title: 13302341 - pool_Col vs pool_Cul

hyb_protocol: pool_Cul Cy5 / pool_Col 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.

extract_protocol: Pool of extract, Cul1:700ng, Cul2:700ng, Cul3:700ng. (Qiagen_RNeasy.pdf)

value: culline 4


title: Sieg_1

status: Public on Mar 27 2012

type: RNA

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

country: Germany

institute: MPI for Evolutionary Biology

hyb_protocol: The microarray was loaded with labeled cRNA as described in the Agilent protocol for One-Color Microarray-Based Gene Expression Analysis (version 6.5, May 2010).

scan_protocol: Microarrays were scanned with an Agilent DNA Microarray Scanner type C with the standard settings for 8 x 15 k Agilent expression arrays.

data_processing: Feature extraction was carried out using the Agilent Feature Extraction software (version 10.7.3.1) and the “gprocessed signal” was taken in the measure for signal intensity. We employed a new normalization procedure, which relates changes in signal intensity to changes in transcript abundance, thereby accounting for observed large differences in probe-binding behavior. This procedure translates measured signal intensities to a percentage of the target transcript’s abundance in a pool previously used for the calibration of the array. Based on this value, new theoretical signal intensity values are calculated based on the same previous calibration. These new theoretical signal intensity values are then normalized for interarray normalization by division by the 75%tile as suggested by Agilent. For a detailed account of the new normalization procedure, please refer to the accompanying publication (Czypionka et al. 2011.Transcriptome changes after genome wide admixture in invasive sculpins Molecular Ecology; no doi yet).

molecule: total RNA

organism: Cottus

source_name: whole fish

label_protocol: Labeled cRNA was prepared from total RNA using the Agilent Low Input Quick Amp Labeling kit.

extract_protocol: Whole fishes were homogenized with a Qiagen Tissue Ruptur  and total RNA was extracted following the Trizol protocol (Invitrogen). Total RNA was quality accessed using an RNA Nano Chip (Agilent) which a was also used for quantification. Quantification was additionally carried out using a NanoDrop-1000 spectrophotometer

tag: species/hybrid

value: invasive hybrid lineage

tag: population

value: Sieg

tag: type

value: invasive

tag: rearing environment

value: lab reared


title: Patient  403; stage IA; Broncho-alveolar

city: Milwaukee

first: Yan

last: Lu

address: 8701 Watertown Plank Rd

country: USA

institute: Medical College of Wisconsin

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the protocols provided by the manufacturer.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

label: BIOTIN

organism: Homo sapiens

source_name: Patient  403

label_protocol: Two hundred ng of total RNA from each sample were labeled and hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

extract_protocol: Total RNA, including miRNA from FFPE lung cancer tissue, RNA was extracted with the Ambion RecoverAll kit (Applied Biosystems, Austin, TX). The recovered RNA was DNAse treated and the quantity and quality were evaluated using a Nanodrop ND-1000 (Thermo Scientific) with an inclusion criterion of A260/A280 ≥1.8.

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: patient id

tag: Stage

value: IA

tag: subtype

value: Broncho-alveolar

tag: age

tag: gender

value: Male


title: Blood, control 16912123-1

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: Affymetrix Power Tools version 1.8.6 RMA model

label: biotin

source_name: Control

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix)

extract_protocol: Total RNA was purified using the Rneasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA)

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.

tag: tissue

value: White Blood Cells

tag: Sex

value: F


title: 13302332 - pool_Cul vs pool_Col

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Antisens and mutnats of the SKP2 and CUL4 genes are comprared to the Wt in order to identify the genes controled by those SCF proteins.

hyb_protocol: pool_Col Cy5 / pool_Cul 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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

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 - The seeds have been sown every two days on MS 255 (Duschefa) without 1% sugar. These plates stayed 6 days in the dark at 4 °s. Then they were transfered to the light for 6 more days.

extract_protocol: Pool of extract, Col1:700ng, Col2:700ng, Col3:700ng. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

value: wild type

tag: treatment


title: Naaf_8

organism: Cottus rhenanus

value: Cottus rhenanus

value: Naaf

value: parental

value: wild reared


title: Blood, control 11014402


title: Blood, control 8491576

value: M


title: Patient  373; stage IA; Large

source_name: Patient  373

value: Large


title: Patient  101167-b; stage IB; SCC

source_name: Patient  101167-b

value: IB

value: SCC

value: Female


title: 13302331 - pool_Cul vs pool_Col

value: culline 4


title: 13301732 - pool_Col vs pool_Cul

hyb_protocol: pool_Cul Cy5 / pool_Col Cy3 : 30pmol.


title: Blood, control 7547283


title: Patient  399; stage IA; Adenosquamous

source_name: Patient  399

value: non-small cell lung cancer (NSCLC)

value: IA

value: Adenosquamous


title: Sieg_3

value: invasive hybrid lineage

value: Sieg

value: invasive


title: Patient  367; stage IA; AD

source_name: Patient  367

value: AD

value: Male


title: Naaf_6

value: Cottus rhenanus

value: Naaf


title: Naaf_5

value: parental

value: wild reared


title: 13301731 - pool_As vs pool_Col

hyb_protocol: pool_Col Cy5 / pool_As 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.

value: columbia

value: wild type

extract_protocol: Pool of extract, As1:700ng, As2:700ng, As3:700ng. (Qiagen_RNeasy.pdf)

value: antisense


title: Naaf_7


title: 13302335 - pool_Col vs pool_As

hyb_protocol: pool_As Cy5 / pool_Col 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: Blood, control 27020842

value: White Blood Cells

value: M


title: Blood, control 1136230

value: F


title: Blood, control 18506903


title: Patient  71997; stage IA; AD

source_name: Patient  71997

value: non-small cell lung cancer (NSCLC)

value: IA


title: Naaf_4

value: lab reared


title: 13690790 - CDC16S 2 vs Col 2

description: Which genes are misregulated when the APC complex activity is reduced?

