title: day 2 post-exposure to S. mansoni (6) 13653201-D2-6

description:
day 2 post-exposure to S. mansoni (6)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

source_name: Biomphalaria glabrata injected with GFP specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia

source_name: Biomphalaria glabrata injected with FREP3 specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia


title: pupa workers of Solenopsis invicta from colony 3, sample no. 2

status: Public on Apr 01 2012

type: RNA

city: San Michele all'Adige

first: Lino

last: Ometto

state: Trento

address: Via Mach 1

department: Department of Biodiversity and Molecular Ecology

country: Italy

institute: Fondazione Edmund Mach

hyb_protocol: The combined Cy3- and Cy5-labeled probes were purified using the Qiaquick PCR Purification Kit (QIAGEN) and eluted in 82ul of elution buffer. We finally added 16.5ul of 20x standard saline citrate (SSC), 3.0ul of yeast transfer RNA (10 lg/ll), 1.8ul of polyA cDNA (2ug/ul; Sigma), and 1.8ul of 10% sodium dodecyl sulfate (SDS), then denatured this reaction mix at 95 °C for 45 s and hybridized to the microarray slides at 64 °C overnight (18–22 h). Excess probe was removed by washing the slides at room temperature twice for 5 min in a 2x SSC/0.1% SDS solution, twice for 1 min in a 0.2x SSC solution, 1 min in a 0.1x SSC solution, and twice for 5 min in a 0.1x SSC/0.1% Triton solution.

scan_protocol: slides were scanned using an Agilent Technologies Scanner

data_processing: signal intensities for each spot were extracted (low-quality spots were flagged and removed prior to analyses) using GenePix software. We used the software package limma to perform adaptive background correction, within-array print-tip loess normalization and between-array normalization of the intensities

molecule: total RNA

organism: Solenopsis invicta

source_name: pupa workers of Solenopsis invicta

label_protocol: Total RNA was amplified (Ambion MessageAmp II kit) and then an ~6ug aliquot of this amplified RNA was mixed with 2ul of random 9mers (2ug/ul), 0.5ul of Alien mRNA Spike mix (Stratagene), and water for a final volume of 17.9ul. The mix was incubated for 10 min at 70 °C, then held for 5 min on ice. Reverse transcription was performed for 2 h at 50 °C after adding 6ul of 5 first-strand buffer, 3ul of 0.1 M dithiothreitol, 0.6ul of 50X aminoallyl-deoxynucleotide triphosphate mix (25 mM deoxyadenosine triphosphate, 25 mM deoxycytidine triphosphate, 25 mM deoxyguanosine triphosphate, 15 mM deoxythymidine triphosphate, and 10 mM aminoallyl-deoxyuridine triphosphate), 0.5ul of RNAse inhibitor (15 U/ll, Invitrogen), and 2ul of SuperScript III reverse transcriptase (200 U/ml, Invitrogen). The residual RNA was hydrolyzed by adding 15ul of 0.1 M NaOH and incubating for 10 min at 70 °C. Subsequently, the pH was returned to neutrality by the addition of 15ul of 0.1 M HCl. The purification of the aminoallyl-labeled cDNA and the coupling to Cy3 or Cy5 dyes (GE Healthcare, Little Chalfont, UK) were done using a modified Qiaquick PCR Purification Kit (QIAGEN) protocol.

growth_protocol: All colonies were collected in the field between 2005 and 2007 and later returned to the laboratory and maintained in a rearing room under standard conditions (see Jouvenaz et al. 1977, The Florida Entomologist 60:275-279).

extract_protocol: ach pooled sample was promptly snap-frozen in liquid nitrogen in tubes containing 1 g of 1.4-mm ceramic beads (Quackenbush) and then homogenized in Trizol (Invitrogen) using a Retsch bead shaker. Both RNA and DNA were extracted according to the manufacturer’s protocol.

tag: caste

value: workers

tag: developmental stage

value: pupa

source_name: Solenopsis invicta common reference

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae


title: B. subtilis ywlE mcsB mutant_stationary phase_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 500 ng of Cy5-labeled cDNA and 500 ng of Cy3-labeled cDNA were hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies). The RNA/primer mixture was incubated at 70 °C for 10 min followed by 5 min incubation on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare) and 2µl of SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 60 min and then heated to 70 °C for 10 min. After 5 min on ice, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min. Labeled cDNA was then purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: B. subtilis 168 wild type, ywlE mutant and ywlE mcsB double mutant cells were grown under vigorous agitation at 37 °C in a defined medium described before (Stülke et al., 1993, J Gen Microbiol 139, 2041-2045).

extract_protocol: Total RNA was isolated by the acid phenol method as described (Majumdar et al., 1991, Biotechniques 11: 94-101).

treatment_protocol: Samples were taken at OD500 0.4 and 1h upon entry into stationary phase.

tag: strain

tag: sample type

value: reference

tag: genotype/variation

value: ywlE mcsB mutant

tag: phase

value: stationary


title: IDC 16S

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Hybridization was run for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640.  Following hybridization, the array was washed and stained on the GeneChip® Fluidics Station 450.

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000

data_processing:
Raw intensity files from the Affymetrix Human Exon 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 32, dated June 23rd, 2011.
HuGene-1_0-st-v1.r4.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

organism: Homo sapiens

source_name: IDC 16S

label_protocol: Amplified single-stranded cDNA was fragmented and labeled using the Encore™ cDNA Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

extract_protocol: Neoplastic epithelial cells and tumor stroma were laser capture microdissected using Leica LCM system (Leica Microsystems, Germany).  Total RNA was extracted using Qiagen microRNA kit.

tag: tissue compartment

value: stroma

tag: phenotype

value: invasive breast cancer

tag: subject

value: IDC 16


title: pupa workers of Solenopsis invicta from colony 2, sample no. 1


title: effect of GC-fed before SDS treatment rep3

city: Yokohama

first: Ritsuro

last: Ideta

address: 2-12-1 Fukuura, Kanazawa-ku

department: Functional Food Research & Development Center

country: Japan

institute: Shiseido Research Center

description: Biological replicate 3 of 3. 12 days after feeding with Gccontaine/non-GC diet, before SDS treatment

hyb_protocol: Two labeled cDNA samples, one from GC-fed mouse and the other from control-fed mouse were combined. For each hybridization, 825 ng of labeled cRNAs were mixed, fragmented, and hybridized at 65°C for 17 hours to an Agilent 4x44K Whole Mouse Genome Microarray (Agilent 14868) in Agilent's G2545A hybridization oven.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Feature extraction software version 9.1.3.1 (Agilent Technologies) was used to assess fluorescent hybridization signals and to normalize signals using linear regression and a Lowess curve-fit technique.
Genespring (Agilent) was used further data processing. Feature extraction software version 9.1.3.1 (Agilent Technologies) was used to assess fluorescent hybridization signals and to normalize signals using linear regression and a Lowess curve-fit technique.Flagged signals were eliminated. Since some genes have multiple probes on the Agilent platform, gene-level expression values were calculated by using the "Gene-level experiment" function in Genespring. Expression values below 200 were floored to 200. Processed signal values of GC-fed mice were divided by processed signal values of references, and these values were used as expression ratio data. Log base 2 of expression ratio (log ratio) was used for further analysis. Grubb's method was used to eliminate outliers.

organism: Mus musculus

source_name: non SDS treated, dorsal skin of GC-fed mouse

label_protocol: 500 ng of total RNA was reverse-transcribed to double-stranded cDNA using a poly dT-T7 promoter primer and MMLV-RT enzyme. cDNA products were used as templates for in vitro transcription to generate fluorescent cRNA using T7 RNA polymerase and Cy5-labeled or Cy3-labeled CTP. Labeled cRNAs were purified using QIAGEN RNeasy mini spin columns and eluted in nuclease-free water. cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 with Bioanalyzer.

