title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep5

source_name: Medicago truncatula  12 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  12 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  12 hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep2

status: Public on Oct 27 2005

type: RNA

city: St Paul

first: Kathryn

middle: A

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep2

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 4.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

molecule: total RNA

organism: Medicago truncatula

label_protocol: 11 ug RNA from each of 3 biological replicates was pooled to make a total of 33 ug for cDNA synthesis with a RT Primer for labeling with either Cy3 or Cy5 dye molecules using a 3DNA Array 50 Expression Array Detection Kit for cDNA Microarrays (Genisophere, Inc., Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 50 Expression Array Detection Kit Appendix A (Genisphere Inc.).

growth_protocol: Medicago truncatula genotype A17 was germinated and grown as previously described (Penmetsa and Cook, 2000).

extract_protocol: Root samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturerés instructions.


title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep6

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep6


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep2

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep2

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  48 hpi after inoculation with Sinorhizobium meliloti

source_name: Medicago truncatula  48 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  48 hpi after mock inoculation


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep6

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep6

source_name: Medicago truncatula  24 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  24 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  24 hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep4

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep4


title: Medicago truncatula  24 hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula  24  hour(s) post inoculation with Sinorhizobium meliloti  rep1


title: Medicago truncatula  48 hpi after Sinorhizobium meliloti inoculation, rep4

description: Medicago truncatula  48  hour(s) post inoculation with Sinorhizobium meliloti  rep4


title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep3


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep6

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep6

source_name: Medicago truncatula  6 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  6 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  6 hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula  12 hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula  12  hour(s) post inoculation with Sinorhizobium meliloti  rep1


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep5


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep4

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep4


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep1


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep2

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep2


title: Medicago truncatula  6 hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula  6  hour(s) post inoculation with Sinorhizobium meliloti  rep3


title: PPARgamma2_DMSO

status: Public on May 31 2005

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

description:
HepG2 tet-off hPPAR gamma2 cells treated with DMSO
(PPAR expressed)

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

label: biotin

organism: Homo sapiens

source_name: HepG2 cells

label_protocol: Total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isogen reagents

tag: HepG2 tet-off hPPAR gamma2 cells


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep6

status: Public on Oct 14 2005

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep6

hyb_protocol: The hybridization and washing rocedures of the 3DNA Array 50 Expression Array Detection Kit were followed. Briefly, the hybridization mix consisted of 2.5 uL of cDNAs from inoculated and uninoculated roots, 2.5 uL of Cy3 and Cy5 dyes, 2 uL of LNA dT blocker 27 and 9 uL of 2X SDS hybridization buffer. Hybridization was carried out at 62.0oC for 20-23 h. Hybridized slides were washed in 2X SSC, 0.2% SDS for 10 min at 55oC, 2X SSC for 10 min at room temperature, and 0.2X SSC for 10 min at room temperatures with gentle agitation

source_name: Medicago truncatula 1hpi after mock inoculation

treatment_protocol: Plants were inoculated with Sinorhizobium meliloti at age of 6 days

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment - 1hpi after mock inoculation

treatment_protocol: Plants were mock inoculated with at age of 6 days

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment - 1hpi after inoculation with Sinorhizobium meliloti


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep1

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep1


title: PPARdelta_GW

description:
HepG2 tet-off hPPAR delta cells treated with GW501516
(PPAR activated)

tag: HepG2 tet-off hPPAR delta cells


title: PPARgamma1_ciglitizone

description:
HepG2 tet-off hPPAR gamma1 cells treated with cigilitazone
(PPAR activated)

tag: HepG2 tet-off hPPAR gamma1 cells


title: PPARgamma1_Dox

description:
HepG2 tet-off hPPAR gamma1 cells treated with doxycycline
(control)


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep5

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep5


title: PPARalpha_DMSO

description:
HepG2 tet-off hPPAR alpha cells treated with DMSO
(PPAR expressed)

tag: HepG2 tet-off hPPAR alpha cells


title: PPARgamma2_Dox

description:
HepG2 tet-off hPPAR gamma2 cells treated with doxycycline
(control)


title: PPARdelta_DMSO

description:
HepG2 tet-off hPPAR delta cells treated with DMSO
(PPAR expressed)


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep2

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep2


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep4

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep4


title: PPARalpha_fenofibric

description:
HepG2 tet-off hPPAR alpha cells treated with fenofibric acid
(PPAR activated)


title: PPARdelta_Dox

description:
HepG2 tet-off hPPAR delta cells treated with doxycycline
(control)


title: PPARgamma2_ciglitizone

description:
HepG2 tet-off hPPAR gamma2 cells treated with ciglitazone
(PPAR activated)


title: PPARalpha_Dox

description:
HepG2 tet-off hPPAR alpha cells treated with doxycycline
(control)


title: Medicago truncatula 1hpi after Sinorhizobium meliloti inoculation, rep3

description: Medicago truncatula 1 hour post inoculation with Sinorhizobium meliloti  rep3


title: Medicago truncatula  72 hpi after Sinorhizobium meliloti inoculation, rep6

description: Medicago truncatula  72  hour(s) post inoculation with Sinorhizobium meliloti  rep6

source_name: Medicago truncatula  72 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  72 hpi after mock inoculation

tag: Medicago truncatula; genotype - A17; tissue- roots; age - 6 days; treatment -  72 hpi after inoculation with Sinorhizobium meliloti


title: PPARgamma1_DMSO

description:
HepG2 tet-off hPPAR gamma1 cells treated with DMSO
(PPAR expressed)


title: Total RNA 11

status: Public on Apr 21 2007

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description: Samples from cell culture

hyb_protocol: for details, see the hybridization section in the direct labeling protocol (2004.10.22) at the UHN Microarray Centre (University Health Network, Princess Margaret Hospital, Ontario Cancer Institute) website

scan_protocol: Slides were digitalized using Axon GenePix 4000B scanner and software using default settings.

