title: 13969467 - V2TS repet1 vs. LUC repet1

hyb_protocol: LUC repet1 Cy5 / V2TS repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: GFP-EtOH, biological rep1

status: Public on Jan 07 2011

type: RNA

city: Philadelphia

first: Clay

last: Comstock

state: PA

department: Dept Cancer Biology

country: USA

institute: Thomas Jefferson University/Kimmel Cancer Center

description: LNCaP passage number was 38

hyb_protocol: 20ug labeled extract was hybridized 16hrs at 45degrees while rotating in a Affymetrix GeneChip Hybridization Oven 640; washed with an Affymetrix Fluidics Station 450; stain: Molecular Probes R-Phycoerythrin Streptavidin, antibody: Vector Laboratories Anti-Streptavidin (goat) biotinylated.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000, CEL files were generated using Affymetrix Microarray Suite 5.0.

data_processing: Individual samples were normalized using the Robust Multichip Analysis (RMA) algorithm in Bioconductor/R and refined using a Custom Definition File (CDF: Hs133 REFSEQ v8). Following RMA normalization, the data was transformed from log 2 to linear values and measurements less than 0.01 were set to 0.01. Per chip normalization was applied: normalize to 50th percentile and per gene normalization was applied: normalize to control samples.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP Cell Culture

label_protocol: Affymetrix Genechip Expression 3' Amplification On-Cyle Target Labeling and Control Reagents Kit was used to prepare biotin-labeled extracts.

growth_protocol: LNCaP cells were plated on poly-l-lysine in phenol red-free IMEM containing 5% charcoal-dextran treated serum 72hrs prior to treatment resulting in a G0/G1 growth arrest.

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

treatment_protocol: LNCaP cells were transduced with GFP- or CCND1-adenovirus then treated for 18hrs with 0.1% ethanol or 1nM DHT.

tag: cell line

value: LNCaP

tag: infection

value: Adenovirus (GFP)

tag: treatment

value: Ethanol


title: Jonasch_R58_Tumor_3-27-08_CMM

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from recesected ccRCC tumors.

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

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

data_processing: The data were analyzed with MBNI re-mapped CDF files, version 12. RMA calculated intensity from MBNI custom annotation with the affy R package.

label: biotin

source_name: tumor

label_protocol:
R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )
10 ug of Qiagen-purified total RNA

tag: disease state

value: ccRCC

tag: agent

value: B


title: CCND1-DHT, biological rep2

description: LNCaP passage number was 38

value: Adenovirus (CCND1)

value: DHT


title: Keratinocytes, DEX-treated 24h, rep2

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

description: dex-24hrs-exp II

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: MAS5 GCOS, RMAExpress summarized using PLM and log2 transformed.

source_name: Epidermal keratinocytes, dexamethasone-treated, 24h

label_protocol: Standard Affymetrix protocol.

growth_protocol: Standard growth protocol (e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642 (PMID 15145954)).

extract_protocol: Standard extraction protocol (e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642 (PMID 15145954)).

treatment_protocol: ~70% confluent keratinocytes were treated with 0.1μM DEX (Sigma).

tag: cell type

value: primary epidermal keratinocytes

value: dexamethasone

tag: treatment duration


title: 13969471 - V2TS repet3 vs. LUC repet3

status: Public on Jan 08 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Determine the level of expression in transgenic plants expressing geminviral gene silencing suppressors.

hyb_protocol: LUC repet3 Cy5 / V2TS repet3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the 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. Analyses were performed in R.

organism: Arabidopsis thaliana

source_name: LUC

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

growth_protocol: Whole plant. Media: MS + kanamycine. Hygrometry: not controlled. Temperature: 22ºC. Light: 16h light-8h darkness.

extract_protocol: LUC repet3:14.21ug. Extraction was performed using Trizol.

treatment_protocol: No treatment.

tag: ecotype

value: Columbia

tag: age

value: 20 days

tag: tissue

value: whole plant

tag: expressing

value: control

extract_protocol: V2TS repet3:15.09ug. Extraction was performed using Trizol.

value: geminiviral silencing suppressor V2


title: Jonasch_R60_Tumor_3-27-08_CMM


title: GFP-EtOH, biological rep3

description: LNCaP passage number was 38


title: Jonasch_R57_Tumor_3-27-08_CMM


title: 13969470 - LUC repet3 vs. V2TS repet3

hyb_protocol: V2TS repet3 Cy5 / LUC repet3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14089402 - Col0-GUS 1 vs. sgs1 1

description: Identification of new genes regulated by SGS1 and SGS6/UBP5 (two genes involved in PTGS) by analysis of the transcriptome of sgs1 and sgs6 mutants compared to wild-type plants in shoot of seedlings. The comparison between transcriptome of sgs3, chr11, chr17 simple mutants impaired differently in PTGS and development (juvenile-to-adult transition and bolting) and transcriptome of sgs3 chr11, sgs3 chr17 double mutants showing additive effect on development (juvenile-to-adult transition and bolting) would allowed a best understanding in genetic link existing between SGS3 and its potential partner, CHR11 (which interacts with SGS3 in two-hybrid and BiFC) and CHR17, 2 homologous proteins of the SWI / SNF2 family.

hyb_protocol: sgs1 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage, 480V,laser power 30%.

