title: Microdissected area # 1 of 2182 tumor

description: Gene expression data from microdissected area # 1 of 2182 tumor

value: Neuroblastoma (Schwannian stroma-poor) with areas of small round neuroblastic cells


title: Whole neuroblastoma tumor_2056

status: Public on Apr 17 2007

type: RNA

city: genoa

first: Domenico

last: Albino

address: L.go R. Benzi, 10

country: Italy

institute: National Institute for Cancer Research (IST)

description: Gene expression data from whole tumor

hyb_protocol: In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed  with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.

scan_protocol: GeneChips were scanned using the laser confocal fluorescence scanner.

data_processing: Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Frozen neuroblastoma tumor

label_protocol: We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).

extract_protocol: Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).

tag: Phenotype

value: Neuroblastoma (Schwannian stroma-poor)


title: Microdissected area # 2 of 2182 tumor

description: Gene expression data from microdissected area # 2 of 2182 tumor

value: Neuroblastoma (Schwannian stroma-poor) with areas of large neuroblastic round cells


title: Whole ganglioneuroblastoma intermixed tumor_1999

description: Gene expression data from whole tumor

source_name: frozen ganglioneuroblastoma intermixed tumor

value: Ganglioneuroblastoma, intermixed (Schwannian stroma-rich)


title: Whole neuroblastoma tumor_2181

description: Gene expression data from whole tumor


title: Whole borderline ganglioneuroma maturing tumor_1761

description: Gene expression data from whole tumor

source_name: Frozen borderline ganglioneuroma maturing tumor

value: Borderline ganglioneuroma maturing


title: Microdissected area # 2 of 1761 tumor

description: Gene expression data from microdissected area # 2 of 1761 tumor

value: Borderline ganglioneuroma maturing with areas of schwannian stromal cells


title: Whole ganglioneuroblastoma tumor_1589

description: Gene expression data from whole tumor


title: Microdissected area # 1 of 1761 tumor

description: Gene expression data from microdissected area # 1 of 1761 tumor


title: Microdissected area # 1 of 1589 tumor

description: Gene expression data from microdissected area # 1 of 1589 tumor

value: Borderline ganglioneuroma maturing with isle of small round neuroblastic cells


title: Microdissected area # 2 of 1919 tumor

description: Gene expression data from microdissected area # 2 of 1919 tumor


title: Whole neuroblastoma tumor_1919

description: Gene expression data from whole tumor


title: Microdissected area # 2 of 1589 tumor

description: Gene expression data from microdissected area # 2 of 1589 tumor


title: Microdissected area # 1 of 1919 tumor

description: Gene expression data from microdissected area # 1of 1919 tumor

value: Neuroblastoma (Schwannian stroma-poor) with areas of large round neuroblastic cells


title: Whole neuroblastoma tumor_1547

description: Gene expression data from whole tumor


title: Whole mature ganglioneuroma tumor_1591

description: Gene expression data from whole tumor

source_name: Frozen ganglioneuroma mature tumor

value: Ganglioneuroma mature


title: Whole neuroblastoma tumor_1538

description: Gene expression data from whole tumor


title: Whole ganglioneuroma tumor_1377

description: Gene expression data from whole tumor

source_name: Frozen ganglioneuroma tumor

value: Ganglioneuroma


title: 30h recovery timepoint control replicate 5b

status: Public on Apr 16 2007

city: Tiburon

first: Jonathon

middle: H

last: Stillman

state: CA

address: 3152 Paradise Drive

department: Romberg Tiburon Center

country: USA

institute: San Francisco State University

description: gene expression data from heat stressed individual at 30h recovery

hyb_protocol: 0.45M NaCl, 45mM NaCitrate, 0.75mg/ml PolyA RNA, 0.2% SDS, and 25mM Hepes, pH 7.4 in a final volume of 48ul.  This volume heat denatured at 100C for 2 min, cooled to room temperature, and pipetted underneath an Erie LifterSlip placed on the microarray slide and incubated in a Genetix hybridization chamber for 12-14 h at 65C.

scan_protocol: 10 um resolution (Axon Instruments, GenePix Personal 4100A; Axon GenePix Pro v.6.0) using the automatic PMT adjustment function.

data_processing:
The data were log2 transformed, lowess normalized, and statistically analyzed using R/maanova using a fixed model and the F3 statistic

Data were analyzed as normalized intensities, not ratios, so the data from n=82 arrays was used to create 164 single channel GEO Sample submissions (one .gpr file = two GEO Samples). Therefore, GEO Samples corresponding to the same .gpr file have identical supplementary .gpr file content (e.g. GSM181590_Cy5.gpr & GSM181591_Cy3.gpr are identical copies of the same .gpr file).

organism: Petrolisthes cinctipes

source_name: crab # 796

label_protocol: Cy dye labeled amino-allyl cDNA was generated by RT from 10ug total RNA using amino-allyl dUTP with subsequent labeling by addition of Cy dye in DMSO.

growth_protocol: samples were immediatley dissected into RNAlater tissue protect and stored at -20C

extract_protocol: Qiagen's RNeasy Mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: crabs were collected at Cape Arago, Oregon, immediately returned to the laboratory at the Oregon Institute of Marine Biology and were either heat stressed (11 to 30C in 4h) or held at 11C for 4h before being placed into a 11C recovery aquarium.

tag: heat-stressed (ramp from 11 to 30C over 4h)


title: 30h recovery timepoint heatstressed replicate 5b

description: gene expression data control individual at 30h recovery

source_name: crab # 791

tag: control (held at 11C for 4h)


title: Whole ganglioneuroma tumor_1172

description: Gene expression data from whole tumor


title: 30h recovery timepoint control replicate 5a


title: 30h recovery timepoint heatstressed replicate 4b

source_name: crab # 790


title: 30h recovery timepoint heatstressed replicate 5a


title: spxB 164880

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: see article SpxB regulates O-acetylation dependent resistance of Lactococcus lactis peptidoglycan to hydrolysis; submitted for publication

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner. Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: L.lactis MG1363 VES3910

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.3) in M17 containing 0.25% glucose (GM17). Cells were harvested by centrifugation for 1 min at 10,000 rpm at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at –80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75–150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Furter purification was done using the High Pure RNA isolation, using the suppliers protocol.

source_name: L.lactis MG1363 VES4075


title: spxB 164885


title: 30h recovery timepoint control replicate 4b

source_name: crab # 795


title: 30h recovery timepoint control replicate 4a


title: spxB 164716


title: Whole ganglioneuroblastoma intermixed tumor_1134

description: Gene expression data from whole tumor

source_name: Frozen ganglioneuroblastoma intermixed tumor


title: 30h recovery timepoint heatstressed replicate 4a


title: 30h recovery timepoint heatstressed replicate 3b

source_name: crab # 789


title: Whole ganglioneuroma tumor_1250

description: Gene expression data from whole tumor


title: 30h recovery timepoint control replicate 3b

source_name: crab # 794


title: 30h recovery timepoint control replicate 3a


title: 30h recovery timepoint heatstressed replicate 3a


title: 30h recovery timepoint control replicate 2a

source_name: crab # 793


title: 30h recovery timepoint control replicate 2b

tag: heatstressed (held at 11C for 4h)


title: 30h recovery timepoint heatstressed replicate 2b

source_name: crab # 788

tag: control (ramp from 11 to 30C over 4h)


title: 30h recovery timepoint heatstressed replicate 1a

source_name: crab # 787


title: 30h recovery timepoint heatstressed replicate 2a


title: 30h recovery timepoint control replicate 1b

source_name: crab # 792


title: 30h recovery timepoint control replicate 1a


title: WS_Input_for_CLF_01

type: genomic

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: Input Genomic DNA

hyb_protocol: Whole Genome Tiling Array was hybridized for 16 hrs, washed, and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner G7

data_processing: Quantile Normalization

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 10-14 day old seedlings

label_protocol: The sample was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Plants were grown under 16 h light on 1/2 X MS media