growth_protocol: 5 weeks old male HR-1 mice were fed with GC-containing / non-containing AIN-93G (Oriental Yeast, Tokyo, Japan) rodent diet for 14 days.

extract_protocol: Total RNA extracted using Isogen. They were further purified using a RNeasy Fibrous Tissue Mini Kit (QIAGEN, Valencia, CA) following manufacturer's instructions.

treatment_protocol: The dorsal skin on the right side of each mouse was treated with 10% SDS for five minutes daily for two days.

tag: tissue

value: skin

tag: age

value: 5 weeks

tag: gender

value: male

source_name: non SDS treated, dorsal skin of control-fed mouse


title: MGUS_991

type: genomic

city: salamanca

first: Maria

middle: Eugenia

last: Sarasquete

state: salamanca

address: Paseo San Vicente 58-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca

description: Hybridized to Affymetrix 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G and AGCC

data_processing: The complete dataset was analyzed by visual inspection using the Genotyping Console 4.0 (Affymetrix) and Chromosome Analysis Suite (ChAS) software (Affymetrix).

molecule: genomic DNA

source_name: Bone Marrow MGUS patient

label_protocol: According to manufacturer’s instructions

extract_protocol: DNA from purified bone marrow plasma cells was extracted using commercially available kits (Allprep kit,Qiagen, Valencia, CA)

tag: cell type

value: Bone Marrow MGUS


title: B. subtilis ywlE mcsB mutant_stationary phase_rep2


title: effect of GC-fed before SDS treatment rep2

description: Biological replicate 2 of 3. 12 days after feeding with Gccontaine/non-GC diet, before SDS treatment


title: MGUS_821

description: Hybridized to Affymetrix 6.0


title: IDC 16E

source_name: IDC 16E

value: epithelium


title: MGUS_850

description: Hybridized to Affymetrix 6.0


title: pupa workers of Solenopsis invicta from colony 12, sample no. 1


title: DCIS 08S

source_name: DCIS 08S

value: ductal carcinoma in situ

value: DCIS 08


title: B. subtilis ywlE mcsB mutant_stationary phase_rep1


title: DCIS 08E

source_name: DCIS 08E


title: pupa workers of Solenopsis invicta from colony 25, sample no. 2

value: workers


title: B. subtilis ywlE mcsB mutant_exponential growth_rep3

value: exponential growth


title: pupa queens of Solenopsis invicta from colony 4, sample no. 2

source_name: pupa queens of Solenopsis invicta

value: queens

value: pupa

value: Mix of workers, queens and males


title: MGUS_727

description: Hybridized to Affymetrix 6.0


title: MGUS_779

description: Hybridized to Affymetrix 6.0


title: B. subtilis ywlE mcsB mutant_exponential growth_rep2

value: reference

value: ywlE mcsB mutant


title: pupa workers of Solenopsis invicta from colony 15, sample no. 1

value: Mix of adults, pupae and larvae


title: DCIS 06E

source_name: DCIS 06E

value: DCIS 06


title: MGUS_1124

description: Hybridized to Affymetrix 6.0


title: MGUS_721

description: Hybridized to Affymetrix 6.0


title: DCIS 02S

source_name: DCIS 02S

value: stroma

value: DCIS 02


title: pupa queens of Solenopsis invicta from colony 3, sample no. 1


title: DCIS 02E

source_name: DCIS 02E


title: B. subtilis ywlE mcsB mutant_exponential growth_rep1


title: MGUS_717

description: Hybridized to Affymetrix 6.0


title: pupa queens of Solenopsis invicta from colony 31, sample no. 1


title: MGUS_693

description: Hybridized to Affymetrix 6.0


title: B. subtilis ywlE mutant_stationary phase_rep3

value: ywlE mutant

value: stationary


title: IDC 15E

source_name: IDC 15E

value: invasive breast cancer

value: IDC 15


title: pupa queens of Solenopsis invicta from colony 25, sample no. 1


title: MGUS_403

description: Hybridized to Affymetrix 6.0

value: Bone Marrow MGUS


title: MGUS_683

description: Hybridized to Affymetrix 6.0


title: pupa queens of Solenopsis invicta from colony 15, sample no. 2


title: B. subtilis ywlE mutant_stationary phase_rep1


title: B. subtilis ywlE mutant_stationary phase_rep2


title: IDC 14E

source_name: IDC 14E

value: epithelium

value: IDC 14


title: pupa queens of Solenopsis invicta from colony 12, sample no. 1


title: MGUS_417

description: Hybridized to Affymetrix 6.0


title: effect of GC-fed before SDS treatment rep1

description: Biological replicate 1 of 3. 12 days after feeding with Gccontaine/non-GC diet, before SDS treatment

value: skin

value: 5 weeks

value: male


title: pupa males of Solenopsis invicta from colony 31, sample no. 1

source_name: pupa males of Solenopsis invicta

value: males

value: pupa

value: Mix of workers, queens and males


title: IDC 13E

source_name: IDC 13E

value: IDC 13


title: Sulfated polysaccharide - Fucoidan vs Glucose Replicate 3

city: Marburg (Lahn)

first: Carl-Eric

last: Wegner

address: Karl von Frisch Straße 10

institute: Max Planck Institute for Terrestrial Microbiology

description: Fucoidan - Biological Replicate 3

hyb_protocol: The hybridisation reaction inlcuding denaturing, hybridisation, washing and drying was done in a HS400 Pro Hybridisation station controlled by respective software (Tecan). Arrays have been blocked by pre-hybridisation buffer and blocking reagent. Differently labelled cDNA was pooled in DIG Easy Hyb hybridisation solution (Roche). After blocking, sample solutions were applied to the arrays followed by denaturation and hybridisation at stringent conditions for more than 12 hrs. ULTRArray low stringency wash buffer (Applied Biosystems) was used for final washing followed by drying.

scan_protocol: Scanner: ScanArray Express MicroArray scanner (Perkin Elmer) Images were quantified using ScanArray Express Software (version 4.0)

data_processing: LOWESS normalisation, MADA software was used (http://www.mpi-bremen.de/en/MADA), for downstream data processing MayDay was applied (http://www-ps.informatik.uni-tuebingen.de/mayday/wp/)

organism: Rhodopirellula baltica

source_name: Mid-exponential phase cultures

label_protocol: 5-10 µg of total RNA have been reverse transcribed using the SuperScript Direct cDNA labelling core kit (Applied Biosystems) following the manufacturers instructions. cDNA was purified using the QUIAEX II Gel extraction kit (Quiagen) according to the instructions described in the manual. Samples have been labelled applying the Platinum BrightTm Alexa 546 and 647 (Kreatech) nucleic acid labeling kits according to the manufacturers protocol.

growth_protocol: R. baltica SH1T was grown on marine mineral medium, supplemented with glucose as reference substrate or substrates of interest. Cultures have been grown to mid-exponential before being harvested. Collected cell material was shock-frozen and kept at -80 °C until being further processed.

extract_protocol: Total RNA was extracted using Ambion's TRI reagent and mechanical lysis following standard procedures.

tag: growth condition

value: glucose

value: fucoidan


title: IDC 07E

source_name: IDC 07E

value: IDC 07


title: Sulfated polysaccharide - Fucoidan vs Glucose Replicate 2

description: Fucoidan - Biological Replicate 2


title: MGUS_736

description: Hybridized to Affymetrix 6.0


title: DCIS 18E

source_name: DCIS 18E

value: ductal carcinoma in situ

value: DCIS 18


title: B. subtilis ywlE mutant_exponential growth_rep1

source_name: pooled RNA (equal amounts of RNA from all samples)

value: reference

value: ywlE mutant

value: exponential growth


title: B. subtilis wild type_stationary phase_rep3

source_name: B. subtilis wild type_stationary phase

value: wild type

value: stationary


title: IDC 04E

source_name: IDC 04E

value: epithelium

value: invasive breast cancer

value: IDC 04


title: B. subtilis ywlE mutant_exponential growth_rep3


title: pupa males of Solenopsis invicta from colony 25, sample no. 1

source_name: Solenopsis invicta common reference

value: Mix of adults, pupae and larvae

value: males


title: pupa males of Solenopsis invicta from colony 2, sample no. 1

value: pupa

value: Mix of workers, queens and males


title: Sulfated polysaccharide - Fucoidan vs Glucose Replicate 1

description: Fucoidan - Biological Replicate 1

value: glucose


title: JNK1-E2, estrogen treated, rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: See the Nimblegen website

hyb_protocol: See the NimbleGen website.

scan_protocol: See the NimbleGen website.