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

growth_protocol: Aerial. Media=MS. in vitro. Hygrometry=80%. Temperature=20°C. Light=23H-7H.

extract_protocol: sgs1 1:15ug. Qiagen RNeasy.

value: seedling shoots

tag: mutant

tag: developmental stage

value: Boyes 1.04 (Boyes et al. Plant Cell 2001)

extract_protocol: Col0-GUS 1:15ug. Qiagen RNeasy.

tag: genotype

value: wild-type


title: Cortex-Sham-Rep1_WT-MCAO

status: Public on Jan 10 2011

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Replicate 1
4421339018_E

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a pmt value=478

data_processing: The data were normalised using median normalisation with GeneSpring Ver 7.3

organism: Mus musculus

source_name: Infarct Cortex

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

growth_protocol: All animal procedures were approved by the Monash University Animal Ethics Committee. Male WT mice on a C57BL/6J background of 8–10 weeks were employed in this study. Gpx1-/- mice demonstrate no overt phenotype and there exist no differences in the cerebral vascular anatomy between the Gpx1-/- mice and their WT counterparts (Crack et al. 2001; de Haan et al. 1998).

extract_protocol: RNA was extracted and cleaned up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: WT mice underwent the mid-cerebral artery occlusion (MCAO) model of cerebral ischemia-reperfusion injury as previously mentioned (Connolly et al. 1996). In experiments examining biochemical end-points and infarct size, a 2-hour ischemic period was used. Reduction in cerebral blood flow upon intraluminal suture insertion was confirmed with laser Doppler. Control sham animals were subjected to the initial anesthetic and neck incision only. All animals were put back onto a 37°C heat pad post-surgery to recover from anesthesia. After 2-hour of ischemic period, the animals underwent reperfusion by withdrawal of the suture under anesthetic condition and return onto the heat pad until euthanized at the designated time-points of 2, 8 or 24 hours.

tag: strain

tag: genotype/variation

value: 8-10 weeks

value: sham

tag: treatment time-point

value: Ctrl


title: Keratinocytes, untreated 72h, rep2

description: Ctrl- 72hrs-exp II

source_name: Epidermal keratinocytes, untreated control, 72h


title: Keratinocytes, DEX-treated 1h, rep2

source_name: Epidermal keratinocytes, dexamethasone-treated, 1h


title: Keratinocytes, DEX-treated 4h, rep2

source_name: Epidermal keratinocytes, dexamethasone-treated, 4h


title: Jonasch_R55_Tumor_3-27-08_CMM

value: ccRCC


title: Keratinocytes, untreated 48h, rep2

source_name: Epidermal keratinocytes, untreated control, 48h


title: Keratinocytes, DEX-treated 72h, rep1

description: Dex-72hrs- Exp I

source_name: Epidermal keratinocytes, dexamethasone-treated, 72h


title: Keratinocytes, DEX-treated 48h, rep1

description: Dex-48hrs- expI

source_name: Epidermal keratinocytes, dexamethasone-treated, 48h


title: Keratinocytes, untreated 24h, rep2

description: Ctrl- 24hrs-exp II

source_name: Epidermal keratinocytes, untreated control, 24h


title: Keratinocytes, untreated 1h, rep2

description: ctrl-1hr-exp II

source_name: Epidermal keratinocytes, untreated control, 1h


title: Keratinocytes, untreated 4h, rep2

description: Ctrl- 4hrs-exp II

source_name: Epidermal keratinocytes, untreated control, 4h


title: Jonasch_R53_Tumor_3-27-08_CMM

value: B


title: Jonasch_R56_Tumor_3-27-08_CMM


title: Jonasch_R44_Tumor_3-27-08_CMM


title: Keratinocytes, DEX-treated 1h, rep1

description: Dex-1hr-exp I


title: Jonasch_R42_Tumor_3-27-08_CMM


title: Keratinocytes, untreated 72h, rep1

description: Ctrl-72hrs-exp I


title: Keratinocytes, untreated 24h, rep1

description: Ctrl-24hrs-exp I


title: Jonasch_R45_Tumor_3-27-08_CMM


title: Jonasch_R50_Tumor_3-27-08_CMM


title: Keratinocytes, untreated 48h, rep1

description: Ctrl 48hrs-exp I


title: Keratinocytes, untreated 4h, rep1

description: Ctrl-4hrs-exp I


title: Keratinocytes, DEX-treated 24h, rep1

description: Dex-24hrs-exp I


title: Jonasch_R52_Tumor_3-27-08_CMM


title: Keratinocytes, DEX-treated 4h, rep1

description: Dex-4hrs-Exp I


title: Keratinocytes, untreated 1h, rep1

description: Ctrl-1hr-exp I


title: Jonasch_R34_Tumor_3-27-08_CMM

value: BE


title: Jonasch_R40_Tumor_3-27-08_CMM


title: Jonasch_R36_Tumor_3-27-08_CMM


title: Jonasch_R32_Tumor_3-27-08_CMM


title: Jonasch_R38_Tumor_3-27-08_CMM


title: Jonasch_R25_Tumor_3-27-08_CMM


title: Jonasch_R28_Tumor_3-27-08_CMM


title: Jonasch_R30_Tumor_3-27-08_CMM


title: 13757372 - GUS polysome 7h repet1 vs. GUS total 7h repet1

description: The impact of the TOR pathway on growth and stress responses.

hyb_protocol: GUS total 7h repet1 Cy5 / GUS polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage 480V, laser power 30%.