extract_protocol: genomic DNA isolation

treatment_protocol: Untreated

tag: Input Genomic DNA


title: 30h recovery timepoint heatstressed replicate 1b


title: 24h recovery timepoint control replicate 5b

description: gene expression data from heat stressed individual at 24h recovery

source_name: crab # 781


title: 24h recovery timepoint control replicate 5a

description: gene expression data control individual at 24h recovery


title: 24h recovery timepoint control replicate 4b

source_name: crab # 780


title: 24h recovery timepoint heatstressed replicate 5a

source_name: crab # 776


title: 24h recovery timepoint heatstressed replicate 4b

source_name: crab # 775


title: 24h recovery timepoint heatstressed replicate 5b


title: 24h recovery timepoint control replicate 3a

source_name: crab # 779


title: 24h recovery timepoint control replicate 4a


title: 24h recovery timepoint heatstressed replicate 2b

source_name: crab # 773


title: 24h recovery timepoint heatstressed replicate 4a


title: 24h recovery timepoint heatstressed replicate 3a

source_name: crab # 774


title: 24h recovery timepoint control replicate 3b


title: 24h recovery timepoint control replicate 2b

source_name: crab # 778


title: 24h recovery timepoint heatstressed replicate 3b


title: 24h recovery timepoint control replicate 2a


title: 24h recovery timepoint heatstressed replicate 2a


title: WS_H3_04

description: Enriched for nucleosomal DNA

extract_protocol: sample was prepared by ChIP using an antibody against H3

tag: Enriched for nucleosomal DNA


title: 18h recovery timepoint control replicate 4b

description: gene expression data control individual at 18h recovery

source_name: crab # 765


title: 24h recovery timepoint control replicate 1a

source_name: crab # 777


title: 18h recovery timepoint control replicate 3a

source_name: crab # 764


title: 18h recovery timepoint heatstressed replicate 4b

description: gene expression data from heat stressed individual at 18h recovery

source_name: crab # 760


title: 24h recovery timepoint control replicate 1b


title: 18h recovery timepoint control replicate 3b


title: 18h recovery timepoint heatstressed replicate 5a

source_name: crab # 761


title: 18h recovery timepoint heatstressed replicate 5b


title: 18h recovery timepoint control replicate 4a


title: WS_H3_03

description: Enriched for nucleosomal DNA


title: 24h recovery timepoint heatstressed replicate 1b

source_name: crab # 772


title: 18h recovery timepoint control replicate 5a

source_name: crab # 766


title: 18h recovery timepoint control replicate 5b

description: gene expression data from heat stressed individual at 6h recovery


title: 18h recovery timepoint heatstressed replicate 4a


title: 18h recovery timepoint heatstressed replicate 3b

source_name: crab # 759


title: 24h recovery timepoint heatstressed replicate 1a


title: WS_H3_02

description: Enriched for nucleosomal DNA

source_name: 10-14 day old seedlings


title: WS_Input_for_CLF_03

description: Input Genomic DNA


title: 18h recovery timepoint control replicate 2b

source_name: crab # 763


title: 18h recovery timepoint heatstressed replicate 3a


title: 18h recovery timepoint heatstressed replicate 2b

source_name: crab # 758


title: 18h recovery timepoint control replicate 2a


title: 18h recovery timepoint heatstressed replicate 2a


title: WS_H3_01

description: Enriched for nucleosomal DNA


title: 18h recovery timepoint control replicate 1b

source_name: crab # 762


title: WS_Input_for_CLF_04

description: Input Genomic DNA


title: WS_3mH3K27_01

description: Enriched for DNA associated with H3K27me3

extract_protocol: sample was prepared by ChIP using an antibody against H3K27me3


title: 18h recovery timepoint heatstressed replicate 1b

source_name: crab # 757


title: 12h recovery timepoint control replicate 5a

description: gene expression data control individual at 12h recovery

source_name: crab # 751


title: 18h recovery timepoint control replicate 1a


title: 12h recovery timepoint heatstressed replicate 4b

description: gene expression data from heat stressed individual at 12h recovery

source_name: crab # 745


title: 12h recovery timepoint heatstressed replicate 5a

source_name: crab # 746


title: 18h recovery timepoint heatstressed replicate 1a


title: 12h recovery timepoint control replicate 5b


title: 12h recovery timepoint control replicate 4b

source_name: crab # 750


title: 12h recovery timepoint heatstressed replicate 3b

source_name: crab # 744


title: 12h recovery timepoint control replicate 4a


title: 12h recovery timepoint heatstressed replicate 5b


title: 12h recovery timepoint heatstressed replicate 2b

source_name: crab # 743


title: 12h recovery timepoint control replicate 2a

source_name: crab # 748


title: 12h recovery timepoint control replicate 2b


title: 12h recovery timepoint control replicate 3b

source_name: crab # 749


title: WS_3mH3K27_02

tag: Enriched for DNA associated with H3K27me3


title: WS_3mH3K27_03


title: 12h recovery timepoint heatstressed replicate 4a


title: 12h recovery timepoint heatstressed replicate 3a


title: 12h recovery timepoint control replicate 3a


title: WS_3mH3K27_04


title: 6h recovery timepoint heatstressed replicate 4b

description: gene expression data control individual at 6h recovery

source_name: crab # 731


title: 12h recovery timepoint control replicate 1a

source_name: crab # 747


title: 12h recovery timepoint heatstressed replicate 1a

source_name: crab # 742


title: 6h recovery timepoint control replicate 4b

source_name: crab # 736


title: 12h recovery timepoint control replicate 1b


title: 12h recovery timepoint heatstressed replicate 1b


title: 12h recovery timepoint heatstressed replicate 2a


title: 6h recovery timepoint heatstressed replicate 4a


title: 6h recovery timepoint control replicate 3a

source_name: crab # 735


title: 6h recovery timepoint heatstressed replicate 1b

source_name: crab # 727


title: 6h recovery timepoint heatstressed replicate 2a

source_name: crab # 729


title: 4h recovery timepoint control replicate 3b

description: gene expression data control individual at 4h recovery

source_name: crab # 721


title: 6h recovery timepoint control replicate 2a

source_name: crab # 734


title: 4h recovery timepoint control replicate 3a


title: 6h recovery timepoint control replicate 4a


title: 6h recovery timepoint heatstressed replicate 3b

source_name: crab # 730


title: 6h recovery timepoint control replicate 3b


title: 6h recovery timepoint heatstressed replicate 1a


title: 6h recovery timepoint heatstressed replicate 2b


title: 4h recovery timepoint heatstressed replicate 3a

description: gene expression data from heat stressed individual at 4h recovery

source_name: crab # 716


title: 6h recovery timepoint control replicate 2b


title: 6h recovery timepoint control replicate 1a

source_name: crab # 732


title: 6h recovery timepoint control replicate 1b


title: 4h recovery timepoint control replicate 2b

source_name: crab # 719


title: 6h recovery timepoint heatstressed replicate 3a


title: 4h recovery timepoint heatstressed replicate 3b

description: gene expression data from heat stressed individual at 2h recovery


title: 4h recovery timepoint heatstressed replicate 2b

source_name: crab # 713


title: 4h recovery timepoint control replicate 1b

source_name: crab # 718


title: 4h recovery timepoint heatstressed replicate 1b

source_name: crab # 712


title: 4h recovery timepoint control replicate 2a


title: 4h recovery timepoint heatstressed replicate 1a


title: 2h recovery timepoint control replicate 5a

description: gene expression data control individual at 2h recovery

source_name: crab # 706


title: 2h recovery timepoint control replicate 4b

source_name: crab # 705


title: 4h recovery timepoint control replicate 1a


title: 2h recovery timepoint control replicate 3b

source_name: crab # 704


title: 2h recovery timepoint control replicate 5b


title: 2h recovery timepoint heatstressed replicate 3b

source_name: crab # 699


title: 2h recovery timepoint control replicate 2b

source_name: crab # 703


title: 2h recovery timepoint heatstressed replicate 2a

source_name: crab # 698


title: 2h recovery timepoint heatstressed replicate 4b