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

source_name: JNK1 ChIP, estrogen treated

label_protocol: See the NimbleGen website.

extract_protocol: MCF-7 breast cancer cells were grown to ~80 to 90% confluence, cross-linked with 10mM DMS in PBS for 10min. at room temp., and 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with antibodies against JNK1. The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.

tag: cell line

value: breast cancer cells

tag: treatment

tag: chip antibody

value: goat polyclonal JNK1 antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #

source_name: Input, estrogen treated


title: pupa males of Solenopsis invicta from colony 15, sample no. 2

tag: caste

tag: developmental stage


title: B. subtilis ywlE mutant_exponential growth_rep2

tag: strain

tag: sample type

tag: genotype/variation


title: DCIS 12E

source_name: DCIS 12E

tag: tissue compartment

tag: phenotype

value: ductal carcinoma in situ

value: DCIS 12


title: pupa males of Solenopsis invicta from colony 12, sample no. 1


title: Sulfated polysaccharide - Carrageenan vs Glucose Replicate 3

description: Carrageenan - Biological Replicate 3

value: carrageenan


title: B. subtilis wild type_stationary phase_rep2

value: reference

tag: phase


title: IDC 03E

source_name: IDC 03E

tag: subject

value: IDC 03


title: MGUS_800

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow MGUS patient

value: Bone Marrow MGUS


title: JNK1-U3A, untreated, rep3 (1 of 2)

description: See the Nimblegen website

source_name: JNK1 ChIP, untreated

value: ethanol control

source_name: Input, untreated


title: JNK1-U2, untreated, rep2

description: See the Nimblegen website


title: Sulfated polysaccharide - Carrageenan vs Glucose Replicate 2

description: Carrageenan - Biological Replicate 2


title: JNK1-U3B, untreated, rep3 (2 of 2)

description: See the Nimblegen website


title: B. subtilis wild type_exponential growth_rep3

value: wild type

value: exponential growth


title: DCIS 09E

source_name: DCIS 09E

value: epithelium

value: DCIS 09


title: JNK1-E3B, estrogen treated, rep3 (2 of 2)

description: See the Nimblegen website


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 9, sample no. 1

organism: Solenopsis invicta x Solenopsis richteri

value: workers

value: pupa

value: Mix of adults, pupae and larvae


title: Sulfated polysaccharide - Chondroitin sulfate vs Glucose Replicate 2

description: Chondroitin Sulfate - Biological Replicate 2

value: glucose

value: chondroitin sulfate


title: Sulfated polysaccharide - Carrageenan vs Glucose Replicate 1

description: Carrageenan - Biological Replicate 1


title: Sulfated polysaccharide - Chondroitin sulfate vs Glucose Replicate 1

description: Chondroitin Sulfate - Biological Replicate 1


title: DCIS 10E

source_name: DCIS 10E

value: DCIS 10


title: DCIS 11E

source_name: DCIS 11E

value: ductal carcinoma in situ

value: DCIS 11


title: DCIS 05E

source_name: DCIS 05E

value: DCIS 05


title: Control - Glucose vs. Glucose Replicate 2

description: Control - Biological Replicate 2

source_name: Mid-exponential phase cultures


title: B. subtilis wild type_exponential growth_rep1

value: reference


title: DCIS 01E

source_name: DCIS 01E

value: DCIS 01


title: JNK1-U1, untreated, rep 1

description: See the Nimblegen website

value: breast cancer cells

value: goat polyclonal JNK1 antibody

value: Santa Cruz


title: B. subtilis wild type_exponential growth_rep2

source_name: pooled RNA (equal amounts of RNA from all samples)

value: wild type

value: exponential growth


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 1

value: Mix of workers, queens and males


title: JNK1-E1, estrogen treated, rep1

description: See the Nimblegen website


title: Control - Glucose vs. Glucose Replicate 1

description: Control - Biological Replicate 1


title: IDC 14S

source_name: IDC 14S

value: stroma

value: invasive breast cancer

value: IDC 14


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 12, sample no. 1

value: Mix of adults, pupae and larvae

value: workers

value: pupa


title: IDC 13S

source_name: IDC 13S

value: IDC 13


title: MGUS_1359

description: Hybridized to Affymetrix 6.0

value: Bone Marrow MGUS


title: delta-env1_cellulose_LL_rep1

city: Vienna

first: Doris

last: Tisch

state: Vienna

address: Gumpendorferstraße 1a

department: Chemical Engineering

country: Austria

institute: Technical University of Vienna

description:
Trichoderma reesei
delta-env1_LL_rep1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trichoderma reesei

source_name: T. reesei delta-env1 grown on cellulose in light

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Trichoderma reesei delta-blr1, delta-blr2 and delta-env1 strains were grown in 1 l Erlenmeyer flasks on a rotary shaker (200 rpm) at 28°C in Mandels-Andreotti minimal medium with 1% microcrystalline cellulose as carbon source in constant light (LL) or constant darkness (DD) for 72 hours.

extract_protocol: Total RNA was extracted as described in Tisch et al., 2011 (New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol, 48 (6): 631 – 40) with supplies provided by the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The quality of the RNA was controlled with the Experion Automated Electrophoresis System (Bio-Rad, Hercules, USA). Total RNA was treated with DNase (Fermentas, Vilnius, Lithuania) and purified using the RNeasy Mini Kit (QIAGEN). cDNA synthesis was done with the RevertAid H- First Strand cDNA Synthesis Kit (Fermentas) and Oligo-d(T) Primer.

treatment_protocol: Mycelium was harvested under red-safety light when cultivated in darkness and frozen in liquid nitrogen.

tag: background strain

value: delta-env1 (reduced growth rate in light, expression induced in light)

tag: condition

value: light


title: DCIS 12S

source_name: DCIS 12S

value: ductal carcinoma in situ

value: DCIS 12


title: delta-env1_cellulose_LL_rep2

description:
Trichoderma reesei
delta-env1_LL_rep2


title: delta-env1_cellulose_DD_rep2

description:
Trichoderma reesei
delta-env1_DD_rep2

source_name: T. reesei delta-env1 grown on cellulose in darkness

value: darkness


title: delta-env1_cellulose_DD_rep1

description:
Trichoderma reesei
delta-env1_DD_rep1


title: delta-blr2_cellulose_DD_rep2

description:
Trichoderma reesei
delta-blr2_DD_rep2

source_name: T. reesei delta-blr2 grown on cellulose in darkness

value: delta-blr2 (blue light receptor 2 deficient mutant strain)


