title: BSG13

status: Public on Dec 01 2010

type: genomic

city: Nottingham

first: Jennifer

middle: Helen

last: Barrow

address: Queen's Medical Centre

department: Clinical Sciences

country: United Kingdom

institute: University of Nottingham, Children's Brain Tumour Research Centre

hyb_protocol: Samples hybridised using Agilent's Hybridisation Kit, following the manufacturer's protocol.

scan_protocol: Arrays washed in accordance with manufacturer's protocol and scanned using an Agilent DNA Microarray Scanner

data_processing: Tiff files from scanner processed/normalized by the Lowess algorithm in Agilent's Feature Extraction software then analysed in CGH Analytics and DNA Analytics software (Agilent).

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA isolated from FFPE high grade glioma sample

label_protocol: Samples digested and labelled using Agilent's labelling kit for array CGH, following the manufacturer's protocol.

extract_protocol:
Tumour samples fixed in formalin and embedded in paraffin.
DNA isolated from FFPE scrolls/cores using RecoverAll Total Nucleic Acid Kit for FFPE (Ambion), following the manufacturer's protocol.

tag: gender (male/female)

value: M

tag: tumour diagnosis

value: GBM

tag: tumour location

value: DIPG (brainstem)

tag: primary/recurrance

value: Primary

source_name: Pooled Normal Human DNA (Promega)

extract_protocol: not applicable

tag: reference

value: Pooled Normal Human DNA (Promega)


title: BSG4

value: F


title: BSG10


title: BSG5


title: HGG21

value: Supratentorial


title: BSG12


title: BSG8


title: HGG22


title: HGG14


title: HGG23

value: 1st rec


title: HGG12


title: BSG6


title: HGG10

value: AA


title: HGG15


title: BSG3

value: LGA


title: HGG11

value: AO


title: BSG9


title: HGG18


title: HGG13


title: BSG11


title: HGG19

value: Infratentorial


title: BSG2


title: HGG9


title: HGG8


title: HGG16


title: HGG20


title: HGG25


title: HGG6


title: BSG7


title: HGG17


title: Ad-orf3-egfp(Cy5)/Ad-egfp(Cy3)_Rep2

type: RNA

city: New Delhi

first: Shahid

last: Jameel

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: The International Centre for Genetic Engineering and Biotechnology (ICGEB)

description: Human hepatoma cell line Huh7 cells with the Ad-orf3-egfp or Ad-egfp recombinant adenoviruses

hyb_protocol: The labelled cDNA was applied to a spotted oligoneucleotide chip using an automated hybridization chamber and hybridization was performed for 18 hours with following step down procedure - 42 degree for 12 hours, 35 degree for 6 hours and 30 degree for 6 hours. Post completion of the hybridization cycles, the slides were removed and washed using Corning Pronto wash buffers and dried by centrifugation.

scan_protocol: The slides were scanned using a dual confocal scanner (Cy3,Cy5) at 10 micron resolution using the auto PMT and gain settings.

data_processing: The scanned images were gridded using GenTAC Integrator software and global normalized background corrected intensity values for each spotted target was determined. This resulted in CSV files entailing the Cy3 and Cy5 values for each gene spotted on the chip. The normalized ratio of Cy5 versus Cy3 was used for subsequent analysis.

molecule: total RNA

source_name: Human hepatoma Huh7 cells infected with Ad-egfp

label_protocol: 20 micrograms of total RNA was reverse transcribed using Superscript II and amino-allyl dUTP. The resulting cDNA was purified and conjugated to corresponding Cy dyes for 2 hours. The labelled cDNA was purified, concentrated and equal portions of the control and test cDNA were mixed, denatured at 95 degree and used for hybridization experiments

growth_protocol: DMEM medium with 10% FCS in a humidified incubator at 37 degree C with 10% CO2.

extract_protocol: The cells were harvested in 1 mL Trizol reagent, homogenized with a 21 gauge needle for 10 times. The RNA was retrieved from the aqueous layer resulting from the addition of 0.2X chloroform and centrifugation. The total RNA from the aqueous layer was purified and concentrated using the RNeasy Mini kit from Qiagen Inc as per the manufacturer's guidelines. The RNA was quantified using Nandrop spectophotometer. All the RNA used in these experiments had a 260/280 ratio >1.8 and 260/230 ratio > 1.8.

treatment_protocol: Huh7 cells infected with ORF3 expressing recombinant adenoviruses (Ad-orf3-egfp) and Huh7 cells infected with control recombinant adenoviruses (Ad-egfp) were cultured for 48 hr post-infection.

tag: cell ine

tag: cell type

value: hepatoma

tag: treatment gp

value: control adenoviral recombinant

source_name: Human hepatoma Huh7 cells infected with the Ad-orf3-egfp

tag: cell line

value: ORF3 expressing adenoviral recombinant


title: a cell, phosphate-starved+alpha pheromone, rep1

city: San Francisco

first: Lauren

middle: N

last: Booth

state: CA

address: 600 16th Street, N374

department: Micobiology and Immunology

country: USA

institute: University of California, San Francisco

hyb_protocol: Equal amounts of the Cy3 and Cy5 labeled cDNA hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.

scan_protocol: Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.

data_processing:
Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed first by averaging the result for all duplicate probes and finally by taking the median of the probes for each ORF. Data was transformed as described for each experiment. Note that comparisons between arrays can only be made if they share a pooled reference (Ch2)
All raw data (gpr) files are complete. However, all of the rep2 files were hybed to the newer 8x15k system, while the other reps were hybed to the 4x44k version of the array where identical probes are duplicated and in some cases triplicated.

organism: Kluyveromyces lactis

source_name: WT a cell

label_protocol: For the individual samples, 1.3 μg of cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. For the pooled samples, 5.9 μg of cDNA was dried and resuspended in 22.5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).

growth_protocol: See Booth, Tuch, Johnson. Nature, 2010

extract_protocol: RNA was isolated and reverse transcribed as previously described (Mitrovich, Q. M., Tuch, B. B., Guthrie, C. & Johnson, A. D. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res 17, 492-502 (2007).) with the exception that the RNA isolation protocol was scaled to 50 mL cultures and that SuperScript II (Invitrogen) was used. Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.

treatment_protocol: See Booth, Tuch, Johnson. Nature, 2010

value: WT a cell

tag: growth condition

value: phosphate-starvation+alpha pheromone

source_name: pooled reference #1

tag: pool used

value: pooled reference #1


title: a/alpha cell, phosphate-starved, rep2

source_name: WT a/alpha cell

value: WT a/alpha cell

value: phosphate-starvation

source_name: pooled reference #2

value: pooled reference #2


title: Ad-orf3-egfp(Cy5)/Ad-egfp(Cy3)_Rep1


title: rme1KO a cell, phosphate-starved, rep1

source_name: rme1KO a cell

value: rme1KO a cell

source_name: pooled reference #3

value: pooled reference #3


title: rme1KO a cell, phosphate-starved+alpha pheromone, rep1


title: a cell, phosphate starved+alpha pheromone, rep3


title: HGG5

value: M

value: GBM

value: Supratentorial

value: Primary

value: Pooled Normal Human DNA (Promega)