data_processing: The data from the final analysis was normalized using the bioconductor (Gentleman et al. 2004) library limma (Wettenhall and Smyth 2004) and the non-print tip lowess approach without background subtraction (Yang et al. 2002) as this increases the accuracy of the obtained measurements (Irizarry et al. 2005). Replicate spots on each array were separated and treated as independent

organism: Mus musculus

source_name: 3T3-eIF4E-induced 5hrs TOTAL RNA-Cy3

label_protocol: direct labeling protocol (2004.10.22) as described at the UHN Microarray Centre (University Health Network, Princess Margaret Hospital, Ontario Cancer Institute) website

extract_protocol: Trizol

tag: NIH3T3/eIF4E cells induced

source_name: 3T3-eIF4E-uninduced TOTAL RNA-Cy5

tag: NIH3T3/eIF4E cells uninduced


title: Heat selected line biological Rep. 1

status: Public on Apr 16 2007

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Gene expression data from heat resistance selected flies

hyb_protocol: As described by Dyrskjot et al (2003), Nat. Gen. 33:90-96..

scan_protocol: As described by Dyrskjot et al (2003), Nat. Gen. 33: 90-96.

data_processing: raw data was GC-RMA normalized using the Bioconductor application for R

label: Biotin

organism: Drosophila melanogaster

source_name: Adult whole female flies of heat selected line 1

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared using the BioArray High Yield RNA Transcript Labelling Kit (Enzo, Farmingdale, NY, USA). After the in vitro transcription (IVT) reaction, the unincorporated nucleotides were removed using RNeasy columns (Qiagen, Hilden, Germany).

extract_protocol: Flies from each vial (10 females) were homogenized with a FP-120 Fast Prep bead beater, according to manufacturer's protocols (Bio-101, Carlsbad, CA, USA), in 1.5 mL Trizol Reagent (Invitrogen, Carlsbad, CA, USA) and 150 mL chloroform. Double-stranded complementary DNA was prepared from 5 microgram total RNA using the SuperScript Choice System (Invitrogen), according to the manufacturer's instructions, except using an oligo-dT primer containing a T7 RNA polymerase promoter site.

tag: Heat resistance selected flies


title: csn51 60hrs aed 4 cy5

status: Public on Apr 12 2007

city: Tel Aviv

first: Danny

last: Chamovitz

address: Ramat aviv

country: Israel

institute: Tel Aviv University

description: Biological replicate 4 of 4

hyb_protocol: FHCRC

scan_protocol: FHCRC

data_processing: LOWESS normalized, background subtracted VALUE data representing log ratios of (mutant/wildtype).

source_name: csn51 Total larva extract

label_protocol: RT REACTION:Oligo-dT 5ug, Random Primers5ug RNA Recommended quantities: 30ug Total RNA,2ug  PolyA Water (RNAse free) (Final Volume = 18.5ul)Incubate RNA/Oligo Mixture @ 70°C - 10 min,Chill on ice (immediately)– 10 min.cDNA Synthesis:5X First Strand Buffer 6ul 0.1M DTT 3ul 50X aa-dUTP/dNTPs 0.6ul SuperScriptII 1.9ul(Final Volume = 11.5) Add 11.5ul Rxn mix to Oligo/RNA mixture.Incubate @ 42°C – 2 hrs. HYDROLYSIS:10ul 1N NaOH 10ul 0.5M EDTA Incubate @ 65 C –15 min. Add: 25ul 1M Tris (pH 7.4)CLEANUP:Add 450ul H2O to a Microcon-30concentrator.Add neutralized reaction (rinse out tube).Spin @ 10,000 x g – 8 min.Decant flo-thru.Wash 2X: Refill original container with 500ulH2O.Elute cDNA – Turn column upside down, Spin @ 10,000 x g – 2 min.(in clean tube).Dry eluate in Speed-Vac.DYE COUPLING :Aliquot 2.25 ul x 16 tubes and store the aliquots in the dark @ 4 C.Coupling Dye to cDNA Resuspend cDNA pellet in 4.5 ulH20.Add 2.25 ul of 0.2M Sodium Bicarbonate to dye aliquot… Immediately! Combine the dye and cDNA. Incubate @ RT - 1 hr in the dark.QUENCHING AND CLEANUP :Add 4.5 ul 4M Hydroxylamine to each reaction.Incubate @ RT – 15 min. in the dark.To remove unincorporated/quenched Cye dye, proceed with Qia-quick PCR Purification Kit.

extract_protocol: TriZol procedure

tag: time aed

value: 60 hrs

source_name: w118 60 hrs aed 4 cy3

tag: Wild type