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 14, sample no. 1

source_name: Solenopsis invicta common reference

value: queens


title: delta-blr2_cellulose_DD_rep1

description:
Trichoderma reesei
delta-blr2_DD_rep1


title: DCIS 11S

source_name: DCIS 11S

value: DCIS 11


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1

value: Mix of workers, queens and males


title: DCIS 10S

source_name: DCIS 10S

value: stroma

value: DCIS 10


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 12, sample no. 1


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 2


title: DCIS 09S

source_name: DCIS 09S

value: DCIS 09


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 11, sample no. 1

value: Mix of adults, pupae and larvae


title: pupa males of Solenopsis invicta X Solenopsis richteri hybrid from colony 9, sample no. 1

value: males


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 1

value: pupa


title: IDC 07S

source_name: IDC 07S

value: invasive breast cancer

value: IDC 07


title: IDC 15S

source_name: IDC 15S

value: IDC 15


title: pupa queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1


title: JNK1-E3A, estrogen treated, rep3 (1 of 2)

description: See the Nimblegen website

source_name: JNK1 ChIP, estrogen treated

tag: cell type

value: breast cancer cells

value: goat polyclonal JNK1 antibody

value: Santa Cruz

source_name: Input, estrogen treated


title: IDC 04S

source_name: IDC 04S

value: IDC 04


title: delta-blr2_cellulose_LL_rep2

description:
Trichoderma reesei
delta-blr2_LL_rep2

source_name: T. reesei delta-blr2 grown on cellulose in light

value: delta-blr2 (blue light receptor 2 deficient mutant strain)

value: light


title: pupa males of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 1


city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
Raw data file:
US83203534_252800512102_S01_GE1_107_Sep09_1_3.txt
gene expression of Sca1+ muscle interstitial cells isolated from TSA treated MDX mice (45 days) replicate 2

hyb_protocol: As recommended by Agilent

scan_protocol: As suggested by Agilent using the illumina scanner

data_processing: Raw data filtered on the absent / detected flag calculated by the Agilent algorithum in GeneSpring GX11 (The data was normalized with quantiles).

label: streptavidin Cy3

source_name: Sca1+ muscle interstitial cells

label_protocol: As suggested by Agilent

growth_protocol: Cells where isolated from DMD/MDX mice using FACS (Fluorescence Activade Cell Sort); Sca1+ muscle interstitial cells were isolated as CD34+/a7-integrin+/Sca1+ while MuSC were isolated as CD34+/a7-integrin+/Sca1-

extract_protocol: total RNA was purified with Rneasy kit (Qiagen) following the manifacturers protocol

treatment_protocol: Mice were treated with TSA  (0.6 mg/Kg) or veichle for 45 days (i.p. injection)

value: DMD/MDX

tag: tissue

value: Muscle

tag: agent

value: TSA


title: delta-blr1_cellulose_DD_rep2

description:
Trichoderma reesei
delta-blr1_DD_replicate 2

source_name: T. reesei delta-blr1 grown on cellulose in darkness

value: delta-blr1 (blue light receptor 1 deficient mutant strain)

value: darkness


title: pupa males of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae


title: adult workers of Solenopsis richteri from colony 33, sample no. 2

organism: Solenopsis richteri

source_name: adult workers of Solenopsis richteri

value: workers

value: adult


description:
Raw data file:
US83203534_252800510534_S01_GE1_107_Sep09_2_1.txt
gene expression of Sca1+ muscle interstitial cells isolated from TSA treated MDX mice (45 days) replicate 1


title: DCIS 01S

source_name: DCIS 01S

value: stroma

value: ductal carcinoma in situ

value: DCIS 01


title: delta-blr2_cellulose_LL_rep1

description:
Trichoderma reesei
delta-blr2_LL_rep1


title: delta-blr1_cellulose_DD_rep1

description:
Trichoderma reesei
delta-blr1_DD_replicate 1


title: C57Bl6_3

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

description: normal adrenal tissue

hyb_protocol: Hybridisation to mouse 430_2 arrays was performed according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent).

data_processing: Signal intensities were RMA normalized using PARTEK Genomics Suite, with the .CEL files as input.

source_name: adrenal

label_protocol: Biotin labelling was performed according the manufacturer's recommendations (Affymetrix).

growth_protocol: Mice transgenic for neural crest specific expression of MYCN, mutated ALK or both were monitored until tumor was palpable and sacrificed afterwards.

extract_protocol: RNA was extracted from tumors or control tissue using the QIAGEN Rneasy mini kit.

value: adrenal

value: normal


title: B. subtilis wild type_stationary phase_rep1

source_name: pooled RNA (equal amounts of RNA from all samples)

value: reference

source_name: B. subtilis wild type_stationary phase

value: wild type

value: stationary


title: pupa males of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 1

source_name: Solenopsis invicta common reference

value: males

value: pupa


title: adult workers of Solenopsis richteri from colony 6, sample no. 1


title: delta-blr1_cellulose_LL_rep1

description:
Trichoderma reesei
delta-blr1_LL_replicate 1

source_name: T. reesei delta-blr1 grown on cellulose in light

value: light


title: 74129_wl

description: tumor driven by MYCN

source_name: tumor

value: tumor

value: MYCN


title: adult workers of Solenopsis richteri from colony 30, sample no. 2

value: Mix of workers, queens and males


title: adult workers of Solenopsis richteri from colony 19, sample no. 2

value: Mix of adults, pupae and larvae


description:
Raw data file:
US83203534_252800512102_S01_GE1_107_Sep09_1_2.txt
gene expression of Sca1+ muscle interstitial cells isolated from veichle treated MDX mice (45 days) replicate 2

value: DMD/MDX

value: Muscle

value: vehicle


title: DCIS 05S

source_name: DCIS 05S

value: stroma

value: ductal carcinoma in situ

value: DCIS 05


title: delta-blr1_cellulose_LL_rep2

description:
Trichoderma reesei
delta-blr1_LL_replicate 2

value: delta-blr1 (blue light receptor 1 deficient mutant strain)


title: IDC 03S

source_name: IDC 03S

value: invasive breast cancer

value: IDC 03


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 1

value: workers


description:
Raw data file:
US83203534_252800510534_S01_GE1_107_Sep09_1_3.txt
gene expression of Sca1+ muscle interstitial cells isolated from veichle treated MDX mice (45 days) replicate 1


title: adult workers of Solenopsis richteri from colony 11, sample no. 1

value: adult


title: 74128_wlr

description: tumor driven by MYCN


title: adult workers of Solenopsis richteri from colony 15, sample no. 2


title: 70660_lu

description: tumor driven by MYCN


title: adult queens of Solenopsis richteri from colony 33, sample no. 2

source_name: adult queens of Solenopsis richteri

value: queens


title: C57Bl6_1

description: normal adrenal tissue

value: adrenal

value: normal


title: adult queens of Solenopsis richteri from colony 30, sample no. 2


title: adult queens of Solenopsis richteri from colony 17, sample no. 2


title: 74128_wr

description: tumor driven by MYCN

value: tumor

value: MYCN


title: 66977_ru

description: tumor driven by mutALK

value: mutALK


title: E12.5 Ret-deficient embryonic kidney, biological rep2

first: Sanjay

middle: K.

last: Nigam

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California San Diego

description: Gene expression data from E12.5 whole embryonic kidney

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: mouse E12.5 embryonic kidney isolated from Ret-knockout pregnant female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA (Expression Analysis Technical Manual, 2011, Affymetrix)

growth_protocol: NA (tissue isolated and RNA extracted directly)

extract_protocol: RNA was extracted with the Qiagen RNEasy Micro kit according to the manufacturer's instructions.

treatment_protocol: Whole embryonic kidneys were isolated from E12.5 pregant female wild-type and knockout mice.

value: Ret Deficient

value: whole embryonic kidney

tag: age

value: gestational day 12.5 (E12.5)


title: adult males of Solenopsis richteri from colony 33, sample no. 1

source_name: adult males of Solenopsis richteri

value: males

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae


title: adult queens of Solenopsis richteri from colony 15, sample no. 2


title: adult queens of Solenopsis richteri from colony 19, sample no. 1


title: 66389_lo

description: tumor driven by mutALK


title: E12.5 wild-type embryonic kidney, biological rep3

source_name: mouse E12.5 embryonic kidney isolated from wild-type pregnant female

value: Wildtype


title: E12.5 Ret-deficient embryonic kidney, biological rep1


title: 66977_ro

description: tumor driven by mutALK


title: E12.5 wild-type embryonic kidney, biological rep1


title: E12.5 wild-type embryonic kidney, biological rep2


title: C57Bl6_2

description: normal adrenal tissue


title: iNSC_4_embryo

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

description:
Gene expression data
Sample name: Mouse-012

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450-0001.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data analysis was carried out by Expression Console 1.1 (Affymetrix). Detection and signal were obtained by MAS5 algorithm with default settings. Global normalization was performed to make average signal intensity of all probesets equal to 100.

source_name: Embryonic fibroblast derived neurosphere (+LIF+cAMP)

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

growth_protocol: Neurospheres were cultured in MHM. iPSC and ESC were cultured in standard conditions.