title: HGG7

value: F

value: 1st rec


title: HGG2

value: Post ALL


title: a cell, phosphate-starved+alpha pheromone, rep2


title: a/alpha cell, phosphate-starved+alpha pheromone, rep1


title: HGG24


title: a cell, phosphate starved, rep3


title: a/alpha cell, phosphate-starved, rep1


title: alpha cell, phosphate-starved, rep2

source_name: WT alpha cell

value: WT alpha cell


title: a/alpha cell, phosphate-starved+alpha pheromone, rep2


title: a/alpha cell YEPD, rep2

value: YEPD growth


title: a cell, phosphate-starved, rep2

value: WT a cell


title: HGG3


title: a cell, phosphate-starved, rep1

value: pooled reference #1


title: alpha cell, phosphate-starved, rep1


title: a/alpha cell YEPD, rep1

value: WT a/alpha cell


title: BSG1

value: DIPG (brainstem)


title: a cell, YEPD, rep2

value: pooled reference #2


title: alpha cell, YPED, rep1


title: Ad-orf3-egfp(Cy5)/Ad-egfp(Cy3)_Rep3

value: hepatoma

value: control adenoviral recombinant

value: ORF3 expressing adenoviral recombinant


title: a cell, YEPD, rep1


title: alpha cell, YEPD, rep2


title: HGG1

value: M

value: GBM


title: B. subtilis_glucose starvation_120min_rep1

city: Greifswald

first: Ulrike

last: Mäder

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

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: B. subtilis grown in minimal medium

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

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

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies). The normalization algorithm is defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol name: GE2_105_Dec08). The normalization/ dye bias correction method is: Linear and Lowess.
MAGE-ML files were imported into the Rosetta Resolver software (version 7.2.1, Rosetta Biosoftware). Then, the error-weighted average of the log ratio values of the individual probes was calculated for each annotated gene. Please see GSE24058.txt.gz supplementary file.

organism: Bacillus subtilis subsp. subtilis str. 168

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

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

growth_protocol: The B. subtilis 168 wild type strain was grown aerobically at 37 °C in BMM medium (Stülke et al., 1993). Glucose and L-malate were added to a final concentration of 0.05 % each to induce glucose starvation after growth to an OD500 of 1.0.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002).

treatment_protocol: Samples were taken before and at different times after the onset of glucose starvation; i.e. at different time points along the growth curve: exponential growth (exp), transition phase (t0), transition phase +30 minutes (t030), +60 minutes (t060) and +120 minutes (t120).

tag: genotype

value: wild type

source_name: 120 min glucose starvation

tag: time point

value: 120 min glucose starvation


title: B. subtilis_glucose starvation_120min_rep2

description: B. subtilis grown in minimal medium


title: B. subtilis_glucose starvation_0min_rep1

description: B. subtilis grown in minimal medium

source_name: glucose starvation - transition phase

value: glucose starvation - transition phase


title: Tissue Comparison at Day 14: Secondary Stem vs. Shoot Tips

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

country: Canada

institute: University of Alberta

description:
ch1: The plants were grown for the tissue comparisons, and secondary stems were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and terminal buds were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-074.txt' and 'GL002-077.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

hyb_protocol: Microarray slides were incubated for 2 hours at 65°C in pre-hybridization buffer (5 × SSC, 0.1% sodium dodecyl sulphate (SDS), 0.2 mg ml−1 bovine serum albumin (BSA), and 0.1 mg ml−1 herring sperm DNA) to prevent nonspecific binding.  Slides were washed twice with 0.1 × SSC, and twice with water at room temperature, and were then transferred to a water bath at 85°C for 90 seconds before drying by centrifugation for 2 minutes at 480 g in a bench top centrifuge (Eppendorf 5804). Alexa Fluor 555 and Alexa Fluor 647 labeled aRNA were denatured at 95°C for 2 minutes, cooled on ice and centrifuged. 51 µl of hybridization buffer (50% formamide, 5 × SSC, 0.1% SDS and 0.1 mg ml−1 herring sperm DNA) was preheated to 46°C, and added to the labeled aRNAs (referred as aRNA probes). The aRNA probes were kept at 46°C until applying to each slide.  Cover-slip (Erie Scientific Company, Portsmouth, NH, USA) was placed on each slide over the subarrays, and aRNA probes were added to one edge of the cover-slip, which allowed the probe to wick underneath it. The slides were put into the hybridization chambers (Corning, New York, NY, USA), with a drop of water being added to dedicated wells to maintain humidity, and incubated for 18 hours in a hybridization oven at 45°C. Cover-slips were then removed by floating the slides in a Coplin jar (Bel-Art Products Inc, Pequannock, NJ, USA) containing 2 × SSC and 0.5% SDS preheated to 45°C. The slides were incubated in the hybridization oven at 45°C for three periods of 15 minutes, with shaking every few minutes: once in 2 × SSC, 0.5% SDS, and twice in 0.5 × SSC, 0.1% SDS. The slides were then washed at room temperature twice with 0.1 × SSC for 1 minute and twice with water for 20 seconds before drying by centrifugation for 2 minutes at 480 g in Eppendorf 5804.

scan_protocol: Microarray images were obtained using a GenePix 4000B microarray scanner and analyzed with Genepix Pro  6.0 (Axon Instruments). Adaptive circles were used to indicate spots (spot diameter resize feature, 80 to 150%; composite pixel intensity, 300). After manual elimination of bad spots (highly irregular spot shape, dust, or salt particles), the median background intensity was subtracted from the mean spot intensity applying the local method (default option).

data_processing:
Within-array data normalization was first applied using print-tip loess detrending procedure, followed by between-array scale normalization to enforce the data having the same median-absolute-deviation across arrays from the same experiment. Taking the normalized data, linear models were fitted using duplicate correlation for each sequence. To reduce the false discovery rate, a nonspecific filtering was applied by removing invalid and low intensity sequences prior statistical analysis.  A moderated t-statistic, empirical Bayes statistic, was used to obtain p-values, and these p-values were further adjusted by Benjamini-Hochberg procedure.  A list of statistically significant differentially expressed (DE) sequences was selected by an adjusted p-value cut-off at 0.01, and this list was further filtered to include sequences with fold change greater than 1.5 or smaller than 0.67.

The VALUEs in the data table represent the averaged values of 4 biological replicates.

label: Alexa 647, Alexa 555

organism: Picea glauca

source_name: Secondary stems at day 14

label_protocol: Two micrograms of total RNA was amplified with the amino allyl antisense RNA (aRNA) procedure (Superscript Indirect RNA Amplification System, Invitrogen). Five micrograms of aRNA was directly labeled using Alexa Fluor 555 and/or 647 Dyes, (Invitrogen). Alexa Fluor 647 conjugates virtually match those of the Cy5 dye, and spectra of the Alexa Fluor 555 conjugates virtually match those of the Cy3 dye. Coupling efficiency was evaluated using the NanoDrop 1000 (Thermo Scientific).

growth_protocol: Seedlings were received from CFS, Quebec. Trees are surplus individuals from starting association population being created by N. Isabel, LFC-CFS. The two-year-old plants were grown using a complete randomized block design in controlled-environment chambers at 20°C and 50-60% humidity, with full illumination for 16 hours and 8 hours of dark.  At 6 to 8 weeks (46-58 days), part of the plant population was switched from a long daylight photoperiod (16h) to a short daylight photoperiod with 8 hours of light and 16 hours of dark for 18 to 25 weeks. A subset was subsequently transferred to low temperature at 2°C to 4°C for 3 to 4 weeks under a short daylight photoperiod. During the long daylight photoperiod, plants were fertilized with 0.5 g/L of 20-20-20. After switching to a short daylight photoperiod, 1.0 g/L of 15-30-15 fertilizations were applied for the first two weeks, 0.5 g/L of 20-20-20 from week 3 to week 8, and 0.5 g/L of 8-20-30 after week 8.