source_name: GUS total 7h

growth_protocol: Seedling. Media=MS(1/5). Hygrometry=75%. Temperature=20°C.

extract_protocol: GUS total 7h repet1:40ug.

treatment_protocol: Name: Induction 7h - compound based treatment - compound addition, ethanol:time 7hour.  inducible RNAi

value: landsberg erecta

value: gus

tag: sample type

value: GUS control

value: seedling

value: Boyes 1.02 (Boyes et al. Plant Cell 2001)

tag: time

source_name: GUS polysome 7h

extract_protocol: GUS polysome 7h repet1:2ug.


title: Jonasch_R15_Tumor_3-27-08_CMM


title: Jonasch_R20_Tumor_3-27-08_CMM


title: Jonasch_R18_Tumor_3-27-08_CMM


title: 13832628 - Tor 6-3 polysome 7h repet2 vs. GUS polysome 7h repet2

hyb_protocol: GUS polysome 7h repet2 Cy5 / Tor 6-3 polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: GUS polysome 7h repet2:2ug.

source_name: Tor 6-3 polysome 7h

extract_protocol: Tor 6-3 polysome 7h repet2:2ug.

value: AtTor

value: tor RNAi mutant


title: 13832626 - Tor 6-3 total 7h repet2 vs. GUS total 7h repet2

hyb_protocol: GUS total 7h repet2 Cy5 / Tor 6-3 total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: GUS total 7h repet2:40ug.

source_name: Tor 6-3 total 7h

extract_protocol: Tor 6-3 total 7h repet2:40ug.


title: Jonasch_R22_Tumor_3-27-08_CMM

source_name: tumor


title: 13757371 - GUS total 7h repet1 vs. GUS polysome 7h repet1

hyb_protocol: GUS polysome 7h repet1 Cy5 / GUS total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Jonasch_R09_Tumor_3-27-08_CMM


title: 13832632 - Tor 5-2 polysome 7h repet2 vs. GUS polysome 7h repet2

hyb_protocol: GUS polysome 7h repet2 Cy5 / Tor 5-2 polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Tor 5-2 polysome 7h

extract_protocol: Tor 5-2 polysome 7h repet2:2ug.


title: Jonasch_R24_Tumor_3-27-08_CMM


title: 13832622 - GUS total 7h repet2 vs. Tor 5-2 total 7h repet2

hyb_protocol: Tor 5-2 total 7h repet2 Cy5 / GUS total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Tor 5-2 total 7h

extract_protocol: Tor 5-2 total 7h repet2:40ug.


title: Jonasch_R11_Tumor_3-27-08_CMM


title: Jonasch_R13_Tumor_3-27-08_CMM


title: 13832623 - Tor 5-2 total 7h repet2 vs. GUS total 7h repet2

hyb_protocol: GUS total 7h repet2 Cy5 / Tor 5-2 total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832621 - Tor 6-3 polysome 7h repet2 vs. Tor 6-3 total 7h repet2

hyb_protocol: Tor 6-3 total 7h repet2 Cy5 / Tor 6-3 polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Jonasch_R16_Tumor_3-27-08_CMM


title: 13832620 - Tor 6-3 total 7h repet2 vs. Tor 6-3 polysome 7h repet2

hyb_protocol: Tor 6-3 polysome 7h repet2 Cy5 / Tor 6-3 total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832624 - GUS total 7h repet2 vs. Tor 6-3 total 7h repet2

hyb_protocol: Tor 6-3 total 7h repet2 Cy5 / GUS total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Jonasch_R05_Tumor_3-27-08_CMM


title: 13832627 - GUS polysome 7h repet2 vs. Tor 5-2 polysome 7h repet2

hyb_protocol: Tor 5-2 polysome 7h repet2 Cy5 / GUS polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832629 - GUS polysome 7h repet2 vs. Tor 6-3 polysome 7h repet2

hyb_protocol: Tor 6-3 polysome 7h repet2 Cy5 / GUS polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Jonasch_R06_Tumor_3-27-08_CMM

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


title: 13832616 - GUS polysome 7h repet2 vs. GUS total 7h repet2

hyb_protocol: GUS total 7h repet2 Cy5 / GUS polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832619 - Tor 5-2 total 7h repet2 vs. Tor 5-2 polysome 7h repet2

hyb_protocol: Tor 5-2 polysome 7h repet2 Cy5 / Tor 5-2 total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832618 - Tor 5-2 polysome 7h repet2 vs. Tor 5-2 total 7h repet2

hyb_protocol: Tor 5-2 total 7h repet2 Cy5 / Tor 5-2 polysome 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NO in asf1-1clr3-735 cells

type: mixed

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled mononucleosomal DNA and Cy3-labeled  genomic DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_107_Sep09 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.

molecule: other

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: Mononucleosomal DNA or genomic DNA was labeled with Cy5 (mononucleosomal DNA) or Cy3 (genomic DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were spheroplasted and incubated with micrococcal nuclease. Mononucleosomal DNA were purified from agarose gel.

treatment_protocol: Exponentially growing cells were fixed in 1% formaldehyde at 30˚C.

molecule: genomic DNA


title: Jonasch_R03_Tumor_3-27-08_CMM


title: Jonasch_R01_Tumor_3-27-08_CMM


title: CF/T43: Cystic Fibrosis (CF) T43 Immortalized human airway (bronchial) epithelial cell line, replicate 3