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

treatment_protocol: Neurospheres were cultured in various conditions.


title: adult males of Solenopsis richteri from colony 15, sample no. 1


title: adult males of Solenopsis richteri from colony 30, sample no. 1


title: pupa workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 14, sample no. 1

value: pupa


title: adult males of Solenopsis richteri from colony 17, sample no. 2


title: adult males of Solenopsis richteri from colony 19, sample no. 1


title: iNSC_3_embryo

description:
Gene expression data
Sample name: Mouse-011

source_name: Embryonic fibroblast derived neurosphere (+LIF)


title: adult workers of Solenopsis invicta from colony 31, sample no. 1

source_name: adult workers of Solenopsis invicta


title: adult workers of Solenopsis invicta from colony 25, sample no. 2


title: adult workers of Solenopsis invicta from colony 2, sample no. 1


title: iNSC_1

description:
Gene expression data
Sample name: Mouse-006

source_name: Adult fibroblast-derived neurosphere (+EGF+cAMP)

value: neurosphere, adult fibroblast-derived


title: E12.5 Ret-deficient embryonic kidney, biological rep3


title: adult workers of Solenopsis invicta from colony 3, sample no. 2

value: workers


title: E14.5 Nanos2 KO Tg 3×FLAG-Nanos2-ΔN10 1

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

institute: National Institute of Genetics

description: Gene expression E14.5 mouse male gonad Nanos2 KO_Tg dN_Nanos2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: embryonic male gonad

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Embryonic male gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: gonad

tag: Sex

value: male

tag: genotype

value: Nanos2-/-_Tg 3×FLAG-tagged Nanos2-ΔN10

tag: genetic background

value: mixed ICR and N2


title: adult workers of Solenopsis invicta from colony 12, sample no. 2

tag: caste

tag: developmental stage

value: adult


title: iNSC_2

description:
Gene expression data
Sample name: Mouse-007

source_name: Adult fibroblast-derived neurosphere (+LIF)


title: adult workers of Solenopsis invicta from colony 15, sample no. 2


title: adult queens of Solenopsis invicta from colony 31, sample no. 2

source_name: adult queens of Solenopsis invicta

value: queens


title: adult queens of Solenopsis invicta from colony 4, sample no. 1


title: E14.5 Nanos2 KO Tg 3×FLAG-Nanos2-ΔN10 2


title: E14.5 Nanos2 Hetero 2

description: Gene expression E14.5 mouse male gonad Nanos2 hetero


title: HEM3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

hyb_protocol: Superamplified cDNA was hybridized according to the Agilent 60-mer oligo microarray processing protocol employing the Agilent Gene Expression Hybridization kit (Agilent Technologies) utilizing 1.25 μg Cy3-labeled fragmented cRNA on Agilent whole mouse genome oligo microarrays.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hematopoietic cell 3

label_protocol: Miltenyi Biotec Protocol

extract_protocol: The isolated cells were lysed in SuperAmp lysis buffer and stored at -80ºC according to the instructions of the SuperAmp Preparation kit (Miltenyi Biotec, Bergisch Gladbach, Germany). SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. The integrity of cDNA was checked using the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Palo Alto, CA). The average length of the library PCR products was 200–1000 bp.

treatment_protocol: C57BL/6JxDBA/2 F1 female mice were subjected to lethal irradiation and intravenously injected with bone marrow cells harvested from C57BL/6J-βactinEGFPxDBA/2 F1 male mice. The livers of female mice were injured with CCl4.  Liver individual cells were laser captured from frozen sections. Bone marrow derived hepatocytes (BMDH), hematopoietic cells, and hepatocytes, were analyzed individually.

tag: gender

value: female

tag: sample type

value: laser captured cells

tag: strain

value: hematopoietic cell


title: E14.5 Nanos2 KO 2

description: Gene expression E14.5 mouse male gonad Nanos2 KO


title: E14.5 Nanos2 Hetero 1


title: adult queens of Solenopsis invicta from colony 15, sample no. 2

source_name: Solenopsis invicta common reference


title: adult queens of Solenopsis invicta from colony 12, sample no. 1


title: E14.5 Nanos2 KO 1


description:
Raw data file:
US83203534_252800510534_S01_GE1_107_Sep09_1_2.txt
gene expression of MuSC cells isolated from veichle treated MDX mice (45 days) replicate 1

source_name: MuSc

tag: genotype/variation

value: DMD/MDX

value: Muscle

value: satellite cell (MuSC; CD34+/a7-integrin+/Sca1-)

value: vehicle


title: adult males of Solenopsis invicta from colony 31, sample no. 1

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae

source_name: adult males of Solenopsis invicta

value: males


title: HEP4

description: C57BL/6JxDBA/2 F1 female mice were subjected to lethal irradiation and intravenously injected with bone marrow cells harvested from C57BL/6J-βactinEGFPxDBA/2 F1 male mice. The livers of female mice were injured with CCl4.

source_name: Hepacocyte 4

value: hepacocyte


title: adult males of Solenopsis invicta from colony 4, sample no. 1


title: HEM1

source_name: Hematopoietic cell 1


title: adult males of Solenopsis invicta from colony 2, sample no. 2


title: HEP3

source_name: Hepacocyte 3


title: BMDH6

source_name: Bone marrow derived hepatocyte 6

value: bone marrow derived hepatocyte


title: BMDH5

source_name: Bone marrow derived hepatocyte 5


title: adult males of Solenopsis invicta from colony 12, sample no. 1


title: HEP1

source_name: Hepacocyte 1


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 9, sample no. 1

value: workers


title: BMDH4

source_name: Bone marrow derived hepatocyte 4


title: adult males of Solenopsis invicta from colony 15, sample no. 1


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 1


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1


title: BMDH7

source_name: Bone marrow derived hepatocyte 7


title: BMDH3

source_name: Bone marrow derived hepatocyte 3


title: HEM2

source_name: Hematopoietic cell 2


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 14, sample no. 1


title: adult queens of Solenopsis invicta from colony 3, sample no. 1


title: adult males of Solenopsis invicta from colony 25, sample no. 1


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 1


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 1


title: SHAM (Cy5) x PMCAO (Cy3) 24h

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of 24 h Brain Sample 2

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1

source_name: Treatment Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Forty male mice (8 to 12-weeks-old, 25 ~ 35 g body weight) were housed at the Animal Institution in Showa University in acrylic cages (8 mice / cage) at 23ºC, and maintained with a standard 12 h light/dark cycle with optimum humidity and temperature control. All animals were given access to tap water and laboratory chow ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: PMCAO control 24 h

value: brain

tag: treatment

value: permanent middle cerebral artery occlusion

tag: time

source_name: Control Cy5

treatment_protocol: Saline control 24 h

value: sham


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 9, sample no. 3

value: queens

value: adult


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 2


title: SHAM (Cy5) x PMCAO (Cy3) 6h

description: Dye-swap (Cy5/Cy3) of 6 h Brain Sample 2

treatment_protocol: PMCAO control 6 h

treatment_protocol: Saline control 6 h


title: SHAM (Cy3) x PMCAO (Cy5) 6h

description: Dye-swap (Cy3/Cy5) of 6 h Brain Sample 1

source_name: Control Cy3

source_name: Treatment Cy5


title: Saline, lymph node pig ID 5

city: Uppsala

first: Viktor

last: Ahlberg

address: PO Box 588

department: Dept of Biomedical Sciences and Veterinary Public Health

country: Sweden

institute: Swedish University of Agricultural Sciences

hyb_protocol: Affymetrix GeneChip® expression arrays (Porcine Genome Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 7G

data_processing: Analysis was performed in R using Bioconductor packages. Normalization using RMA. Differentially expressed genes was calculated using Bayes moderated t-test (limma package) and false-discovery rate was calculated using the method of Benjamini and Hochberg.