hyb_protocol: Col 2 Cy5 / CDC16S 2 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,650V,laser power 33%, Cy5:635nm,pmt voltage 650V,laser power 33%

source_name: Col 2

growth_protocol: whole plant - Media : MS Hygrometry : 54% Temperature : 22°C Light : 16 light/ 8h darkness

extract_protocol: Col 2:10.16ug. (Qiagen_RNeasy.pdf)

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

source_name: CDC16S 2

extract_protocol: CDC16S 2:9.39ug. (Qiagen_RNeasy.pdf)

value: cdc16 down regulated


title: Patient  70761; stage IB; SCC

source_name: Patient  70761

value: IB

value: SCC


title: patient 152; stage IA; Poorly differentiated

source_name: patient 152

value: Poorly differentiated

value: Female


title: Naaf_3

value: Cottus rhenanus

value: Naaf


title: 13690789 - Col 2 vs CDC16S 2

hyb_protocol: CDC16S 2 Cy5 / Col 2 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: 13690788 - APC10S 2 vs Col 2

hyb_protocol: Col 2 Cy5 / APC10S 2 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: APC10S 2

extract_protocol: APC10S 2:10.65ug. (Qiagen_RNeasy.pdf)

value: apc10 down regulated


title: Patient  70906; stage IA; AD

source_name: Patient  70906

value: AD


title: 13690785 - Col 1 vs CDC16S 1

hyb_protocol: CDC16S 1 Cy5 / Col 1 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: CDC16S 1

extract_protocol: CDC16S 1:10.31ug. (Qiagen_RNeasy.pdf)

source_name: Col 1

extract_protocol: Col 1:8.17ug. (Qiagen_RNeasy.pdf)

value: wild type


title: patient 178; stage IB; AD

source_name: patient 178


title: LB_9

organism: Cottus perifretum

source_name: whole fish

value: Cottus perifretum

value: Laarse Beek (LB)

value: parental


title: 13690787 - Col 2 vs APC10S 2

hyb_protocol: APC10S 2 Cy5 / Col 2 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: Blood, control 21473827

value: White Blood Cells

value: F


title: Blood, control 11908009

value: M


title: Naaf_1

value: wild reared


title: Blood, control 18000027


title: Blood, control 19297865-2


title: Naaf_2


title: Blood, control 19802493


title: 13690784 - APC10S 1 vs Col 1

hyb_protocol: Col 1 Cy5 / APC10S 1 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: APC10S 1

extract_protocol: APC10S 1:9.88ug. (Qiagen_RNeasy.pdf)


title: LB_6

value: lab reared


title: patient 125; stage IA; AD

source_name: patient 125

value: non-small cell lung cancer (NSCLC)

value: IA

value: Male


title: patient 105; stage IB; AD

source_name: patient 105

value: IB

value: Female


title: Blood, control 8478360

source_name: Control


title: Blood, control 17930391


title: Blood, control 29091703


title: patient 108; stage IA; SCC

source_name: patient 108

value: SCC


title: 13690783 - Col 1 vs APC10S 1

hyb_protocol: APC10S 1 Cy5 / Col 1 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.

value: apc10 down regulated


title: patient 423; stage IA; AD

source_name: patient 423

value: AD


title: patient 366; stage IB; SCC

source_name: patient 366


title: patient 398; stage IA; SCC

source_name: patient 398


title: LB_11


title: patient 71061; stage IA; Adenosquamous

source_name: patient 71061

value: Adenosquamous


title: LB_13

value: Cottus perifretum


title: LB_8

value: Laarse Beek (LB)


title: Blood, control 32378500


title: LB_12

value: parental


title: LB_10


title: Blood, control 3511111

value: White Blood Cells


title: Broel_4

value: Cottus rhenanus

value: Broel


title: patient 141-b; stage IA; Broncho-alveolar

source_name: patient 141-b

value: Broncho-alveolar


title: LB_5

value: lab reared


title: patient 70904; stage IB; Large

source_name: patient 70904

value: non-small cell lung cancer (NSCLC)

value: Large


title: Blood, control 22680057

value: F


title: Blood, control 10378715


title: Blood, control 13057592

value: M


title: Blood, control 32292315


title: Broel_3

value: wild reared


title: patient 147; stage IB; AD

source_name: patient 147

value: IB

value: Female


title: Broel_2


title: Broel_9


title: patient 175; stage IB; AD

source_name: patient 175

value: AD

value: Male


title: patient 56361; stage IB; AD

source_name: patient 56361


title: Blood, control 19107727


title: patient 107; stage Ib; AD

source_name: patient 107


title: Blood, control 20591195


title: Blood, control 16952213


title: patient 101; stage IA; AD

source_name: patient 101

value: IA


title: Blood, control 35028656


title: Broel_1

source_name: whole fish


title: Broel_10


title: Broel_11


title: Blood, control 19297865-1


title: patient 112; stage IA; Broncho-alveolar

source_name: patient 112


title: Blood, control 1829766


title: Broel_12


title: Blood, control 17587105


title: Blood, control 8915966


title: 12961296 - Pool_Col0 vs Pool_SKP2

hyb_protocol: Pool_SKP2 Cy5 / Pool_Col0 Cy3 : 40pmol. (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,650V,laser power 100%, Cy5:635nm,pmt voltage 650V,laser power 100%

growth_protocol: cotyledons - MS255 + agar (8g/L) + 1% sucrose. 48h at 4°C then 22°C hygrometry : 70% Light : 2000 lux, Day/night : 16h/8h.

extract_protocol: Pool of extract, SKP2_2:1ug, SKP2_3:1ug, SKP2_1:1ug.

value: columbia

extract_protocol: Pool of extract, C1:1ug, C2:1ug, C3:1ug.

value: wild type


title: 12961294 - Pool_SKP2 vs Pool_Col0

hyb_protocol: Pool_Col0 Cy5 / Pool_SKP2 Cy3 : 40pmol. (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: Blood, control 22062194

value: White Blood Cells


title: 12949725 - Pool_Col0 vs Pool_SKP2


title: 12949724 - Pool_SKP2 vs Pool_Col0


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 6

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 6

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction and dye-normalization were used.