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

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

tag: cell line

tag: Sex

value: unknown


title: CF/T43: Cystic Fibrosis (CF) T43 Immortalized human airway (bronchial) epithelial cell line, replicate 2

tag: disease state


title: 13757369 - Tor 5-2 polysome 7h repet1 vs. Tor 5-2 total 7h repet1

hyb_protocol: Tor 5-2 total 7h repet1 Cy5 / Tor 5-2 polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Tor 5-2 total 7h repet1:40ug.

extract_protocol: Tor 5-2 polysome 7h repet1:2ug.


title: BEAS-2B: Immortalized human airway (bronchial) epithelial cell line Rep 3

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


title: 13757368 - Tor 5-2 total 7h repet1 vs. Tor 5-2 polysome 7h repet1

hyb_protocol: Tor 5-2 polysome 7h repet1 Cy5 / Tor 5-2 total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NO in wild-type cells

tag: cell type


title: BEAS-2B: Immortalized human airway (bronchial) epithelial cell line Rep 1


title: C38 cells: Cystic Fibrosis (CF) immortalized human airway (bronchial) epithelial cell line expressing wtCFTR


title: NO in clr3-735 cells


title: LAN-5 NB cell Treated Day 5 Rep3

source_name: Treated Day 5

treatment_protocol: Human NB cell lines LAN-5 were incubated with 10 µM of all-trans retinoic acid or untreated as control, and total RNA harvested after 24 hours, 72 hours and 120 hours of exposure to retinoic acid.

value: neuroblastoma

value: unkown


title: LAN-5 NB cell Treated Day 5 Rep2


title: LAN-5 NB cell Treated Day 5 Rep1


title: 13757364 - GUS polysome 7h repet1 vs. Tor 5-2 polysome 7h repet1

hyb_protocol: Tor 5-2 polysome 7h repet1 Cy5 / GUS polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: BEAS-2B: Immortalized human airway (bronchial) epithelial cell line Rep 2


title: 13705713 - GUS total 7h repet1 vs. Tor 5-2 total 7h repet1

hyb_protocol: Tor 5-2 total 7h repet1 Cy5 / GUS total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756985 - Tor 6-3 polysome 7h repet1 vs. GUS polysome 7h repet1

hyb_protocol: GUS polysome 7h repet1 Cy5 / Tor 6-3 polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Tor 6-3 polysome 7h repet1:2ug.


title: LAN-5 NB cell Treated Day 3 Rep3

source_name: Treated Day 3


title: 13705712 - Tor 6-3 total 7h repet1 vs. GUS total 7h repet1

hyb_protocol: GUS total 7h repet1 Cy5 / Tor 6-3 total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Tor 6-3 total 7h repet1:40ug.


title: 13756917 - Tor 5-2 total 7h repet1 vs. GUS total 7h repet1

hyb_protocol: GUS total 7h repet1 Cy5 / Tor 5-2 total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757370 - Tor 5-2 polysome 7h repet1 vs. GUS polysome 7h repet1

hyb_protocol: GUS polysome 7h repet1 Cy5 / Tor 5-2 polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756984 - GUS polysome 7h repet1 vs. Tor 6-3 polysome 7h repet1

hyb_protocol: Tor 6-3 polysome 7h repet1 Cy5 / GUS polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CF/T43: Cystic Fibrosis (CF) T43 Immortalized human airway (bronchial) epithelial cell line, replicate 1


title: 13832614 - GUS total 7h repet2 vs. GUS polysome 7h repet2

hyb_protocol: GUS polysome 7h repet2 Cy5 / GUS total 7h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757367 - Tor 6-3 polysome 7h repet1 vs. Tor 6-3 total 7h repet1

hyb_protocol: Tor 6-3 total 7h repet1 Cy5 / Tor 6-3 polysome 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: LAN-5 NB cell Treated Day 3 Rep1


title: LAN-5 NB cell Treated Day 3 Rep2


title: 13705711 - GUS total 7h repet1 vs. Tor 6-3 total 7h repet1

hyb_protocol: Tor 6-3 total 7h repet1 Cy5 / GUS total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757366 - Tor 6-3 total 7h repet1 vs. Tor 6-3 polysome 7h repet1

hyb_protocol: Tor 6-3 polysome 7h repet1 Cy5 / Tor 6-3 total 7h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Gliomatosis cerebri, NCH_1474

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

description: Primary gliomatosis cerebri vs. non-neoplastic adult brain tissue.

hyb_protocol: Purified tagged miRNA was hybridized to an epoxy-coated glass slide printed with miRNA probes in the antisense orientation. Purified tagged miRNA was diluted 1:1 in 2X Hybridization solution. The so-obtained mix was held at the hybridization temperature (52°C) until loading the array. After loading the array the chamber was sealed. Maintaining controlled humidity during hybridization is crucial for successful microarray experiments to prevent the slide from drying out. The hybridization chamber was placed in an incubator at 52°C, and incubated overnight (16–20 hours). Washing steps was performed as follows: array was washed in wash solution 1 (2X SSC/0.2% SDS) for 15 minutes at 50°C, in wash solution 2 (2X SSC) for 15 minutes at room temperature, and finally in wash solution 3 (0.2X SSC). Finally array was dried by centrifugation.

