Parameter Pixel Size = 10; Parameter Laser on time = 332259; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.83; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger


title: Lung_unstim_3

city: Vancouver

first: Timotheus

middle: You Fu

last: Halim

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with FlexArray 1.4.1, data was processed by RMA using standard settings.

source_name: Lung leukocytes

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

treatment_protocol: stimulated samples were incubated in 200 microlitre of RPMI-1640, 10% FCS, Pen/Strep, 2-Me, 500 ng/ml ionomycin, 60 ng/ml PMA for 3 days

tag: cell type

value: Lung leukocytes

tag: stimulation


title: Lung_P/I_1

value: PMA + ionomycin


title: Pooled retinal RNA from room air-exposed post-natal day 6 SD rats, biological replicate 2


title: Lung_P/I_2


title: Pooled retinal RNA from room air-exposed post-natal day 6 F344 rats, biological replicate 1


title: 06_29662

description: FFPE material/DASL processed

source_name: FFPE block, diffuse astrocytic glioma

value: diffuse astrocytic glioma

value: EPL

value: mut

value: M

tag: pten del

tag: pdgfra ihc

tag: p53 ihc

tag: p-pras40 ihc


title: 02_22877_2

description: FFPE material/DASL processed

tag: who grade

tag: subclass

value: U


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 6 F344 rats, biological replicate 1

value: retina

value: cyclic hyperoxia-exposed


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 6 SD rats, biological replicate 1

value: Sprague Dawley


title: Lung_unstim_2


title: Expt. #8.2-13028381

tag: Reference

tag: Test


title: Pooled retinal RNA from room air-exposed post-natal day 5 SD rats, biological replicate 2

source_name: Retinae, exposed to room air to post-natal day 5

tag: strain

tag: tissue


title: Lung_unstim_1


title: Pooled retinal RNA from room air-exposed post-natal day 6 SD rats, biological replicate 1

tag: treatment

tag: age


title: Saracatinib resistant PIK3CA mutant rep2

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Gene expression data from baseline, before treatment

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

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

data_processing: The data were analyzed with RMA using Affymetrix Power Tools.

source_name: Resistant, PIK3CA mutant rep2

value: Human colorectal tumor  xenografted in six-week-old female athymic nude mice

tag: genotype

value: PIK3CA mutant resistant to saracatinib


title: Saracatinib resistant PIK3CA mutant rep1

source_name: Resistant, PIK3CA mutant rep1


title: Pooled retinal RNA from room air-exposed post-natal day 5 SD rats, biological replicate 1


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 5 SD rats, biological replicate 1

source_name: Retinae, exposed to cyclic hyperoxia to post-natal day 5


title: Saracatinib sensitive PIK3CA mutant rep1

source_name: Sensitive, PIK3CA mutant rep1

value: PIK3CA mutant sensitive to saracatinib


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 5 SD rats, biological replicate 2


title: Saracatinib sensitive PIK3CA mutant rep2

source_name: Sensitive, PIK3CA mutant rep2


title: Pooled retinal RNA from room air-exposed post-natal day 5 F344 rats, biological replicate 2

value: Fischer 344

value: room air-exposed


title: NormalBrain

description: FFPE material/DASL processed

source_name: Normal Brain

tag: tumor type

value: normal brain


title: shgc151|PR00381 Gibbon

description: Simple annotation: Comparative genomics, aCGH cell line

source_name: Normal human male genomic DNA

tag: Normal human male genomic DNA

organism: Hylobates sp.

source_name: Gibbon genomic DNA

tag: Gibbon genomic DNA


title: shgc150|PR00242 Macaque

source_name: Macaque genomic DNA

tag: Macaque genomic DNA


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 5 F344 rats, biological replicate 2


title: si-hnRNP L, biological rep1

city: Newark

first: Wencheng

last: Li

state: NJ

address: MSB-E501, 185 South Orange Ave.

institute: UMDNJ

description: si-hnRNP L, biological rep1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Affymetrix exon arrays were normalized by the RMA method in the Affymetrix Power Tools (APT) program. Probe sets with detection above background (DABG) P value < 0.05 in at least one sample group were used for further analysis.
HuEx-1_0-st-v2.r2.pgf

source_name: si-hnRNP L, biological rep1

label_protocol: Standard Affymetrix protocol

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% FBS (Hyclone). All the cells were maintained in 5% CO2.