source_name: Peripheral blood cells from vasculitis patient 6

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The RNAs of TA patients' and normal volunteers' PBMCs were prepared by a standard method. Briefly, heparinized venous blood (10 mL) was mixed with an equal volume of 2% dextran/saline solution and incubated at room temperature for 30 min to precipitate the red blood cells. The PBMCs in the supernatant were then purified by density-gradient centrifugation on Percoll (density=1.064 g/mL). Total RNA was extracted from the PBMC pellets by adding guanidine-thiocyanate solution and the samples were used for acid guanidinium-phenol-chloroform extraction followed by ethanol precipitation and DNase I treatments for microarray analysis.

tag: age (y)

value: Takayasu's vasculitis

tag: cell type

value: peripheral blood cells

source_name: Peripheral mononuclear blood cells from 17 healthy controls

value: 11 females and 6 males

value: healthy controls without any identified diseases

value: Peripheral mononuclear blood cells


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 3

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 3

source_name: Peripheral blood cells from vasculitis patient 3


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 7

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 7

source_name: Peripheral blood cells from vasculitis patient 7


title: 13690786 - CDC16S 1 vs Col 1

hyb_protocol: Col 1 Cy5 / CDC16S 1 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: Col 1

source_name: CDC16S 1

value: cdc16 down regulated


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 4

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 4

source_name: Peripheral blood cells from vasculitis patient 4

value: F

value: ND


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 1

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 1

source_name: Peripheral blood cells from vasculitis patient 1


title: mock at T24 hpi, biological rep2

city: LODI

first: PAMELA

last: ABBRUSCATO

state: LO

address: via Einstein

department: RICE GENOMICS UNIT

country: Italy

institute: PARCO TECNOLOGICO PADANO

description: gene expression data from rice leaf sample not inoculated with B. graminis f. sp. hordei (Bgh) but incubated at the same conditions of tretaed plants

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized according to the GeneChip standard protocol (Eukaryotic Target Preparation, Affymetrix) on the  GeneChip® Rice Genome Array.

scan_protocol: According to the GeneChip standard protocol (Eukaryotic Target Preparation, Affymetrix) using GeneArray® Scanner at the excitation wavelength of 488 nm.

data_processing: The data were analysed in R 2.12.0 applying the RMA algorithm from affy package. The default settings for all normalization procedures were used as implemented in the BioConductor.

organism: Oryza sativa

source_name: non treated plants 24 hours post incubation with treated plants

label_protocol: Biotin-labelled cRNA targets obtained by direct in vitro transcription reaction.

growth_protocol: Plants grown in a glasshouse under a day-time temperature of 27°C, a night-time temperature of 22°C and 60% humidity.

extract_protocol: Total RNA of each biological replicate was purified, using the TRIZOL protocol (Invitrogen, Carlsbad, CA), following the manufacturer's instructions.

treatment_protocol: Two week-old rice plants were inoculated with Bgh conidia by shaking inoculated barley plants over test plants in a settling tower of approximately 60 X 60 X 60 cm,  in analogy to barley plants inoculation as previously described by Zellerhoff et al. (2010). Inoculations were done 1 to 2 h after the onset of light at an average density of 10 conidia mm leaf area. Control plants were left nontreated. Control and inoculated plants were incubated at a constant temperature of 20 °C and natural daylight (no direct sunlight) until RNA extraction.

tag: cultivar

value: Nipponbare

tag: protocol

tag: test

value: control sample

value: rice leaf


title: mock at T24 hpi, biological rep1

value: not inoculated with B. graminis f. sp. hordei (Bgh) but incubated at the same conditions of tretaed plants


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 8

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 8

source_name: Peripheral blood cells from vasculitis patient 8

tag: disease state


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 2

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 2

source_name: Peripheral blood cells from vasculitis patient 2


title: Bgh at 24 hpi, biological replicate 3

description: gene expression data from rice leaf sample inoculated with B. graminis f. sp. hordei (Bgh)

source_name: 24 hours post inoculation with  B. graminis f. sp. hordei

value: treated sample


title: Peripheral mononuclear blood cells in patients with Takayasu's arteritis 5

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu's arteritis 5

source_name: Peripheral blood cells from vasculitis patient 5


title: Lung_SS_biological rep4

city: New York

first: Rui

last: Xiao

state: NY

address: 630 West 168th Street

department: Anesthesiology

institute: Columbia University

description: Left lung from 15-week-old male Balb/c mice with in-utero exposure to SHS, adult exposure to SHS.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays in a GeneChip Hybridization Oven 640, followed by washing and staining in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with the R/Bioconductor platform. Packages used: AffyExpress, Limma, Heatplus, etc.

organism: Mus musculus

source_name: Left lung, in-utero exposure to SHS, adult exposure to SHS

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

growth_protocol: We housed and handled Balb/c mice on a 12-hr light-dark cycle. Mice had food and water ad libitum except when in the exposure chambers.

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

treatment_protocol: Animals were exposed to sidestream smoke with a suspended particle load of 10 mg/m3 during the smoke exposure or to filtered-air as control (5 hr/day, 7 days a week).

tag: strain

value: Balb/c

value: male

value: 15 weeks

value: left lung


title: mock at T24 hpi, biological rep3


title: Blood, control 4609399

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix

source_name: Control

value: White Blood Cells


title: mock at T24 hpi, biological replicate 1

description: gene expression data from rice leaf sample inoculated with gelatin suspension without fungal spores

source_name: 24 hours post treatment with 0.5% gelatin suspension

treatment_protocol: Inoculations with Magnaporthe strains were performed on rice plantlets 2 wk after sowing by spraying with conidial suspensions. Rice plants were then kept for 16 h in a controlled climatic chamber at 25°C and 95% relative humidity. Plants were then transferred back to the glasshouse according to Faivre-Rampant et al. 2008 (doi: 10.1111/j.1469-8137.2008.02621.x)


title: Lung_SS_biological rep2

value: in-utero exposure to SHS, adult exposure to SHS


title: Lung_SS_biological rep1


title: Bgh at 24 hpi, biological replicate 2

value: inoculated with B. graminis f. sp. hordei (Bgh)


title: Lung_SS_biological rep3


title: Bgh at 24 hpi, biological replicate 1


title: Lung_SA_biological rep3

description: Left lung from 15-week-old male Balb/c mice with in-utero exposure to SHS, adult exposure to air.