scan_protocol: After hybridization, arrays were scanned using a confocal laser scanner (Affymetrix 428 scanner) at a resolution of 10 um. Data from the laser scans were collected as graphics (.tiff format) for each channel. To maximize the dynamic range of microarrays, the same arrays were scanned using different photo-multiplier settings (PMT). The use of different intensities allows the quantification of both the high and low copy expressed genes.

data_processing: The images were combined and processed using the ScanAnalyze program (written by Michael Eisen, http://rana.Stanford.EDU/software/) and the positions on the images were assigned to grid coordinates for the matching of spot identity with average pixel intensity at that region. Background corrected, log converted intensity ratios were determined for each element of the array. The image processing analysis also extracted information regarding spot quality and assigned a quality score to each ratio measurement. The definition of the quality metric was based on the notion that unreliable data points usually result from weak target intensity, high local background, small target area, and inconsistent target intensity within a given target. Implementation of the quality metric enabled unified and universally applicable data filtering before downstream higher-level data analysis. ScanAlyze data was imported in GeneSpring and GenePattern for further elaboration (Silicon Genetics, Redwood City, CA). To import data a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. Parameters are not numerical but define the sample nature or tissue type. The normalization of each sample was performed dividing each signal intensity by the 50th- percentile of all genes in that array. The normalization of each gene between samples was performed on the median of signal intensity of that gene in the reference sample. Genes were also analyzed using GeneSpring for differential expression between sample classes. The software allow the data filtering upon signal intensity and detection value. To select differentially expressed genes we used several approaches: for two class matching we utilized the Scatter Plot selecting the genes with an expression fold >2. To identify differentially expressed genes in a multi class match we calculated the log2 of normalized data. In this way over-expressed genes was the ones with a value >0, while the down-expressed was the ones with a value <0. For statistical validation we used t-test with a p-value of 0.01.

source_name: gliomatosis cerebri tumour tissue

label_protocol: The labelling protocol consisted of two steps: a prehybridization target tagging and a post hybridization incubation with capture labelled reagents. The target was tagged with the following steps: 1. miRNAs were added of a poly(A) tail using a polyA polymerase; 2. a short  highly specific tag was ligated to each tailed miRNA using a bridging oligo. Following a purification, tagged miRNAs could be hybridized to the microarray.

extract_protocol: Total RNA was extracted from tissue using TRIZOL, after pulverizing the tissue in a stainless steel mortar and pestle that was chilled on liquid nitrogen. miRNA was isolated by PureLink™ miRNA Isolation Kit (Invitrogen) following manufacturer’s instructions.

value: gliomatosis cerebri

tag: sample

source_name: non-neoplastic adult brain tissue

value: brain

value: adult


title: Gliomatosis cerebri, NCH_1477


title: LAN-5 NB cell Treated Day 1 Rep1

source_name: Treated Day 1


title: LAN-5 NB cell Treated Day 1 Rep2


title: LAN-5 NB cell Treated Day 1 Rep3


title: LAN-5 NB cell Control Day 5 Rep2

source_name: Control Day 5


title: LAN-5 NB cell Control Day 5 Rep3


title: LAN-5 NB cell Control Day 5 Rep1


title: LAN-5 NB cell Control Day 3 Rep3

source_name: Control Day 3


title: NO in asf1-1 cells


title: Gliomatosis cerebri, NCH_1457


title: Gliomatosis cerebri, NCH_1448


title: Gliomatosis cerebri, NCH_1437


title: Gliomatosis cerebri, NCH_1443


title: Gliomatosis cerebri, NCH_1461


title: Gliomatosis cerebri, NCH_1441


title: Gliomatosis cerebri, NCH_1436


title: Gliomatosis cerebri, NCH_1429


title: LAN-5 NB cell Control Day 1 Rep2

source_name: Control Day 1


title: LAN-5 NB cell Control Day 1 Rep3


title: Gliomatosis cerebri, NCH_1420


title: LAN-5 NB cell Control Day 3 Rep1


title: Gliomatosis cerebri, NCH_1428


title: LAN-5 NB cell Control Day 3 Rep2


title: Gliomatosis cerebri, NCH_1432


title: Gliomatosis cerebri, NCH_1419


title: Gliomatosis cerebri, NCH_1410


title: LAN-5 NB cell Control Day 1 Rep1


title: Gliomatosis cerebri, NCH_1413


title: Primary IgG Plasma cell:Primary IgG Plasma cell, replicate #2

source_name: CD19+ B Cell

value: Unknown

value: wild-type

value: healthy


title: Gliomatosis cerebri, NCH_1409


title: Primary IgG Plasma cell:Primary IgG Plasma cell, replicate #1


title: CD8 T cells Day 15

source_name: CD8 T cells Day 15

value: P14 TCR transgenic


title: Normal B-cell:CD19+ B-Cell, replicate #2

source_name: Plasma Cell


title: CD8 T cells Memory (>Day 40)

source_name: CD8 T cells Memory (>Day 40)


title: Gliomatosis cerebri, NCH_1397


title: Normal B-Cell:CD19+ B cell, replicate #1


title: Gliomatosis cerebri, NCH_1396


title: Gliomatosis cerebri, NCH_1399


title: CD8 T cells Day 8

source_name: CD8 T cells Day 8


title: Gliomatosis cerebri, NCH_1398


title: Gliomatosis cerebri, NCH_1386


title: CD8 T cells Naive

source_name: CD8 T cells Naive


title: Gliomatosis cerebri, NCH_1384


title: CD8+ Lymphocyte, Activated with IL2/IL4, replicate #3

source_name: CD8 Lymphocytes activated with IL2/IL4

treatment_protocol: In brief, the experimental protocol is as follows: splenocytes are isolated from C57Bl/6 mice (6-10 wks old) and cultured for 0, 24, 48 and 72 hrs. Cultures containe either anti-CD3/IL2/IL4 or anti-IgM/IL4 to activate T cells and B cells respectively. At each time point, B, CD4+ and CD8+ cells are purified by positive selection using magnetic beads and total RNA is prepared from each cell type.