organism: Sus scrofa

source_name: Internal iliac lymph node (draining), 24 h post saline i.m. injection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit Manual).

extract_protocol: Combination of Trizol separation and subsequent purification with the E.Z.N.A Total RNA Kit

treatment_protocol: Samples were transfered to RNAlater and stored according to the manufacturer's instructions.

tag: breed

value: Yorkshire x Landrace

value: Castrated male

value: 11 weeks

value: Internal iliac lymph node (draining)

value: saline


title: Saline, lymph node pig ID 4


title: adult workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 11, sample no. 1

source_name: Solenopsis invicta common reference


title: Saline, lymph node pig ID 6


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 14, sample no. 2


title: adult males of Solenopsis invicta X Solenopsis richteri hybrid from colony 9, sample no. 1


title: ISCOM-Matrix, lymph node pig ID 2

source_name: Internal iliac lymph node (draining), 24 h post Matrix M i.m. injection

value: intramuscular ISCOM-Matrix vaccine adjuvant treatment


title: adult males of Solenopsis invicta X Solenopsis richteri hybrid from colony 4, sample no. 1

value: Mix of workers, queens and males


title: HCT116_mir-493_rep3

city: Chuo-ku

first: koji

last: okamoto

state: Tokyo

address: 5-1-1 Tsukiji

department: Division of Cancer Differentiation

institute: National Cancer Center Research Institute

description: Gene expression aftermir-493 transfection

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HCT116, mir-493, replicate 3

label_protocol: Cy3-labeled cRNA was prepared from 0.2 ug RNA using Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HCT116 cells were grown in DMEM medium supplemented with 10% heat-inactivated fetal calf serum.

extract_protocol: Total RNAs from the transfected HCT116 cells were extracted using miRNeasy mini kit (QIAGEN) according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer. RNA quality control was performed in 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: 2 x 105 of HCT116 cells were transfected with 4 pmol of control oligonucleotide or mir-493 mimic for 24 hrs.

tag: cell line

value: HCT116 cells


title: ISCOM-Matrix, lymph node pig ID 3


title: 716NT

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
716NT_B8.A

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

scan_protocol: see manufacturer's web site www.nimblegen.com

data_processing: HELP assay data analysis was performed using the published pipeline (Thompson, Reimers, Khulan, Gissot, Richmond, Chen, Zheng, Kim and Greally 2008), an open source resource available through BioConductor (HELP package). Quantile normalized, log2 HpaII/MspI ratio data is available on a Series records [Final_Qnormalized_ratio.txt]

source_name: LM-PCR products from HpaII digested DNA

label_protocol: The HELP samples were labeled for microarray analysis as described previously [Selzer, Genes Chromosomes Cancer 44:305–319] using Cy3 or Cy5-conjugated oligonucleotides and random primers.

extract_protocol: DNA was isolated using proteinase K digestion, phenol-chloroform extraction, dialysis against 0.2X SSC and concentration by surrounding the dialysis bag with PEG 20,000 to reduce water content by osmosis.  The quality of the DNA was checked by gel electrophoresis and spectrophotometry.

value: Lung

tag: phenotype

value: non-tumor

value: female

tag: tumor histology

value: adenocarcinoma (Ad)

tag: smoking status

value: Current

tag: restriction enzyme

value: HpaII

source_name: LM-PCR products from MspI digested DNA

value: MspI


title: 713T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
713T_B8.A

tag: tissue

value: tumor

value: Never


title: ISCOM-Matrix, lymph node pig ID 1

value: Yorkshire x Landrace

tag: age


title: Saline, muscle, pig ID 5

source_name: Biceps femoris, 24 h post saline injection

value: Castrated male

value: Biceps femoris


title: adult queens of Solenopsis invicta from colony 25, sample no. 2

city: San Michele all'Adige

first: Lino

last: Ometto

address: Via Mach 1

institute: Fondazione Edmund Mach

hyb_protocol: The combined Cy3- and Cy5-labeled probes were purified using the Qiaquick PCR Purification Kit (QIAGEN) and eluted in 82ul of elution buffer. We finally added 16.5ul of 20x standard saline citrate (SSC), 3.0ul of yeast transfer RNA (10 lg/ll), 1.8ul of polyA cDNA (2ug/ul; Sigma), and 1.8ul of 10% sodium dodecyl sulfate (SDS), then denatured this reaction mix at 95 °C for 45 s and hybridized to the microarray slides at 64 °C overnight (18–22 h). Excess probe was removed by washing the slides at room temperature twice for 5 min in a 2x SSC/0.1% SDS solution, twice for 1 min in a 0.2x SSC solution, 1 min in a 0.1x SSC solution, and twice for 5 min in a 0.1x SSC/0.1% Triton solution.

scan_protocol: slides were scanned using an Agilent Technologies Scanner

data_processing: signal intensities for each spot were extracted (low-quality spots were flagged and removed prior to analyses) using GenePix software. We used the software package limma to perform adaptive background correction, within-array print-tip loess normalization and between-array normalization of the intensities

label_protocol: Total RNA was amplified (Ambion MessageAmp II kit) and then an ~6ug aliquot of this amplified RNA was mixed with 2ul of random 9mers (2ug/ul), 0.5ul of Alien mRNA Spike mix (Stratagene), and water for a final volume of 17.9ul. The mix was incubated for 10 min at 70 °C, then held for 5 min on ice. Reverse transcription was performed for 2 h at 50 °C after adding 6ul of 5 first-strand buffer, 3ul of 0.1 M dithiothreitol, 0.6ul of 50X aminoallyl-deoxynucleotide triphosphate mix (25 mM deoxyadenosine triphosphate, 25 mM deoxycytidine triphosphate, 25 mM deoxyguanosine triphosphate, 15 mM deoxythymidine triphosphate, and 10 mM aminoallyl-deoxyuridine triphosphate), 0.5ul of RNAse inhibitor (15 U/ll, Invitrogen), and 2ul of SuperScript III reverse transcriptase (200 U/ml, Invitrogen). The residual RNA was hydrolyzed by adding 15ul of 0.1 M NaOH and incubating for 10 min at 70 °C. Subsequently, the pH was returned to neutrality by the addition of 15ul of 0.1 M HCl. The purification of the aminoallyl-labeled cDNA and the coupling to Cy3 or Cy5 dyes (GE Healthcare, Little Chalfont, UK) were done using a modified Qiaquick PCR Purification Kit (QIAGEN) protocol.

extract_protocol: ach pooled sample was promptly snap-frozen in liquid nitrogen in tubes containing 1 g of 1.4-mm ceramic beads (Quackenbush) and then homogenized in Trizol (Invitrogen) using a Retsch bead shaker. Both RNA and DNA were extracted according to the manufacturer’s protocol.