source_name: Left lung, in-utero exposure to SHS, adult exposure to air


title: mock at T24 hpi, biological replicate 3

value: inoculated with gelatin suspension without fungal spores


title: mock at T24 hpi, biological replicate 2


title: Lung_SA_biological rep4

value: in-utero exposure to SHS, adult exposure to air


title: FR13 at 24 hpi, biological replicate 3

description: gene expression data from rice leaf sample inoculated with Magnaporthe oryzae isolate FR13

source_name: 24 hours post inoculation with Magnaporthe oryzae isolate FR13


title: FR13 at 24 hpi, biological replicate 2

value: inoculated with Magnaporthe oryzae isolate FR13


title: synovial fibroblasts incubated with Tenascin-C vs. incubated with BSA

city: Sapporo

first: Asano

last: Tsuyoshi

address: Kita-15, Nishi-7, Kita-ku

department: Graduate School of Medicine

institute: Hokkaido University

hyb_protocol: overnight hybridizatio using Oligo GEArray HybTube Protocol

scan_protocol: Scanned on a LAS-1000LC scanner (FUJIFILM). Images were quantified using Image Reader LAS-1000 Lite for LAS-1000 plus (Version 1.2) (FUJIFILM).

data_processing: Background subtracted data obtained from log2 of Tenascin-C/BSA.

source_name: synovial fibroblast treated with Tenascin-C

label_protocol: 5ug of total RNA are labeling with TrueLabeling-AMP 2.0 cRNA Synthesis and Labeling

growth_protocol: Synovial fibroblasts separated from human rheumatoid arthritis synovial tissue were used

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

treatment_protocol: Synovial fibroblasts were incubated on plates coated with 10ug/ml of BSA or Tenascin-C for 48 hours

value: primary rheumatoid synovial fibroblasts, passage 3

value: Tenascin-C

source_name: synovial fibroblast treated with BSA

value: BSA


title: CL367 at 24 hpi, biological replicate 1

description: gene expression data from rice leaf sample inoculated with Magnaporthe oryzae isolate CL367

source_name: 24 hours post inoculation with Magnaporthe oryzae isolate CL367

value: Nipponbare


title: FR13 at 24 hpi, biological replicate 1

value: rice leaf


title: Lung_AS_biological rep1

description: Left lung from 15-week-old male Balb/c mice with in-utero exposure to air, adult exposure to SHS.

source_name: Left lung, in-utero exposure to air, adult exposure to SHS


title: CL367 at 24 hpi, biological replicate 2

value: inoculated with Magnaporthe oryzae isolate CL367


title: CL367 at 24 hpi, biological replicate 3

value: treated sample


title: Lung_AA_biological rep4

description: Left lung from 15-week-old male Balb/c mice with in-utero exposure to air, adult exposure to air.

source_name: Left lung, in-utero exposure to air, adult exposure to air

value: Balb/c


title: Lung_SA_biological rep2

value: male


title: Lung_AS_biological rep4

value: 15 weeks

value: in-utero exposure to air, adult exposure to SHS


title: Lung_SA_biological rep1

value: left lung


title: Lung_AS_biological rep2


title: Lung_AA_biological rep3

value: in-utero exposure to air, adult exposure to air


title: BR32 at 24 hpi, biological replicate 2

description: gene expression data from rice leaf sample inoculated with Magnaporthe oryzae isolate BR32

source_name: 24 hours post inoculation with Magnaporthe oryzae isolate BR32


title: Lung_AA_biological rep1


title: BR32 at 24 hpi, biological replicate 1

value: inoculated with Magnaporthe oryzae isolate BR32


title: Lung_AA_biological rep2


title: BR29 at 24 hpi, biological replicate 2

description: gene expression data from rice leaf sample inoculated with Magnaporthe grisea isolate BR29

source_name: 24 hours post inoculation with Magnaporthe grisea isolate BR29


title: WT Xylose-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[14104535]

status: Public on Mar 26 2012

city: Tianjin Airport Economic Area

first: Chaoguang

last: Tian

state: Tianjin

address: Xiqi Dao 32

country: China

institute: Tianjin Institute of Industrial Biotechnology, CAS

description:
Hyb name: 14104535
RNA in hybs cy3 @ cy5: WT Xylose-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylose for 4h

hyb_protocol: The Pronto! Hybridization Kit (Corning, catalog no. 40076) was used for microarray hybridization according to the manufacturer's specifications

scan_protocol: Scanned on a GenePix 4000B scanner (Axon Instruments)

data_processing:
GenePix Pro6 software was used to quantify hybridization signals and collect the raw data (ie, gpr files); normalized gene relative expression values were analyzed by using BAGEL (Bayesian Analysis of Gene Expression Levels).
Normalized ratio (SJ635/J532) representing cy5/cy3 ; gene relative expression were generated by BAGEL based on loop design, the lowest genes expression of the RNA sample will set as 1.0, the gene expression in other RNA samples will relative to this lowest one.
Software for normalization/relative gene expression/Statistics: Bayesian Analysis of Gene Expression Levels (BAGEL); http://www.yale.edu/townsend/jeffreytownsend.html
Details: Once we have GPR file for each hyb, we normalized the ratio of cy5/cy3 of each hyb using BAGEL normalized function first (see data table below). But our conclusion were not directly based on this ratio, we use the normalized ratio data as BAGEL input data, using BAGEL second function-to generate the gene relative expression, this BAGEL result called BAR output file, will give every gene relative expression in each RNA sample. Our conclusion were based on BAR files.
I run BAGEL using two different subset,  one is Avicel condition sample hybs, the second was xylan-xylose condition hybs. So, there are two Relative Gene Expression tables (ie, BAGEL_BAR_outputfiles, linked as supplementary files on the Series record).  My conclusion were based on these relative expression under different condition dataset.