extract_protocol: Total RNA was isolated from cells using TRIZOL (Invitrogen)

tag: cell line

value: HeLa

value: sihnRNP L


title: Pooled retinal RNA from room air-exposed post-natal day 5 F344 rats, biological replicate 1


title: shgc157|PR00254 Lemur

source_name: Normal human female genomic DNA

tag: Normal human female genomic DNA

organism: Lemur sp.

source_name: Lemur genomic DNA

tag: Lemur genomic DNA


title: shgc149|PR00295 Marmoset

organism: Callithrix sp.

source_name: Marmoset genomic DNA

tag: Marmoset genomic DNA


title: shgc148|PR00789 Marmoset


title: RNA: OCI-AML2

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28019.gif

source_name: CRH

tag: reference

value: CRH


title: RNA: K-562

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35295.gif


title: RNA: KG-1

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34469.gif


title: si-hnRNP L, biological rep2

description: si-hnRNP L, biological rep2

source_name: si-hnRNP L, biological rep2


title: RNA: KASUMI-1

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34465.gif


title: RNA: HL-60

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34467.gif


title: Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 5 F344 rats, biological replicate 1


title: RNA: UT-7

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28018.gif


title: Cadmium

city: La Jolla

first: Julian

middle: I

last: Schroeder

address: 9500 Gilman Drive #0116

department: Biology

institute: UCSD

description: 7-day old Arabidopsis thaliana seedlings exposed to Cd for 4 hours

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Seedling

growth_protocol: Arabidopsis thaliana plants were grown on quarter-strength MS media at 28oC with 16-h-light/8-h-dark cycle

extract_protocol: RNeasy column (Qiagen) using the manufacturers’ protocols

treatment_protocol: 200um Cd for 6 hours

value: 7-day old

value: seedling

value: Cd for 4 hours

tag: ecotype


title: shgc154|PR00036 Baboon

source_name: Baboon genomic DNA

tag: Baboon genomic DNA


title: RNA: ME-1

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35296.gif


title: si-Med23, biological rep1

description: si-Med23, biological rep1

source_name: si-Med23, biological rep1


title: shgc156|PR00266 Lemur


title: RNA: OCI-AML5

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28016.gif


title: si-Med23, biological rep2

description: si-Med23, biological rep2

source_name: si-Med23, biological rep2


title: Normal #22

status: Public on Feb 23 2012

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

description: mRNA expression in healthy donor

hyb_protocol: 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent)  for 1min at 37C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol : GE1-v5_95_Feb07  and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng total RNA using the Low RNA Linear Amplification Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations.  The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly drawn peripheral blood from ATL patients and healthy volunteers was subjected to PBMC isolation. Then PBMC from healthy donor was further subjected to isolation of CD4+ T-cells by negative isolation.

tag: cell type

value: CD4+ T-cell

tag: atl subtype

value: HTLV-1 uninfected

tag: age (y)

tag: gender

value: F

tag: disease state

value: normal


title: si-hnRNP L, biological rep3

description: si-hnRNP L, biological rep3

source_name: si-hnRNP L, biological rep3

tag: treatment


title: RNA: CMK

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34468.gif

source_name: CMK

value: CMK


title: Normal #20

description: mRNA expression in healthy donor

value: M


title: si-Med23, biological rep3

description: si-Med23, biological rep3

source_name: si-Med23, biological rep3


title: shgc147|PR00644 Marmoset


title: siRNA control, biological rep3

description: siRNA control, biological rep3

source_name: siRNA control, biological rep3

value: siRNA control


title: shgc153|PR00721 Gibbon

source_name: Normal human male genomic DNA


title: shgc155|PR00338 Lemur


title: siRNA control, biological rep2

description: siRNA control, biological rep2

source_name: siRNA control, biological rep2


title: Hep G2 vs. Hep G2-HGF

city: Taipei

first: Yung-Ming

last: Jeng

address: 7 Chung-Shan South Road

department: Department of Pathology

country: Taiwan

institute: National Taiwan University Hospital

description: Comparison of the transcriptional profile of HepG2 cells treated with HGF and control cells

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to the microarray membrane at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: Hep G2 cells

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: The cells are grown in serum-free DMEM for 24 hours

