title: HPTE_5_cAMP 3

status: Public on Jun 10 2009

city: New Brunswick

first: Mehmet

last: Uzumcu

state: NJ

address: 84 Lipman Drive Bartlett 119

department: Department of Animal ScienceS

institute: Rutgers University

description:
Briefly, intact, non-primed, immature female rats (21-27 days old) were sacrificed by cervical dislocation. Ovaries were removed from the animals, cleaned free of associated fat, oviduct, and bursa ovary, and then placed in ice-cold DMEM/F-12. Granulosa cells were isolated using a non-enzymatic needle puncture method with a sterile bundle of beading needles to release the cells from follicles. Cell viability was determined by the trypan blue exclusion method.   The cells were plated and cultured (24-well plates) at approximately 3-4 x 105 viable cells/ml/well and incubated at 37°C for 24 h in the DMEM/F-12 containing FBS (5%) in an atmosphere of 5% CO2 in air. Following the 24 h acclimation period, the medium was replaced with serum-free DMEM/F12 containing androstenedione (0.1 M) as a substrate for aromatization.
Cells were treated with increasing doses of HPTE (0, 1, 5, and 10µM) in the absence (basal) or presence of 3 ng FSH/ml or 1 mM cAMP for 48 h. The doses of FSH and cAMP were selected based on a dose-response curve that provided a maximum level of stimulation for E2 production (data not shown). Cultures were terminated at 48 h following the addition of treatments. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat # 74106) followed by DNase I treatment. RNA quality was assessed by electrophoresis using the Agilent Bioanalyzer 2100 and spectrophotometric analysis prior to cDNA synthesis (data not shown). Forty nanograms of total RNA from each sample were used to generate a high fidelity cDNA for array hybridization using the NuGen Ovation Biotin RNA Amplification and Labeling system (NuGen). After fragmentation and biotin labeling, the samples were hybridized to Affymetrix Rat Genome 230 2.0 arrays, which have eleven pairs of oligonucleotide probes per chip. Washing and staining of all arrays were carried out in the Affymetrix fluidics module as per the manufacturer’s protocol. The detection and quantification of target hybridization was performed with an Affymetrix GeneChip Scanner. Three separate samples were analyzed for each of the treatment groups.Initially, raw data were analyzed using Robust Multichip Analysis (RMA) with a logarithmic base 2 conversion utilizing the Affymetrix ArrayAssist Suite (Affymetrix, Inc., Santa Clara, CA). One-way ANOVA analysis of each group (basal, FSH, or cAMP) was used to determine genes that are significantly affected by HPTE. This was followed by an unpaired t-test to determine changes in global gene expression between HPTE-treated groups and the control groups to determine the levels of fold change. All statistical analyses were performed using P < 0.005  as the level of statistical significance.

hyb_protocol: Samples were hybridized to Affymetrix Rat Genome 230 2.0 arrays. Arrays were washed and stained in the Affymetrix fluidics module as per the manufacturer’s instructions.

source_name: Granulosa cells from post-natal days 21-27 female Sprague Dawley Rats

growth_protocol: Granulosa cells were plated and cultured at 37°C for 24 h in DMEM/F-12 containing FBS (5%).

extract_protocol: RNA extractions were performed using Qiagen RNeasy Mini-kits followed by DNase1 treatment. RNA quality was assessed by electrophoresis using the Agilent Bioanalyzer 2100 and spectrophotometric analysis.

tag: Charles River outbred immature female rats


title: HPTE_5_FSH 3

type: RNA

country: USA

scan_protocol: The detection and quantification of target hybridization was performed with an Affymetrix GeneChip Scanner.

data_processing: Initially, raw data were analyzed using Robust Multichip Analysis (RMA) with a logarithmic base 2 conversion utilizing the Affymetrix ArrayAssist Suite (Affymetrix, Inc., Santa Clara, CA). One-way ANOVA analysis of each group (basal, FSH, or cAMP) was used to determine genes that are significantly affected by HPTE. This was followed by an unpaired t-test to determine changes in global gene expression between HPTE-treated groups and the control groups to determine the levels of fold change. All statistical analyses were performed using P < 0.005  as the level of statistical significance.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Forty nanograms of total RNA from each sample were used to generate a high fidelity cDNA for array hybridization using the NuGen Ovation Biotin RNA Amplification and Labeling system (NuGen).


title: HPTE_0_FSH 3


title: HPTE_5_Basal 3


title: HPTE_1_Basal 3


title: HPTE_0_cAMP 3


title: HPTE_10_FSH 3


title: HPTE_10_cAMP 2


title: HPTE_1_cAMP 3


title: HPTE_10_cAMP 3


title: HPTE_10_FSH 2


title: HPTE_0_ Basal 3


title: HPTE_10_Basal 3


title: Listeria monocytogenes LMB0429_bile stress_rep1

status: Public on Jun 15 2009

city: Pullman

first: Devendra

middle: H

last: Shah

state: WA

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

institute: Washington State University

description:
Slide Bar Code: 126292
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

hyb_protocol: The labeled cDNA pellets were resuspended in 70uL of hybridization buffer (5x denhardt’s/4x SSC) and boiled for 2 minutes. Samples were centrifuged for 1 minute and applied to the slides under Erie Scientific Lifter slips (24x60mM). Hybridizations were conducted in a 45oC water bath in corning hybridization chambers for 18 hours. Post hybridization washes consisted of three 1 minute TNT (Tris/NaCl/Tween) washes (gently shaking). The slides were dried using a Microarray High-Speed Centrifuge (TeleChem International, Inc).

scan_protocol: Applied Precisions ArrayWorx Scanner employing the following settings: CY3 for 0.1s and A488 for 0.3s with a resolution of 9.6um.

data_processing: TIFF images were processed using SPOTfinder software (TIGR TM4 software suite) using the otsu spot setting and employing background subtraction within the spotfinding software. The resultant median intensities were imported into MATlab software (Mathworks, Inc) for lowess normalization. The normalized intensities and ratios were imported into an access database. Spot quality control filtering was conducted in access (Microsoft) and consisted of the following criterion: 1) Signal:Noise ratio must be greater than 2 (A488) or 10 (A555); 2) The mean spot intensity must be within 25% of the median spot intensity; 3) The coefficient of variance for replicate spots must be less than 0.2; 4)Those spots with only a single channel passing the previous three filters were then low-intensity filtered with a cutoff of 4000.

label: AlexaFluor 488

organism: Listeria monocytogenes

label_protocol:
cDNA was generated as follows: 3μg of total RNA and 150ng of random hexamers (RHs) were combined and heated to 70oC for 10 minutes. This RNA:RHs mixture was snap cooled on ice for 1 minute. The remaining reagents from the SuperScriptTM III First Strand Synthesis Kit® (Invitrogen) were added to the following final concentrations: 1.2x RT Buffer; 6.1mM MgCl2; 12mM DTT; 2.7mM dNTP’s (Promega) which contained aa-dUTP (Ambion) at a ratio of 3.5:1; 40U RNaseOUTTM; and 760U SuperScriptTM III. This mixture was incubated for 18h at 42oC. Following the 42oC incubation, EDTA (pH 8.0) and NaOH were added to a final concentration of 0.1M and 0.2M, respectively. This mixture was incubated at 65oC for 15 minutes in order to hydrolyze the RNA. The solution was neutralized by the addition of 1M Tris-HCl pH 7.0 to a final concentration of 0.3M. The cDNA was cleaned up using a QiaQuick PCR clean-up column (Qiagen) with the following modifications: all spins except the elution step were conducted at 6,000 rpms and the column drying spin (step 6) was extended to 5 minutes; the wash buffer and elution buffers consisted of 5mM KPO4/80% EtOH and 4mM KPO4, respectively, to avoid Tris contamination in the cDNA; finally, the elution buffer was preheated to 37oC and the column was incubated at 37oC for 5 minutes prior to elution from the column. The eluted cDNA was dried down in a centrivap for 45 minutes at 40oC. The resultant pellet was either stored at -20oC until later use or resuspended in 5ul of water and incubated for 2-3 hours at 55oC in preparation for a labeling reaction.
The labeling reactions were performed utilizing AlexaFluor 555 and AlexaFluor 488 as per manufacturer’s instructions with the minor modification of an overnight incubation (instead of 1 hour). Labeling reactions were cleaned up as described above for cDNA clean-up, with the replacement of the KPO4 buffers with manufacturer supplied buffers. The eluted labeled cDNA was quantified on a spectrophotometer. cDNA concentrations were calculated and combined such that the same amount of cDNA was used for each condition (control vs. stress). Each hybridization consisted of between 2.4 – 4.6nM cDNA (per condition) and 60 – 480 pmol dye incorporation (per dye)

growth_protocol: All strains were passaged 3 times in BHI at 37oC with moderate shaking for 18 hours prior to stress protocol.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) as per the manufacturer’s instructions with only minor modifications. Briefly, bacterial pellets were resuspended in 3-mL of TRIzol followed by the addition of 0.1mm Zirconia beads (BIOSPEC Products Inc) for cell disruption. This mixture underwent rapid horizontal vortexing for 1 hour at 4oC. The beads were pelleted out by centrifugation and chloroform was added for organic extraction. Phase separation was achieved through centrifugation at which time the aqueous phase was removed to a separate tube. The organic phase was back-extracted by the addition of ultra-pure RNase-free water (ISC Bioexpress) and the phases were separated again as described. This second aqueous phase was added to the first and precipitated with the addition of isopropanol . The RNA was pelleted, washed once in 75% ethanol, air-dried for 15 minutes and resuspended in ultra-pure RNase-free water. A DNase reaction was performed as per manufacturer’s instructions (Promega). Following the DNase reaction, a second organic extraction was performed using TRIzol LS (Invitrogen) as per the manufacturer’s instructions with the following minor modifications: phase-lock heavy gel tubes (Eppendorf) were employed for the phase separation step and the co-precipitant glycoblue (Ambion) was added in the final precipitation step. The final RNA pellet was resuspended in RNAsecure (Ambion) and quantitated using a spectrophotometer. A measure of RNA quality was assessed through 260/280 and 260/230 ratios.

treatment_protocol: A 50-mL culture was grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and half was resuspended in 1x PBS/BHI broth, pH 7.4. This was incubated for 1 hour at 37oC. The culture was again pelleted via centrifugation and resuspended in  1xPBS/BHI broth, pH 7.4. This was incubated for 1 hour at 37oC. Finally, the culture was pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth, pH 5.5. This was incubated for 1 hour at 37oC. 5-mL was subsequently pelleted for RNA extraction.

tag: Strain

value: Environmental, serotype 4b, lineage 1

label: AlexaFluor 555

growth_protocol: All strains were passaged 3 times in BHI at 37oC with moderate shaking for 18 hours.

treatment_protocol: A 50-mL culture was grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and half was resuspended in HCl acidified 1x PBS/BHI broth, pH 5.5. This was incubated for 1 hour at 37oC. The culture was again pelleted via centrifugation and resuspended in HCl acidified 1xPBS/BHI broth, pH 3.5. This was incubated for 1 hour at 37oC. Finally, the culture was pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth, pH 5.5, that also contained 0.3% BILE. This was incubated for 1 hour at 37oC. 10-mL was subsequently pelleted for RNA extraction.