organism: Neurospora crassa

source_name: N. crassa  WT transferred to Xylose for 4h from a 16h MM culture

label_protocol: 10ug of total RNA were used; ChipShot Indirect Labeling/Clean-Up System (Promega, catalog no. Z4000) and CyDye Post-Labeling Reactive Dye Pack (GE, catalog no. RPN5661) were used to synthesize and label cDNA according to the manufacturer's  instruction

growth_protocol:
Growth medium: MM: 1xVogel's (Vogel, 1956 Microbiol. Genet. Bull. 13:42-43) salts with 2% sucrose as a sole carbon source; Avicel: 1xVogel's salts with 2% Avicel as a sole carbon source;Xylan:1xVogel's salts with 2% Xylan as a sole carbon source;Xylose:1xVogel's salts with 2% Xylose as a sole carbon source
N. crassa was pregrown in minimal medium (MM) for 16h

treatment_protocol: The pregrown hyphae were washed by 1x Vogel's media then transferred into either MM or Avicel (Avi)or Xylan or Xylose for 4h

tag: strain fgsc number

value: FGSC 2489

value: WT

tag: growth medium

value: Xylose

value: hyphae

source_name: N. crassa  WT transferred to  MM for 4h from a 16h MM culture

value: MM


title: xlr-1 Xylose-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C[14104537]

description:
Hyb name: 14104537
RNA in hybs cy3 @ cy5: xlr-1 Xylose-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylose for 4h

source_name: N. crassa xlr-1 transferred to Xylose for 4h from a 16h MM culture

source_name: N. crassa  xlr-1 transferred to MM for 4h from a 16h MM culture


title: BR29 at 24 hpi, biological replicate 3

value: inoculated with Magnaporthe grisea isolate BR29


title: WT MM-4h_transfer from 16h MM@25C vs WT Xylose-4h_transfer from 16h MM@25C[14104534]

description:
Hyb name: 14104534
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Xylose-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylose for 4h


title: C. elegans cultured on : Bacillus strain 67 vs. E. coli OP50 exposure; Biological Replicate 4. Dye-swap-2

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 4 of 4. This is also a dye-swap.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans young adults, cultured on E.coli OP50

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

value: N2 Bristol

tag: bacteria

value: E. coli OP50

source_name: C. elegans young adults, cultured on Bacillus strain 67

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on lawns of Bacillus strain 67 at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: Bacillus strain 67


title: Lung_AS_biological rep3

value: Balb/c

tag: gender

tag: age

tag: tissue


title: BR29 at 24 hpi, biological replicate 1

value: Nipponbare

value: treated sample

value: rice leaf


title: C. elegans cultured on : Bacillus strain 67 vs. E. coli OP50 exposure; Biological Replicate 2

description: Biological replicate 2 of 4.


title: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Xylan-4h_transfer from 16h MM@25C[13790884]

description:
Hyb name: 13790884
RNA in hybs cy3 @ cy5: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Xylan-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h

tag: genotype/variation

source_name: N. crassa xlr-1 transferred to Xylan for 4h from a 16h MM culture

value: Xylan


title: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Xylose-4h_transfer from 16h MM@25C[14104536]

description:
Hyb name: 14104536
RNA in hybs cy3 @ cy5: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Xylose-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylose for 4h


title: WT Avicel-4h_transfer from 16h MM@25C vs xlr-1 Avicel-4h_transfer from 16h MM@25C[13790872]

description:
Hyb name: 13790872
RNA in hybs cy3 @ cy5: WT Avicel-4h_transfer from 16h MM@25C vs xlr-1 Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

source_name: N. crassa  WT transferred to Avicel for 4h from a 16h MM culture

value: Avicel

source_name: N. crassa xlr-1 transferred to Avicel for 4h from a 16h MM culture


title: WT MM-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C[13929884]

description:
Hyb name: 13929884
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h

source_name: N. crassa  WT transferred to Xylan for 4h from a 16h MM culture


title: WT MM-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C[13989825]

description:
Hyb name: 13929825
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Avicel-4h_transfer from 16h MM@25C[13790883]

description:
Hyb name: 13790883
RNA in hybs cy3 @ cy5: xlr-1 MM-4h_transfer from 16h MM@25C vs xlr-1 Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h


title: C. elegans cultured on : Bacillus strain 67 vs. E. coli OP50 exposure; Biological Replicate 1

description: Biological replicate 1 of 4.


title: WT Xylan-4h_transfer from 16h MM@25C vs xlr-1 Xylan-4h_transfer from 16h MM@25C[13791357]

description:
Hyb name: 13791357
RNA in hybs cy3 @ cy5: WT Xylan-4h_transfer from 16h MM@25C vs xlr-1 Xylan-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: C. elegans cultured on : Bacillus strain 67 vs. E. coli OP50 exposure; Biological Replicate 3. Dye-swap-1

description: Biological replicate 3 of 4. This is also a dye-swap.


title: WT Xylan-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[13929879]

description:
Hyb name: 13929879
RNA in hybs cy3 @ cy5: WT Xylan-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: WT Xylan-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[13989800]

description:
Hyb name: 13989800
RNA in hybs cy3 @ cy5: WT Xylan-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: xlr-1 Xylan-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C[13791354]

description:
Hyb name: 13791354
RNA in hybs cy3 @ cy5: xlr-1 Xylan-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: Xlr-1 Xylan-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C[13791355]

description:
Hyb name: 13791355
RNA in hybs cy3 @ cy5: Xlr-1 Xylan-4h_transfer from 16h MM@25C vs WT Xylan-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Xylan for 4h


title: xlr-1 Avicel-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C[13790882]

description:
Hyb name: 13790882
RNA in hybs cy3 @ cy5: xlr-1 Avicel-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h


title: Subject 4- Haired

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

hyb_protocol: Affymetrix GeneChip Technical Manual: standard hybridization cocktail at 45C for 16hr.

scan_protocol: Affymetrix GeneChip Technical Manual: GeneChip Scanner 3000 7G

data_processing: GCRMA signal intensities were calculated from cel files using GeneSpring version 7. To be included probe set must be present in 2 of 10 subjects

source_name: Scalp epidermis and dermis

label_protocol: Affymetrix One-Cycle Target Labeling Kit: Linear amplification and biotinylation by T7 RNA polymerase in vitro transcription.