extract_protocol: Total RNA was extracted according to a modified procedure of Chang et al. 1993, a simple and efficient method for isolating RNA from pine trees [Plant Molecular Biology Reporter, 11(2):113-116].  Ground tissue was treated with 750 µL CTAB + b-ME extraction buffer, and incubated in water bath at 65°C for 10 minutes, vortexed periodically.  Each tube received 500 µl of chloroform:isoamyl alcohol (24:1 v/v), vortexed vigorously, and centrifuged at 14000 rpm for 15 minutes.  The aqueous phase was transferred to new tubes, and purified with chloroform:isoamyl alcohol again.  The volume of aqueous phase recovered after the second purification was determined, and mixed with an equal volume of LiCl-EDTA (7.5 M LiCl, 50mM EDTA) gently by inverting the tubes several times.  These tubes were placed at -20°C freezer for one hour, and centrifuged for 15 minutes at 14000 rpm at 4ºC. Pellet from each tube was collected, and washed with 800 µL of 80% ethanol, followed by a brief vortex.  Another 5 minutes of centrifugation at 14000 rpm at room temperature was applied to separate out the ethanol.  After drying the pellet by removing the supernatant, the pellet was resuspended in sterile water. NanoDrop 1000 (Thermo Scientific, ON, Canada) and 2100 Bioanalyzer (Agilent, ON, Canada) were used to determine the relative quality and quantity of the extracted RNA.

tag: tissue

value: secondary stems

value: day 14

tag: daylight

value: short day

label: Alexa 555, Alexa 647

source_name: Shoot tips at day 14

value: shoot tips (terminal buds)


title: B. subtilis_glucose starvation_60min_rep2

description: B. subtilis grown in minimal medium

source_name: 60 min glucose starvation

value: 60 min glucose starvation


title: B. subtilis_glucose starvation_0min_rep2

description: B. subtilis grown in minimal medium


title: Tissue Comparison at Day 14: Secondary Stems vs. Needles

description:
ch1: The plants were grown for the tissue comparisons, and secondary stems were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and needles were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-073.txt' and 'GL002-082.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Needles at day 14

value: needles


title: B. subtilis_glucose starvation_30min_rep2

description: B. subtilis grown in minimal medium

source_name: 30 min glucose starvation

value: 30 min glucose starvation


title: B. subtilis_glucose starvation_30min_rep1

description: B. subtilis grown in minimal medium


title: LD Day 28 vs. SD Day 28

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 28 days after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 28 days after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-014.txt' and 'GL002-010.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 28

value: day 28

value: long day

source_name: Shoot tips, SD, day 28


title: Tissue Comparison at Day 70: Shoot Tips vs. Needles

description:
ch1: The plants were grown for the tissue comparisons, and terminal buds were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and needles were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-059.txt' and 'GL002-062.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips at day 70

value: day 70

source_name: Needles at day 70


title: LD Day 70 vs. SD Day 70

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 10 weeks after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-018.txt' and 'GL002-031.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 70

source_name: Shoot tips, SD, day 70


title: B. subtilis_glucose starvation_exp_rep1

description: B. subtilis grown in minimal medium

source_name: exponential growth

value: exponential growth


title: LD Day 14 vs. SD Day 14

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 14 days after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 14 days after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-005.txt' and 'GL002-009.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 14

source_name: Shoot tips, SD, day 14


title: LD Day 3 vs. SD Day 3

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 3 days after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 3 days after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-023.txt' and 'GL002-015.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 3

value: day 3

source_name: Shoot tips, SD, day 3


title: Tissue Comparison at Day 70: Secondary Stem vs. Shoot Tips

description:
ch1: The plants were grown for the tissue comparisons, and secondary stems were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and terminal buds were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-054.txt' and 'GL002-057.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Secondary stems at day 70


title: LD Day 0 vs. SD Day 0

description:
ch1: The plants were grown for the LD/SD comparisons, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

ch2: The plants were grown for the LD/SD comparisons, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-024.txt' and 'GL002-022.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 0

value: day 0

source_name: Shoot tips, SD, day 0


title: B. subtilis_glucose starvation_60min_rep1

description: B. subtilis grown in minimal medium

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

source_name: 60 min glucose starvation


title: LD Day 1 vs. SD Day 1

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 1 day after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 1 day after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-027.txt' and 'GL002-013.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 1

value: day 1

source_name: Shoot tips, SD, day 1


title: Tissue Comparison at Day 70: Secondary Stems vs. Needles

description:
ch1: The plants were grown for the tissue comparisons, and secondary stems were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and needles were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-058.txt' and 'GL002-063.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: LD Day 7 vs. SD Day 7

description:
ch1: The plants were grown for the LD/SD comparisons.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 7 days after the long photoperiods treatment.

ch2: The plants were grown for the LD/SD comparisons, and terminal buds were harvested 7 days after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-028.txt' and 'GL002-029.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 7

value: day 7

source_name: Shoot tips, SD, day 7


title: Tissue Comparison at Day 14: Shoot Tips vs. Needles

description:
ch1: The plants were grown for the tissue comparisons, and terminal buds were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the tissue comparisons, and needles were harvested 2 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

4 biological replicates were used. Raw data files 'GL002-076.txt' and 'GL002-072.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips at day 14

source_name: Needles at day 14


title: LD Day 70 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 10 weeks after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-039.txt' and 'GL002-049.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 70


title: B. subtilis_glucose starvation_exp_rep2

description: B. subtilis grown in minimal medium

value: wild type

source_name: exponential growth


title: LD Day 14 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 14 days after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-048.txt' and 'GL002-045.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 14


title: LD Day 7 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 7 days after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-050.txt' and 'GL002-053.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: LD Day 3 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 3 days after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-036.txt' and 'GL002-047.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: LD Day 1 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 1 day after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-044.txt' and 'GL002-046.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: LD Day 28 vs. LD Day 0

description:
ch1: The plants were grown for the LD time course experiment.  At the end of 6-8 weeks long photoperiods for synchronization, they remained in the long photoperiods.  Shoot tips were harvested 28 days after the long photoperiods treatment.

ch2: The plants were grown for the LD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'GL002-051.txt' and 'GL002-055.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, LD, day 28


title: Low Temperature vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment. About 18-23 weeks after switching from long photoperiods to short photoperiods, they were exposed to low temperature (2°C to 4°C) for another 3 to 4 weeks.  Terminal buds were harvested after the low temperature treatment.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-057.txt' and 'HA013-029.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, SD, low temperature

tag: temperature

value: low


title: SD Day 7 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 7 days after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-049.txt' and 'HA013-025.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: SD Day 28 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 28 days after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-052.txt' and 'HA013-037.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, SD, day 28


title: SD Day 1 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 1 day after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-053.txt' and 'HA013-032.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).


title: SD Day 70 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 10 weeks after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-031.txt' and 'HA013-062.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, SD, day 70


title: HGG4

source_name: DNA isolated from FFPE high grade glioma sample

value: M

value: GBM

value: Supratentorial

value: 1st rec

source_name: Pooled Normal Human DNA (Promega)

value: Pooled Normal Human DNA (Promega)


title: SD Day 3 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 3 days after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-058.txt' and 'HA013-063.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, SD, day 3

value: shoot tips (terminal buds)

value: short day

source_name: Shoot tips, SD, day 0


title: Adipose, High Triglyceride, Rep 8

city: Knoxville

first: Arnold

last: Saxton

state: TN

address: Dept. of Animal Science

institute: University of Tennessee

description: Mouse 540

hyb_protocol: Hybridizations were performed at the University of Tennessee Affymetrix Facility (Knoxville, TN) using Affymetrix GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA) following the standard protocol.