value: 3 months


title: CD8+ Lymphocyte, Activated with IL2/IL4, replicate #1


title: CD8+ Lymphocyte, Activated with IL2/IL12, replicate #3

source_name: CD8 Lymphocytes activated with IL2/IL12


title: CD8+ Lymphocyte, Activated with IL2/IL12, replicate #2


title: CD8+ Lymphocyte, Activated with IL2/IL4, replicate #2


title: CD8 T cells Day 22

source_name: CD8 T cells Day 22


title: Gliomatosis cerebri, NCH_1380


title: Gliomatosis cerebri, NCH_1383


title: Gliomatosis cerebri, NCH_1381


title: 13969993 - Tor 5-2 total 24h repet1 vs. GUS total 24h repet1

hyb_protocol: GUS total 24h repet1 Cy5 / Tor 5-2 total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: GUS total 24h

extract_protocol: GUS total 24h repet1:40ug. (Extraction-ARNs-totaux.doc)

treatment_protocol: Name: Induction 24h - compound based treatment - compound addition, ethanol:time 24hour. inducible RNAi

tag: ecotype

value: landsberg erecta

value: gus

source_name: Tor 5-2 total 24h

extract_protocol: Tor 5-2 total 24h repet1:40ug.


title: CD8+ Lymphocyte, Activated with IL2/IL12, replicate #1

tag: age


title: Gliomatosis cerebri, NCH_1379

source_name: gliomatosis cerebri tumour tissue

tag: tissue


title: Gliomatosis cerebri, NCH_1390

source_name: non-neoplastic adult brain tissue


title: 13969992 - GUS total 24h repet1 vs. Tor 5-2 total 24h repet1

hyb_protocol: Tor 5-2 total 24h repet1 Cy5 / GUS total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: seedling

value: GUS control


title: Gliomatosis cerebri, NCH_1377


title: CD8+ Lymphocyte, Activated with IL2, replicate #3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: CD8 Lymphocytes activated with IL2


title: 13969995 - Tor 6-3 total 24h repet1 vs. GUS total 24h repet1

hyb_protocol: GUS total 24h repet1 Cy5 / Tor 6-3 total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Boyes 1.02 (Boyes et al. Plant Cell 2001)

source_name: Tor 6-3 total 24h

extract_protocol: Tor 6-3 total 24h repet1:40ug.

value: AtTor


title: Gliomatosis cerebri, NCH_1374


title: Gliomatosis cerebri, NCH_1375


title: Gliomatosis cerebri, NCH_1368


title: CD8+ Lymphocyte, fresh, replicate #3

source_name: Unactivated CD8 lymphocytes

value: unknown


title: 13970195 - Tor 6-3 total 24h repet1 vs. GUS total 24h repet1

value: tor RNAi mutant


title: 13970194 - GUS total 24h repet1 vs. Tor 6-3 total 24h repet1

hyb_protocol: Tor 6-3 total 24h repet1 Cy5 / GUS total 24h repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD8+ Lymphocyte, Activated with IL2, replicate #2


title: CD8+ Lymphocyte, Activated with IL2, replicate #1


title: 13970193 - Tor 5-2 total 24h repet1 vs. GUS total 24h repet1


title: 13970192 - GUS total 24h repet1 vs. Tor 5-2 total 24h repet1


title: Gliomatosis cerebri, NCH_1367


title: Gliomatosis cerebri, NCH_1362


title: Gliomatosis cerebri, NCH_1376


title: CD4+ Lymphocyte, Activated with IL2/IL4, replicate #3

source_name: CD4 Lymphocytes activated with IL2/IL4


title: CD8+ Lymphocyte, fresh, replicate #1


title: Gliomatosis cerebri, NCH_1355


title: CD4+ Lymphocyte, Activated with IL2/IL4, replicate #2


title: CD8+ Lymphocyte, fresh, replicate #2


title: 13970189 - GUS total 24h repet1 vs. Tor 5-2 total 24h repet1


title: 13970191 - Tor 5-2 total 24h repet1 vs. GUS total 24h repet1


title: 13969994 - GUS total 24h repet1 vs. Tor 6-3 total 24h repet1


title: 13970188 - Tor 6-3 total 24h repet1 vs. GUS total 24h repet1


title: 279 Smad1 CKO

city: Los Angeles

first: Wei

last: Shi

address: 4650 Sunset Boulevard

department: Surgery

institute: Children's Hospital Los Angeles

description: GSM651589_G279-A-Mouse430_2-01-1_28-5E_.CEL

hyb_protocol: According to standard Affymetrix protocol: hybridize with GeneChip Mouse Genome 430A 2.0 arrays

scan_protocol: Images were acquired by using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Data were analyzed using a RMA method to perform background adjustment and quantitative normalization (Bolstad et al., 2003).