title: HPTE_1_FSH 2


title: HPTE_1_Basal 2


title: HPTE_10_Basal 2


title: HPTE_5_Basal 2


title: HPTE_1_cAMP 2


title: HPTE_10_cAMP 1

description:
Briefly, intact, non-primed, immature female rats (21-27 days old) were sacrificed by cervical dislocation. Ovaries were removed from the animals, cleaned free of associated fat, oviduct, and bursa ovary, and then placed in ice-cold DMEM/F-12. Granulosa cells were isolated using a non-enzymatic needle puncture method with a sterile bundle of beading needles to release the cells from follicles. Cell viability was determined by the trypan blue exclusion method.   The cells were plated and cultured (24-well plates) at approximately 3-4 x 105 viable cells/ml/well and incubated at 37°C for 24 h in the DMEM/F-12 containing FBS (5%) in an atmosphere of 5% CO2 in air. Following the 24 h acclimation period, the medium was replaced with serum-free DMEM/F12 containing androstenedione (0.1 M) as a substrate for aromatization.
Cells were treated with increasing doses of HPTE (0, 1, 5, and 10µM) in the absence (basal) or presence of 3 ng FSH/ml or 1 mM cAMP for 48 h. The doses of FSH and cAMP were selected based on a dose-response curve that provided a maximum level of stimulation for E2 production (data not shown). Cultures were terminated at 48 h following the addition of treatments. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat # 74106) followed by DNase I treatment. RNA quality was assessed by electrophoresis using the Agilent Bioanalyzer 2100 and spectrophotometric analysis prior to cDNA synthesis (data not shown). Forty nanograms of total RNA from each sample were used to generate a high fidelity cDNA for array hybridization using the NuGen Ovation Biotin RNA Amplification and Labeling system (NuGen). After fragmentation and biotin labeling, the samples were hybridized to Affymetrix Rat Genome 230 2.0 arrays, which have eleven pairs of oligonucleotide probes per chip. Washing and staining of all arrays were carried out in the Affymetrix fluidics module as per the manufacturer’s protocol. The detection and quantification of target hybridization was performed with an Affymetrix GeneChip Scanner. Three separate samples were analyzed for each of the treatment groups.Initially, raw data were analyzed using Robust Multichip Analysis (RMA) with a logarithmic base 2 conversion utilizing the Affymetrix ArrayAssist Suite (Affymetrix, Inc., Santa Clara, CA). One-way ANOVA analysis of each group (basal, FSH, or cAMP) was used to determine genes that are significantly affected by HPTE. This was followed by an unpaired t-test to determine changes in global gene expression between HPTE-treated groups and the control groups to determine the levels of fold change. All statistical analyses were performed using P <  0.005  as the level of statistical significance.


title: HPTE_0_ Basal 2


title: HPTE_5_cAMP 2


title: HPTE_5_FSH 2


title: HPTE_0_FSH 2


title: HPTE_0_cAMP 2


title: HPTE_1_FSH 3


title: HPTE_10_FSH 1


title: HPTE_5_cAMP 1


title: HPTE_10_Basal 1


title: HPTE_1_FSH 1


title: HPTE_0_FSH 1


title: HPTE_1_Basal 1


title: HPTE_5_Basal 1


title: HPTE_1_cAMP 1


title: HPTE_0_Basal 1


title: HPTE_0_cAMP 1


title: HPTE_5_FSH 1


title: Control13

status: Public on Jun 01 2009

city: Los Angeles

first: Yelena

last: Bykhovskaya

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description:
4037951027D_Control13
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Raw data for each sample was output using the Illumina BeadStudio. Default data transformation to set measurements below 0.01 to 0.01 was applied. Default settings were used for experiment normalization which included chip normalization to 50th percentile and gene normalization to the median

label: Biotin-Labeled cRNA

organism: Homo sapiens

source_name: EBV-transformed cell line of lymphoblasts extrated from peripheral blood

label_protocol: Illlumina® TotalPrep RNA amplification kit, manufactured by Ambion, Inc (Austin, TX) according to the manufacturer’s protocol

growth_protocol: RPMI-1640 medium (Invitrogen, Inc., Carlsbad, CA), containing 2 mmol/L L-glutamine, 100 ug/ml streptomycin, and 10% fetal calf serum

extract_protocol: Trizol reagent (Invitrogen, Inc.)

treatment_protocol: No treatment

tag: Immortalized lymphoblastoid cell line


title: Affected12

description:
4037951027F_Affected12
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: Unaffected12

description:
4037951027E_Unaffected13
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected14

description:
4037951019F_Affected14
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control14

description:
4037951019A_Control14
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control15

description:
4037951019D_Control15
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected13

description:
4037951019B_Unaffected14
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected13

description:
4037951019C_Affected13
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Listeria monocytogenes LMB0622_acid adaptation_rep3

description:
Slide Bar Code: 00091588
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0622, neutral pH

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The cultures were split, pelleted via centrifugation (rcf), and resuspended in neutral (pH 7.4) 1x PBS/BHI broth. These were incubated for 1 hour at 37oC. 5-mL pellets were collected for subsequent RNA extraction.

value: Environmental, serotype 1/2c, lineage 2

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The cultures were split, pelleted via centrifugation (rcf), and resuspended in HCl acidified 1xPBS/BHI broth pH 5.5. These were incubated for 1 hour at 37oC. 5-mL pellets were collected for subsequent RNA extraction.


title: Unaffected11

description:
4037951027B_Unaffected12
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected9

description:
4037951030C_Affected9
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control11

description:
4037951030D_Control11
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected10

description:
4037951030F_Affected10
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control12

description:
4037951027A_Control12
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected14

description:
4037951019E_Unaffected15
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected9

description:
4037951030B_Unaffected10
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected10

description:
4037951030E_Unaffected11
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected7

description:
4019227009B_Unaffected8
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control9

description:
4019227009D_Control9
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control10

description:
4037951030A_Control10
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control8

description:
4019227009A_Control8
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected8

description:
4019227009E_Unaffected9
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected7

description:
4019227009C_Affected7
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control7

description:
4019227010D_Control7
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected5

description:
4019227024E_Unaffected5
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control6

description:
4019227010A_Control6
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected6

description:
4019227010B_Unaffected6
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control4

description:
4019227024A_Control4
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected5

description:
4019227024F_Affected5
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected6

description:
4019227010C_Affected6
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected8

description:
4019227009F_Affected8
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected4

description:
4019227024B_Unaffected4
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control5

description:
4019227024D_Control5
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected3

description:
1825389067C_Affected3
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected1

description:
1825389041A_Unaffected1
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected2

description:
1825389041B_Unaffected2_1; 1825389041F_Unaffected2_2
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Unaffected3

description:
1825389041D_Unaffected3
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Affected4

description:
4019227024C_Affected4
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control1

description:
1825389041C_Control1
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Control3

description:
1825389067E_Control3
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: Wild-type_vivo_sample

status: Public on May 22 2009

city: Beijing

first: Li

last: Zhu

address: 20 Dongdajie, Fengtai District

department: State Key Laboratory of Pathogens and Biosecurity

country: China

institute: Beijing Institute of Biotechnology

hyb_protocol: Available at manufacturer's website: www.nimblegen.com

organism: Shigella flexneri

source_name: Wild-type bacteria of stationary-phase resuspended in PBS and then placed in Rabbit ileum

growth_protocol: wild-type strain were maintained at TSA plates with 30 μg/ml naladixic acid at 30 degree and cultured in LB broth at 37 degree.

extract_protocol: use QIAGEN RNAeasy mini kit

treatment_protocol: The Rabbit (about 3 kg) was fasted for 24 hours before operation. 50 ml of an overnight culture of the wild-type strain in LB broth was harvested and resuspended in 20 ml PBS buffer in dialysis bag (MWCO 25kD) and then placed in Rabbit ileum for 4 hours.

tag: Shigella flexneri 2a str. 2457T

value: wild-type strain


title: Affected1

description:
1825389041E_Affected1_1; 1825389067A_Affected1_2; 1825389067F_Affected1_3
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: liver sample time 40.0 hours mx-cre PLUS replicate E batch PHX2

status: Public on May 01 2009

city: Basel

first: Alessandro

last: Di Cara

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: liver sample collected at 40.0 hours following partial hepatectomy in a mx-cre PLUS transgenic mice homozygous for the RPS6 floxed mutation

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA Normalized values

label: biotin

organism: Mus musculus

source_name: liver following partial hepatectomy

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

extract_protocol: Total RNA was extracted from frozen liver samples using Trizol (Invitrogen), folowing the manufacturer's instructions

tag: Genetic

value: RPS6 homozygous floxed

value: mx-cre transgene PLUS

tag: Age

value: 3 months

tag: Gender

value: male

tag: Batch


title: liver sample time 40.0 hours mx-cre PLUS replicate D batch PHX2


title: liver sample time 40.0 hours mx-cre PLUS replicate C batch PHX3


title: Affected2

description:
1825389067B_Affected2
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: liver sample time 30.0 hours mx-cre PLUS replicate B batch PHX2

description: liver sample collected at 30.0 hours following partial hepatectomy in a mx-cre PLUS transgenic mice homozygous for the RPS6 floxed mutation


title: liver sample time 30.0 hours mx-cre MINUS replicate C batch PHX2

description: liver sample collected at 30.0 hours following partial hepatectomy in a mx-cre MINUS transgenic mice homozygous for the RPS6 floxed mutation

value: mx-cre transgene MINUS


title: liver sample time 40.0 hours mx-cre PLUS replicate B batch PHX3


title: liver sample time 40.0 hours mx-cre MINUS replicate C batch PHX3

description: liver sample collected at 40.0 hours following partial hepatectomy in a mx-cre MINUS transgenic mice homozygous for the RPS6 floxed mutation


title: liver sample time 40.0 hours mx-cre MINUS replicate D batch PHX2


title: liver sample time 30.0 hours mx-cre PLUS replicate C batch PHX2


title: liver sample time 40.0 hours mx-cre PLUS replicate A batch PHX3


title: Control2

description:
1825389067D_Control2
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls


title: liver sample time 30.0 hours mx-cre MINUS replicate D batch PHX2


title: liver sample time 40.0 hours mx-cre MINUS replicate A batch PHX3


title: liver sample time 40.0 hours mx-cre MINUS replicate B batch PHX3


title: liver sample time 30.0 hours mx-cre MINUS replicate B batch PHX3


title: liver sample time 30.0 hours mx-cre PLUS replicate A batch PHX3


title: liver sample time 30.0 hours mx-cre MINUS replicate A batch PHX3


title: liver sample time 20.0 hours mx-cre PLUS replicate D batch PHX2

description: liver sample collected at 20.0 hours following partial hepatectomy in a mx-cre PLUS transgenic mice homozygous for the RPS6 floxed mutation


title: liver sample time 20.0 hours mx-cre PLUS replicate B batch PHX3


title: liver sample time 20.0 hours mx-cre MINUS replicate B batch PHX3

description: liver sample collected at 20.0 hours following partial hepatectomy in a mx-cre MINUS transgenic mice homozygous for the RPS6 floxed mutation


title: liver sample time 20.0 hours mx-cre PLUS replicate A batch PHX3


title: liver sample time 20.0 hours mx-cre MINUS replicate A batch PHX3


title: liver sample time 20.0 hours mx-cre MINUS replicate D batch PHX2


title: liver sample time 20.0 hours mx-cre MINUS replicate C batch PHX2


title: liver sample time 0.0 hours mx-cre PLUS replicate B batch PHX3

description: liver sample collected at 0.0 hours following partial hepatectomy in a mx-cre PLUS transgenic mice homozygous for the RPS6 floxed mutation


title: liver sample time 0.0 hours mx-cre PLUS replicate C batch PHX2


title: liver sample time 0.0 hours mx-cre MINUS replicate C batch PHX3

description: liver sample collected at 0.0 hours following partial hepatectomy in a mx-cre MINUS transgenic mice homozygous for the RPS6 floxed mutation


title: Wild-type_in_vitro_control

scan_protocol: Available at manufacturer's website: www.nimblegen.com

source_name: Wild-type bacteria of stationary-phase resuspended in PBS

treatment_protocol: 50 ml of an overnight culture of the wild-type strain in LB broth was harvested and resuspended in 20 ml PBS buffer and then stored at 37 degree for 4 hours.