source_name: crab # 700


title: 2h recovery timepoint heatstressed replicate 5a

source_name: crab # 701


title: 2h recovery timepoint control replicate 3a


title: 4h recovery timepoint heatstressed replicate 2a


title: 2h recovery timepoint control replicate 4a


title: 2h recovery timepoint heatstressed replicate 4a


title: 2h recovery timepoint heatstressed replicate 5b


title: 2h recovery timepoint control replicate 1a

source_name: crab # 702


title: 2h recovery timepoint heatstressed replicate 2b


title: 2h recovery timepoint heatstressed replicate 3a


title: 2h recovery timepoint heatstressed replicate 1b

source_name: crab # 697


title: 2h recovery timepoint control replicate 2a


title: 2h recovery timepoint heatstressed replicate 1a


title: 2h recovery timepoint control replicate 1b


title: 1h recovery timepoint heatstressed replicate 4b

description: gene expression data from heat stressed individual at 1h recovery

source_name: crab # 686


title: 1h recovery timepoint control replicate 4a

description: gene expression data control individual at 1h recovery

source_name: crab # 691


title: 1h recovery timepoint heatstressed replicate 4a


title: 1h recovery timepoint heatstressed replicate 3b

source_name: crab # 685


title: 1h recovery timepoint control replicate 3b

source_name: crab # 690


title: 1h recovery timepoint control replicate 3a


title: 1h recovery timepoint control replicate 2a

source_name: crab # 689


title: 1h recovery timepoint heatstressed replicate 1b

source_name: crab # 683


title: 1h recovery timepoint heatstressed replicate 3a


title: 1h recovery timepoint control replicate 4b


title: 0.5h recovery timepoint heatstressed replicate 5a

description: gene expression data from heat stressed individual at 0.5h recovery

source_name: crab # 671


title: 1h recovery timepoint control replicate 2b


title: 0.5h recovery timepoint control replicate 4a

description: gene expression data control individual at 0.5h recovery

source_name: crab # 675


title: 1h recovery timepoint heatstressed replicate 2b

source_name: crab # 684


title: 1h recovery timepoint control replicate 1a

source_name: crab # 687


title: 1h recovery timepoint heatstressed replicate 1a


title: 1h recovery timepoint control replicate 1b


title: 0.5h recovery timepoint control replicate 4b


title: 0.5h recovery timepoint control replicate 3b

source_name: crab # 674


title: 0.5h recovery timepoint heatstressed replicate 2b

source_name: crab # 668


title: 0.5h recovery timepoint heatstressed replicate 4b

source_name: crab # 670


title: 0.5h recovery timepoint heatstressed replicate 3b

source_name: crab # 669


title: 1h recovery timepoint heatstressed replicate 2a


title: 0.5h recovery timepoint control replicate 3a


title: 0.5h recovery timepoint heatstressed replicate 3a


title: 0.5h recovery timepoint control replicate 2b

source_name: crab # 673


title: 0.5h recovery timepoint control replicate 5a

source_name: crab # 677


title: 0.5h recovery timepoint heatstressed replicate 5b


title: 0.5h recovery timepoint control replicate 5b


title: 0.5h recovery timepoint control replicate 2a


title: 0.5h recovery timepoint heatstressed replicate 4a


title: 0.5h recovery timepoint heatstressed replicate 2a


title: 0.5h recovery timepoint heatstressed replicate 1b

source_name: crab # 667


title: 0.5h recovery timepoint control replicate 1a

source_name: crab # 672


title: Desiccation selected line biological Rep. 3

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 desiccation 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 desiccation selected line 3

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: desiccation resistance selected flies


title: 0.5h recovery timepoint heatstressed replicate 1a


title: 0.5h recovery timepoint control replicate 1b


title: Heat selected line biological Rep. 3

description: Gene expression data from heat resistance selected flies

source_name: Adult whole female flies of heat selected line 3

tag: Heat resistance selected flies


title: Knock_down selected line biological Rep. 1

description: Gene expression data from knock_down resistance selected flies

source_name: Adult whole female flies of knock_down selected line 1

tag: knock_down resistance selected flies


title: Desiccation selected line biological Rep. 2

source_name: Adult whole female flies of desiccation selected line 2


title: Starvation selected line biological Rep. 2

description: Gene expression data from starvation resistance selected flies

source_name: Adult whole female flies of starvation selected line 2

tag: starvation resistance selected flies


title: Knock_down selected line biological Rep. 3

source_name: Adult whole female flies of knock_down selected line 3


title: Heat selected line biological Rep. 2

source_name: Adult whole female flies of heat selected line 2


title: Starvation selected line biological Rep. 1

source_name: Adult whole female flies of starvation selected line 1


title: Starvation selected line biological Rep. 3

source_name: Adult whole female flies of starvation selected line 3


title: Constant 30 line biological Rep. 3

description: Gene expression data from flies held at 30 degrees

source_name: Adult whole female flies of constant 30 line 3

tag: Constant 30 selected flies


title: Knock_down selected line biological Rep. 2

source_name: Adult whole female flies of knock_down selected line 2


title: Longevity selected line biological Rep. 3

description: Gene expression data from longevity selected flies

source_name: Adult whole female flies of longevity selected line 3

tag: Longevity selected flies


title: Longevity selected line biological Rep. 2

source_name: Adult whole female flies of longevity selected line 2


title: Constant 30 line biological Rep. 1

source_name: Adult whole female flies of constant 30 line 1


title: Cold selected line biological Rep. 3

description: Gene expression data from cold resistance selected flies

source_name: Adult whole female flies of cold selected line 3

tag: Cold resistance selected flies


title: Constant 30 line biological Rep. 2

source_name: Adult whole female flies of constant 30 line 2


title: Desiccation selected line biological Rep. 1

source_name: Adult whole female flies of desiccation selected line 1


title: Longevity selected line biological Rep. 1

source_name: Adult whole female flies of longevity selected line 1


title: Control line biological Rep. 3

description: Gene expression data from non-selected (control) flies

source_name: Adult whole female flies of control line 3

tag: non-selected control flies


title: Cold selected line biological Rep. 1

source_name: Adult whole female flies of cold selected line 1


title: Cold selected line biological Rep. 2

source_name: Adult whole female flies of cold selected line 2


title: Control line biological Rep. 2

source_name: Adult whole female flies of control line 2


title: Heat Shock Dif HS_DIF_3

city: College Park

first: Subhamoy

last: Pal

state: MD

address: 5126 Plant Sciences Building

department: Center for Biosystems Research

institute: University of Maryland

description: The experiment is meant to determine the role of ectopic expression of HS-Dif on Drosophila gene expression.

hyb_protocol: Detailed protocols can be downloaded from the GE/Amersham website (Amersham CyScribe First-Strand cDNA Labeling Kit)

data_processing: Spot intensities generated using TIGR Spotfinder, Data normalized using TIGR MIDAS-- Lowess and Standard deviation Normalization. Dividing IB by IA gives Value.

source_name: Wildtype

label_protocol: Direct Labelling using Amersham Biosciences' Cyscribe First Strand Labelling Kit.

growth_protocol: Using standard protocol, larvae were kept in Fly vials with fly food consisting of mollasses, yeast, and agar.

extract_protocol: RNA was extracted from a pooled sample of 20 larvae with STAT-60 Buffer, according to the manufacturer's protocols (Isotex Diagnostics).

treatment_protocol: Expose staged third instar larvae to heat shock at 37C for one hour.

tag: Wildtype OR strain, staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.

source_name: HS-DIF

tag: HS-DIF third instar larvae, with identical staging to the wildtype larvae used for channel 1.