scan_protocol: Scanning of arrays was done with an Affymetrix Genechip scanner.

data_processing: Individual probe data were extracted using Bioconductor (www.bioconductor.org), and gcRMA was used to produce a signal measure for each gene. Statistical analysis was performed using SAS software (Cary, NC). A mixed ANOVA model was run on the normalized data, fitting genotype and tissue treatment effects, and using array variation as the experimental error. Genes with significant (P<0.05) ANOVA interaction, and significant pair-wise False Discovery Rate were considered differentially expressed.

label: biotin

organism: Mus musculus

source_name: Pooled fat pads, high triglyceride

label_protocol: cDNA formation and biotin labeling was done using standard Affymetrix protocols.

growth_protocol: Mice were maintained on standard rodent chow with 4% fat [Harlan Teklad Rodent Diet (W) 8604, Madison, WI] ad libitum with free access to water (HCl acidified, pH 2.8-3.2) under controlled temperature and humidity with a 12-hour light and dark cycle. All animal studies were carried out with the approvals of The University of Tennessee Animal Care and Use Committee and Marshall University Animal Care and Use Committee. Mice were euthanized at 24 weeks of age by CO2 asphyxiation.

extract_protocol: Total RNA was isolated from liver, muscle (combined soleus and gastrocnemius), pancreas, and adipose tissue (combined inguinal, epididymal, retroperitoneal, perirenal, and subscapular fat pads) using RNeasy Lipid Tissue Midi Kit (75842, QIAGEN, Valencia, CA) according to the manufacturer's instructions. For adipose tissue, muscle and pancreas, the entire tissue was homogenized and total RNA extracted, whereas approximately 50% of the liver was homogenized. Total RNA was further purified using RNeasy MinElute Cleanup Kit (74204, QIAGEN) for microarray analysis.

treatment_protocol: 16 mice were chosen for microarray analysis from the upper and lower tails (8 each) for plasma triglyceride distribution of all the male F2 mice, excluding overtly diabetic mice. Four tissues were dissected from each mouse, producing the 64 samples.

tag: strain

value: TALLYHO x C57BL6 F2 mice

value: Adipose

tag: trigyceride

value: High

tag: mouse number

value: Mouse 540


title: Adipose, Low Triglyceride, Rep 6

description: Mouse 521

source_name: Pooled fat pads, low triglyceride

value: Low

value: Mouse 521


title: Muscle, Low Triglyceride, Rep 8

description: Mouse 532

source_name: Pooled soleus and gastrocnemius muscle, low triglyceride

value: Muscle

value: Mouse 532


title: Adipose, High Triglyceride, Rep 3

description: Mouse 319

value: Mouse 319


title: Adipose, Low Triglyceride, Rep 3

description: Mouse 342

value: Mouse 342


title: Adipose, High Triglyceride, Rep 2

description: Mouse 297

value: Mouse 297


title: SD Day 14 vs. SD Day 0

description:
ch1: The plants were grown for the SD time course experiment, and terminal buds were harvested 14 days after switching from 6-8 weeks long photoperiods to short photoperiods.

ch2: The plants were grown for the SD time course experiment, and shoot tips were harvested at the end of 6-8 weeks long photoperiods.

4 biological replicates were used. Raw data files 'HA013-064.txt' and 'HA013-028.txt' were dye-swaps (ch1: Alexa 555, ch2: Alexa 647).

source_name: Shoot tips, SD, day 14

value: day 14

value: day 0


title: Adipose, High Triglyceride, Rep 1

description: Mouse 293

value: Mouse 293


title: Adipose, High Triglyceride, Rep 5

description: Mouse 492

value: Mouse 492


title: Adipose, High Triglyceride, Rep 6

description: Mouse 516

value: Mouse 516


title: Adipose, Low Triglyceride, Rep 1

description: Mouse 258

value: Mouse 258


title: Adipose, Low Triglyceride, Rep 4

description: Mouse 425

value: TALLYHO x C57BL6 F2 mice

value: Mouse 425


title: Muscle, Low Triglyceride, Rep 6

description: Mouse 521


title: Adipose, High Triglyceride, Rep 4

description: Mouse 447

value: Adipose

value: High

value: Mouse 447


title: Adipose, Low Triglyceride, Rep 5

description: Mouse 434

value: Low

value: Mouse 434


title: Adipose, Low Triglyceride, Rep 2

description: Mouse 260

value: Mouse 260


title: Adipose, High Triglyceride, Rep 7

description: Mouse 525

value: Mouse 525


title: Muscle, Low Triglyceride, Rep 2

description: Mouse 260

value: Muscle


title: Adipose, Low Triglyceride, Rep 8

description: Mouse 532

value: Mouse 532


title: Muscle, Low Triglyceride, Rep 4

description: Mouse 425


title: Adipose, Low Triglyceride, Rep 7

description: Mouse 639

value: Mouse 639


title: Muscle, Low Triglyceride, Rep 5

description: Mouse 434


title: Muscle, Low Triglyceride, Rep 7

description: Mouse 639


title: Muscle, High Triglyceride, Rep 8

description: Mouse 540

source_name: Pooled soleus and gastrocnemius muscle, high triglyceride

value: Mouse 540


title: Muscle, Low Triglyceride, Rep 1

description: Mouse 258


title: Muscle, High Triglyceride, Rep 6

description: Mouse 516


title: Muscle, Low Triglyceride, Rep 3

description: Mouse 342

value: Mouse 342


title: Muscle, High Triglyceride, Rep 7

description: Mouse 525


title: Muscle, High Triglyceride, Rep 5

description: Mouse 492

value: Mouse 492


title: Muscle, High Triglyceride, Rep 1

description: Mouse 293

value: Mouse 293


title: Muscle, High Triglyceride, Rep 4

description: Mouse 447


title: Muscle, High Triglyceride, Rep 3

description: Mouse 319

value: Mouse 319


title: Muscle, High Triglyceride, Rep 2

description: Mouse 297

value: TALLYHO x C57BL6 F2 mice

value: Mouse 297


title: abKOvsaKO3

city: Orlando

first: Christoph

last: Zechner

state: FL

address: 6400 Sanger Road

institute: Sanford-Burnham Medical Research Institute at Lake Nona

hyb_protocol: Samples were hybridized in 3 hybridizations per KO group, each normalized to control. Agilent platform Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F was used.

scan_protocol: Arrays were scanned on an Axon Scanner to detect Cy3 and Cy5 flourescence.

data_processing:
GenePix Pro 6.0 acquisition and analysis software was used to visualize and analyze the 16-bit TIFF files generated by the scanner. After cluster analysis, sample 6 and 12 were excluded.
For further analysis, GenePix 4000B with global normalization was used to normalize the ratio of medians (635/532) representing KO vs control was used for probes with flag = 0 (present).

source_name: Gastrocnemius muscle PGC-1alpha -/-

label_protocol: 1 ug Cy3 and Cy5-labeled cRNA was mixed and fragmented according to the Agilent technologies protocol.

extract_protocol: Total RNA was extracted using the Trizol method.