value: wild-type strain.


title: liver sample time 0.0 hours mx-cre PLUS replicate D batch PHX2


title: liver sample time 0.0 hours mx-cre MINUS replicate D batch PHX2


title: 2nd-ALD+RU

city: Minatoku, Tokyo

first: NORITADA

last: YOSHIKAWA

address: Shirokanedai 4-6-1

department: Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, University of Tokyo

description: Gene expression data from 2nd experiment of ALD and RU486-treated neonatal rat cardiomyocyte primary culture cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3007G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Per-chip normalization  was carried out with GeneSpringｨ7.3.1 (Agilent Technologies, Palo Alto, CA). A raw intensity value was divided by the median value of the chip measurements.

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with ALD and RU486 for 3 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The ventricles of 1-day-old neonatal Wistar rats (CLEA Japan, Tokyo, Japan) were dissociated in 0.03% trypsin, 0.03% collagenase, and 20 µg/mL of DNase I. The cardiomyocytes and cardiac fibroblasts were separately prepared on the basis of their differential adhesiveness. Attached cells (mostly cardiac fibroblasts) were subcultured twice to deplete cardiomyocytes, and the third passage cells were used. Cardiomyocytes were seeded at a density of 1x105 cells/cm2 on gelatin-coated dishes and grown in medium 199/DMEM (Invitrogen) supplemented with 10% FCS and antibiotics in a humidified atmosphere at 37˚C with 5% CO2.

extract_protocol: Total RNA was isolated using TRIZOL-Reagent (Invitrogen) according to the manufacturer’s protocol and further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Primary cultures of cardiomyocytes, grown in OPTI-MEM for 24 h, were treated with vehicle (ethanol) or various ligands for 3 h with or without pretreatment of 10 µM RU486.

tag: one-day-old neonatal Wistar rats


title: 2nd-ALD

description: Gene expression data from 2nd experiment of ALD-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with ALD for 3 h


title: 2nd-COR

description: Gene expression data from 2nd experiment of COR-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with COR for 3 h


title: 2nd-COR+RU

description: Gene expression data from 2nd experiment of COR and RU486-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with COR and RU486 for 3 h


title: liver sample time 20.0 hours mx-cre PLUS replicate C batch PHX2


title: 1st-COR

description: Gene expression data from 1st experiment of COR-treated neonatal rat cardiomyocyte primary culture cells

source_name: 1st experiment: neonatal rat cardiomyocytes primary culture cells treated with COR for 3 h


title: liver sample time 0.0 hours mx-cre MINUS replicate A batch PHX3


title: 2nd-CVZ

description: Gene expression data from 2nd experiment of CVZ-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with CVZ for 3 h


title: 2nd-CVZ+RU

description: Gene expression data from 2nd experiment of CVZ and RU486-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with CVZ and RU486 for 3 h


title: 2nd-vehicle

description: Gene expression data from 2nd experiment of ethanol-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with ethanol for 3 h


title: 1st-ALD

description: Gene expression data from 1st experiment of ALD-treated neonatal rat cardiomyocyte primary culture cells

source_name: 1st experiment: neonatal rat cardiomyocytes primary culture cells treated with ALD for 3 h


title: 2nd-RU

description: Gene expression data from 2nd experiment of RU486-treated neonatal rat cardiomyocyte primary culture cells

source_name: 2nd experiment; neonatal rat cardiomyocytes primary culture cells treated with RU486 for 3 h


title: liver sample time 0.0 hours mx-cre MINUS replicate B batch PHX2


title: 7130T (U133A): Lung metastasis

city: Houston

first: Xiang

last: Zhang

state: TX

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

description: Lung metastasis

hyb_protocol: Test3 arrays (Affymetrix), standard Affymetrix protocol

data_processing: RMA algorithm

source_name: Lung

label_protocol: Biotinylated nucleotides (Enzo Biochem), standard Affymetrix protocol

extract_protocol: TRIzol (GIBCO/BRL)

tag: Breast cancer


title: 4059T (U133A): Lung metastasis

description: Lung metastasis


title: 1st-CVZ

description: Gene expression data from 1st experiment of CVZ-treated neonatal rat cardiomyocyte primary culture cells

source_name: 1st experiment: neonatal rat cardiomyocytes primary culture cells treated with CVZ for 3 h


title: 1st-vehicle

description: Gene expression data from 1st experiment of ethanol-treated neonatal rat cardiomyocyte primary culture cells

source_name: 1st experiment: neonatal rat cardiomyocytes primary culture cells treated with ethanol for 3 h


title: 5381T (U133A): Lung metastasis

description: Lung metastasis


title: 15112T (U133A): Lung metastasis

description: Lung metastasis


title: 6752T (U133A): Bone metastasis

description: Bone metastasis

source_name: Bone


title: 1813T (U133A): Lung metastasis

description: Lung metastasis


title: Affected11

description:
4037951027C_Affected11
Comparison of genome-wide expression in EBV-transformed lymphoblastoid cell lines of patients and controls

source_name: EBV-transformed cell line of lymphoblasts extrated from peripheral blood


title: 6565T (U133A): Lung metastasis

description: Lung metastasis


title: 14891T (U133A): Bone metastasis

description: Bone metastasis


title: 12749T (U133A): Liver metastasis

description: Liver metastasis

source_name: Liver


title: 12740T (U133A): Lung metastasis

description: Lung metastasis


title: 12367T (U133A): Bone metastasis

description: Bone metastasis


title: liver sample time 0.0 hours mx-cre PLUS replicate A batch PHX3

source_name: liver following partial hepatectomy


title: 109714T (U133A): Brain metastasis

description: Brain metastasis

source_name: Brain


title: 103696T (U133A): Lung metastasis

description: Lung metastasis


title: 109506T (U133A): Brain metastasis

description: Brain metastasis


title: 3032T (U133A): Liver metastasis

description: Liver metastasis


title: 109594T (U133A): Bone metastasis

description: Bone metastasis


title: 109734T (U133A): Brain metastasis

description: Brain metastasis


title: 106389T (U133A): Liver metastasis

description: Liver metastasis


title: 107426T (U133A): Brain metastasis

description: Brain metastasis


title: 105188T (U133A): Brain metastasis

description: Brain metastasis


title: 107482T (U133A): Bone metastasis

description: Bone metastasis


title: 10519T (U133A): Lung metastasis

description: Lung metastasis


title: 14045T (U133A): Lung metastasis

description: Lung metastasis


title: 106570T (U133A): Lung metastasis

description: Lung metastasis


title: 3878T (U133A): Bone metastasis

description: Bone metastasis


title: 101258T (U133A): Lung metastasis

description: Lung metastasis


title: 11887T (U133A): Bone metastasis

description: Bone metastasis


title: 105880T (U133A): Bone metastasis

description: Bone metastasis


title: B41-Met (U133A): Liver metastasis

description: Liver metastasis


title: 100184T (U133A): Brain metastasis

description: Brain metastasis


title: B34-Met (U133A): Lung metastasis

description: Lung metastasis


title: B22-Met (U133A): Lung metastasis

description: Lung metastasis


title: 106201T (U133A): Lung metastasis

description: Lung metastasis


title: B35-Met (U133A): Lung metastasis

description: Lung metastasis


title: 102962T (U133A): Brain metastasis

description: Brain metastasis


title: 101815T (U133A): Liver metastasis

description: Liver metastasis


title: MZL patient 10-N

status: Public on Apr 01 2009

type: genomic

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

description: SMZL

hyb_protocol: standard Affymetrix procedures using Fluidics Station

scan_protocol: standard Affymetrix procedures using GeneChip Scanner 3000

data_processing:
Affymetrix GeneChip GCOS 1.4, GTYPE 4.1 (HMM 100kb), the LOH values were processed using the dCHIP software.
We have used the following 30 HapMap samples (corresponding to maternal individuals from the trio sets) as normal reference samples:

CEU_NA06985_NSP.CEL
CEU_NA07000_NSP.CEL
CEU_NA07055_NSP.CEL
CEU_NA07056_NSP.CEL
CEU_NA07345_NSP.CEL
CEU_NA11830_NSP.CEL
CEU_NA11832_NSP.CEL
CEU_NA11840_NSP.CEL
CEU_NA11882_NSP.CEL
CEU_NA11993_NSP.CEL
CEU_NA11995_NSP.CEL
CEU_NA12004_NSP.CEL
CEU_NA12006_NSP.CEL
CEU_NA12044_NSP.CEL
CEU_NA12057_NSP.CEL
CEU_NA12145_NSP.CEL
CEU_NA12156_NSP.CEL
CEU_NA12234_NSP.CEL
CEU_NA12236_NSP.CEL
CEU_NA12239_NSP.CEL
CEU_NA12249_NSP.CEL
CEU_NA12717_NSP.CEL
CEU_NA12751_NSP.CEL
CEU_NA12761_NSP.CEL
CEU_NA12763_NSP.CEL
CEU_NA12813_NSP.CEL
CEU_NA12815_NSP.CEL
CEU_NA12873_NSP.CEL
CEU_NA12875_NSP.CEL
CEU_NA12892_NSP.CEL

molecule: genomic DNA

source_name: MZL patient 10-N

label_protocol: standard Affymetrix protocol starting from 250 ng of DNA.