title: LDI-DL_ctr-2aDros-s1

description: The image data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. "Single array analysis can be used to build databases of gene expression profiles, facilitate sample classification and transcript clustering, and monitor gross expression characteristics. In addition, the analyses provide the initial data required to perform comparisons between experiment and baseline (Control) arrays. This analysis generates a Detection p-value, which is evaluated against user-definable cut-offs to determine the detection call. This call indicates whether a transcript is reliably detected (Present) or not detected (Absent). Additionally, a Signal value is calculated which assigns a relative measure of abundance to the transcript.? (See Affymetrix Manuals for more details)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

source_name: Dorsal Replicate 3

label_protocol: Approximately 25 ?g of total RNA was processed to produce biotinylated cRNA targets. (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted from a pooled sample of 20 larvae with STAT-60 Buffer, according to the manufacturer's protocols (Isotex Diagnostics). RNA was purified using QIAGEN RNeasy Mini kit according to manufacturer's protocols.

treatment_protocol: Larvae were injected with about 0.1 microliter of E. coli bacteria suspended in PBS.  RNA was harvested two hours later.

tag: Dorsal 1 mutant staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.


title: Heat Shock Dorsal HS_DL_1

description: The experiment is meant to determine the role of ectopic expression of HS-Dorsal on Drosophila gene expression.

source_name: HS-Dorsal


title: LDI-inj2h-2bDros-s1

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

source_name: Injected Replicate 3

label_protocol: Approximately 25 microgram of total RNA was processed to produce biotinylated cRNA targets. (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: Wildtype staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.


title: LDI-inj2h-1aDros-s1

source_name: Injected Replicate 1


title: LDI-DL_ctr-1aDros-s1

source_name: Dorsal Replicate 1


title: WS_Input_for_CLF_02

description: Input Genomic DNA

source_name: 10-14 day old seedlings


title: LDI-E20_ctr-3aDros-s1

source_name: Relish Replicate 3

tag: Relish E20 mutant staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.


title: LDI-E20_ctr-2aDros-s1

source_name: Relish Replicate 2


title: Heat Shock Dif HS_DIF_2


title: LDI-E20_ctr-1aDros-s1

source_name: Relish replicate 1

tag: RelishE20 mutant staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.


title: Heat Shock Dorsal HS_DL_3

tag: HS-Dorsal third instar larvae, with identical staging to the wildtype larvae used for channel 1.


title: LDI-ctr-2aDros-s1

source_name: Control Replicate 2

treatment_protocol: Control flies were injected with about 0.1 microliter of Phosphate Buffered Saline.  RNA was harvested two hours later.


title: Control line biological Rep. 1

source_name: Adult whole female flies of control line 1


title: LDI-DL_ctr-1bDros-s1

source_name: Dorsal Replicate 2


title: LDI-Dif_ctr-2aDros-s1

source_name: Dif Replicate 2

treatment_protocol: Control flies were injected with about 0.1 microliter of E. coli bacteria suspended in Phosphate Buffered Saline.  RNA was harvested two hours later.

tag: Dif1 mutant staged third instar larvae. Staging performed by feeding larvae yeast mixed with bromophenol blue, to observe thickening of gut, as described in Andres, A.J. and Thummel, C.S. (1994) Methods for quantitative analysis of transcription in larvae and prepupae. Methods Cell Biol, 44, 565-573.


title: LDI-inj2h-2aDros-s1

source_name: Injected Replicate 2


title: LDI-Dif_ctr-1aDros-s1

source_name: Dif Replicate 1


title: LDI-ctr-2bDros-s1

source_name: Control Replicate 3


title: Day 2_L_+RA_Achip

status: Public on Apr 13 2007

city: Toronto

first: William

middle: L

last: Stanford

state: Ontario

address: 164 College St

department: IBBME

country: Canada

institute: University of Toronto

description: gene expression of 2 day RA differentiated ESCs

hyb_protocol: Amplified and biotin labeled cRNA was hybridized to both the Affymetrix GeneChips MG_U74av2 and MG_U74bv2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Mus musculus

source_name: embryonic stem cell, low Oct4 subpopulation, 2 days following RA treatment

label_protocol: The protocol was modified from the Affymetrix GeneChip technical note entitled: Eukaryotic Small Sample Target Labeling.  500 ng of cRNA was used for the second cycle of amplification and 1 g of purified cDNA from the second cycle was used for biotin labeling.  It was determined that this resulted in optimized linearity of amplification. Amplified and biotin labeled cRNA was hybridized to both the Affymetrix GeneChips MG_U74av2 and MG_U74bv2.

growth_protocol: R1 ESCs and Oct4:eGFP ESCs (Viswanathan et al., 2003) were cultured at 37°C and 5% CO2, on a layer of mitomycin-treated embryonic fibroblasts (MEFs) in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100 µM beta-mercaptoethanol (Sigma).  Differentiation media consisted of either ESC media without LIF, or ESC media without LIF and supplemented with 0.1 uM retinoic acid.  Selection media consisted of ESC media supplemented with 150 g/mL G418 (Gibco).  ESCs were passaged every two days at a ratio of 1:5 by washing with PBS (Gibco), dissociating with 0.05% trypsin (Gibco) for 5 minutes at 37°C and resuspending in ESC media. Media was changed daily.

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

treatment_protocol: Oct4:eGFP ESCs were plated on 10-cm tissue culture treated dishes (Falcon) coated with 0.1% gelatin in differentiation media at a density of 0.5x106 cells/dish for 5 days of differentiation, 106 cells/dish for 3 days of differentiation, 2x106 cells/dish for 2 days of differentiation or 3.5x106 cells/dish for 1 day of differentiation.  Control, cells were harvested two days after plating in +LIF media.  Differentiating cells were FACS sorted by eGFP expression following trypsinization and resuspension in 2% FBS in PBS at a dilution of 8x106 cells/mL.

tag: R1 cell line


title: LDI-ctr-1aDros-s1

description: The image data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. "Single array analysis can be used to build databases of gene expression profiles, facilitate sample classification and transcript clustering, and monitor gross expression characteristics. In addition, the analyses provide the initial data required to perform comparisons between experiment and baseline (Control) arrays. This analysis generates a Detection p-value, which is evaluated against user-definable cut-offs to determine the detection call. This call indicates whether a transcript is reliably detected (Present) or not detected (Absent). Additionally, a Signal value is calculated which assigns a relative measure of abundance to the transcript.” (See Affymetrix Manuals for more details)

source_name: Control Replicate 1

label_protocol: Approximately 25 µg of total RNA was processed to produce biotinylated cRNA targets. (Expression Analysis Technical Manual, 2001, Affymetrix).


title: Heat Shock Dif HS-Dif_1

source_name: Wildtype

source_name: HS-DIF


title: LDI-Dif_ctr-3aDros-s1

source_name: Dif Replicate 3


title: Heat Shock Dorsal HS_DL_2

source_name: HS-Dorsal


title: Day 3_H_-LIF_Achip

description: gene expression of 3 day LIF differentiated ESCs

source_name: embryonic stem cell, high Oct4 subpopulation, 3 days following LIF withdrawal


title: Day 1_H_+RA_Achip

description: gene expression of 1 day RA differentiated ESCs

source_name: embryonic stem cell, high Oct4 subpopulation, 1 day following RA treatment


title: Day 3_L_-LIF_Achip

source_name: embryonic stem cell, low Oct4 subpopulation, 3 days following LIF withdrawal


title: Day 1_H_-LIF_Achip_rep1

description: gene expression of 1 day LIF differentiated ESCs

source_name: embryonic stem cell, high Oct4 subpopulation, 1 day following LIF withdrawal


title: Day 2_M_+RA_Achip

source_name: embryonic stem cell, medium Oct4 subpopulation, 2 days following RA treatment


title: Day 1_L_+RA_Achip

source_name: embryonic stem cell, low Oct4 subpopulation, 1 day following RA treatment


title: Day 5_L_-LIF_Bchip

description: gene expression of 5 day LIF differentiated ESCs

source_name: embryonic stem cell, low Oct4 subpopulation, 5 days following LIF withdrawal