tag: sex

value: male

tag: age

value: 12 week old

value: Gastrocnemius muscle

value: C57BL6/J x sv129

tag: genotype/variation

value: PGC-1alpha -/-

source_name: Gastrocnemius muscle PGC-1alpha-/- beta f/f/Mlc1fCre

value: PGC-1alpha-/- beta f/f/Mlc1fCre


title: abKOvsaKO2


title: abKOvsbflox3

source_name: Gastrocnemius muscle PGC-1beta f/f

value: PGC-1beta f/f


title: abKOvsaKO1


title: Pancreas, Low Triglyceride, Rep 7

description: Mouse 639

source_name: Pancreas, low triglyceride

value: Pancreas

value: Low


title: abKOvsbflox1


title: abKOvsbflox2


title: Pancreas, Low Triglyceride, Rep 8

description: Mouse 532

value: Mouse 532


title: Pancreas, Low Triglyceride, Rep 5

description: Mouse 434

value: Mouse 434


title: Pancreas, Low Triglyceride, Rep 6

description: Mouse 521

value: Mouse 521


title: Pancreas, Low Triglyceride, Rep 4

description: Mouse 425

value: Mouse 425


title: Pancreas, Low Triglyceride, Rep 3

description: Mouse 342

value: Mouse 342


title: Pancreas, High Triglyceride, Rep 7

description: Mouse 525

source_name: Pancreas, high triglyceride

value: High

value: Mouse 525


title: Pancreas, Low Triglyceride, Rep 1

description: Mouse 258

value: TALLYHO x C57BL6 F2 mice

value: Mouse 258


title: aKOvsbflox1

value: male

value: 12 week old


title: bKOvsbflox3

value: Gastrocnemius muscle

value: C57BL6/J x sv129


title: Pancreas, High Triglyceride, Rep 8

description: Mouse 540

value: Mouse 540


title: Pancreas, Low Triglyceride, Rep 2

description: Mouse 260

value: Mouse 260


title: aKOvsbflox2

value: PGC-1beta f/f


title: bKOvsbflox1

value: PGC-1alpha -/-


title: Pancreas, High Triglyceride, Rep 6

description: Mouse 516

value: Pancreas

value: Mouse 516


title: Liver, Low Triglyceride, Rep 7

description: Mouse 639

source_name: Whole liver, low triglyceride

value: Liver

value: Low

value: Mouse 639


title: Pancreas, High Triglyceride, Rep 4

description: Mouse 447

value: High

value: Mouse 447


title: aKOvsbflox3

value: PGC-1alpha-/- beta f/f/Mlc1fCre


title: Pancreas, High Triglyceride, Rep 5

description: Mouse 492

value: TALLYHO x C57BL6 F2 mice

value: Mouse 492


title: bKOvsbflox2

value: male

value: 12 week old


title: Pancreas, High Triglyceride, Rep 2

description: Mouse 297

value: Mouse 297


title: Liver, Low Triglyceride, Rep 8

description: Mouse 532

value: Mouse 532


title: Pancreas, High Triglyceride, Rep 3

description: Mouse 319

value: Mouse 319


title: Pancreas, High Triglyceride, Rep 1

description: Mouse 293

value: Mouse 293


title: Liver, Low Triglyceride, Rep 2

description: Mouse 260

value: Mouse 260


title: Liver, Low Triglyceride, Rep 4

description: Mouse 425

value: Mouse 425


title: Liver, High Triglyceride, Rep 6

description: Mouse 516

source_name: Whole liver, high triglyceride

value: Mouse 516


title: Liver, Low Triglyceride, Rep 6

description: Mouse 521

value: Liver

value: Mouse 521


title: Liver, High Triglyceride, Rep 7

description: Mouse 525

value: Mouse 525


title: Liver, Low Triglyceride, Rep 5

description: Mouse 434

value: Low

value: Mouse 434


title: Liver, Low Triglyceride, Rep 1

description: Mouse 258

value: Mouse 258


title: Liver, Low Triglyceride, Rep 3

description: Mouse 342

value: TALLYHO x C57BL6 F2 mice

value: Mouse 342


title: Liver, High Triglyceride, Rep 4

description: Mouse 447

value: High

value: Mouse 447


title: Liver, High Triglyceride, Rep 5

description: Mouse 492

value: Mouse 492


title: Liver, High Triglyceride, Rep 8

description: Mouse 540

value: Mouse 540


title: lactating ileum 2

status: Public on Nov 21 2010

city: Lexington

first: Mary

last: Vore

state: KY

address: 1095 Va Drive

department: Graduate Center of Toxicology

institute: University of Kentucky

description: RMA expression value derived from Expression Console software; extended-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Rat Exon 1.0 ST Arrays (Affymetrix) and scanned at the Uiversity of Kentucky Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: .CEL files were analyzed in Affymetrix Expression Console(EC) using the RMA algorithm on the Extended dataset to background correct, normalize, and log 2 transform the dataset.

organism: Rattus norvegicus

source_name: day 10-11 16h lactating dam

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix) according to the manufacutrer's instructions.(www.Affymetrix.com)

extract_protocol: Total RNA was isolated using TRIzol reagent followed by purification with Quiagen's RNAeasy kit.

treatment_protocol: Day 10-11 lactating Sprague-Dawley rats or virgin controls were sacrificed and whole liver, duodenum, jejunum, and ileum homogenates were used for RNA extraction.

tag: treatment

value: lactation

value: ileum


title: lactating ileum 3


title: lactating jejunum 4

value: jejunum


title: lactating ileum 4


title: Liver, High Triglyceride, Rep 2

description: Mouse 297

value: Mouse 297


title: Liver, High Triglyceride, Rep 1

description: Mouse 293

value: Mouse 293


title: lactating ileum 1


title: lactating jejunum 3


title: lactating jejunum 2


title: Liver, High Triglyceride, Rep 3

description: Mouse 319

value: Liver

value: Mouse 319


title: lactating duodenum 4

value: duodenum


title: lactating duodenum 1


title: 13833008 - pten2-Q-Fertile vs pten2-Q-Sterile

status: Public on Nov 30 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description:
ch1: arabidopsis thaliana (columbia)  mutant (pten2a) -  dev.stage (boyes et al. plant cell 2001): boyes: 6.50
ch2: arabidopsis thaliana (columbia)  mutant (pten2a) -  dev.stage (boyes et al. plant cell 2001): boyes: 6.50
The impact of the TOR pathway on growth and stress responses.

hyb_protocol: pten2-Q-Sterile Cy5 / pten2-Q-Fertile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

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

growth_protocol: flower - Media=humus  hygrometry=60%  Temperature=20  Light=100 uEinstein