extract_protocol: genomic DNA was extracted using the Qiagen DNA Mini kit (Qiagen, Hilden, Germany) dissolved in reduced EDTA TE buffer

tag: human MZL clinical sample

tag: SMZL


title: MZL patient 12-N

description: SMZL

source_name: MZL patient 12-N


title: MZL patient 8-N

description: NMZL

source_name: MZL patient 8-N

tag: NMZL


title: MZL patient 11-N

description: SMZL

source_name: MZL patient 11-N


title: MZL patient 17-C

description: EMZL

source_name: MZL patient 17-C

tag: EMZL


title: MZL patient 4-N

description: NMZL

source_name: MZL patient 4-N


title: MZL patient 12-C

description: SMZL

source_name: MZL patient 12-C


title: MZL patient 16-C

description: NMZL

source_name: MZL patient 16-C


title: MZL patient 9-N

description: SMZL

source_name: MZL patient 9-N


title: MZL patient 13-N

description: SMZL

source_name: MZL patient 13-N


title: MZL patient 5-N

description: SMZL

source_name: MZL patient 5-N


title: MZL patient 2-N

description: SMZL

source_name: MZL patient 2-N


title: MZL patient 7-C

description: EMZL

source_name: MZL patient 7-C


title: MZL patient 1-N

description: SMZL

source_name: MZL patient 1-N


title: MZL patient 14-C

description: NMZL

source_name: MZL patient 14-C


title: MZL patient 18-C

description: NMZL

source_name: MZL patient 18-C


title: MZL patient 5-C

description: NMZL

source_name: MZL patient 5-C


title: MZL patient 3-C

description: EMZL

source_name: MZL patient 3-C


title: MZL patient 3-N

description: EMZL

source_name: MZL patient 3-N


title: MZL patient 4-C

description: EMZL

source_name: MZL patient 4-C


title: MZL patient 11-C

description: NMZL

source_name: MZL patient 11-C


title: MZL patient 8-C

description: EMZL

source_name: MZL patient 8-C


title: MZL patient 10-C

description: EMZL

source_name: MZL patient 10-C


title: MZL patient 6-N

description: SMZL

source_name: MZL patient 6-N


title: MZL patient 6-C

description: NMZL

source_name: MZL patient 6-C


title: MZL patient 9-C

description: EMZL

source_name: MZL patient 9-C


title: MZL patient 15-C

description: EMZL

source_name: MZL patient 15-C


title: N40F:M (NSP)

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Application Study: Genotyping data from patients with unexplained mental retardation

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: We identified genome-wide CNV using both the Copy Number Analyzer for Affymetrix GeneChip (CNAG) software and Affymetrix Genotyping Console (GTC), which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

source_name: Genomic DNA from blood

label_protocol: Standard Affymetrix protocol

extract_protocol: Salt-extraction from blood, no extra purification

tag: Unaffected parent male


title: N37F:M (NSP)


title: N38F:M (NSP)


title: N39F:M (NSP)


title: N39C:M (NSP)

tag: Affected child male


title: N31M:F (NSP)

tag: Unaffected parent female


title: N36C:F (NSP)

tag: Affected child female


title: N37M:F (NSP)


title: N35M:F (NSP)


title: N36M:F (NSP)


title: N38M:F (NSP)


title: N40M:F (NSP)


title: N33C:M (NSP)


title: N39M:F (NSP)


title: N32M:F (NSP)


title: N32F:M (NSP)


title: N36F:M (NSP)


title: N34F:M (NSP)


title: N40C:F (NSP)


title: N35F:M (NSP)


title: N32C:M (NSP)


title: N34C:M (NSP)


title: N33M:F (NSP)


title: N35C:F (NSP)


title: N37C:F (NSP)


title: N33F:M (NSP)


title: N34M:F (NSP)


title: N38C:M (NSP)


title: N31F:M (NSP)


title: N30C:M (NSP)


title: N31C:F (NSP)


title: N30M:F (NSP)


title: N28F:M (NSP)


title: N30F:M (NSP)


title: N29F:M (NSP)


title: N29C:M (NSP)


title: N27M:F (NSP)


title: N25M:F (NSP)


title: N26F:M (NSP)


title: N26M:F (NSP)


title: N27C:F (NSP)


title: N26C:F (NSP)


title: N27F:M (NSP)


title: N29M:F (NSP)


title: N28M:F (NSP)


title: N23C:M (NSP)


title: N22M:F (NSP)


title: N23M:F (NSP)


title: N25C:M (NSP)


title: N25F:M (NSP)


title: N24C:F (NSP)


title: N24F:M (NSP)


title: N22C:M (NSP)


title: N22F:M (NSP)


title: N21M:F (NSP)


title: N23F:M (NSP)


title: N24M:F (NSP)


title: N20M:F (NSP)


title: N19M:F (NSP)


title: N28C:M (NSP)


title: N20F:M (NSP)


title: N18M:F (NSP)


title: N19F:M (NSP)


title: N19C:M (NSP)


title: N20C:F (NSP)


title: N15F:M (NSP)


title: N17M:F (NSP)


title: N18C:F (NSP)


title: N18F:M (NSP)


title: N17F:M (NSP)


title: N16C:M (NSP)


title: N16M:F (NSP)


title: N16F:M (NSP)


title: N14F:M (NSP)


title: N21C:F (NSP)


title: N13C:F (NSP)


title: N15C:M (NSP)


title: N13M:F (NSP)


title: N15M:F (NSP)


title: N14C:M (NSP)


title: N13F:M (NSP)


title: N14M:F (NSP)


title: N12M:F (NSP)


title: N12C:M (NSP)


title: N12F:M (NSP)


title: N11F:M (NSP)


title: N10F:M (NSP)


title: N21F:M (NSP)


title: N17C:F (NSP)


title: N10M:F (NSP)


title: N11C:F (NSP)


title: N9M:F (NSP)


title: N11M:F (NSP)


title: N8F:M (NSP)


title: N10C:F (NSP)


title: N8M:F (NSP)


title: N7F:M (NSP)


title: N9C:M (NSP)


title: N9F:M (NSP)


title: N6M:F (NSP)


title: N7C:F (NSP)


title: N5M:F (NSP)


title: N6C:M (NSP)


title: N4F:M (NSP)


title: N6F:M (NSP)


title: N5C:F (NSP)


title: N7M:F (NSP)


title: N4M:F (NSP)


title: N3M:F (NSP)


title: N5F:M (NSP)


title: N3F:M (NSP)


title: N3C:M (NSP)


title: N8C:F (NSP)


title: N2F:M (NSP)


title: N2M:F (NSP)


title: N4C:F (NSP)


title: N2C:M (NSP)


title: T40F:M (NSP)


title: N1M:F (NSP)


title: N1C:F (NSP)


title: T40M:F (NSP)


title: T37M:F (NSP)


title: T39C:M (NSP)


title: T40C:F (NSP)


title: T39F:M (NSP)


title: T39M:F (NSP)


title: T38C:F (NSP)


title: T38F:M (NSP)


title: T37F:M (NSP)


title: T36M:F (NSP)


title: N1F:M (NSP)


title: T36C:M (NSP)


title: T35M:F (NSP)


title: T36F:M (NSP)


title: T34M:F (NSP)


title: T38M:F (NSP)


title: T34F:M (NSP)


title: T35F:M (NSP)


title: T35C:M (NSP)


title: T34C:M (NSP)


title: T33C:M (NSP)


title: T33M:F (NSP)


title: T32M:F (NSP)


title: T33F:M (NSP)


title: T32C:F (NSP)


title: T37C:F (NSP)


title: T31M:F (NSP)


title: T30M:F (NSP)


title: T31F:M (NSP)


title: T32F:M (NSP)


title: T29C:F (NSP)


title: T30F:M (NSP)


title: T28C:M (NSP)


title: T27F:M (NSP)


title: T28M:F (NSP)


title: T29M:F (NSP)


title: T30C:F (NSP)


title: T31C:M (NSP)


title: T27C:M (NSP)


title: T26M:F (NSP)


title: T29F:M (NSP)


title: T28F:M (NSP)


title: T25C:M (NSP)


title: T26F:M (NSP)


title: T27M:F (NSP)


title: T24C:M (NSP)


title: T24M:F (NSP)


title: T25F:M (NSP)


title: T23M:F (NSP)


title: T24F:M (NSP)


title: T23F:M (NSP)


title: T25M:F (NSP)


title: T26C:F (NSP)


title: T19C:M (NSP)


title: T22F:M (NSP)


title: T20M:F (NSP)


title: T22M:F (NSP)


title: T20C:F (NSP)


title: T22C:M (NSP)


title: T21M:F (NSP)


title: T19M:F (NSP)


title: T21C:M (NSP)


title: T20F:M (NSP)


title: T16M:F (NSP)


title: T23C:M (NSP)


title: T19F:M (NSP)


title: T21F:M (NSP)


title: T17M:F (NSP)


title: T16C:F (NSP)


title: T18M:F (NSP)


title: T18C:M (NSP)


title: T18F:M (NSP)


title: T17F:M (NSP)


title: T17C:M (NSP)


title: T16F:M (NSP)


title: T14F:M (NSP)


title: T14C:M (NSP)


title: T15F:M (NSP)


title: T13F:M (NSP)


title: T14M:F (NSP)


title: T15C:M (NSP)


title: T15M:F (NSP)


title: T12M:F (NSP)


title: T12F:M (NSP)


title: T10F:M (NSP)


title: T12C:M (NSP)


title: Populus_trichocarpa_rep1_ozone_exposed_200ppb_9hrs

city: Umeå

first: Nathaniel

middle: Robert

last: Street

address: Umeå University

department: Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

hyb_protocol: 1 L pre-hybridisation solution (5X SSC, 0.1% SDS, 2% BSA) was heated for 30 min at 50 °C in an oven. Slides was placed in a UV cross-linker (Stratagene, California, USA) set at 90 mJ and then washed for 30 s in 0.1% SDS, 30 s in MQ water and incubated for 3 min in near boiling water followed by 95% EtOH for 90 s, and centrifuged for 5 min at 500 rpm. Slides were immediately transferred to a staining dish containing pre-heated pre-hybridisation solution. The preparation was transferred to an oven and incubated at 50 °C. Slides were removed from the pre-hybridisation solution and washed for 30 s in MQ H2O and 30 s in 95% EtOH and centrifuged for 5 min at 500 rpm. A lifter slip (Erie Scientific, Portsmouth, USA) (pre-washed in 0.1% SDS, MQ H2O, and EtOH) was then placed on the spotted area of each slide. 2 µl poly-A, and 48 µl hybridisation buffer 3 (Ambion, Cambridgeshire, UK) were added to the probe and mixed. The probe was denatured by incubation at 96 °C for 2 min, and centrifuged at 13000 rpm for 30 s. The probe was then added to the slide adjacent to the lifter slip. Slides were incubated in a hybridisation chamber (Genetix, Hampshire, UK) at 50 °C for 16-18 hrs. Slides were then washed in coplain staining jars by gently agitated in wash buffer1 (2X SSC, 0.5% SDS) to remove the lifter slip and transferred to fresh wash buffer 1. The jar was incubated in an oven for 15 min at 50 °C. Slides were then transferred to wash buffer 2 (0.5X SSC, 0.5% SDS) for 15 min at 50 °C, wash buffer 3 (0.5X SSC) at room temperature for 5 min, WB4 (0.2X SSC) at room temperature for 1 min and WB5 (0.06X SSC) at room temperature for 1 min and then centrifuged for 5 min at 500 rpm.

scan_protocol: Slides were scanned using a ScanArray500 (PerkinElmer Life and Analytical Sciences, Boston, MA). Initially, a line scan was performed on a row of spots at 90 % laser power, and the Cy3 and Cy5 laser intensities equalised on the basis of this. The final scan was performed at 5 µm resolution, and the data saved in TIFF format.

data_processing: QC and normalisation was run in R using limma and sma function (R script linked as supplementary file).