title: Day 1_L_+RA_Bchip


title: Control H_Achip_rep1

description: gene expression of undifferentiated ESCs

source_name: embryonic stem cell, high Oct4 subpopulation, +LIF conditions


title: Day 1_L_-LIF_Achip

source_name: embryonic stem cell, low Oct4 subpopulation, 1 day following LIF withdrawal


title: Day 1_M_-LIF_Achip

source_name: embryonic stem cell, medium Oct4 subpopulation, 1 day following LIF withdrawal


title: Day 5_M_-LIF_Achip

source_name: embryonic stem cell, medium Oct4 subpopulation, 5 days following LIF withdrawal


title: Day 1_H_+RA_Bchip


title: Day 2_M_+RA_Bchip


title: Day 5_H_-LIF_Achip

source_name: embryonic stem cell, high Oct4 subpopulation, 5 days following LIF withdrawal


title: Day 1_M_+RA_Achip

source_name: embryonic stem cell, medium Oct4 subpopulation, 1 day following RA treatment


title: Day 5_L_-LIF_Achip


title: Control H_Achip_rep2


title: Day3_L_-LIF_Bchip


title: Day 5_H_-LIF_Bchip


title: Day 2_L_+RA_Bchip

source_name: embryonic stem cell, low Oct4 subpopulation, 2 days following RA treatment


title: Day 1_M_+RA_Bchip


title: Day 1_H_-LIF_Achip_rep2


title: Day 3_M_-LIF_Achip

source_name: embryonic stem cell, medium Oct4 subpopulation, 3 days following LIF withdrawal


title: Day 5_M_-LIF_Bchip


title: Day 3_M_-LIF_Bchip


title: Day 3_H_-LIF_Bchip


title: Day 1_L_-LIF_Bchip


title: Control M_Bchip_rep1

source_name: embryonic stem cell, medium Oct4 subpopulation, +LIF conditions


title: Day 1_H_-LIF_Bchip_rep2


title: Day 1_H_-LIF_Bchip_rep1


title: Control M_Achip_rep1


title: RCG-12 cells cultured at nonpermissive temperature for 3 days-1

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: A rat conditionally immortalized astrocyte cell line, RCG-12, derived from primary cultured rat cortical glia cells infecting with a temperature-sensitive simian virus 40 large T-antigen was used. RCG-12 cells were cultured at nonpermissive temperature (39°C) for 3 days.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: phycoerythrin

organism: Rattus norvegicus

source_name: Rat astrocyte cell line RCG-12

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K.K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Rat astrocyte cell line RCG-12


title: Control H_Bchip_rep1


title: csn51 60hrs aed 3 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 3 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 1 cy3

tag: Wild type


title: RCG-12 cells cultured at permissive temperature for 3 days-2

description: A rat conditionally immortalized astrocyte cell line, RCG-12, derived from primary cultured rat cortical glia cells infecting with a temperature-sensitive simian virus 40 large T-antigen was used. RCG-12 cells were cultured at permissive temperature (33°C) for 3 days.


title: RCG-12 cells cultured at permissive temperature for 3 days-1


title: Day 1_M_-LIF_Bchip


title: RCG-12 cells cultured at nonpermissive temperature for 3 days-2


title: csn51 60hrs aed 2 cy3

description: Biological replicate 2 of 4

source_name: w118 60 hrs aed 1 cy5


title: Progesterone treated versus control Ishikawa cells replicate 3

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

description: Biological replicate 3 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone

hyb_protocol: Hybridizations were carried out with a TECAN HS4800 instrument using the formamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 micro grams COT1 DNA/micro grams RNA at 37 degrees C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with 0.2xSSC for 30 sec.

scan_protocol: Scanned on an AXON 4000B scanner Images were quantified using GenePix pro 6.0 software

data_processing: Quality control ( SNR >3 and saturation level <30%  to be eligible) of individual spots. Dye-swap normalized, using technical replicate in which the dye-orientation was reversed.

source_name: total RNA from endometrial adenocarcinoma cells (Ishikawa)

label_protocol: 5 micro grams of total RNA was reverse transcribed and labelled with Cy5-attached dendrimer using the Genisphere 3DNA 350 HS kit (Genisphere) as described in the manufacturer’s protocol

tag: Ishikawa cell line (ECACC #99040201) derived from a well-differentiated endometrial adenocarcinoma

label_protocol: 5 micro grams of total RNA and Arabidopsis thaliana mRNA (Stratagene Spotreporter) was reverse transcribed and labelled with Cy3-attached dendrimer using the Genisphere 3DNA 350 HS kit (Genisphere) as described in the manufacturer’s protocol.

growth_protocol: Monolayer cultures of Ishikawa cells were established in RPMI-1640 medium containing 10% fetal calf serum including 0.2% ethanol and 30  micro gram/ml progesterone

tag: Ishikawa cell line (ECACC #99040201) derived from a well-differentiated endometrial adnocarcinoma


title: Progesterone treated versus control Ishikawa cells replicate 2

description: Biological replicate 2 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone

growth_protocol: Monolayer cultures of Ishikawa cells were established in RPMI-1640 medium containing 10% fetal calf serum including 0.2% ethanol


title: csn51 60hrs aed 1 cy3

description: Biological replicate 1 of 4


title: Control H_Bchip_rep2


title: Progesterone treated versus control Ishikawa cells replicate 5

description: Biological replicate 5 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone

hyb_protocol: Hybridizations were carried out with a TECAN HS4800 instrument using the formamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 micro grams COT1 DNA/micro grams  RNA at 37 degrees C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with 0.2xSSC for 30 sec.

data_processing: Quality control ( SNR >3 and saturation level <30%  to be eligible). Lowess normalized

growth_protocol: Monolayer cutures of Ishikawa cells were established in RPMI-1640 medium containing 10% fetal calf serum including 0.2% ethanol

growth_protocol: Monolayer cultures of Ishikawa cells were established in RPMI-1640 medium containing 10% fetal calf serum including 0.2% ethanol and 30 micro grams/ml progesterone


title: Progesterone treated versus control Ishikawa cells replicate 4

description: Biological replicate 4 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone


title: Progesterone treated versus control Ishikawa cells replicate 1

description: Biological replicate 1 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone


title: Progesterone treated versus control Ishikawa cells replicate 6

description: Biological replicate 6 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone


title: csn4null 60hrs aed 2 cy5

description: Biological replicate 2 of 3.

source_name: csn4null Total larva extract

source_name: w118 60 hrs aed 2 cy3


title: csn4null 60hrs aed 1 cy3

description: Biological replicate 1 of 3.


title: csn53 96hrs aed 5 cy5

description: Biological replicate 5 of 5

source_name: csn53Total larva extract

value: 96 hrs

source_name: w118 96 hrs aed 5 cy3


title: csn51 72hrs aed 1 cy3

description: Biological replicate 1 of 4

value: 72 hrs

source_name: w118 72 hrs aed 1 cy5


title: csn53 96hrs aed 4 cy5

description: Biological replicate 4 of 5

source_name: w118 96 hrs aed 4 cy3


title: csn53 96hrs aed 2 cy3

description: Biological replicate 2 of 5

source_name: csn53 Total larva extract

source_name: w118 96 hrs aed 2 cy5


title: csn53 60hrs aed 3 cy5

description: Biological replicate 3 of 5

source_name: w118 60 hrs aed 3 cy3


title: Progesterone treated versus control Ishikawa cells replicate 7

description: Biological replicate 7 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone


title: Progesterone treated versus control Ishikawa cells replicate 8

description: Biological replicate 8 of 8. Control Ishikawa cells vs Ishikawa cells treated with progesterone


title: csn51 96hrs aed 3 cy5

description: Biological replicate 3 of 5

source_name: csn51Total larva extract

source_name: w118 96 hrs aed 3 cy3


title: csn51 96hrs aed 5 cy5

description: Biological replicate 5 of 5


title: csn53 60hrs aed 4 cy5

description: Biological replicate 4 of 5

source_name: w118 60 hrs aed 4 cy3


title: csn51 72hrs aed 3 cy5

description: Biological replicate 3 of 4

source_name: w118 72 hrs aed 3 cy3


title: csn53 96hrs aed 3 cy5

description: Biological replicate 3 of 5


title: csn53 60hrs aed 5 cy5

description: Biological replicate 5 of 5

source_name: w118 60 hrs aed 5 cy3


title: csn51 96hrs aed 2 cy3

description: Biological replicate 2 of 5

source_name: csn51 Total larva extract


title: csn53 60hrs aed1 cy3

description: Biological replicate 1 of 5

source_name: w118 60 hrs aed 1 cy5


title: csn53 60hrs aed 2 cy3

description: Biological replicate 2 of 5

source_name: w118 60 hrs aed 2 cy5


title: csn51 96hrs aed 4 cy5

description: Biological replicate 4 of 5


title: csn4null 60hrs aed 3 cy3

description: Biological replicate 3 of 3.