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: pten2a overexpressor

tag: developmental stage

value: boyes 6.50

value: pten2a control


title: lactating duodenum 2


title: 13833009 - pten2-Q-Sterile vs pten2-Q-Fertile

hyb_protocol: pten2-Q-Fertile Cy5 / pten2-Q-Sterile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833010 - pten2-O13-Fertile vs pten2-O13-Sterile

hyb_protocol: pten2-O13-Sterile Cy5 / pten2-O13-Fertile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833013 - pten2-I17-Fertile vs pten2-I17-Sterile

hyb_protocol: pten2-I17-Sterile Cy5 / pten2-I17-Fertile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: lactating liver 2

value: liver


title: lactating liver 4


title: lactating liver 3


title: 13833012 - pten2-O13-Sterile vs pten2-O13-Fertile

hyb_protocol: pten2-O13-Fertile Cy5 / pten2-O13-Sterile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: lactating duodenum 3


title: lactating jejunum 1


title: control ileum 1

source_name: virgin dam

value: control


title: 13833015 - pten2-I17-Sterile vs pten2-I17-Fertile

hyb_protocol: pten2-I17-Fertile Cy5 / pten2-I17-Sterile Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: control ileum 3


title: lactating liver 1


title: control ileum 4


title: control duodenum 3


title: control duodenum 4


title: control jejunum 4


title: control jejunum 3


title: control jejunum 2


title: control ileum 2


title: control jejunum 1


title: control duodenum 2


title: control duodenum 1


title: control liver 2


title: control liver 3


title: control liver 4


title: control liver 1


title: CGH: FSCS sorted CD105+ cells from case73

city: new york

first: Viviane

last: Tabar

state: NY

address: 411 east 67th street

department: neurosurgery

institute: MSKCC

hyb_protocol: standard Agilent CGH protocol

scan_protocol: standard Agilent protocol.

data_processing: standard Agilent protocol CGH_v4_10_27_aug08, Log2 ratios were normalized by Lowess against probe intensity and mean %GC of the genomic region mapped to by the probe. Segmentation of normalized log2 ratios was by Circular Binary Segmentation (CBS, R package DNAcopy)

source_name: sorted cell from case73

label_protocol: standard Agilent CGH directly labellling protocol

growth_protocol: GBM specimen were dissociated into single cell and then labelled with fluorochrome-labelled antibodies fro FACS sorting

extract_protocol: Genomic DNA were extracted from freshly sorted cell population by using the Picopure DNA extraction Kit, followed by phenol extraction.

tag: cell type

value: CD105+  cell from GBM tumor

tag: gender

value: female

source_name: normal human genomic DNA-Roche

tag: sample type

value: normal human genomic DNA-Roche


title: CGH: FSCS sorted CD133+/CD144- cells from case62

source_name: sorted cell from case62

value: CDCD144-  cell from GBM tumor


title: CGH: FSCS sorted CD31+ cells from case71

source_name: sorted cell from case71

value: CD31+  cell from GBM tumor

value: male


title: CGH: FSCS sorted CD133-/CD144+ cells from case71

value: CDCD144+  cell from GBM tumor


title: CGH: FSCS sorted CD133+/CD144- cells from case73


title: CGH: FSCS sorted CD105+ cells from case71


title: CGH: FSCS sorted CD133+/CD144- cells from case71


title: CGH: FSCS sorted CD133+/CD144+ cells from case71


title: CGH: FSCS sorted CD31+ cells from case73


title: CGH: FSCS sorted CD133-/CD144- cells from case71


title: CGH: FSCS sorted CD133-/CD144- cells from case62

value: CDCD144- expression cell from GBM tumor


title: CGH: FSCS sorted CD133-/CD144+ cells from case73


title: CGH: FSCS sorted CD133+/CD144+ cells from case62

value: CDCD144+ expression cell from GBM tumor


title: Exon: GBM_case26

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

source_name: brain tumor

label_protocol: standard Affymetrix protocol

growth_protocol: Tissue were collected during surgery

extract_protocol: Total RNA were extracted by facility protocol

value: brain glioblastoma tumor


title: Exon: GBM_case20


title: Exon: GBM_case46

value: unknown


title: Exon: GBM_case34


title: Exon: GBM_case24


title: Exon: GBM_case31


title: CGH: FSCS sorted CD105+ cells from case62

value: CD105+ cell from GBM tumor


title: Exon: GBM_case37


title: Exon: GBM_case41


title: Exon: GBM_case33


title: Exon: GBM_case38


title: Exon: GBM_case40


title: Exon: GBM_case29


title: Exon: GBM_case27


title: Exon: GBM_case44


title: Exon: GBM_case2


title: Exon: GBM_case14


title: NA16 cells injected subcutaneously for tumor formation, biological replicate 2 (RMA)

status: Public on Nov 14 2010

city: Hyderabad

first: Dr. Gopal

last: Pande

state: Andhra Pradesh

address: Uppal Road

institute: Centre for Cellular and Molecular Biology

description: Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells

hyb_protocol: The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.

label: Biotin

source_name: F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells

label_protocol: 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)

growth_protocol: A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.

extract_protocol: 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)

treatment_protocol: A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days

tag: cell line

value: tumor


title: NA16 cells injected subcutaneously for tumor formation, biological replicate 1, technical replicate 1 (RMA)


title: NA16 cells injected subcutaneously for tumor formation, technical replicate 2 (RMA)


title: NA16 cells injected subcutaneously for tumor formation, technical replicate 2 (PLIER)


title: NA16 cells injected subcutaneously for tumor formation, biological replicate 2 (PLIER)


title: A16 vs Tumor F111 cells 16 h adhesion, biological replicate 2 (RMA)

description: Expression profile of F111 fibroblast cell lines, 16 h after adhesion

source_name: F111 fibroblast cell lines, adherent for 16h


title: NA16 cells injected subcutaneously for tumor formation, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs Tumor F111 cells 16 h adhesion, technical replicate 2 (RMA)


title: A16 vs Tumor F111 cells 16 h adhesion, biological replicate 2 (PLIER)


title: A16 vs Tumor F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs Tumor F111 cells 16 h adhesion, technical replicate 2 (PLIER)


title: A16 vs Tumor F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (RMA)


title: NA16 cells plated on soft agar for colony formation, biological replicate 1, technical replicate 1 (RMA)

description: Expression profile of F111 fibroblast cell lines, 7 days after colony formation by NA16 cells

source_name: F111 fibroblast cell lines, colony formation after 7 days of NA16 cells plating on softagar

value: colony


title: NA16 cells plated on soft agar for colony formation, biological replicate 2 (PLIER)


title: NA16 cells plated on soft agar for colony formation, biological replicate 2 (RMA)


title: NA16 cells plated on soft agar for colony formation, , technical replicate 2 (RMA)


title: NA16 cells plated on soft agar for colony formation, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs COLONY F111 cells 16 h adhesion, technical replicate 2 (RMA)


title: NA16 cells plated on soft agar for colony formation, , technical replicate 2 (PLIER)


title: CGH: GBM_case29

data_processing: standard Agilent protocol.

source_name: brain

label_protocol: standard Agilent CGH directly labeling protocol

growth_protocol: GBM specimen from operation room were quickly frozen for assay

extract_protocol: phenol chloroform


title: CGH: GBM_case31


title: A16 vs COLONY F111 cells 16 h adhesion, technical replicate 2 (PLIER)


title: CGH: GBM_case41


title: A16 vs COLONY F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs COLONY F111 cells 16 h adhesion, biological replicate 2 (RMA)


title: A16 vs COLONY F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (RMA)


title: CGH: GBM_case14


title: CGH: GBM_case38


title: CGH: GBM_case24


title: A16 vs NA16 F111 cells 16 h suspension, technical replicate 2 (RMA)

description: Expression profile of F111 fibroblast cell lines, 16 h after suspension

source_name: F111 fibroblast cell lines, suspended for 16h


title: CGH: GBM_case2


title: CGH: GBM_case26


title: A16 vs COLONY F111 cells 16 h adhesion, biological replicate 2 (PLIER)


title: CGH: GBM_case20


title: CGH: GBM_case40


title: A16 vs NA16 F111 cells 16 h suspension, biological replicate 2 (PLIER)


title: A16 vs NA16 F111 cells 16 h suspension, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs NA16 F111 cells 16 h suspension, technical replicate 2 (PLIER)