organism: Populus trichocarpa

label_protocol:
1 µl oligo dT (Invitrogen, Paisley, UK) was added to 25 µg total RNA in 15.5 µl RNase free water. The sample was heated at 65 °C in a heating block for 10 min and then was placed on ice for 1 min. A reverse transcription mastermix was prepared, consisting of 6 µl 5X first strand buffer, 3 µl DTT, 3 µl 10X amino-allyl dNTP mix, 0.5 µl Super RNase inhibitor and 1 µl SuperScript III per reaction (all from Invitrogen, Paisley, UK). 13.5 µl mastermix was then added to each sample, and the preparation incubated at 46 °C for 1 hr. 1 µl MMLV-RT RNase H point mutant (Promega, Southampton, UK) was added to each sample, and further incubated for 1 hr. 2 µl fresh 5M NaOH and 8 µl 0.5M EDTA were added and the samples incubated for 15 min at 65 °C to stop the reverse transcription and degrade remaining RNA. The reaction was neutralised with 20 µl 1M HEPES (pH 7.5).
40 µl water and 500 µl PB were added to each sample and mixed thoroughly. The sample was transferred to a QiaQuick column, and centrifuged at maximum speed for 1 min. The flow-through was discarded and 750 µl fresh phosphate–ethanol wash buffer added to the column. The column was centrifuged for 1 min and the flow through discarded. The column was then centrifuged for 1 min and transferred to a labelled 1.5 ml microfuge tube. 30 µl H-2O was added to the column, incubated at room temperature for 1 min and centrifuged for 1 min. A further 20 µl H¬2O was added and the column centrifuged for 1 min. The sample was dried in a speed vac (Savant, Minnesota, USA) to 27 µl.
A tube of dye ester was re-suspended in 73 µl water-free DMSO, and 4.5 µl aliquots made, which were stored at -80°C. 3 µl 1M NaHCO3 (pH 9.3) were added to the cDNA sample. From this point onwards all steps are carried out in minimal light. 4.5 µl Cy-dye (Amersham, Buckinghamshire, UK) were added to the sample and incubated at room temperature for 1 hr. 4.5 µl 4M hydroxylamine were added to stop the reaction. The Cy3 and Cy5 reactions were mixed and 22 µl H2O added. The reaction was then dried in a speed-vac.

growth_protocol: Cuttings were planted in John Innes No. 2 compost (John Innes Manufacturers Association, Harrogate, UK) in 1.75 L pots with two buds above soil level. Pots were assigned randomly to two controlled environment rooms set at 22 ?C, PAR 160 µmol m-2s-1 and 16 hr photoperiod, and were watered daily. Thirty three days after planting, the plants were transferred to the ozone enrichment chambers. The growth chambers were described in detail by Warwick and Taylor (1995). Plants were acclimated for 48 hrs under continuous light before the ozone treatment was initiated, at a mean temperature of 24 °C and PAR 120 µmol m-2 s-1. Mean airflow through the chambers was 2.5 m s-1.

extract_protocol: Total RNA was extracted from the fifth leaf of each plant using a modified version of the method described in Chang et al (1993): Spermidine was omitted from the extraction buffer, and 2.67 % ß-mercaptoethanol was added. After precipitation, two additional CHISAM extractions were performed. RNA concentration was determined using an Eppendorf Biophotometer (Eppendorf, Hamburg, Germany), and quality was assessed using a 1 % (w/v) agarose gel.

treatment_protocol: The fifth leaf below the first fully unfurled leaf was sampled from three replicate plants after 9 hrs exposure to ambient air in growth chambers. RNA was extracted from each leaf and then equal quantities of RNA from each replicate pooled to form a single sample for cDNA synthesis and hybridisation.

tag: Female P. trichocarpa 'Torr. and Gray', clone 93-968 from western Washington, USA

treatment_protocol: The fifth leaf below the first fully unfurled leaf was sampled from three replicate plants after 9 hrs exposure to 200 ppb ozone in growth chambers. RNA was extracted from each leaf and then equal quantities of RNA from each replicate pooled to form a single sample for cDNA synthesis and hybridisation.


title: T11M:F (NSP)


title: T13M:F (NSP)


title: T10M:F (NSP)


title: T11C:M (NSP)


title: T13C:F (NSP)


title: T11F:M (NSP)


title: T9C:M (NSP)


title: T10C:M (NSP)


title: Populus_trichocarpa_rep2_ozone_exposed_200ppb_9hrs


title: Populus_deltoides_rep3_ozone_exposed_200ppb_9hrs

organism: Populus deltoides

tag: Male P. deltoides 'Bart ex. Marsh', clone ILL-129 from central Illinois, USA


title: Populus_deltoides_rep2_ozone_exposed_200ppb_9hrs


title: T7C:F (NSP)


title: T6F:M (NSP)


title: T8M:F (NSP)


title: T9F:M (NSP)


title: T5M:F (NSP)


title: T8C:M (NSP)


title: T9M:F (NSP)


title: T7M:F (NSP)


title: T6M:F (NSP)


title: T8F:M (NSP)


title: Populus_trichocarpa_rep3_ozone_exposed_200ppb_9hrs


title: T6C:F (NSP)


title: T7F:M (NSP)


title: T5C:M (NSP)


title: Populus_deltoides_rep1_ozone_exposed_200ppb_9hrs

tag: Male P. deltoides 'Bart' ex. March, clone ILL-129 from central Illinois, USA


title: T4C:F (NSP)


title: T5F:M (NSP)


title: T4F:M (NSP)


title: T4M:F (NSP)


title: T3M:F (NSP)


title: T2F:M (NSP)


title: T3F:M (NSP)


title: T2M:F (NSP)


title: T2C:M (NSP)


title: T3C:M (NSP)


title: B39C:F (NSP)


title: B40F:M (NSP)


title: B38C:M (NSP)


title: T1C:M (NSP)


title: B40C:M (NSP)


title: B40M:F (NSP)


title: B36C:M (NSP)


title: B37M:F (NSP)


title: B37C:M (NSP)


title: B37F:M (NSP)


title: B38F:M (NSP)


title: B39M:F (NSP)


title: B35M:F (NSP)


title: T1M:F (NSP)


title: B36F:M (NSP)


title: B38M:F (NSP)


title: B39F:M (NSP)


title: T1F:M (NSP)


title: B36M:F (NSP)


title: B34F:M (NSP)


title: B34C:M (NSP)


title: B35C:F (NSP)


title: B33C:F (NSP)


title: B34M:F (NSP)


title: B35F:M (NSP)


title: B33F:M (NSP)


title: B32C:M (NSP)


title: B33M:F (NSP)


title: B32M:F (NSP)


title: B31M:F (NSP)


title: B31F:M (NSP)


title: B30F:M (NSP)


title: N40C:F (STY)


title: B30C:F (NSP)


title: B31C:M (NSP)


title: N39C:M (STY)


title: B30M:F (NSP)


title: N38C:M (STY)


title: B28M:F (NSP)


title: B28F:M (NSP)


title: B27C:M (NSP)


title: N37M:F (STY)


title: N39M:F (STY)


title: B27M:F (NSP)


title: N37C:F (STY)


title: B28C:M (NSP)


title: B32F:M (NSP)


title: N36C:F (STY)


title: B29F:M (NSP)


title: B27F:M (NSP)


title: N35M:F (STY)


title: N34C:M (STY)


title: B29C:M (NSP)


title: B29M:F (NSP)


title: N33C:M (STY)


title: N33M:F (STY)


title: Non-Recurrent-NSCLC-2

status: Public on Dec 01 2009

city: Minneapolis

first: David

middle: A.

last: Potter

state: MN

address: 420 Delaware St. SE

department: Division of Hematology, Oncology and Transplantation

institute: University of Minnesota

description: Gene expression data from patient with non-recurrent cancer (frozen NSCLC tumor tissue)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: non-recurrent NSCLC tumor

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

extract_protocol: Resected tumor tissue was placed in liquid nitrogen immediately following resection. Specimens were homogenized using a Polytron homogenizer (Brinkmann Instruments, Westbury, NY) in ice-cold Trizol reagent (Gibco BRL, Gaithersburg, MD). Trizol extraction was followed by clean-up using the Qiagen RNeasy Mini-kit.

tag: from patient with non-recurrent cancer


title: N35C:F (STY)


title: B26C:M (NSP)


title: N32C:M (STY)


title: N29M:F (STY)


title: B26M:F (NSP)


title: N31M:F (STY)


title: N30C:M (STY)


title: N29C:M (STY)


title: N31C:F (STY)


title: B26F:M (NSP)2


title: B25F:M (NSP)


title: N26C:F (STY)


title: N24C:F (STY)


title: N23M:F (STY)


title: B24C:M (NSP)


title: N27C:F (STY)


title: N25C:M (STY)


title: N28C:M (STY)


title: B25C:F (NSP)


title: N27M:F (STY)


title: B24M:F (NSP)


title: B25M:F (NSP)


title: N23C:M (STY)


title: N22C:M (STY)


title: N21M:F (STY)


title: B23C:F (NSP)


title: B24F:M (NSP)


title: B23M:F (NSP)


title: N19C:M (STY)


title: N25M:F (STY)


title: N21C:F (STY)


title: N18C:F (STY)


title: N20C:F (STY)


title: N19M:F (STY)


title: B23F:M (NSP)


title: N17C:F (STY)


title: N17M:F (STY)


title: N13C:F (STY)


title: B21C:M (NSP)


title: N15C:M (STY)


title: B22C:F (NSP)


title: N15M:F (STY)


title: N16C:M (STY)


title: N14C:M (STY)


title: B21M:F (NSP)


title: N10C:F (STY)


title: N11C:F (STY)


title: B22M:F (NSP)


title: N9M:F (STY)


title: N12C:M (STY)


title: B22F:M (NSP)


title: N9C:M (STY)


title: N5M:F (STY)


title: B21F:M (NSP)


title: N5C:F (STY)


title: N7C:F (STY)


title: N6C:M (STY)


title: N8C:F (STY)


title: N7M:F (STY)


title: B20C:F (NSP)


title: N4C:F (STY)


title: N11M:F (STY)


title: B20F:M (NSP)


title: B20M:F (NSP)


title: B19C:F (NSP)


title: N3C:M (STY)


title: N1M:F (STY)


title: T40C:F (STY)


title: N13M:F (STY)


title: N3M:F (STY)


title: N1C:F (STY)


title: B19M:F (NSP)


title: T37C:F (STY)


title: B18M:F (NSP)


title: B18F:M (NSP)


title: T39C:M (STY)


title: N2C:M (STY)


title: T33C:M (STY)


title: T35C:M (STY)


title: B18C:M (NSP)


title: B17C:F (NSP)


title: T31C:M (STY)


title: B19F:M (NSP)


title: T34C:M (STY)


title: T38C:F (STY)


title: T30C:F (STY)


title: B16C:M (NSP)


title: T36C:M (STY)


title: T32C:F (STY)


title: B17M:F (NSP)


title: B17F:M (NSP)


title: T29C:F (STY)


title: T28C:M (STY)


title: B16F:M (NSP)


title: B15C:F (NSP)


title: T27C:M (STY)


title: T25C:M (STY)


title: T26C:F (STY)


title: T23C:M (STY)


title: T24C:M (STY)


title: B16M:F (NSP)


title: T19M:F (STY)


title: B15M:F (NSP)


title: T20C:F (STY)


title: T22C:M (STY)