source_name: csn4null Total larva extract

source_name: w118 60 hrs aed 3 cy5


title: csn51 72hrs aed 4 cy5

description: Biological replicate 4 of 4

source_name: w118 72 hrs aed 4 cy3


title: csn53 72hrs aed 4 cy5

description: Biological replicate 4 of 4


title: csn51 72hrs aed 2 cy5

description: Biological replicate 2 of 4

source_name: w118 72 hrs aed 2 cy3


title: csn51 96hrs aed 1 cy3

description: Biological replicate 1 of 5

source_name: w118 96 hrs aed 1 cy5


title: csn53 72hrs aed 1 cy3

description: Biological replicate 1 of 4

source_name: w118 72 hrs aed 1 cy5


title: 13561517 - SA+W1+MeOH 2 vs SA 2

city: evry

first: taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Genes activated by s.a through the activity of phosphatidylinositol 4-kinase

hyb_protocol: SA 2 Cy5 / SA+W1+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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

source_name: SA 2

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

growth_protocol: cell culture - Media : Gamborg B5	 hygrometry : 70%	 Temperature : 22degreeC	 Light : 100 mmol.m-2.s-1	 Cell suspension culture, constant light, constant horizontal agitation 130 RPM.

extract_protocol: Pool of extract, SA F:.33ug, SA E:.33ug, SA D:.33ug.

treatment_protocol: Name:SA250 - compound based treatment - compound addition,salicylic acid:time 4hour . salicylic acid (250(u)M)was added as sodium salt solubilized in water (50 mM stock solution); wortmannin was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.

tag: Arabidopsis thaliana (columbia)  - age:5day

source_name: SA+W1+MeOH 2

extract_protocol: Pool of extract, SA+W1+MeOH F:.33ug, SA+W1+MeOH E:.33ug, SA+W1+MeOH D:.33ug.

treatment_protocol: Name:SA250+W1+methanol - compound based treatment - compound addition,sa250+w1+methanol:time 4hour . salicylic acid (250(u)M) was added as sodium salt solubilized in water (50 mM stock solution); wortmannin (1(u)M) was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.


title: 13561406 - SA 2 vs SA+W1+MeOH 2

hyb_protocol: SA+W1+MeOH 2 Cy5 / SA 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: csn53 96hrs aed 1 cy3

description: Biological replicate 1 of 5

source_name: csn53 Total larva extract


title: csn5null 96hrs aed 3 cy5

description: Biological replicate 3 of 4

source_name: csn5null Total larva extract


title: csn5null 60hrs aed 4 cy5

description: Biological replicate 4 of 5

source_name: w118 60 hrs aed 1 cy3


title: csn53 72hrs aed 2 cy3

description: Biological replicate 2 of 4

source_name: w118 72 hrs aed 2 cy5


title: 13561543 - W30+MeOH 2 vs W1+MeOH 2

hyb_protocol: W1+MeOH 2 Cy5 / W30+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: W1+MeOH 2

extract_protocol: Pool of extract, W1+MeOH F:.33ug, W1+MeOH E:.33ug, W1+MeOH D:.33ug.

treatment_protocol: Name:W1+methanol - compound based treatment - compound addition,w1+methanol:time 4hour . salicylic acid was added as sodium salt solubilized in water (50 mM stock solution); wortmannin (1(u)M) was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.

source_name: W30+MeOH 2

extract_protocol: Pool of extract, W30+MeOH F:.33ug, W30+MeOH E:.33ug, W30+MeOH D:.33ug.

treatment_protocol: Name:W30+methanol - compound based treatment - compound addition,w30+methanol:time 4hour . salicylic acid was added as sodium salt solubilized in water (50 mM stock solution); wortmannin (30(u)M) was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.


title: csn5null 60hrs aed 3 cy5

description: Biological replicate 3 of 5


title: csn5null 96hrs aed 2 cy3

description: Biological replicate 2 of 4

source_name: w118 96 hrs aed 2 cy5


title: csn5null 60hrs aed 5 cy5

description: Biological replicate 5 of 5


title: 13561536 - W1+MeOH 2 vs MeOH 2

hyb_protocol: MeOH 2 Cy5 / W1+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: MeOH 2

extract_protocol: Pool of extract, MeOH F:.33ug, MeOH E:.33ug, MeOH D:.33ug.

treatment_protocol: Name:methanol - compound based treatment - compound addition,methanol:time 4hour . salicylic acid was added as sodium salt solubilized in water (50 mM stock solution); wortmannin was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.


title: csn5null 60hrs aed 1 cy3

description: Biological replicate 1 of 5

source_name: w118 60 hrs aed 1 cy5


title: csn5null 60hrs aed 2 cy3

description: Biological replicate 2 of 5


title: 13561407 - SA+W1+MeOH 2 vs SA+W30+MeOH 2

hyb_protocol: SA+W30+MeOH 2 Cy5 / SA+W1+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: SA+W30+MeOH 2

extract_protocol: Pool of extract, SA+W30+MeOH F:.33ug, SA+W30+MeOH E:.33ug, SA+W30+MeOH D:.33ug.

treatment_protocol: Name:SA250+W30+methanol - compound based treatment - compound addition,sa250+w30+methanol:time 4hour . salicylic acid (250(u)M) was added as sodium salt solubilized in water (50 mM stock solution); wortmannin (30(u)M) was added as stock solution in methanol to produce final 0.5% methanol (v/v) and desired final concentration of wortmannin.


title: csn5null 96hrs aed 4 cy5

description: Biological replicate 4 of 4

source_name: w118 96 hrs aed 4 cy3


title: 13561521 - MeOH 2 vs W1+MeOH 2

hyb_protocol: W1+MeOH 2 Cy5 / MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13371038 - W30+MeOH vs W1+MeOH

hyb_protocol: W1+MeOH Cy5 / W30+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, W1+MeOH C:.33ug, W1+MeOH B:.33ug, W1+MeOH A:.33ug.

extract_protocol: Pool of extract, W30+MeOH C:.33ug, W30+MeOH B:.33ug, W30+MeOH A:.33ug.


title: 13561414 - SA+W30+MeOH 2 vs SA+W1+MeOH 2

hyb_protocol: SA+W1+MeOH 2 Cy5 / SA+W30+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561540 - W1+MeOH 2 vs W30+MeOH 2

hyb_protocol: W30+MeOH 2 Cy5 / W1+MeOH 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557356 - SA 2 vs Water 2

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

source_name: Water 2

extract_protocol: Pool of extract, Water F:.33ug, Water E:.33ug, Water D:.33ug.

treatment_protocol: Name:Water - control buffer - control buffer,water:time 4hour .