value: Mix of adults, pupae and larvae

source_name: adult queens of Solenopsis invicta

value: queens

value: adult


title: HCT116_mir-493_rep2

source_name: HCT116, mir-493, replicate 2


title: 716T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
716T_B8.A


title: Saline, muscle, pig ID 4

value: 11 weeks

value: saline


title: HCT116_mir-493_rep1

source_name: HCT116, mir-493, replicate 1

value: HCT116 cells


title: adult males of Solenopsis invicta X Solenopsis richteri hybrid from colony 13, sample no. 1

value: Mix of workers, queens and males

value: males


title: Saline, muscle, pig ID 6


title: HCT116_control_rep3

description: Gene expression after control transfection

source_name: HCT116, control, replicate 3


title: adult males of Solenopsis invicta X Solenopsis richteri hybrid from colony 17, sample no. 1


title: SHAM(Cy3) x PMCAO (Cy5) 24h

description: Dye-swap (Cy3/Cy5) of 24 h Brain Sample 1

value: brain

value: sham

value: permanent middle cerebral artery occlusion


title: 713NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
713NT_B8.A

value: Lung

value: non-tumor

value: female

value: adenocarcinoma (Ad)

value: HpaII

value: MspI


title: WT, Dark, biol rep 4

city: Davis

first: Wei

last: Hu

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

description: gene expression from dark-grown WT

hyb_protocol: Fifteen micrograms (15 µg) of aRNA were fragmented, and used for hybridization for 16 hr at 45 degree on GeneChip Arabidopsis ATH1 Array in the Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 3000 GeneChip Scanner with Autoloader.

data_processing: The data were analyzed in R/Bioconductor. Data were normalized with the 'RMA' function, ABS calls were obtained by Affymetrix GCOS algorithm, and statistical analysis were performed by LIMMA.

organism: Arabidopsis thaliana

source_name: Arabidopsis 4-day-old seedling

label_protocol: Biotinylated aRNA were prepared using the GeneChip 3' IVT Express Kit (Affymetrix) from 500ng total RNA according to the manufacturer's instructions.

growth_protocol: Surface sterilized seeds were sown on 1x MS salt medium solidified with 0.8% phytoagar, imbibed in darkness at 4 degree for 4 days, then exposed to white light for 3 hours to promote germination, and finally wrapped with aluminum foil for dark growth, or put into LED red light growth chamber for continuous red light growth (50 µmol m-2 s-1 irradiance).

extract_protocol: QIAGEN RNeasy Plant Mini kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: After 4 days of growth, during the subjective morning time, continuous red light-grown seedlings (R50) were directly harvested under red light, dark-grown seedlings (D) were harvested under safe dim green light (approximately 1 µmol m-2 s-1 irradiance). For DR2h samples, dark-grown seedlings were exposed to red light (50 µmol m-2 s-1 irradiance) for 2 hours before harvest under red light.

value: whole seedling

tag: genotype

value: wild type

tag: genetic background

value: Ler

value: 4 d old

value: Dark


title: adult queens of Solenopsis invicta X Solenopsis richteri hybrid from colony 11, sample no. 2

tag: caste

value: queens

tag: developmental stage

value: adult

value: Mix of adults, pupae and larvae


title: HCT116_control_rep1

source_name: HCT116, control, replicate 1

value: HCT116 cells


title: WT, Rc50, biol rep 1

description: gene expression from Rc50-grown WT

value: red light


title: HCT116_control_rep2

source_name: HCT116, control, replicate 2


title: WT, Rc50, biol rep 2

description: gene expression from Rc50-grown WT


title: ISCOM-Matrix, muscle, pig ID 1

source_name: Biceps femoris, 24 h post Matrix M injection

value: Yorkshire x Landrace

tag: gender

value: Castrated male

value: 11 weeks

value: Biceps femoris

value: intramuscular ISCOM-Matrix vaccine adjuvant treatment


title: 699NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
699NT_B8.A

value: Lung

value: non-tumor

value: male

value: adenocarcinoma (Ad)

value: Never

value: HpaII


title: 692T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
692T_B7.A

value: tumor

value: female

value: Current

value: MspI


title: ISCOM-Matrix, muscle, pig ID 2


title: 6-13-64 T-cell hybridoma ICOS(-) vs ICOS(+)

city: Noda

first: Ryo

last: Abe

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biological Sciences

institute: Tokyo University of Science

description: 6-13-64-ICOS(-) vs. ICOS(+)

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on Scanarray Express (Perkin Elmer). Images were quantified using QuantArray 3.0 software (Perkin Elmer).

data_processing: Data processing was perfomed using GeneSpring 6.2.1 software (Silicon Genetics).

label_protocol: Total RNA was reverse transcribed and labeled using SuperScript Indirect cDNA Labeling System (Invitrogen) following manufacturer's instructions.

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

tag: cell type

value: T-cell hybridoma

tag: background

value: AKR/J x BALB/c hybrid

tag: cell subpopulation

value: ICOS(-)

value: ICOS(+)


title: ISCOM-Matrix, muscle, pig ID 3

value: Yorkshire x Landrace

value: Castrated male

value: 11 weeks

tag: treatment


title: 699T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
699T_B8.A

value: Lung


title: 675T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
675T_B7.AS

value: adenosquamous carcinoma (AdSq)

value: Former


title: 692NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
692NT_B7.A

value: non-tumor

value: adenocarcinoma (Ad)


title: 675NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
675NT_B7.AS

value: HpaII


title: 670T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
670T_B5.AS

value: tumor


title: 59A vs. 59A NADPH Bdh_200mM replicate 3

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

country: France

institute: INRA

description: Biological replicate 3 of 3 of 59A vs. Biological replicate 3 of 3 of 59A NADPH Bdh200.

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: print-tip-loess within-array normalization, quantile between-array normalization. R 2.10.1 software and limma bioconductor package used.

organism: Saccharomyces cerevisiae

source_name: Total RNA of 59A strain

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: strain

source_name: Total RNA of 59A NADPH Bdh 200 mM strain

tag: state

value: NADPH Bdh 200


title: 59A vs. 59A NADPH Bdh_300mM replicate 3

description: Biological replicate 3 of 3 of 59A vs. Biological replicate 3 of 3 of 59A NADPH Bdh300.

source_name: Total RNA of 59A NADPH Bdh 300 mM strain

value: NADPH Bdh 300


title: 14268693 - dcl234 Generation11 not infected Repet3 vs dcl234 Generation11 infected Repet3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description: 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process?

hyb_protocol: dcl234 Generation11 infected Repet3 Cy5 / dcl234 Generation11 not infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

source_name: dcl234 Generation11 infected Repet3

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

growth_protocol: rosette - Media hygrometry Temperature=22ºC Light=Long day

extract_protocol: dcl234 Generation11 infected Repet3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:TCV - biotic stress - pathogen infection,tcv virus infection:time 10day . Col-0 and dcl2/3/4 were grown until rosette state and inoculated with TCV virus. Ten days post-inoculation, leaves and flowers were harvested and frozen with liquid nitrogen. They were kept at -80 until the TRNA was extracted. The same was made for Fisrt, Last generations and Fitness experiment.

tag: ecotype

value: columbia

value: mutant (dcl2/3/4)

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

tag: generation

tag: disease state

value: infected

source_name: dcl234 Generation11 not infected Repet3

extract_protocol: dcl234 Generation11 not infected Repet3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: not infected


title: 59A vs. 59A NADH Bdh_200mM replicate 3

description: Biological replicate 3 of 3 of 59A vs. Biological replicate 3 of 3 of 59A NADH Bdh200.