title: B14C:M (NSP)


title: T20M:F (STY)


title: B14M:F (NSP)


title: T19C:M (STY)


title: T21M:F (STY)


title: T22M:F (STY)


title: B15F:M (NSP)


title: T17C:M (STY)


title: T17M:F (STY)


title: B14F:M (NSP)


title: T18C:M (STY)


title: T16M:F (STY)


title: T15C:M (STY)


title: B13C:M (NSP)


title: T15M:F (STY)


title: T21C:M (STY)


title: T14M:F (STY)


title: B13F:M (NSP)


title: B13M:F (NSP)


title: T16C:F (STY)


title: B12C:F (NSP)


title: T13M:F (STY)


title: T14C:M (STY)


title: T13C:F (STY)


title: B12M:F (NSP)


title: T12F:M (STY)


title: T11M:F (STY)


title: T7M:F (STY)


title: B11F:M (NSP)


title: T7C:F (STY)


title: T10C:M (STY)


title: T10M:F (STY)


title: T12M:F (STY)


title: T6M:F (STY)


title: T11C:M (STY)


title: B12F:M (NSP)


title: B10C:F (NSP)


title: B10M:F (NSP)


title: T9C:M (STY)


title: B11C:F (NSP)


title: T12C:M (STY)


title: B11M:F (NSP)


title: T5C:M (STY)


title: T5F:M (STY)


title: T6C:F (STY)


title: T4C:F (STY)


title: T5M:F (STY)


title: T2M:F (STY)


title: T4M:F (STY)


title: T3M:F (STY)


title: B9C:F (NSP)


title: B10F:M (NSP)


title: B9M:F (NSP)


title: T1M:F (STY)


title: T3C:M (STY)


title: B9F:M (NSP)


title: T2C:M (STY)


title: B8C:M (NSP)


title: B40C:M (STY)


title: B38C:M (STY)


title: B35C:F (STY)


title: B39C:F (STY)


title: B7C:F (NSP)


title: B8F:M (NSP)


title: B36C:M (STY)


title: B34C:M (STY)


title: B33C:F (STY)


title: T1C:M (STY)


title: B7M:F (NSP)


title: B8M:F (NSP)


title: B30C:F (STY)


title: T8M:F (STY)


title: B32C:M (STY)


title: B37C:M (STY)


title: B6M:F (NSP)


title: B6C:F (NSP)


title: B28C:M (STY)


title: B27C:M (STY)


title: B26C:M (STY)


title: B25C:F (STY)


title: B23C:F (STY)


title: B6F:M (NSP)


title: B31C:M (STY)


title: B5C:F (NSP)


title: B29C:M (STY)


title: B22C:F (STY)


title: B7F:M (NSP)


title: B21C:M (STY)


title: B19C:F (STY)


title: B22M:F (STY)


title: B4M:F (NSP)


title: B21M:F (STY)


title: B4C:F (NSP)


title: B24C:M (STY)


title: B20C:F (STY)


title: B5M:F (NSP)


title: B20M:F (STY)


title: B17C:F (STY)


title: B5F:M (NSP)


title: B18C:M (STY)


title: B18M:F (STY)


title: B4F:M (NSP)


title: B19M:F (STY)


title: B15C:F (STY)


title: B17M:F (STY)


title: B3M:F (NSP)


title: B15M:F (STY)


title: B3C:M (NSP)


title: B13C:M (STY)


title: B14C:M (STY)


title: B2F:M (NSP)


title: B10C:F (STY)


title: B16C:M (STY)


title: B16M:F (STY)


title: B3F:M (NSP)


title: B12C:F (STY)


title: B12M:F (STY)


title: B2C:F (NSP)


title: B9M:F (STY)


title: B13M:F (STY)


title: B7C:F (STY)


title: B1M:F (NSP)


title: B1C:F (NSP)


title: B14M:F (STY)


title: B11C:F (STY)


title: B8M:F (STY)


title: B10M:F (STY)


title: B9C:F (STY)


title: B1F:M (NSP)


title: B8C:M (STY)


title: B10 (NSP)

description: Validation Study: Genotyping data from patients with known CNV aberration

tag: interstitial Xp22 del


title: B2M:F (NSP)


title: B6C:F (STY)


title: B5M:F (STY)


title: B5C:F (STY)


title: B6M:F (STY)


title: B7M:F (STY)


title: B4M:F (STY)


title: 05_1113 (NSP)

tag: DGS


title: B12 (NSP)


title: B2C:F (STY)


title: B1C:F (STY)


title: B4C:F (STY)


title: B3M:F (STY)


title: B12 (STY)


title: B10 (STY)


title: B3C:M (STY)


title: B11 (NSP)

tag: SMS


title: 05_1113 (STY)


title: 05_1183 (STY)

tag: 20qter dup and 22qter del


title: B9 (NSP)

tag: interstitial 20q11 dup


title: 05_1183 (NSP)


title: 04_1429 (NSP)

tag: PWS


title: ID680 (NSP)

tag: interstitial 17q21 del


title: B6 (NSP)


title: B11 (STY)


title: ID3635 (STY)

tag: interstitial 17q25 dup


title: ID3635 (NSP)


title: B1M:F (STY)


title: B7 (NSP)

tag: interstitial 13q14 del


title: 05_04365 (NSP)

tag: 12pter del


title: 04_1429 (STY)


title: ID680 (STY)


title: B9 (STY)


title: B6 (STY)


title: B5 (NSP)

tag: 11qter del


title: 05_04365 (STY)


title: B7 (STY)


title: B5 (STY)


title: B2 (STY)

tag: 10pte del


title: 03_04084Z (NSP)

tag: 9qter del


title: 03_03060 (NSP)

tag: 9qter dup


title: ID350 (STY)

tag: interstitial 9q33 del


title: 7312 (STY)

tag: 9pter dup


title: 03_03060 (STY)


title: ID298 (STY)


title: 03_04084Z (STY)


title: 26833 (STY)

tag: 8pter del


title: B13 (STY)

tag: interstitial 8q13 del


title: 7312 (NSP)


title: 04_03654 (NSP)

tag: 9pter dup and 11pter dup


title: 06_1047 (STY)

tag: WBS dup


title: B2 (NSP)


title: ID293 (STY)

tag: interstitial 6q15 dup


title: ID350 (NSP)


title: Tolerant_F2_genotype3_ozone_exposed_200ppb_9hrs

hyb_protocol: Pre-hybridisation was performed by placing slides in a Coplin staining jar containing pre-warmed pre-hybridisation buffer, and incubated for 1 hour at 42 °C. Slides were removed and placed immediately in WB III (0.2X SSC) for 5 min. Slides were then transferred to fresh WB III for 5 min, and to MQ H2O for 30 s. Targets were denatured by placing slides in boiling water for 1 min, and then transferring to 4 °C EtOH. Slides were then transferred to 50 ml Falcon tubes and immediately centrifuged at 3000 g for 1 min. The sample containing the Cy3 labelled sample was dissolved in 25 μl MQ H2O and 50 μl formamide. The sample was then transferred to the corresponding Cy5 sample and 25 μl Amersham hybridisation buffer added. The probe was denatured at 95 °C for 1 min and then placed on ice for 30 s. Hybridisation was performed in an HS400 hybridisation station (Tecan, Reading, UK). Slides were washed for 1 min in pre-hybridisation buffer. The prepared probe was then added, and slides hybridised for 16 hr at 42 °C with low agitation frequency. Slides were then washed 5 times for 1 min in each of WBI (1X SSC, 0.2% SDS), WBII (0.1X SSC, 0.1% SDS) and WBIII, and then for 1 min in MQ H2O, and 1 min in 100% EtOH and then dried with nitrogen gas.

scan_protocol: Slides were scanned on a Genetix Aquire scanner (Genetix, Hampshire, UK) at 5 μm resolution. PMT settings were adjusted to equalise the channel intensities. TIFF images were analysed using GenePixPro 5.1 (Axon Instruments, Union City, California). Spots were flagged as “bad” if the median signal intensity was less than 256 or equal to 65535. For the grand-parental experiment, spots were also flagged if less than 150 µm in diameter. Images were also checked manually.

organism: Populus trichocarpa x Populus deltoides

growth_protocol: Cuttings were planted in John Innes No. 2 compost (John Innes Manufacturers Association, Harrogate, UK) in 1.75 L pots with two buds above soil level. Pots were assigned randomly to two controlled environment rooms set at 22 C, PAR 160 µmol m-2s-1 and 16 hr photoperiod, and were watered daily. Thirty three days after planting, the plants were transferred to the ozone enrichment chambers. The growth chambers were described in detail by Warwick and Taylor (1995). Plants were acclimated for 48 hrs under continuous light before the ozone treatment was initiated, at a mean temperature of 24 °C and PAR 120 µmol m-2 s-1. Mean airflow through the chambers was 2.5 m s-1.

extract_protocol: Total RNA was extracted from the fifth leaf of each plant using a modified version of the method described in Chang et al (1993): Spermidine was omitted from the extraction buffer, and 2.67 % β-mercaptoethanol was added. After precipitation, two additional CHISAM extractions were performed. RNA concentration was determined using an Eppendorf Biophotometer (Eppendorf, Hamburg, Germany), and quality was assessed using a 1 % (w/v) agarose gel.

treatment_protocol: The fifth leaf below the first fully unfurled leaf was sampled from three replicate plants after 9 hrs exposure ambient air in growth chambers. RNA was extracted from each leaf and then equal quantities of RNA from each replicate pooled to form a single sample for cDNA synthesis and hybridisation.

tag: The inbred F2 population Family 331 was created from a cross between a female P. trichocarpa (clone 93-968 from western Washington, USA) and a male P. deltoides (clone ILL-129 from central Illinois, USA). Two siblings, 53-242 (female) and 53-246 (male), from the resulting F1 family (Family 53; Bradshaw and Stettler 1993) were crossed in 1988 to form an F2 family of 90 genotypes and again in 1990 to obtain an additional 320 genotypes (Family 331; Bradshaw et al., 1994, Wu et al., 1998). This pedigree was imported into the UK in 1999.


title: B13 (NSP)


title: ID298 (NSP)


title: 26833 (NSP)


title: Sensitive_F2_genotype1_ozone_exposed_200ppb_9hrs


title: Tolerant_F2_genotype2_ozone_exposed_200ppb_9hrs


title: 06_01465 (STY)

tag: 2qter del


title: Sensitive_F2_genotype3_ozone_exposed_200ppb_9hrs


title: Tolerant_F2_genotype1_ozone_exposed_200ppb_9hrs


title: Sensitive_F2_genotype2_ozone_exposed_200ppb_9hrs


title: B3 (STY)

tag: 6pter del


title: 03_1593 (STY)

tag: interstitial Xp22 dup and 4pter del


title: 05_04780 (STY)

tag: 5qter dup


title: ID71 (STY)

tag: interstitial 3q26 del


title: 04_03654 (STY)


title: 04_00746Z (STY)

tag: 3qter del


title: B4 (STY)

tag: interstitial 2q37 del and 10pter dup


title: 06_1047 (NSP)


title: B14 (STY)

tag: interstitial 6p21 dup


title: Heterozygous periphilin knockout mice II

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description: Each cRNA generated from whole brain was hybridized on one microarray separately.