extract_protocol: Qiangen Fibrous RNA kit

tag: subject

tag: haired or bald

value: Haired

value: Scalp epidermis and dermis


title: Subject 2- Bald

value: Bald


title: Subject 4- Bald


title: Subject 3- Bald


title: WT MM-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C[13769160]

description:
Hyb name: 13769160
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs xlr-1 MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

value: FGSC 2489

value: WT


title: xlr-1 MM-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[13990062]

description:
Hyb name: 13990062
RNA in hybs cy3 @ cy5: xlr-1 MM-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

source_name: N. crassa  xlr-1 transferred to  MM for 4h from a 16h MM culture

value: MM

value: hyphae

source_name: N. crassa  WT transferred to MM for 4h from a 16h MM culture


title: Subject 5- Haired


title: xlr-1 Avicel-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C[13790881]

description:
Hyb name: 13790881
RNA in hybs cy3 @ cy5: xlr-1 Avicel-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h


title: Subject 5- Bald


title: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C[13929871]

description:
Hyb name: 13929871
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

source_name: N. crassa wildtype (WT) transferred to  MM for 4h from a 16h MM culture

source_name: N. crassa  WT transferred to  Avicel for 4h from a 16h MM culture


title: chondrocyte_24h_IL1beta

city: Shanghai

first: Jing

last: Li

address: South Chongqing Road

institute: Institue of Health Sciences

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

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

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
Averages are derived from LOWESS normalized data from all probes per miRNA.

organism: Rattus norvegicus

source_name: chondrocyte, IL1beta, 24h

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from 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 dye staining.

extract_protocol: Total RNA extracted using miRNeasy Mini Kit (Qiagen) following manufacturer's instructions

value: Rat primary chondrocyte

tag: culture intensity

tag: treatment protocol

value: treated with 10 ng/ml IL1beta, collected after 24h


title: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C[13927383]

description:
Hyb name: 13927383
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h


title: Subject 3- Haired


title: WT Avicel-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[13927197]

description:
Hyb name: 13927197
RNA in hybs cy3 @ cy5: WT Avicel-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

source_name: N. crassa wildtype (WT) transferred to  Avicel for 4h from a 16h MM culture


title: Subject 1- Haired


title: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C[13927193]

description:
Hyb name: 13927193
RNA in hybs cy3 @ cy5: WT MM-4h_transfer from 16h MM@25C vs WT Avicel-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h


title: Subject 2- Haired


title: BR32 at 24 hpi, biological replicate 3

description: gene expression data from rice leaf sample inoculated with Magnaporthe oryzae isolate BR32

source_name: 24 hours post inoculation with Magnaporthe oryzae isolate BR32

tag: cultivar


title: Subject 1- Bald


title: WT Avicel-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C[13927384]

description:
Hyb name: 13927384
RNA in hybs cy3 @ cy5: WT Avicel-4h_transfer from 16h MM@25C vs WT MM-4h_transfer from 16h MM@25C
N. crassa was pregrown in MM for 16h then transferred into either MM or Avicel for 4h

source_name: N. crassa  WT transferred to  MM for 4h from a 16h MM culture


title: chondrocyte_6h_IL1beta

source_name: chondrocyte, IL1beta, 6h

tag: cell type

value: treated with 10 ng/ml IL1beta, collected after 6h


title: Control-Diaphragm-4

city: Gainesville

first: Vipa

last: Bernhardt

state: FL

address: 1600 Archer Rd

institute: University of Florida

description: US83800208_252827910157_S01_GE1-v5_10_0-2D_2_3.txt

hyb_protocol: Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 5.7).

scan_protocol: An Axon GenePix®4000B Microarray Scanner (Molecular Deviced Inc., Concord, Ontario, Canada) was used to scan the microarrays.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA).

source_name: Diaphragm muscle from surgical control rat

label_protocol: One microgram of total RNA was used for all hybridizations. Complementary cDNA synthesis, cRNA labeling, and hybridizations were performed following the manufacturer’s kits and protocols (QuickAmp Labeling Kit; Agilent Technologies, Palo Alto, CA).

growth_protocol: Male Sprague-Dawley rats were housed two per cage in a temperature-controlled room (72°F) on a 12:12 light:dark cycle, and with free access to food and water. All animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Florida.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen Life Science, Carlsbad, CA)

treatment_protocol: During the experimental session the rats underwent repeated trials of 5-8 second occlusions followed by approximately 25 s of recovery. Control animals did not receive occlusions. Occlusion and control sessions were performed daily for 10 days. On day 10, the rats were sacrificed via overdose of anesthetic, the left diaphragm and 3rd parasternal muscles were debrided of connective tissue and then flash-frozen in liquid nitrogen.