title: A16 vs NA16 F111 cells 16 h adhesion, technical replicate 2 (RMA)


title: A16 vs NA16 F111 cells 16 h adhesion, biological replicate 2 (PLIER)


title: A16 vs NA16 F111 cells 16 h suspension, biological replicate 2 (RMA)


title: Proliferating 3

status: Public on Nov 15 2010

city: Durham

first: Luftig

last: Laboratory

state: NC

address: 220 CARL Bldg Duke U Med Center

department: MGM

institute: Duke University

description: Prolif3_1743_3638_18387_8_HuEx-1+0-st-v1.CEL

hyb_protocol: Hybridization targets were prepared from totalRNA and hybridized to GeneChip HuEx 1.0 ST arrays according to standard Affymetrix (Santa Clara,CA) GeneChip HuEx 1.0 ST and GeneChip Hybridization, Wash, and Stain protocols

scan_protocol: GeneChip Scanner 3000 7G with GeneChip Fluidics Station 450

data_processing: Raw .CEL data was normailized and consolidated into a total .GCT metadata file via ExpressionFileCreator RMA normalization of the 12 .CEL files in GenePattern

source_name: CFSE stained, proliferating, CD19+ cells from EBV-infected PBMCs

label_protocol: cDNA preparation, labeling, fragmentation performed with Gene Chip cDNA synthesis/amplification kit (Affymetrix # 900673) and Exon Array Labeling kit (Affymetrix #900671)

growth_protocol: Infected cells (PBMCs) were maintained in RPMI 1640 + 15% FCS + cyclosporin A + Pen/Strep

extract_protocol: CD19+ B cells were purified from PBMC using the BD iMag Negative Isolation Kit (BD #558007). Total RNA was isolated via miRvana organic extraction (Ambion Inc) according to manufacturer's protocol

treatment_protocol: Infected cells were incubated with EBV for 1h at 37 C. CFSE treatment was performed as described (Quah et al, Nature Protocols 2007).

tag: ebv staus

value: infected, proliferating

value: CD19+ B cells, EBV-infected, sorted

tag: day post infection or extraction


title: CGH: GBM_case37

tag: tissue


title: LCL 3

description: LCL3_1743_3808_19354_6_HuEx-1+0-st-v1.CEL

source_name: Monoclonal LCL derived by limited EBV dilution on PBMCs

value: infected, immortalized

value: Lymphoblastoid Cell Line, EBV-infected, monoclonal


title: A16 vs NA16 F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (PLIER)


title: A16 vs NA16 F111 cells 16 h suspension, biological replicate 1, technical replicate 1 (RMA)


title: Proliferating 1

description: Prolif1_1743_3638_18384_2_HuEx-1+0-st-v1.CEL


title: Proliferating 2

description: Prolif2_1743_3808_19353_5_HuEx-1+0-st-v1.CEL


title: LCL 2

description: LCL2_1743_3638_18385_3_HuEx-1+0-st-v1.CEL


title: B Cell 1

source_name: Purified B Cells from PBMCs

value: uninfected

value: Purified B Cells, from negative selection of PBMCs


title: Proliferating 4

description: Prolif4_1743_4013_20995_Donor3_EBV_prolif_HuEx-1+0-st-v1.CEL


title: A16 vs NA16 F111 cells 16 h adhesion, technical replicate 2 (PLIER)


title: B Cell 4


title: Patient 66

status: Public on Nov 13 2010

city: North Ryde

first: Iain

last: Beeston

state: NSW

address: 11 Julius Avenue

country: Australia

institute: Clinical Genomics

description: Patient 66

hyb_protocol: The custom microarrays were processed using standard Affymetrix protocols developed for the HuGene ST 1.0 array described in (Pradervand, et al., 2008).  Importantly, this method differed from the HGU133 protocols used for discovery by using a random primer RNA amplification instead of the poly-dT method used previously.  The use of random primers was advantageous for measuring along the whole transcript including the 5’ terminus, thereby providing better exon-level resolution of transcripts originating from target loci.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with a 48 array autoloader.

data_processing: Expression values were calculatated using R and Bioconductor, and normalised using RMA

source_name: Colorectal mucosa

label_protocol: For each RNA extract, DNA end labelled with biotin was synthesized from 100ng of total RNA as previously described (Pradervand, et al., 2008).

extract_protocol: RNA was extracted from frozen tissue samples using Trizol (Invitrogen, San Diego US) as recommended by manufacturer.  Briefly, frozen tissues were homogenized in 300mL of Trizol reagent using a modified Dremel drill and sterilised disposable pestles. 200mL of Trizol reagent was added to the homogenate and samples were incubated at room temperature (25°C)  (RT) for 10 minutes.  100mL of chloroform was then added, samples were vortexed for 15 seconds, and incubated at RT for a further 3 minutes.  The aqueous phase containing target RNA was obtained by centrifugation at 12,000g for 15 min, 40°C.  RNA was then precipitated by incubating samples at RT for 10 min with 250mL isopropanol.  Purified RNA precipitate was collected by centrifugation at 12,000g for 10 minutes, 40°C and supernatants were discarded.

tag: phenotype

value: Cancer


title: B Cell 3

description: Bcell3_1743_3638_18386_7_HuEx-1+0-st-v1.CEL


title: A16 vs NA16 F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (RMA)


title: Patient 65

description: Patient 65


title: A16 vs NA16 F111 cells 16 h adhesion, biological replicate 2 (RMA)


title: B Cell 2

description: Bcell2_1743_3638_18383_1_HuEx-1+0-st-v1.CEL


title: Patient 62

description: Patient 62


title: Patient 63

description: Patient 63


title: Patient 67

description: Patient 67


title: Patient 59

description: Patient 59


title: Patient 56

description: Patient 56


title: LCL 1


title: Patient 60

description: Patient 60


title: Patient 64

description: Patient 64


title: Patient 57

description: Patient 57


title: Patient 53

description: Patient 53


title: Patient 61

description: Patient 61


title: Patient 54

description: Patient 54


title: Patient 58

description: Patient 58


title: Patient 55

description: Patient 55


title: LCL 4

description: LCL4_1743_3638_18388_9_HuEx-1+0-st-v1.CEL


title: Patient 52

description: Patient 52


title: Patient 49

description: Patient 49

value: Adenoma


title: Patient 50

description: Patient 50


title: Patient 51

description: Patient 51


title: Patient 48

description: Patient 48


title: Patient 47

description: Patient 47


title: Patient 44

description: Patient 44


title: Patient 45

description: Patient 45


title: Patient 46

description: Patient 46


title: Patient 43

description: Patient 43


title: Patient 40

description: Patient 40


title: Patient 38

description: Patient 38


title: Patient 41

description: Patient 41


title: Patient 35

description: Patient 35


title: Patient 32

description: Patient 32


title: Patient 42

description: Patient 42


title: Patient 29

description: Patient 29

value: Normal


title: Patient 37

description: Patient 37


title: Patient 68

description: Patient 68


title: Patient 39

description: Patient 39


title: Patient 36

description: Patient 36


title: Patient 30

description: Patient 30


title: Patient 34

description: Patient 34


title: Patient 33

description: Patient 33


title: Patient 27

description: Patient 27


title: Patient 24

description: Patient 24


title: Patient 26

description: Patient 26


title: Patient 28

description: Patient 28


title: Patient 31

description: Patient 31


title: Patient 21

description: Patient 21


title: Patient 23

description: Patient 23


title: Patient 20

description: Patient 20


title: Patient 18

description: Patient 18


title: Patient 25

description: Patient 25


title: Patient 22

description: Patient 22


title: Patient 15

description: Patient 15


title: Patient 19

description: Patient 19


title: Patient 16

description: Patient 16


title: Patient 7

description: Patient 7


title: Patient 4

description: Patient 4


title: Patient 12

description: Patient 12


title: Patient 14

description: Patient 14


title: Patient 17

description: Patient 17


title: Patient 11

description: Patient 11


title: Patient 10

description: Patient 10


title: Patient 9

description: Patient 9


title: Patient 13

description: Patient 13


title: Patient 1

description: Patient 1


title: Patient 6

description: Patient 6


title: Patient 8

description: Patient 8


title: Patient 3

description: Patient 3


title: hippocampus_deldup_rep5

status: Public on Nov 10 2010

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissue separately.