hyb_protocol: Labeled, fragmented cRNA (15 µg) was hybridized for 16 h at 45°C to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix) according to the GeneChip® Expression Analysis Technical Manual (701021rev1; Affymetrix).

scan_protocol: After hybridization, the microarrays were automatically washed and stained with streptavidin–phycoerythrin. The probe arrays were scanned using a GeneChip®-Scanner 3000 (Affymetrix).

data_processing: In total, six cRNA samples were analyzed (three Periphilin+/- mice and three controls). To filter for transcripts that are differentially expressed between the two genotypes, the signals were first filtered for an absolute change in signal level of 2-fold (corresponding to a signal log ratio of 1.0). The remaining transcripts were subjected to statistical analysis using a t-test. Transcripts with a minimum fold change of 2.0 and a p-value of 0.05 or less were considered as statistically significant regulated. Categorization was based on the NetAffx™ Analysis Center annotations (https://www.affymetrix.com/analysis/netaffx/index.affx).

source_name: Whole brains from knockout mice

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each cell culture using GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix) with a T7-oligo(dT) primer incorporating a T7 RNA polymerase promoter. cRNA was prepared, biotin labeled and subsequently fragmented using the same set of reagents.

extract_protocol: Isolation of RNA was performed using RNAeasy® Kit (Qiagen, Germany) according to the manufacturer’s conditions. The quality of isolated RNA was controlled by Lab-on-Chip-System Bioanalyser 2100 (Agilent).

treatment_protocol: Whole brains of three male 2-months-old periphilin+/-knockout mice and three C57BL/6-wild type littermates were dissected, snap-frozen and kept at -80°C until further processing.


title: wt mice III

source_name: Whole brains from wild type mice

tag: Whole brains of three C57BL/6-wild type littermates


title: wt mice I


title: wt mice II


title: Heterozygous periphilin knockout mice III

tag: Whole brains of three male 2-months-old periphilin+/-knockout mice


title: B1 (NSP)

tag: WBS del


title: Heterozygous periphilin knockout mice


title: Time 3, Experimental Replicate 2

status: Public on Mar 31 2009

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

country: Canada

institute: National Research Council

description: All experimental samples run against universal RNA (cDNA prepared from 1 ug of a pooled universal RNA consisting of equal amounts of RNA from five developmental stages from hatching until post-metamorphosis).

hyb_protocol: Hybridization was completed using the 3DNA kit from Genisphere, (60 uL) was carefully applied to one corner of the Lifter Slip on the slide and immediately placed in the hybridization chamber (Die Tech, San Jose, CA, USA) for ON hyb. The hybridization process is 2 step where the initial hyb is cDNA only, and the second hyb is to couple the fluorophore. After hybridization slides were washed.

scan_protocol: Scanned on Perkin Elmer ScanArray 5000XL, ScanArray Express software v3.0.1

data_processing: Limma LOWESS normalized, background subtracted data obtained from log2 of processed Experimental signal/processed Reference signal. Arraypipe software was used.

organism: Hippoglossus hippoglossus

source_name: TEx2 (Time 3)

label_protocol: RNA (1 ug) from control RNA reference and experimental samples was reverse transcribed and labeled using the 3DNA Genisphere Array 900 expression array detection kit (Genisphere Inc,Hatfield PA, USA) with Alexa fluorophores according to manufacturers instructions.

extract_protocol: Total RNA extracted using Triazole according to the manufacturers protocol

tag: distal intestine

tag: Day 20 of diet

source_name: Univ RNA CEx


title: Time 3, Experimental Replicate 3

source_name: TEx3 (Time 3)


title: ID412 (STY)

tag: interstitial 2p22 dup


title: ID293 (NSP)


title: B1 (STY)


title: B8 (STY)

tag: interstitial 1p36 del


title: 05_0018 (STY)

tag: 1pter del


title: Endothelial_highShear_rep10

city: Durham

first: Ji

state: NC

address: Room 136 Hudson Hall

department: Department of Biomedical Engineering

institute: Duke University

hyb_protocol: • Make hybridization buffer fresh each time.  • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA.  • Add 1ul each poly dA and appropriate Cot-1 DNA.  • Heat at 95ºC for 2 minutes and put on ice to cool down.  • Mix well and load sample to the array slide with lifter cover slip.  • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized, include genes with signal in at least 16 of the 32 arrays, Agilent GeneSpring GX was used.

organism: Sus scrofa

source_name: Left iliac arterial endothelial cells exposed to high shear

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). 20 ng of total RNA for each sample, two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Reference endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum

extract_protocol: Qiagen RNeasy Micro kit following manufacturer's protocol

tag: Left iliac from Animal No. 6

source_name: Pooled referece RNA

tag: cultured porcine aortic endothelial cells


title: 20946 (STY)

tag: 1qter del


title: Endothelial_mediumShear_rep10

source_name: Left iliac arterial endothelial cells exposed to medium shear


title: Endothelial_lowShear_rep10

source_name: Left iliac arterial endothelial cells exposed to low shear


title: Time 3, Experimental Replicate 1

source_name: TEx1 (Time 3)


title: B14 (NSP)


title: ID166 (STY)

tag: interstitial 2q23 del


title: Time 3, Control Replicate 1

source_name: TC1 (Time 3)

source_name: Univ RNA CC


title: Time 2, Experimental Replicate 3

source_name: TEx3 (Time 2)

tag: Day 10 of diet


title: Endothelial_highShear_rep9

source_name: Right iliac arterial endothelial cells exposed to high shear

tag: Right iliac from Animal No. 5


title: 05_04780 (NSP)

tag: 5qter dup


title: Time 3, Control Replicate 2

source_name: TC2 (Time 3)


title: B3 (NSP)

source_name: Genomic DNA from blood

tag: 6pter del


title: Endothelial_highShear_rep11

tag: Right iliac from Animal No. 6


title: 04_00746Z (NSP)

tag: 3qter del


title: Time 2, Experimental Replicate 2

source_name: TEx2 (Time 2)


title: Endothelial_mediumShear_rep11

source_name: Right iliac arterial endothelial cells exposed to medium shear


title: Time 2, Experimental Replicate 1

source_name: TEx1 (Time 2)


title: Endothelial_highShear_rep8

tag: Left iliac from Animal No. 5


title: Endothelial_lowShear_rep9

source_name: Right iliac arterial endothelial cells exposed to low shear


title: Endothelial_mediumShear_rep9


title: Time 2, Control Replicate 3

source_name: TC3 (Time 2)


title: Time 2, Control Replicate 2

source_name: TC2 (Time 2)


title: Endothelial_mediumShear_rep8


title: ID71 (NSP)

tag: interstitial 3q26 del


title: Endothelial_lowShear_rep8


title: Endothelial_highShear_rep7

tag: Right iliac from Animal No. 4


title: Time 2, Control Replicate 1

source_name: TC1 (Time 2)

tag: distal intestine


title: Time 1, Experimental Replicate 2

source_name: TEx2 (Time 1)

tag: Day 1 of diet

source_name: Univ RNA CEx


title: Endothelial_mediumShear_rep7

source_name: Pooled referece RNA


title: 06_01465 (NSP)

tag: 2qter del


title: Endothelial_lowShear_rep7


title: Endothelial_highShear_rep5

tag: Right iliac from Animal No. 3


title: Endothelial_mediumShear_rep6

source_name: Left iliac arterial endothelial cells exposed to medium shear

tag: Left iliac from Animal No. 4


title: Time 3, Control Replicate 3

source_name: TC3 (Time 3)

tag: Day 20 of diet


title: Endothelial_lowShear_rep6

source_name: Left iliac arterial endothelial cells exposed to low shear

tag: cultured porcine aortic endothelial cells


title: 20946 (NSP)

tag: 1qter del


title: B8 (NSP)

tag: interstitial 1p36 del


title: ID412 (NSP)

tag: interstitial 2p22 dup


title: Time 1, Control Replicate 2

source_name: TC2 (Time 1)

source_name: Univ RNA CC


title: Time 1, Control Replicate 1

source_name: TC1 (Time 1)


title: B4 (NSP)

source_name: Genomic DNA from blood

tag: interstitial 2q37 del and 10pter dup


title: ID166 (NSP)

tag: interstitial 2q23 del


title: Endothelial_lowShear_rep4

tag: Right iliac from Animal No. 2


title: 03_1593 (NSP)

tag: interstitial Xp22 dup and 4pter del


title: Day 30 Replicate 3

description: Three separate RNAs made from control samples at each time point, pooled and used as reference

tag: whole larval tissue

tag: 30 Days after microdiet start


title: Endothelial_mediumShear_rep4


title: Endothelial_mediumShear_rep5


title: 05_0018 (NSP)

tag: 1pter del


title: Endothelial_highShear_rep4

source_name: Right iliac arterial endothelial cells exposed to high shear


title: Endothelial_highShear_rep3

source_name: Left iliac arterial endothelial cells exposed to high shear

tag: Left iliac from Animal No. 2


title: Day 30 Replicate 1


title: Day 30 Replicate 2


title: Time 1, Experimental Replicate 1

source_name: TEx1 (Time 1)

tag: distal intestine

tag: Day 1 of diet


title: Day 20 Replicate 2

tag: 20 Days after microdiet start


title: Endothelial_mediumShear_rep2

source_name: Right iliac arterial endothelial cells exposed to medium shear

tag: Right iliac from Animal No. 1


title: Endothelial_mediumShear_rep3


title: Endothelial_lowShear_rep5

source_name: Right iliac arterial endothelial cells exposed to low shear

tag: Right iliac from Animal No. 3


title: Endothelial_highShear_rep1

tag: Left iliac from Animal No. 1

tag: cultured porcine aortic endothelial cells


title: Endothelial_highShear_rep2


title: Endothelial_lowShear_rep3


title: Endothelial_lowShear_rep2


title: Endothelial_lowShear_rep1


title: Day 20 Replicate 1


title: Day 20 Replicate 3


title: Endothelial_mediumShear_rep1


title: Day 10 Replicate 3

tag: 10 Days after microdiet start


title: Day 10 Replicate 1


title: Day 2 Replicate 3

tag: 2 Days after microdiet start

source_name: C T20 D2


title: Day 2 Replicate 2


title: Day 10 Replicate 2


title: Day 2 Replicate 1


title: ATJ_038

city: Paris

first: Julien

last: Laffaire

address: 10 rue Vauquelin

country: France

institute: ESPCI - CNRS UMR 7637

description: The level of expression of each gene was evaluated by calculating the mean ratio "signal/background" for each corresponding  spot from the 2 dye-swap experiments. Genes were considered to be expressed if their mean ratio was higher or equal to 1.2. Genes with mean ratio<1.2 in the 2 conditions were not used for further analysis.

hyb_protocol: RNG-MRC_MM25K_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dissecator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt's, 4X SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes 0.2X SSC and 5 minutess 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarrays images were obtained using ScanArray Gx scanner (perkin Elmer). Median signal and medin local background intensities were extracted from the images using Genepix 4.1 software (Axon Instruments).

data_processing: Filtered data were processed under R software for lowess fit normalization and  Analysis of variance (ANOVA).