value: Sprague-Dawley

value: male

tag: treatment

value: Control


title: Control-Diaphragm-3

description: US83800208_252827910157_S01_GE1-v5_10_0-1D_2_2.txt


title: chondrocyte_0h_con

source_name: chondrocyte, untreated, 0h

value: No treatment


title: chondrocyte_12h_IL1beta

source_name: chondrocyte, IL1beta, 12h

value: treated with 10 ng/ml IL1beta, collected after 12h


title: Occlusion-Diaphragm-2

description: US83800208_252827910157_S01_GE1-v5_10_9-3D_1_3.txt

source_name: Diaphragm muscle from rat that received tracheal occlusions

value: tracheal occlusions


title: Occlusion-Diaphragm-1

description: US83800208_252827910157_S01_GE1-v5_10_9-1D_1_1.txt


title: Occlusion-Diaphragm-4

description: US83800208_252827910157_S01_GE1-v5_10_0-4D_2_4.txt


title: Control-Diaphragm-1

description: US83800208_252827910157_S01_GE1-v5_10_9-2D_1_2.txt


title: Occlusion-Diaphragm-3

description: US83800208_252827910157_S01_GE1-v5_10_9-5D_1_4.txt


title: Control-Intercostal-4

description: US83800208_252827910156_S01_GE1-v5_10_0-6I_2_4.txt

source_name: Intercostal muscle from surgical control rat


title: Control-Diaphragm-2

description: US83800208_252827910157_S01_GE1-v5_10_9-8D_2_1.txt


title: Control-Intercostal-2

description: US83800208_252827910156_S01_GE1-v5_10_9-8I_2_1.txt


title: Occlusion-Intercostal-4

description: US83800208_252827910156_S01_GE1-v5_10_0-4I_2_3.txt

source_name: Intercostal muscle from rat that received tracheal occlusions


title: Occlusion-Intercostal-1

description: US83800208_252827910156_S01_GE1-v5_10_9-1I_1_1.txt


title: Control-Intercostal-3

description: US83800208_252827910156_S01_GE1-v5_10_9-0I_2_2.txt


title: Control-Intercostal-1

description: US83800208_252827910156_S01_GE1-v5_10_9-2I_1_2.txt


title: Occlusion-Intercostal-3

description: US83800208_252827910156_S01_GE1-v5_10_9-5I_1_4.txt


title: HEK293

status: Public on Mar 25 2012

city: Montreal

first: Diana

middle: Paola

last: Granados

state: Quebec

address: C.P. 6128, succursale Centre-ville

department: Medecine

country: Canada

institute: IRIC

hyb_protocol: Labeled RNA was hybridized to the Agilent Human microRNA Microarray Release 16.0 (G4872A-031181 Agilent Technologies) with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Slides were scanned with a GenePix 4000B scanner (Molecular Devices) at a 5uM/pixel resolution .

data_processing: Features were extracted with the GenePix 6.1 software. Analyses were performed using BRB-ArrayTools Version 4.2.0 Stable Release developed by Dr. Richard Simon and the BRB-ArrayTools Development Team (http://en.bio-soft.net/chip/BRBArrayTools.html). The data were background-subtracted and quantile normalized. To estimate a single intensity measure for each miRNA, we calculated the mean of its different probes.

source_name: HEK293 human embryonic kidney

label_protocol: 100 ng of each RNA sample was labeled with the microRNA complete labeling and hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: B-LCLs and B cells were grown in RPMI 1640 medium supplemented with 25mM HEPES, 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. HEK293 and HeLa cells were grown in DMEM medium supplemented with 2mM L-glutamine, 10% heat-inactivated fetal bovine serum and penicillin-streptomycin. Exponential growth under normal conditions.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit, including on-column DNase I treatment (Qiagen), according to the manufacturer’s instructions. Total RNA was quantified using the NanoDrop 2000 (Thermo Scientific) and RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Not treated.

tag: cell line

value: embryonic kidney

tag: origin

value: non-lymphoid


title: CD19+CD20-_2.1

source_name: CD19+CD20- B cells sorted from peripheral blood mononuclear cells of subject 2.1

value: primary CD19+CD20- B cells

value: lymphoid


title: HeLa

source_name: HeLa from human cervix cancer

value: HeLa

value: cervical cancer


title: Occlusion-Intercostal-2

description: US83800208_252827910156_S01_GE1-v5_10_9-3I_1_3.txt

tag: strain


title: BLCL_1.1

source_name: EBV-transformed lymphoblastoid cell line from subject 1.1

value: EBV-transformed lymphoblastoid cells


title: BLCL_1.2

source_name: EBV-transformed lymphoblastoid cell line from subject 1.2


title: CD19+CD20+_2.1

source_name: CD19+CD20+ B cells sorted from peripheral blood mononuclear cells of subject 2.1

value: primary CD19+CD20+ B cells


title: 13415173 - Cadmium 24h 1 vs Control 24h 1

description: trancriptional and post-transcriptional response to cadmium.

hyb_protocol: Control 24h 1 Cy5 / Cadmium 24h 1 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 24h 1

growth_protocol: cell culture/primary cell - Murashige and Skoog salts (Sigma), 0.5 mM kinetin, 0.34 mM 2-4D, vitamins mix (4 mM Nicotinic Acid, 1.26 uM Calcium Dpantothenate, 2.66 mM Glycine, 150 uM Thiamine-HCl, 110 uM Folic acid, 0.25 mM Pyridoxine-HCl, 20 uM Biotine and 28 mM Myo-inositol) and 3 % sucrose with pH adjusted to 5.6.

extract_protocol: Control 24h 1:91ug. (RNA_extraction-protocol.doc)

tag: ecotype

value: columbia

tag: harvest date

source_name: Cadmium 24h 1

extract_protocol: Cadmium 24h 1:91ug. (RNA_extraction-protocol.doc)

treatment_protocol: Name:CdCl2 - abiotic stress - abiotic stress,cadmium:quantity 0.2mM . After 5 days of grown in a fresh medium (5% PCV at day0), CdCl2 was added to tested cells (Cad) to a final concentration of 200(u)M. Nothing was added to control cells (Tem). After 12 and 24 hours of growth +/- cadmium, cells were harvested and frozen in liquid nitrogen.

value: CdCl2 was added to tested cells (Cad) to a final concentration of 200(u)M. After 24 hours of growth +/- cadmium cells were harvested.


title: BLCL_2.2

source_name: EBV-transformed lymphoblastoid cell line from subject 2.2


title: BLCL_2.1

source_name: EBV-transformed lymphoblastoid cell line from subject 2.1


title: 13415174 - Control 24h 1 vs Cadmium 24h 1

hyb_protocol: Cadmium 24h 1 Cy5 / Control 24h 1 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: 13415179 - Control 24h 2 vs Cadmium 24h 2

hyb_protocol: Cadmium 24h 2 Cy5 / Control 24h 2 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: Cadmium 24h 2

extract_protocol: Cadmium 24h 2:55ug. (RNA_extraction-protocol.doc)

source_name: Control 24h 2

extract_protocol: Control 24h 2:43ug. (RNA_extraction-protocol.doc)


title: 13415175 - Cadmium 12h 2 vs Control 12h 2

hyb_protocol: Control 12h 2 Cy5 / Cadmium 12h 2 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 12h 2

extract_protocol: Control 12h 2:80ug. (RNA_extraction-protocol.doc)

source_name: Cadmium 12h 2

extract_protocol: Cadmium 12h 2:77ug. (RNA_extraction-protocol.doc)

value: CdCl2 was added to tested cells (Cad) to a final concentration of 200(u)M. After 12 hours of growth +/- cadmium cells were harvested.