title: 13557354 - Water 2 vs SA 2

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


title: csn5null 96hrs aed 1 cy3

description: Biological replicate 1 of 4


title: csn4null 96hrs aed 4 cy5

description: Biological replicate 4 of 4

source_name: csn4null Total larva extract


title: SCLC NCI-H526 cell line (NCI-H526ps3)

city: Abbott Park

first: Mark

last: Anderson

state: IL

address: 100 Abbott Park Road

institute: Abbott Laboratories

hyb_protocol: Affy protocol, midi_euk_2v3

data_processing: GCOS

source_name: cell line

label_protocol: Enzo kit

extract_protocol: Trizol

tag: SCLC NCI-H526 cell line


title: csn4null 96hrs aed 3 cy5

description: Biological replicate 3 of 4

source_name: w118 96 hrs aed 3 cy3


title: 13371033 - SA+W30+MeOH vs SA+W1+MeOH

hyb_protocol: SA+W1+MeOH Cy5 / SA+W30+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, SA+W1+MeOH C:.33ug, SA+W1+MeOH B:.33ug, SA+W1+MeOH A:.33ug.

extract_protocol: Pool of extract, SA+W30+MeOH C:.33ug, SA+W30+MeOH B:.33ug, SA+W30+MeOH A:.33ug.


title: csn4null 96hrs aed 1 cy3

description: Biological replicate 1 of 4

source_name: w118 96 hrs aed 1 cy5


title: 13371034 - W1+MeOH vs MeOH

hyb_protocol: MeOH Cy5 / W1+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: MeOH

extract_protocol: Pool of extract, MeOH C:.33ug, MeOH B:.33ug, MeOH A:.33ug.


title: csn5null 72hrs aed 4 cy5

description: Biological replicate 4 of 4

hyb_protocol: FHCRC

source_name: w118 72 hrs aed 4 cy3


title: 13371035 - MeOH vs W1+MeOH

hyb_protocol: W1+MeOH Cy5 / MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: csn5null 72hrs aed 3 cy5

description: Biological replicate 3 of 4

source_name: csn5null Total larva extract

source_name: w118 72 hrs aed 3 cy3


title: csn4null 96hrs aed 2 cy3

description: Biological replicate 2 of 4


title: 13371032 - SA+W1+MeOH vs SA+W30+MeOH

hyb_protocol: SA+W30+MeOH Cy5 / SA+W1+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SCLC NCI-H526 cell line (NCI-H526ps2)


title: 13371031 - SA+W1+MeOH vs SA

hyb_protocol: SA Cy5 / SA+W1+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: SA

extract_protocol: Pool of extract, SA C:.33ug, SA B:.33ug, SA A:.33ug.


title: 13371036 - W1+MeOH vs W30+MeOH

hyb_protocol: W30+MeOH Cy5 / W1+MeOH Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: csn5null 72hrs aed 1 cy3

description: Biological replicate 1 of 4

source_name: w118 72 hrs aed 1 cy5


title: csn4null 72hrs aed 3 cy5

description: Biological replicate 3 of 4


title: csn4null 72hrs aed 4 cy5

description: Biological replicate 4 of 4


title: 13371030 - SA vs SA+W1+MeOH

hyb_protocol: SA+W1+MeOH Cy5 / SA Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: csn5null 72hrs aed 2 cy3

description: Biological replicate 2 of 4

source_name: w118 72 hrs aed 2 cy5


title: SCLC NCI-H526 cell line (NCI-H526ps.1)


title: 13371024 - Water vs SA

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

source_name: Water

extract_protocol: Pool of extract, Water C:.33ug, Water B:.33ug, Water A:.33ug.


title: csn4null 72hrs aed 2 cy3

description: Biological replicate 2 of 4


title: 13371026 - SA vs Water

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


title: csn4_72_cy3_1

hyb_protocol: done by FHCRC genomic unit

scan_protocol: done by FHCRC genomic unit

source_name: csn4null, 72hrs AED

label_protocol:
I. RT REACTION
Oligo-dT/Random Prime RNA
Reagent Final Quantity in Rxn Volume
Oligo-dT* 5ug
Random Primers** 5ug
RNA Recommended quantities: 30ug Total RNA,
2ug PolyA or 4ug aRNA(not modified)
Water (RNAse free)
Final Volume = 18.5ul
* Use Oligo-dT when labeling Total RNA
** Use Random primers when labeling amplified RNA that is not modified or poly-A selected RNA
Incubate RNA/Oligo Mixture @ 70°C - 10 min.
Chill on ice (immediately) – 10 min.
cDNA Synthesis
Reagent Volume for 1 Rxn
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.
II. HYDROLYSIS
Add:
10ul 1N NaOH
10ul 0.5M EDTA
Incubate @ 65ºC –15 min.
Neutralize
Add: 25ul 1M Tris (pH 7.4)

III. CLEANUP
To continue with the Amino-Allyl dye coupling procedure, all Tris must be removed from the
reaction to prevent monofunctional NHS-ester Cye dyes from coupling with free amine groups in solution.
Add 450ul H2O to a Microcon-30 concentrator.
Add neutralized reaction (rinse out tube).
Spin @ 10,000 x g – 8 min.
Decant flo-thru.
Wash 2X: Refill original container with 500ul H2O.
Elute cDNA – Turn column upside down, Spin @ 10,000 x g – 2 min. (in clean tube).
Dry eluate in Speed-Vac.
IV. DYE COUPLING
Aliquoting Cy3 and Cy5 Monoreactive Dyes
Resuspend fresh tube of dye in 36 ul of DMSO that has been treated with Molecular Sieves.
Technical Note: DMSO should be dried using 100g/L of 4 Å molecular sieve pellets from Sigma (cat. #M-0133).
Prior to use, the pellets should be baked @ 300-350ºC for 3 hrs, followed by cooling and storage with desiccant until needed. Pellets should be introduced directly into the DMSO container and followed with occasional shaking.
Aliquot 2.25 ul x 16 tubes and store the aliquots in the dark @ 4ºC.
Coupling Dye to cDNA
Resuspend cDNA pellet in 4.5 ul H20.
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.
V. QUENCHING AND CLEANUP
Before combining Cy3 and Cy5 labeled samples for hybridization, the reactions must be quenched to prevent cross-coupling.
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.
Combine Cy3 and Cy5 reactions.
Add 70 ul H2O.
Add 500 ul Buffer PB – Mix.
Apply to Qia-quick column – Spin @ 13,000 x g – 2 min.
Discard flo-thru.
Add 750 ul Buffer PE – Spin @ 13,000 x g – 2 min.
Discard flo-thru – Repeat wash.
Discard flo-thru – Spin @ max rpm to dry column.
Transfer to clean/new Eppendorf tube.
Add 30 ul Buffer EB to center of filter – Allow to stand 1 min. @ RT.
Spin @ 13,000 x g – 2 min.
Repeat elution step again.
Final volume should be ~ 60 ul.

VI. SAMPLE PREPARATION FOR HYBRIDIZATION
Dry down eluate (Qiaquick) in speed-vac.
Standard Format 16 block Arrays: Large Format 32 block Arrays:
Resuspend in 20 ul H2O Resuspend in 27.8 ul H2O
Add 4 ul 20X SSC Add 5.4 ul 20X SSC
Add 2 ul Poly A (10mg/ml stock) Add 2.8 ul Poly A (10 mg/ml stock)
Filter in Millipore 0.45 um spin column.
Prewet filter with 20 ul H20
Spin @ 10,000 x g – 2 min. and Decant completely.
Apply sample to side of column avoiding probe contact with filter.
Spin @ 10,000 x g – 2 min.
Store sample @ -20ºC until ready for hybridization.

extract_protocol: RNA was extracted with TRIZOL® Reagent (Invitrogen) according to manufacturer protocol

source_name: wild type, 72hrs AED


title: NCI-H524 cell line (NCI-H524a)

tag: NCI-H524 cell line


title: NCI-H524 cell line (NCI-H524c)


city: Créteil

first: Jacques

last: Bourbon

address: 8 rue du Général Sarrail

department: Faculté de Médecine

institute: Université de Paris 12

description: pooled cells from 4 pups (21-day old, terminated secondary septation) from litter 3

hyb_protocol: Following fragmentation, 10 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were obtained by processing raw CEL files through the Affy package. Background correction method RMA, normalization method qspline, probe-level correction Pmonly, and summarization method Li-Wong model were used.