source_name: Whole hippocampus, duplication and deletion

label_protocol: The synthesis of cRNA was performed using the GeneChip® One-Cycle cDNA Synthesis (for cerebellum, testis, kidney and heart) and the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification (hippocampus) kits according to the manufacturers' protocols (Affymetrix, Santa Clara, CA, USA and Applied Biosystems/Ambion, Austin, TX, respectively). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: Heterozygous mice carrying a duplication, Dp(11)17/+, a deletion, Df(11)17)/+, or both rearrangements, Df(11)17/Dp(11)17, were analyzed in a pure C57BL/6-Tyrc-Brd genetic background.

extract_protocol: Whole hippocampus, cerebellum, testis, kidney and heart from +/+, Dp(11)17/+, Df(11)17)/+ and Df(11)17/Dp(11)17 adult males were dissected and immediately frozen on dry ice. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, NM, USA) and cleaned on RNeasy columns (Qiagen). RNA quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and Agilent 2100 bio-analyzer chips, respectively.

tag: genotype

value: duplication, Dp(11)17/+ and a deletion Df(11)17)/+ on chromosome 11

value: male


title: hippocampus_del/+_rep5

description: MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification

source_name: Whole hippocampus, deletion

value: deletion Df(11)17)/+ on chromosome 11


title: hippocampus_del/+_rep3


title: hippocampus_del/+_rep2


title: hippocampus_+/+_rep1

source_name: Whole hippocampus, wild-type

value: wild-type


title: Patient 2

description: Patient 2


title: hippocampus_deldup_rep2


title: hippocampus_deldup_rep4


title: hippocampus_del/+_rep1


title: hippocampus_dup/+_rep3

source_name: Whole hippocampus, duplication

value: duplication, Dp(11)17/+ on chromosome 11


title: hippocampus_+/+_rep2


title: hippocampus_dup/+_rep1


title: Patient 5

description: Patient 5


title: hippocampus_deldup_rep3


title: hippocampus_dup/+_rep2


title: hippocampus_del/+_rep4


title: hippocampus_deldup_rep1


title: testis_+/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole testis, wild-type


title: testis_+/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: testis_+/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_dup/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole kidney, duplication


title: kidney_+/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole kidney, wild-type


title: testis_deldup_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole testis, duplication and deletion


title: testis_del/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole testis, deletion


title: testis_dup/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole testis, duplication


title: testis_del/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: testis_dup/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: testis_del/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: testis_dup/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_+/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_dup/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_dup/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_del/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole kidney, deletion


title: kidney_del/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: testis_deldup_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_del/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole heart, deletion


title: heart_dup/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole heart, duplication


title: kidney_deldup_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole kidney, duplication and deletion


title: heart_dup/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_+/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole heart, wild-type


title: kidney_del/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_del/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_deldup_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_+/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_dup/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_del/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_+/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: kidney_deldup_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_+/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole cerebellum, wild-type


title: cerebellum_del/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole cerebellum, deletion


title: cerebellum_dup/+_rep3

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole cerebellum, duplication


title: cerebellum_del/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: heart_deldup_rep2

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole heart, duplication and deletion


title: heart_deldup_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_+/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_dup/+_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_deldup_rep1

description: GeneChip® One-Cycle cDNA Synthesis

source_name: Whole cerebellum, duplication and deletion


title: heart_deldup_rep1

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_deldup_rep3

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_+/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_dup/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_del/+_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: cerebellum_deldup_rep2

description: GeneChip® One-Cycle cDNA Synthesis


title: 13489191 - L_St10d vs L_St2d

status: Public on Nov 03 2010

description: Nitrogen starvation and re-supply.

hyb_protocol: L_St2d Cy5 / L_St10d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 610V,laser power 100%

growth_protocol: rosette - Media : 2(KNO3)/Ca(NO3)2 = 1.5mM MgSO4/KH2PO4 = 2 mM K2SO4 = 1 mM CaCl2 = 0.7 mM Oligo(Cooc and Lesaint, 1975)= 1 ml.L-1 Fer-EDTA = 10 mg.L-1 hygrometry : 70 % Temperature : day : 21°C, night :17 °C Light : 8 h WS Arabidopsis ecotype and colza were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 (T+1).

value: rosette

tag: nitrogen starvation time

value: wassilewskija

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


title: 13485533 - L_T0 vs L_St2d

description: Nitrogen starvation and re-supply.

hyb_protocol: L_St2d Cy5 / L_T0 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485530 - R_St10d vs R_St2d

description: Nitrogen starvation and re-supply.

hyb_protocol: R_St2d Cy5 / R_St10d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: roots - Media : 2(KNO3)/Ca(NO3)2 = 1.5mM MgSO4/KH2PO4 = 2 mM K2SO4 = 1 mM CaCl2 = 0.7 mM Oligo(Cooc and Lesaint, 1975)= 1 ml.L-1 Fer-EDTA = 10 mg.L-1 hygrometry : 70 % Temperature : day : 21°C, night :17 °C Light : 8 h WS Arabidopsis ecotype and colza were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 (T+1).

value: roots


title: 13485531 - R_St10d vs R_St10d+1h

description: Nitrogen starvation and re-supply.

hyb_protocol: R_St10d+1h Cy5 / R_St10d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Nitrogen_1h - environmental treatment - azote concentration,nitrate:quantity 6mM time 1hour . WS Arabidopsis ecotype and colza were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 hour (T+1).


title: 13485532 - R_St10d+1h vs R_St10d

description: Nitrogen starvation and re-supply.

hyb_protocol: R_St10d Cy5 / R_St10d+1h Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13489189 - L_St2d vs L_St10d

description: Nitrogen starvation and re-supply.

hyb_protocol: L_St10d Cy5 / L_St2d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485536 - L_St2d vs L_T0

description: Nitrogen starvation and re-supply.

hyb_protocol: L_T0 Cy5 / L_St2d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485526 - R_St2d vs R_St10d

description: Nitrogen starvation and re-supply.

hyb_protocol: R_St10d Cy5 / R_St2d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13489195 - L_St10d+1h vs L_St10d

description: Nitrogen starvation and re-supply.

hyb_protocol: L_St10d Cy5 / L_St10d+1h Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13489192 - L_St10d vs L_St10d+1h

description: Nitrogen starvation and re-supply.

hyb_protocol: L_St10d+1h Cy5 / L_St10d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13485529 - R_St2d vs R_T0

description: Nitrogen starvation and re-supply.

hyb_protocol: R_T0 Cy5 / R_St2d Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.