source_name: Cerebellum P7 Ts1Cje

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5 µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

extract_protocol: Total RNA was extracted from frozen individual cerebella and treated with DNAse using RNeasy Minikit (Qiagen) in accordance with the manufacturer's protocol. RNA quality and quantity were then checked on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

tag: Strain

value: B6EiC3SnF1/J A/a

tag: Genotype

tag: Stage

tag: Tissue

value: Cerebellum

source_name: Cerebellum P3 euploid

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5 µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

value: euploid


title: NPC_corticosterone_3

city: Suita

first: Taira

last: Mayanagi

state: Osaka

address: Yamadaoka 2-2

institute: Osaka University Graduate School of Medicine

description: gene expression data from rat NPC treated with corticosterone

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: NPC treated with 1 uM corticosterone for 48 hr

label_protocol: cDNA were synthesized by GeneChip T7-Oligo(dT) Promoter Primer Kit（Affymetrix) and TaKaRa cDNA Synthesis Kit (TaKaRa Bio)  from 3ug total RNA. Biotinylated cRNA were synthesized by IVT Labeling Kit (Affymetrix) .

growth_protocol: Neuronal progenitor cells were prepared from cerebral cortices of rat embryo at E15.5. Cells were cultured with 20 ng/ml bFGF on fibronectin coated dish.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen). Quality of the RNA was certificated using Agilent 2100 Bioanalyzer (Agilent Technlogies).

treatment_protocol: Cells were treated with 1 uM corticosterone or vehicle (DMSO) for 48 hr.

tag: Wister

tag: NPC from cerebral cortices of embryo at E15.5


title: NPC_corticosterone_2


title: ATJ_009

source_name: Cerebellum P10 Ts1Cje

source_name: Cerebellum P10 euploid


title: ATJ_026

source_name: Cerebellum P7 euploid


title: ATJ_014

source_name: Cerebellum P3 Ts1Cje


title: NPC_control_1

description: gene expression data from rat NPC treated with control DMSO

source_name: NPC treated with DMSO for 48 hr


title: ATJ_041


title: ATJ_012

source_name: Cerebellum P0 euploid

source_name: Cerebellum P0 Ts1Cje


title: ATJ_010


title: NPC_control_3


title: ATJ_039


title: ATJ_037


title: NPC_corticosterone_1


title: NPC_control_2


title: ATJ_013


title: ATJ_006

hyb_protocol: RNG-MRC_MM25K_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dissecator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt's, 4X SSC and 0.1% SDS solution at 42Ã‚Â°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes 0.2X SSC and 5 minutess 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.


title: ATJ_015

value: Euploid


title: ATJ_011


title: ATJ_007


title: ATJ_008


title: ATJ_004


title: Time 1, Experimental Replicate 3

source_name: TEx3 (Time 1)

source_name: Univ RNA CEx


title: ATJ_002

hyb_protocol: RNG-MRC_MM25K_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dissecator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. 	Hybridizations were performed in 50% formamide, 5X Denhardt's, 4X SSC and 0.1% SDS solution at 42Â°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes 0.2X SSC and 5 minutess 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.


title: ATJ_003


title: ASJ_016


title: ASJ_011

scan_protocol: Microarrays images were obtained using ScanArray Gx scanner (perkin Elmer). Median signal and medin local background intensities weree xtracted from the images using Genepix 4.1 software (Axon Instruments).

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

extract_protocol: Total RNA was extracted from frozen individual cerebella and treated with DNAse using RNeasy Minikit (Qiagen) in accordance with the manufacturer’s protocol. RNA quality and quantity were then checked on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).


title: ASJ_012

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5Ã‚ÂµM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5Ã‚ÂµM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).


title: ATJ_005


title: EZH2 siRNA 3 with UMUC3

status: Public on Mar 11 2009

first: Jeffrey

last: Friedman

address: 1441 Eastlake Ave.

institute: USC/Norris Comprehensive Cancer Center

description: Note PMT1 settings

hyb_protocol: Illumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were extracted with Illumina BeadStudio software. Quantile normalization was performed.

source_name: Bladder cancer cell line treated with EZH2 siRNA

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: Trizol

tag: UM-UC-3 cells transfected with EZH2 siRNA for 72 hours


title: ASJ_018


title: ASJ_017


title: miR-101 2 with UMUC3

description: Note PMT1 settings

source_name: Bladder cancer cell line treated with miR-101

tag: UM-UC-3 cells transfected with miR-101 for 72 hours


title: ASJ_010

hyb_protocol: RNG-MRC_MM25K_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dissecator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt's, 4X SSC and 0.1% SDS solution at 42Â°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes 0.2X SSC and 5 minutess 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

label_protocol: 5 Âµg of total RNA were reverse transcribed in the presence of 7.5ÂµM random hexamers (Pasteur Institute), 75 ÂµM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37Â°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

extract_protocol: Total RNA was extracted from frozen individual cerebella and treated with DNAse using RNeasy Minikit (Qiagen) in accordance with the manufacturerâ€™s protocol. RNA quality and quantity were then checked on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

label_protocol: 5 Âµg of total RNA were reverse transcribed in the presence of 7.5ÂµM random hexamers (Pasteur Institute), 75 ÂµM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37Â°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).


title: ASJ_014


title: wt 80 days rep 3

status: Public on Mar 08 2009

city: Providence

first: Nicola

last: Neretti

state: RI

address: Box G-L158

institute: Brown University

description: wt 80 days rep 3

hyb_protocol: DNA was made with random hexamer primers and Superscript II reverse transcriptase in the presence of Cy3 or Cy5 fluorescent-tagged dUTP. cDNA was hybridized to the arrays for 16 - 18 hours at 65°C in humidified incubation chambers. Cy3 was used for labeling the reference sample and Cy5 for experimental or control samples (Kevin P. White, Scott A. Rifkin, Patrick Hurban, David S. Hogness: Microarray Analysis of Drosophila Development During Metamorphosis, Science 1999, 284: 2179-2184).

scan_protocol: Scanned on a GenePix 4000B scanner

data_processing: Arrays were background adjusted and normalized via the LIMMA package of bioconducto with the following options: normexp, printtiploess, Gquantile

organism: Drosophila melanogaster

source_name: universal reference (pool of all RNA samples from wt control flies at all ages)

label_protocol: 2 μg of total RNA from each sample was amplified with T7 RNA polymerase (Promega) using one-round linear amplification protocol as described

growth_protocol: Flies were cultured on standard laboratory food as previously described (35). Indy206 flies heterozygous over Canton-S (Indy206/CS) and genetically matched heterozygous controls (2216/CS) were placed on cold block and head and thorax were dissected at age: 5, 10, 20, 30, 40, 50, 70 and 80.

extract_protocol: Three replicates of 15 males were homogenized in Trizol reagent (Invitrogen) and RNA was isolated by standard method of Chomczynski and Sacchi.

tag: head and thorax

source_name: wt

growth_protocol: Flies were cultured on standard laboratory food as previously described (Bross TG, Rogina B, & Helfand SL (2005) Behavioral, physical, and demographic changes in Drosophila populations through dietary restriction.  Aging cell 4(6):309-317). Indy206 flies heterozygous over Canton-S (Indy206/CS) and genetically matched heterozygous controls (2216/CS) were placed on cold block and head and thorax were dissected at age: 5, 10, 20, 30, 40, 50, 70 and 80.


title: miR-101 3 with UMUC3

description: Note PMT1 settings


title: Control miRNA 3 with UMUC3

description: Note PMT1 settings

source_name: Bladder cancer cell line treated with control miRNA

tag: UM-UC-3 cells transfected with control miRNA for 72 hours


title: EZH2 siRNA 2 with UMUC3

description: Note PMT1 settings


title: control siRNA 1 with UMUC3

description: Note PMT1 settings

source_name: Bladder cancer cell line treated with control siRNA

tag: UM-UC-3 cell transfected with control siRNA for 72 hours


title: control siRNA 3 with UMUC3

description: Note PMT1 settings

tag: UM-UC-3 cells transfected with control siRNA for 72 hours


title: miR-101 1 with UMUC3

description: Note PMT1 settings


title: Time 1, Control Replicate 3

source_name: TC3 (Time 1)

tag: distal intestine

tag: Day 1 of diet

source_name: Univ RNA CC


title: control siRNA 2 with UMUC3

description: Note PMT1 settings


title: Control miRNA 1 with UMUC3

description: Note PMT1 settings

tag: UM-UC-3 cells transfected with control miRNA for 72 hours.


title: Control miRNA 2 with UMUC3

description: Note PMT1 settings


title: ASJ_013


title: wt 80 days rep 2

description: wt 80 days rep 2


title: wt 70 days rep 3

description: wt 70 days rep 1


title: wt 80 days rep 1

description: wt 80 days rep 1


title: wt 50 days rep 2

description: wt 50 days rep 2


title: wt 50 days rep 1

description: wt 50 days rep 1


title: wt 30 days rep 3

description: wt 30 days rep 3


title: wt 20 days rep 3

description: wt 20 days rep 3


title: wt 40 days rep 1

description: wt 40 days rep 1


title: wt 70 days rep 1

description: wt 70 days rep 1


title: wt 30 days rep 1

description: wt 30 days rep 1


title: wt 10 days rep 2

description: wt 10 days rep 2


title: wt 5 days rep 3

description: wt 5 days rep 3


title: indy 80 days rep 1

description: indy 80 days rep 1

source_name: indy


title: wt 5 days rep 1

description: wt 5 days rep 1


title: indy 70 days rep 2

description: indy 70 days rep 2


title: wt 30 days rep 2

description: wt 30 days rep 2


title: wt 50 days rep 3

description: wt 50 days rep 3


title: wt 20 days rep 1

description: wt 20 days rep 1


title: indy 70 days rep 3

description: indy 70 days rep 3


title: wt 40 days rep 2

description: wt 40 days rep 2


title: indy 40 days rep 3

description: indy 40 days rep 3


title: wt 10 days rep 1

description: wt 10 days rep 1


title: indy 70 days rep 1

description: indy 70 days rep 1


title: indy 80 days rep 3

description: indy 80 days rep 3


title: wt 20 days rep 2

description: wt 20 days rep 2


title: Endothelial_highShear_rep6

source_name: Left iliac arterial endothelial cells exposed to high shear

tag: Left iliac from Animal No. 4

source_name: Pooled referece RNA

tag: cultured porcine aortic endothelial cells


title: indy 80 days rep 2

description: indy 80 days rep 2


title: indy 50 days rep 1

description: indy 50 days rep 1


title: indy 50 days rep 3

description: indy 50 days rep 3


title: indy 40 days rep 1

description: indy 40 days rep 1


title: indy 10 days rep 1

description: indy 10 days rep 1


title: indy 40 days rep 2

description: indy 40 days rep 2


title: indy 10 days rep 2

description: indy 10 days rep 2


title: indy 30 days rep 2

description: indy 30 days rep 2


title: indy 30 days rep 3

description: indy 30 days rep 3


title: indy 30 days rep 1

description: indy 30 days rep 1


title: indy 50 days rep 2

description: indy 50 days rep 2


title: indy 20 days rep 2

description: indy 20 days rep 2


title: indy 20 days rep 1

description: indy 20 days rep 1


title: indy 5 days rep 2

description: indy 5 days rep 2


title: indy 5 days rep 1

description: indy 5 days rep 1