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: The experiment group is treated with HGF (10ng/ml) for 8 hours

source_name: Hep G2 cells treated with HGF


title: Normal #17

description: mRNA expression in healthy donor


title: Normal #16

description: mRNA expression in healthy donor


title: Normal #21

description: mRNA expression in healthy donor


title: Normal #18

description: mRNA expression in healthy donor


title: RNA: SIG-M5

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34471.gif


title: RNA: NB-4

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28015.gif


title: RNA: MONO-MAC-1

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28573.gif


title: siRNA control, biological rep1

description: siRNA control, biological rep1

source_name: siRNA control, biological rep1


title: RNA: M-07e

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34466.gif


title: Normal #15

description: mRNA expression in healthy donor


title: Normal #12

description: mRNA expression in healthy donor


title: Normal #13

description: mRNA expression in healthy donor


title: Normal #11

description: mRNA expression in healthy donor


title: Normal #14

description: mRNA expression in healthy donor


title: shgc152|PR00495 Gibbon

source_name: Gibbon genomic DNA


title: RNA: THP-1

description:
Simple annotation: Myeloid Leukemias, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43990.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 8160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 23:16:03; Parameter PMT Volts = 630; Parameter Scan Date = 2003-08-12; Parameter Pixel Size = 10; Parameter Laser on time = 110043; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 23:16:03; Parameter PMT Volts = 670; Parameter Scan Date = 2003-08-12; Parameter Pixel Size = 10; Parameter Laser on time = 329035; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.89; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger


title: Normal #9

description: mRNA expression in healthy donor


title: Normal #8

description: mRNA expression in healthy donor


title: Normal #6

description: mRNA expression in healthy donor


title: Normal #7

description: mRNA expression in healthy donor


title: Control

description: 7-day old Arabidopsis thaliana seedlings

tag: age

tag: tissue


title: Normal #10

description: mRNA expression in healthy donor


title: Normal #5

description: mRNA expression in healthy donor


title: ATL #52

description: mRNA expression in ATL

value: Adult T-cell Leukemia (ATL) cells

value: Chronic

value: Adult T-cell Leukemia (ATL)


title: Normal #1

description: mRNA expression in healthy donor

value: unknown


title: Normal #4

description: mRNA expression in healthy donor


title: ATL #48

description: mRNA expression in ATL

value: Acute


title: Normal #3

description: mRNA expression in healthy donor


title: ATL #51

description: mRNA expression in ATL


title: ATL #49

description: mRNA expression in ATL


title: ATL #45

description: mRNA expression in ATL


title: ATL #46

description: mRNA expression in ATL


title: ATL #50

description: mRNA expression in ATL


title: ATL #43

description: mRNA expression in ATL


title: ATL #40

description: mRNA expression in ATL


title: ATL #41

description: mRNA expression in ATL


title: ATL #37

description: mRNA expression in ATL


title: ATL #39

description: mRNA expression in ATL


title: ATL #47

description: mRNA expression in ATL


title: ATL #44

description: mRNA expression in ATL


title: ATL #36

description: mRNA expression in ATL

value: Lymphoma


title: ATL #38

description: mRNA expression in ATL


title: ATL #42

description: mRNA expression in ATL


title: ATL #34

description: mRNA expression in ATL


title: ATL #32

description: mRNA expression in ATL


title: ATL #30

description: mRNA expression in ATL


title: ATL #29

description: mRNA expression in ATL


title: ATL #31

description: mRNA expression in ATL


title: ATL #27

description: mRNA expression in ATL


title: ATL #24

description: mRNA expression in ATL


title: ATL #23

description: mRNA expression in ATL


title: Normal #19

description: mRNA expression in healthy donor


title: ATL #26

description: mRNA expression in ATL


title: ATL #25

description: mRNA expression in ATL


title: ATL #22

description: mRNA expression in ATL


title: ATL #21

description: mRNA expression in ATL


title: ATL #15

description: mRNA expression in ATL

value: Smoldering


title: ATL #18

description: mRNA expression in ATL


title: ATL #16

description: mRNA expression in ATL


title: ATL #17

description: mRNA expression in ATL


title: ATL #20

description: mRNA expression in ATL


title: ATL #13

description: mRNA expression in ATL


title: ATL #11

description: mRNA expression in ATL


title: ATL #9

description: mRNA expression in ATL


title: ATL #19

description: mRNA expression in ATL


title: ATL #12

description: mRNA expression in ATL


title: ATL #14

description: mRNA expression in ATL


title: ATL #6

description: mRNA expression in ATL


title: ATL #4

description: mRNA expression in ATL


title: ATL #5

description: mRNA expression in ATL


title: ATL #3

description: mRNA expression in ATL


title: ATL #10

description: mRNA expression in ATL


title: ATL #8

description: mRNA expression in ATL


title: ATL #2

description: mRNA expression in ATL


title: ATL #7

description: mRNA expression in ATL


title: ATL #1

description: mRNA expression in ATL


title: ATL #33

description: mRNA expression in ATL


title: ATL #35

description: mRNA expression in ATL

value: Unknown