title: 13415172 - Control 12h 2 vs Cadmium 12h 2

hyb_protocol: Cadmium 12h 2 Cy5 / Control 12h 2 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: 13415171 - Cadmium 12h 1 vs Control 12h 1

hyb_protocol: Control 12h 1 Cy5 / Cadmium 12h 1 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 12h 1

extract_protocol: Control 12h 1:74ug. (RNA_extraction-protocol.doc)

source_name: Cadmium 12h 1

extract_protocol: Cadmium 12h 1:77ug. (RNA_extraction-protocol.doc)


title: 13281470 - ca1Xca2-1 vs wt1

description: Identification of genes differentially expressed in leaves of single CA1 and CA2 T-DNA insertional mutants and in the corresponding double mutant vs wild type

hyb_protocol: wt1 Cy5 / ca1Xca2-1 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.

growth_protocol: rosette - Media : Soil hygrometry : 65% day, 50% night Temperature : 22°C Day, 18°C night Light : 370 umol.m-2.s-1, 8 hours/day

value: wild type

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

value: mutant (carbonic anhydrases double mutant)


title: 13281471 - wt1 vs ca1Xca2-1

hyb_protocol: ca1Xca2-1 Cy5 / wt1 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: 13281472 - ca2-2 vs wt2

hyb_protocol: wt2 Cy5 / ca2-2 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.

value: mutant (carbonic anhydrase ca2 mutant)


title: 13281481 - ca1Xca2-2 vs wt2

hyb_protocol: wt2 Cy5 / ca1Xca2-2 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: 13415177 - Cadmium 24h 2 vs Control 24h 2

hyb_protocol: Control 24h 2 Cy5 / Cadmium 24h 2 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: 13281462 - wt1 vs ca1-1

hyb_protocol: ca1-1 Cy5 / wt1 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: 13281458 - ca2-1 vs wt1

hyb_protocol: wt1 Cy5 / ca2-1 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: 13281473 - wt2 vs ca2-2

hyb_protocol: ca2-2 Cy5 / wt2 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: 13281460 - ca1-1 vs wt1

hyb_protocol: wt1 Cy5 / ca1-1 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: 13281482 - wt2 vs ca1Xca2-2

hyb_protocol: ca1Xca2-2 Cy5 / wt2 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: 13281459 - wt1 vs ca2-1

hyb_protocol: ca2-1 Cy5 / wt1 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: HUVEC_VEGF 48 hour

city: Toon-shi

first: Hidetaka

last: Ohnuki

state: Ehime

address: Shitsukawa

department: Department of Biochemistry and Molecular Genetics

institute: Ehime University

hyb_protocol: Cy5 labeled aRNA was hybridized to the custum array using MAUI HYB (BioMicro systems) at 50°C for 16 hours.

scan_protocol: The arrays were scanned at 5-mm resolution with a CRBIOIIe (Hitachi Solutions), images of the hybridized arrays were processed with DNASIS Array ImageScanner  (Hitachi Solutions) and signal intensities quantified

data_processing: Initial data analysis for each chip was performed using DNASIS-Array software (Hitachi Solutions). We used a software "DNASIS array" to generate 'Normalized total signal intensity'.

source_name: Human umbilical vein endothelial cells

label_protocol: cDNA was synthesized and purified, and amino allyl-labeledRNA was synthesized using an Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).  Subsequently, the purified, amino allyl modifed aRNA was fragmented into 50-150-nucleotide fragments. Fragmented amino allyl aRNA (5 mg) reacted with Cy5 mono-reactive dye (Amersham Biosciences) according to the manufacute’s protocol.

growth_protocol: HUVEC were cultured with MCDB131 medium (Gibco) containing 10% fetal bovine serum, basic FGF (10 ng/ml), heparin (18 U/ml), L-glutamine (2 mM), hydrocortisone (1 mg/ml), amphotericine B (250 ng/ml), streptmycin (100 mg/ml) and penicillin (100 U/ml).

extract_protocol: After treatments, HUVEC were collected using TRIzol regent (Invitrogen). Total RNA was prepared according the manufacture's protocol.

treatment_protocol: Before a treatment of 50 ng/ml VEGF-A (recombinant human VEGF165 protein) (R&D systems), HUVEC were serum-starved for 12 hours.

value: Human umbilical vein endothelial cells

tag: agent

tag: time point

value: 48 hour


title: HUVEC_VEGF 6 hour

value: 6 hour


title: 13281477 - wt2 vs ca1-2

hyb_protocol: ca1-2 Cy5 / wt2 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.

value: mutant (carbonic anhydrase ca1 mutant)

tag: age


title: HUVEC_VEGF 12 hour

value: 12 hour


title: HUVEC_VEGF 0 hour

data_processing: Initial data analysis for each chip was performed using DNASIS-Array software (Hitachi Solutions). We used a software "DNASIS array" to generate 'Normalized total signal intensity'. We used a software "DNASIS array" to generate 'Normalized total signal intensity'.

value: 0 hour


title: HUVEC_VEGF 2 hour

value: 2 hour


title: HUVEC_VEGF 1 hour

value: 1 hour


title: HUVEC_VEGF 24 hour

value: 24 hour


title: 13415176 - Control 12h 1 vs Cadmium 12h 1

hyb_protocol: Cadmium 12h 1 Cy5 / Control 12h 1 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: 6C-secondary-day25-suspension

city: Toronto

first: David

last: Fluri

address: 160 College Street

institute: University of Toronto

hyb_protocol: Samples were hybridized and washed using FS450_0007 protocol

scan_protocol: Affimetrix GeneChip Scanner 3000

data_processing: Data was processed using Affimetrix Expression Console (RMA normalization)

label_protocol: Ambion Wt Kit

growth_protocol: cells were reprogrammed in standard cell culture conditions

extract_protocol: total RNA was extracted using the QIAGEN RNAeasy extraction kit according to the manufacturer's protocol

treatment_protocol: cells were treated with doxycycline at day 0 to induce reprogramming

tag: strain background

value: mixed (mainly R1 and ICR)

tag: tissue

value: secondary mouse embryonic fibroblasts

value: suspension cells


title: 6C-secondary-day15-suspension


title: 6C-secondary-day6-suspension