source_name: mouse embryonic lung knockout

label_protocol: According to standard Affymetrix protocol: biotinylated cRNA

growth_protocol: E18.5 mouse embryonic lung

extract_protocol: isolated using RNeasy kit (Qiagen)

value: lung, left lobe

value: Smad1 CKO


title: 13970187 - GUS total 24h repet1 vs. Tor 6-3 total 24h repet1


title: 278 wild type

description: GSM651588_G278-A-Mouse430_2-01-1_28-3C_.CEL

source_name: mouse embryonic lung wildtype

value: wild type


title: 639 Smad1 CKO

description: GSM651587_F639-A-Mouse430_2-01-1_Knockout-lung_.CEL


title: 638 wild type

description: GSM651586_F638-A-Mouse430_2-01-1_Control-lung_.CEL


title: 603 Smad1 CKO

description: GSM651585_E603-A-Mouse430_2-01-1_72-2_.CEL


title: Gliomatosis cerebri, NCH_1349

value: gliomatosis cerebri

value: brain

value: adult


title: CD4+ Lymphocyte, Activated with IL2/IL4, replicate #1

value: wild-type

value: healthy


title: CD4+ Lymphocyte, Activated with IL2/IL12, replicate #2

source_name: CD4 Lymphocytes activated with IL2/IL12

value: 3 months


title: CD4+ Lymphocyte, Activated with IL2/IL12, replicate #3


title: CD4+ Lymphocyte, Activated with IL2/IL12, replicate #1


title: 13970204 - GUS polysome 24h repet2 vs. Tor 6-3 polysome 24h repet2

hyb_protocol: Tor 6-3 polysome 24h repet2 Cy5 / GUS polysome 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Tor 6-3 polysome 24h

extract_protocol: Tor 6-3 polysome 24h repet2:2ug.

value: landsberg erecta

source_name: GUS polysome 24h

extract_protocol: GUS polysome 24h repet2:2ug.


title: 13970205 - Tor 6-3 polysome 24h repet2 vs. GUS polysome 24h repet2

hyb_protocol: GUS polysome 24h repet2 Cy5 / Tor 6-3 polysome 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: gus


title: CD4+ Lymphocyte, Activated with IL2, replicate #2

source_name: CD4 Lymphocytes activated with IL2


title: CD4+ Lymphocyte, Activated with IL2, replicate #3


title: 13970203 - Tor 5-2 polysome 24h repet2 vs. GUS polysome 24h repet2

hyb_protocol: GUS polysome 24h repet2 Cy5 / Tor 5-2 polysome 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: seedling

source_name: Tor 5-2 polysome 24h

extract_protocol: Tor 5-2 polysome 24h repet2:2ug.


title: 13970202 - GUS polysome 24h repet2 vs. Tor 5-2 polysome 24h repet2

hyb_protocol: Tor 5-2 polysome 24h repet2 Cy5 / GUS polysome 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: GUS control


title: SETDB1-2.121009

city: Karp 7

first: Yariv

last: Houvras

state: MA

address: 1 Blackfan Circle

institute: Childrens Hospital Boston

description: Gene expression data from WM451-Lu melanoma cells after lentiviral infection with SETDB1 (experimental) virus.

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 and Affymetrix GeneChip Hybridization, Wash and Stain Kit according to the manufacturer's recommendations.

data_processing: The data were analyzed with Affymetrix Command Console using RMA.

source_name: WM451-Lu, SETDB1

label_protocol: Affymetrix GeneChip WT cDNA synthesis and amplification kit, and Affymetrix GeneChip WT terminal labeling kit, used according to the manufacturer's reccomendations.

growth_protocol: WM451-Lu melanoma short-term cultures were grown on gelatin-coated plates.

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

treatment_protocol: Lentiviral infections were performed for 24 hours. Total RNA was harvested after 48 hours.

value: melanoma

tag: lentiviral infection


title: SETDB1-3.121009


title: SETDB1-1.121009


title: CD4+ Lymphocyte, fresh, replicate #3

source_name: Unactivated CD4 lymphocytes


title: EGFP-2.121009

description: Gene expression data from WM451-Lu melanoma cells after lentiviral infection with GFP (control) virus.

source_name: WM451-Lu, GFP

value: GFP


title: CD4+ Lymphocyte, Activated with IL2, replicate #1

value: unknown


title: EGFP-1.121009


title: 13970200 - GUS total 24h repet2 vs. Tor 6-3 total 24h repet2

hyb_protocol: Tor 6-3 total 24h repet2 Cy5 / GUS total 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Tor 6-3 total 24h repet2:40ug.

value: AtTor

value: tor RNAi mutant

value: Boyes 1.02 (Boyes et al. Plant Cell 2001)

source_name: GUS total 24h

extract_protocol: GUS total 24h repet2:40ug.


title: EGFP-3.121009


title: Adult Lung_IL4RA-ko+IL13_rep1

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description:
SMP8_IL4RA-ko_1
Lungs isolated from mice that were treated with IL13 whose genotype was IL4R -/-, BALB/c background; replicate pool #1.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MOE 430 Plus 2.0 Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: RMA processing of CEL files, standard Affymetrix CDF.

source_name: adult mouse whole lung, IL4R KO

label_protocol: Standard Affymetrix labeling protocol to generate biotinylated cRNA applied to 2ug total RNA for MOE 430 plus 2.0 GeneChip.

growth_protocol: Microisolator housed mice in clean mouse facility.