source_name: Total RNA of 59A NADH Bdh 200 mM strain

value: NADH Bdh 200


title: WT, Dark, biol rep 3

description: gene expression from dark-grown WT

tag: tissue

value: whole seedling

value: wild type

value: Ler

value: 4 d old

value: Dark


title: 14268694 - dcl234 Generation11 infected Repet3 vs dcl234 Generation11 not infected Repet3

hyb_protocol: dcl234 Generation11 not infected Repet3 Cy5 / dcl234 Generation11 infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age


title: 14268702 - dcl234 Generation11 not infected Repet3 vs Col0 Generation11 infectedFA Repet3

hyb_protocol: Col0 Generation11 infectedFA Repet3 Cy5 / dcl234 Generation11 not infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 Generation11 infectedFA Repet3

extract_protocol: Col0 Generation11 infectedFA Repet3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:TCV FA - biotic stress - pathogen infection,tcv virus infection:time 10day . A.ColO and dcl234 were grown until resette state and innoculated with TCV. Ten days postinnoculation, leaves were harvested. TCV from these tissues were used to innoculate next set of plants. The process was done 10 times. B. TCV from dcl234 G10 was inoculated on ColO plants (FA).

tag: genotype


title: WT, Dark, biol rep 2

description: gene expression from dark-grown WT

tag: genetic background


title: 653T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
653T_B3.A

source_name: LM-PCR products from HpaII digested DNA

value: Lung

tag: phenotype

value: female

tag: tumor histology

tag: smoking status

value: Former

tag: restriction enzyme

source_name: LM-PCR products from MspI digested DNA

value: MspI


title: 14268701 - Col0 Generation11 infectedFA Repet3 vs dcl234 Generation11 not infected Repet3

hyb_protocol: dcl234 Generation11 not infected Repet3 Cy5 / Col0 Generation11 infectedFA Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 653NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
653NT_B3.A

value: non-tumor

tag: gender

value: adenocarcinoma (Ad)

value: HpaII


title: 642NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
642NT_B3.A

value: Current


title: 14268700 - dcl234 Generation11 not infected Repet2 vs Col0 Generation11 infectedFA Repet2

hyb_protocol: Col0 Generation11 infectedFA Repet2 Cy5 / dcl234 Generation11 not infected Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 Generation11 infectedFA Repet2

extract_protocol: Col0 Generation11 infectedFA Repet2:10ug. (Qiagen_RNeasy.pdf)

value: columbia

source_name: dcl234 Generation11 not infected Repet2

extract_protocol: dcl234 Generation11 not infected Repet2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (dcl2/3/4)


title: 670NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
670NT_B5.AS

value: adenosquamous carcinoma (AdSq)


title: 619T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
619T_B5.AS

value: tumor


title: 59A vs. 59A NADPH Bdh_300mM replicate 2

description: Biological replicate 2 of 3 of 59A vs. Biological replicate 2 of 3 of 59A NADPH Bdh300.

value: NADPH Bdh 300mM


title: 619NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
619NT_B5.AS


title: 642T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
642T_B3.A


title: 59A vs. 59A NADPH Bdh_200mM replicate 1

description: Biological replicate 1 of 3 of 59A vs. Biological replicate 1 of 3 of 59A NADPH Bdh200.

value: NADPH Bdh 200


title: 59A vs. 59A NADH Bdh_200mM replicate 2

description: Biological replicate 2 of 3 of 59A vs. Biological replicate 2 of 3 of 59A NADH Bdh200.

value: NADH Bdh 200mM


title: 610T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
610T_B5.A


title: 14268698 - dcl234 Generation11 infected Repet3 vs Col0 Generation11 infectedFA Repet3

hyb_protocol: Col0 Generation11 infectedFA Repet3 Cy5 / dcl234 Generation11 infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: infected


title: 59A vs. 59A NADPH Bdh_200mM replicate 2

description: Biological replicate 2 of 3 of 59A vs. Biological replicate 2 of 3 of 59A NADPH Bdh200.

value: NADPH Bdh 200mM


title: 59A vs. 59A NADH Bdh_200mM replicate 1

description: Biological replicate 1 of 3 of 59A vs. Biological replicate 1 of 3 of 59A NADH Bdh200.

value: NADH Bdh 200


title: 59A vs. 59A NADPH Bdh_300mM replicate 1

description: Biological replicate 1 of 3 of 59A vs. Biological replicate 1 of 3 of 59A NADPH Bdh300.

value: NADPH Bdh 300


title: 14268695 - Col0 Generation11 infectedFA Repet2 vs dcl234 Generation11 infected Repet2

hyb_protocol: dcl234 Generation11 infected Repet2 Cy5 / Col0 Generation11 infectedFA Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 Generation11 infected Repet2

extract_protocol: dcl234 Generation11 infected Repet2:10ug. (Qiagen_RNeasy.pdf)


title: 14268697 - Col0 Generation11 infectedFA Repet3 vs dcl234 Generation11 infected Repet3

hyb_protocol: dcl234 Generation11 infected Repet3 Cy5 / Col0 Generation11 infectedFA Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 606Tr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
606Tr_B6.A

value: Lung

value: female


title: 14268699 - Col0 Generation11 infectedFA Repet2 vs dcl234 Generation11 not infected Repet2

description: 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process?

hyb_protocol: dcl234 Generation11 not infected Repet2 Cy5 / Col0 Generation11 infectedFA Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: not infected


title: 14268696 - dcl234 Generation11 infected Repet2 vs Col0 Generation11 infectedFA Repet2

hyb_protocol: Col0 Generation11 infectedFA Repet2 Cy5 / dcl234 Generation11 infected Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 606NTo

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
606NTo_B3.A

value: non-tumor

value: adenocarcinoma (Ad)

value: MspI


title: 14268692 - dcl234 Generation1 infected Repet3 vs dcl234 Generation11 infected Repet3

hyb_protocol: dcl234 Generation11 infected Repet3 Cy5 / dcl234 Generation1 infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia

source_name: dcl234 Generation1 infected Repet3

extract_protocol: dcl234 Generation1 infected Repet3:10ug. (Qiagen_RNeasy.pdf)


title: 14268655 - dcl234 Generation11 not infected Repet1 vs Col0 Generation11 infectedFA Repet1

hyb_protocol: Col0 Generation11 infectedFA Repet1 Cy5 / dcl234 Generation11 not infected Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 Generation11 infectedFA Repet1

extract_protocol: Col0 Generation11 infectedFA Repet1:10ug. (Qiagen_RNeasy.pdf)

source_name: dcl234 Generation11 not infected Repet1

extract_protocol: dcl234 Generation11 not infected Repet1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (dcl2/3/4)


title: 14268690 - Col0 Generation11 not infected Repet2 vs Col0 Generation11 infectedFA Repet2

hyb_protocol: Col0 Generation11 infectedFA Repet2 Cy5 / Col0 Generation11 not infected Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 Generation11 not infected Repet2

extract_protocol: Col0 Generation11 not infected Repet2:10ug. (Qiagen_RNeasy.pdf)


title: 14268688 - Col0 Generation11 infectedFA Repet2 vs Col0 Generation11 not infected Repet2

hyb_protocol: Col0 Generation11 not infected Repet2 Cy5 / Col0 Generation11 infectedFA Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 603T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
603T_B4.A

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

value: Never

value: HpaII


title: 610NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
610NT_B5.A

value: Former


title: 603NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
603NT_B4.A


title: 14268691 - dcl234 Generation11 infected Repet3 vs dcl234 Generation1 infected Repet3

hyb_protocol: dcl234 Generation1 infected Repet3 Cy5 / dcl234 Generation11 infected Repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 596T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
596T_B6.AS

value: tumor

value: squamous cell carcinoma (Sq)


title: 596NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
596NT_B6.AS