source_name: Lung fibroblasts isolated on postnatal day 21, biological repl3 (litter 3)

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 10 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rat lung fibroblasts were extemporaneously isolated on postnatal days 2 (saccular stage), 7 (alveolar stage, progressing secondary septation) and 21 (alveolar stage, terminated secondary septation)

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

treatment_protocol: Lung cells were dispersed by trypsin and collagenase, then plated onto plastic Petri dishes in MEM-10% FBS and allowed to adhere for 45 min. Non-adherent cells were discarded, and the adherent fibroblasts were rinsed and immediately scrapped and pelleted. Freshly isolated cells were stored at -80°C until RNA extraction.

tag: Sprague Dawley

tag: pooled cells from 4 pups (21-day old) from litter 3


description: pooled cells from 4 pups (21-day old, terminated secondary septation) from litter 1

source_name: Lung fibroblasts isolated on postnatal day 21, biological repl1 (litter 1)

tag: pooled cells from 4 pups (21-day old) from litter 1


title: Backskin_Get1_e18_WT2

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Get1, grainyhead epithelial transactivator 1. Also known as grainyhead-like 3 (Grhl3)

hyb_protocol: Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Genome 430 2.0 array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Strain C57BL/6

tag: Tissue

value: Backskin

tag: Age


description: pooled cells from 4 pups (7-day old, progressing secondary septation) from litter 2

source_name: Lung fibroblasts isolated on postnatal day 7, biological repl2 (litter 2)

tag: pooled cells from 4 pups (7-day old) from litter 2


description: pooled cells from 4 pups (7-day old, progressing secondary septation) from litter 3

source_name: Lung fibroblasts isolated on postnatal day 7, biological repl3 (litter 3)

tag: pooled cells from 4 pups (7-day old) from litter 3


description: pooled cells from 5 pups (2-day old, before septation) from litter 3

source_name: Lung fibroblasts isolated on postnatal day 2, biological repl3 (litter 3)

tag: pooled cells from 5 pups (2-day old) from litter 3


description: pooled cells from 4 pups (7-day old, progressing secondary septation) from litter 1

source_name: Lung fibroblasts isolated on postnatal day 7, biological repl1 (litter 1)

tag: pooled cells from 4 pups (7-day old) from litter 1


title: AML sample 7 diagnosis

status: Public on Apr 11 2007

city: London

first: Manoj

last: Raghavan

address: Charterhouse Square

department: Centre for Medical Oncology, Institute of Cancer

country: United Kingdom

institute: Barts and the London, Queen Mary's School of Medicine and Dentistry

description: SNP genotype data from AML patient at diagnosis

hyb_protocol: Affymetrix 10K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

source_name: AML blood/marrow cells relapse

label_protocol: Affymetrix 10K mapping assay protocol

growth_protocol: Not applicable

extract_protocol: Phenol chloroform

treatment_protocol: AML cells collected from blood or bone marrow. Ficoll separation, and cryopreserved in liquid nitrogen.

tag: FAB type = M5


title: AML sample 75 diagnosis

tag: cytogenetics = 46,XX


title: AML sample 57 diagnosis

tag: FAB type = M1


title: AML sample 62 diagnosis


description: pooled cells from 4 pups (21-day old, terminated secondary septation) from litter 2

source_name: Lung fibroblasts isolated on postnatal day 21, biological repl2 (litter 2)

tag: pooled cells from 4 pups (21-day old) from litter 2


title: AML sample 23 diagnosis

tag: FAB type = M2


title: AML sample 38 diagnosis

tag: cytogenetics = 46,del(5)(q31)XY


description: pooled cells from 5 pups (2-day old, before septation) from litter 1

source_name: Lung fibroblasts isolated on postnatal day 2, biological repl1 (litter 1)

tag: pooled cells from 5 pups (2-day old) from litter 1


title: AML sample 17 diagnosis

tag: cytogenetics = 46,XY,t(15;17)


title: AML sample 60 diagnosis


title: Backskin_Get1_e18_WT1


title: AML sample 82 diagnosis

tag: cytogenetics = 45,X-Y


title: AML sample 63 diagnosis


description: pooled cells from 5 pups (2-day old, before septation) from litter 2

source_name: Lung fibroblasts isolated on postnatal day 2, biological repl2 (litter 2)

tag: Sprague Dawley

tag: pooled cells from 5 pups (2-day old) from litter 2


title: AML sample 64 diagnosis

tag: FAB type = M3


title: Backskin_Get1_e18_WT3

tag: Strain C57BL/6

tag: Tissue

tag: Age


title: AML sample 300 diagnosis

tag: FAB type = M4

tag: cytogenetics = 46,XY


title: csn53 72hrs aed 3 cy5

description: Biological replicate 3 of 4

source_name: csn53 Total larva extract

extract_protocol: TriZol procedure

tag: time aed

source_name: w118 72 hrs aed 3 cy3

tag: Wild type


title: AML sample 37 diagnosis

tag: cytogenetics = 46,XX


title: AML sample 74 diagnosis

tag: FAB type = M1

tag: cytogenetics = 46,XX,t(15;17),idem17


title: AML sample 66 diagnosis


title: AML sample 50 diagnosis


title: AML sample 20 diagnosis


title: AML sample 68 diagnosis

tag: FAB type = M2

tag: cytogenetics = 48,XY,+11,+13


title: AML sample 51 diagnosis


title: AML sample 18 diagnosis

tag: cytogenetics = 46,XY,inv(16)(p13q22)


title: AML sample 15 diagnosis

tag: cytogenetics = 46,XY,t(8;21)


title: AML sample 39 diagnosis


title: AML sample 70 diagnosis


title: AML sample 54 diagnosis


title: AML sample 56 diagnosis


title: AML sample 61 diagnosis


title: AML sample 19 diagnosis

tag: cytogenetics = 46,XY,dir ins(6;11)(q27;q13q23)


title: AML sample 79 diagnosis


title: AML sample 52 diagnosis


title: AML sample 76 diagnosis


title: AML sample 34 diagnosis

tag: cytogenetics = 45,XY,-7,+mar. ish ider(7)add(7)(wcp7+,CEP7+,D75486-)


title: AML sample 65 diagnosis


title: AML sample 77 diagnosis

tag: FAB type = M5


title: AML sample 36 diagnosis


title: AML sample 80 diagnosis


title: AML sample 78 diagnosis


title: AML sample 31 diagnosis

tag: cytogenetics = 46,XY,-9,+17


title: AML sample 11 diagnosis paired with sample 12

source_name: AML marrow cells remission

tag: FAB type = NA

tag: cytogenetics = not analysed


title: AML sample 12 diagnosis paired with sample 11


title: AML sample 43 diagnosis paired with sample 42


title: cy3:SHR treated w/ nifedipine and then washed out, biological rep 5g; cy5:pool of 6 WKY control rats

city: Seattle

first: Lynn

middle: M

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: 60 C for 17 hours

scan_protocol: Agilent DNA Microarray scanner

data_processing: images analyzed with Agilent Feature Extraction v7.1,

source_name: medial layer of thorassic and abdominal aorta from pool of 6 WKY control rats

label_protocol: fluorescent linear amplification kit from Agilent

extract_protocol: Qiagen RNeasy kit

tag: mean systolic blood pressure = 107+/-8 mm HG

source_name: medial layer of thorassic and abdominal aorta from SHR rat treated w/ nifedipine and then washed out

tag: mean systolic blood pressure = 151+/-4 mm HG


title: cy5:SHR treated w/ nifedipine and then washed out, biological rep 4r; cy3:pool of 6 WKY control rats


title: cy3:SHR treated w/ nifedipine and then washed out, biological rep 1g; cy5:pool of 6 WKY control rats


title: AML sample 42 remission paired with sample 43