treatment_protocol: Mice were treated with 2-3 micrograms of IL-13, intratracheally 1x/day x 7 days. Lungs were collected 24 hours after final administration.

tag: strain/background

value: BALB/c

value: whole lung

tag: il4r genotype

tag: smp8-il4r transgene

tag: treatment


title: 602 wild type

description: GSM651584_E602-A-Mouse430_2-01-1_72-1_.CEL

tag: strain

tag: developmental stage

value: lung, left lobe

tag: genotype/variation

value: wild type


title: Adult Lung_IL4RA-ko-SMP8-IL4RA-het+IL13_rep2

description:
SMP8_IL4RA-het_2
Lungs isolated from mice that were treated with IL13 whose genotype was IL4R -/-, SMP8-IL4R transgenic +/-, BALB/c background; replicate pool #2.

source_name: adult mouse whole lung, IL4R KO, SMP8-IL4R transgenic

value: adult


title: 13970199 - Tor 5-2 total 24h repet2 vs. GUS total 24h repet2

hyb_protocol: GUS total 24h repet2 Cy5 / Tor 5-2 total 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

tag: sample type

tag: time

source_name: Tor 5-2 total 24h

extract_protocol: Tor 5-2 total 24h repet2:40ug.


title: Adult Lung_wt1+IL13_rep1

description:
WT_1
Lungs isolated from mice that were treated with IL13 whose genotype was WT, BALB/c background; replicate pool #1.

source_name: adult mouse whole lung, WT


title: Adult Lung_IL4RA-ko+IL13_rep2

description:
SMP8_IL4RA-ko_2
Lungs isolated from mice that were treated with IL13 whose genotype was IL4R -/-, BALB/c background; replicate pool #2.


title: Adult Lung_IL4RA-ko-SMP8-IL4RA-het+IL13_rep1

description:
SMP8_IL4RA-het_1
Lungs isolated from mice that were treated with IL13 whose genotype was IL4R -/-, SMP8-IL4R transgenic +/-, BALB/c background; replicate pool #1.


title: Adult Lung_wt1+IL13_rep2

description:
WT_2
Lungs isolated from mice that were treated with IL13 whose genotype was WT, BALB/c background; replicate pool #2.


title: 13970201 - Tor 6-3 total 24h repet2 vs. GUS total 24h repet2

hyb_protocol: GUS total 24h repet2 Cy5 / Tor 6-3 total 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Tor 6-3 total 24h


title: 56 day Placebo: 592

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

country: Germany

institute: HelmholtzZentrum

description: Gene expression data from transplanted rat kidneys (56d post-transplantation)

hyb_protocol: We used standard Affymetrix procedures for hybridization

scan_protocol: Reactions were performed essentially according to the Affymetrix protocol.

data_processing: The resultant .CEL files were analyzed using the ChipInspector software V.0.92 (CI; Genomatix Software GmbH, Munich, Germany). CI does not supply probeset signal intensitites for individual arrays.  Processed log2 (placebo/control) ratio data provided as supplementary files on the Series record.

organism: Rattus norvegicus

source_name: transplanted kidney

label_protocol: Standard Affymetrix protocol.  20µg of total RNA were reverse-transcribed and used for biotinylation.

extract_protocol: Total RNA was isolated by the method of Chomczynski and Sacci. RNA quality was characterized using a RNA6000 Nanochip (Agilent

treatment_protocol:
transplantation protocol: Inbred male rats were purchased from Charles River Laboratories GmbH (Sulzfeld, Germany) and were used in all experiments. Kidney transplantation was performed by a modified technique originally described by Lee (1967) under general ether anaesthesia. Unlike the original model, the recipient's right kidney was left in place and no immunosuppressive agent was given, in order to enhance the contribution of rejection to CAD.
Rats were not treated with any medication including Cyclosporine A.

tag: Transplants

value: F344 RT1lvl

tag: Recipients

value: LEW RT1l


title: 56 day Placebo: 593


title: 13970198 - GUS total 24h repet2 vs. Tor 5-2 total 24h repet2

description: The impact of the TOR pathway on growth and stress responses.

hyb_protocol: Tor 5-2 total 24h repet2 Cy5 / GUS total 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: landsberg erecta


title: 56 day Placebo: 574


title: 56 day Placebo: 587


title: CD4+ Lymphocyte, fresh, replicate #1

tag: Sex

value: wild-type

tag: disease state

value: healthy

value: 3 months


title: 56 day Placebo: 572


title: B Cells, Activated with aIgM, replicate #3

source_name: B Cells activated with algM

tag: age


title: 14 day Placebo: 248

description: Gene expression data from transplanted rat kidneys (14d post-transplantation)


title: B Cells, Activated with aIgM, replicate #2


title: 14 day Placebo: 546


title: 13970197 - Tor 6-3 polysome 24h repet2 vs. Tor 6-3 total 24h repet2

hyb_protocol: Tor 6-3 total 24h repet2 Cy5 / Tor 6-3 polysome 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: tissue

value: seedling


title: 14 day Placebo: 246


title: 14 day Placebo: 531


title: 13970196 - Tor 6-3 total 24h repet2 vs. Tor 6-3 polysome 24h repet2

hyb_protocol: Tor 6-3 polysome 24h repet2 Cy5 / Tor 6-3 total 24h repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: B Cells, fresh, replicate #3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the scrGLYCO-v1GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Unactivated B Cells