title: T-LBL_13

description: primary LBL diagnosis sample

value: T-cell; Age:12 yrs; Gender:F


title: Zhong You 821 stem-24 hour Control vs Infection-Replicate 2

status: Public on Feb 01 2009

type: RNA

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Biological replicate 2 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.

hyb_protocol: Hybridizations were performed at 37°C for 16 h in the dark, after which the slides were washed in 2 x SSC, 0.1 % SDS at 37°C for 5 min, followed by 2 washes in 1 x SSC for 2 min each and 2 washes in 0.1 x SSC for 1 min each. Washed slides were dried by centrifugation at 1000 rpm for 1 min at 20°C.

scan_protocol: The slides were scanned using a Virtek Chip Reader (Bio-Rad Laboratories). For each scan, the signal intensity of the two channels was initially adjusted based on the control spots so that an average red/green signal ratio of approximately 1 was achieved and the spots were not saturated.

data_processing: Spot intensities from scanned slides were quantified using ArrayPro 4.0 (Bio-Rad Laboratories) and the data imported into the BioArray Software Environment (BASE version 1.0). Spots with intensities lower than the background were eliminated. Gene Spring 7.3 (Agilent Technologies, Inc.) was used to select spots with intensity values > 50 in at least half of the samples (slides) for further analysis. Normalization was conducted using the per spot and per-chip Lowess normalization procedure with a smooth factor of 20. A one-way ANOVA with a parametric test and variances not assumed to be equal was performed. A multiple test correction (Benjamini and Hochberg, 1995) was applied and a False Discovery Rate (FDR) of < 0.0001 was used.

molecule: total RNA

organism: Brassica napus

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 24 hours after infection

label_protocol: 5 mg aRNA was coupled with either Cy3 or Cy5 dye. The coupling reaction mixture was incubated at 20°C for 30 min, quenched with 4 M hydroxylamine for 15 min and purified. Cy3/Cy5 labelled aRNA was completely dried in a vacuum, dissolved in 9 ml ddH2O and fragmented by adding 1 ml of fragmentation reagent followed by incubation at 70°C for 15 min. The reaction was stopped with 1 ml of stop solution and 47 ml of hybridization solution was added.

growth_protocol: Seeds of ZY821 were sown in Redi-Earth soil mixture (Scotts Fertilizer Company) amended with coconut fibre to improve drainage and Osmocote 15-7-12 for controlled release of fertilizer. The plants were grown in a growth chamber under 200 mmol m-2 s-1 light with a 16 h photoperiod provided by fluorescent and incandescent light. The temperature was maintained at 20°C in the light and 16°C in the dark. Two seeds were planted in each of 36 cells and seedlings were thinned to one plant per cell eleven days after planting. Four week-old seedlings were vernalized in a cold room at 5 - 8°C for 4 weeks under an 8 h photoperiod and half of the previous light intensity. After vernalization, each plant was transplanted to a six-inch pot and returned to the growth chamber. Seeds of Westar were planted directly in six-inch pots and plants were grown under the same conditions as ZY821 except for the vernalization treatment. Excess plants were grown and only those with uniform stem size and architecture were used. Plants were selected for inoculation and sampling using a randomized design with three biological replicates for each cultivar.

extract_protocol: Total RNA was isolated from 1 g of ground tissue using the plant RNeasy kit (Qiagen) and stored at -80°C. RNase-Free DNase was applied during RNA isolation to remove any DNA contamination (Qiagen). The concentration of total RNA was determined using a Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and verified by agarose gel electrophoresis.

treatment_protocol: One replicate consisted of 60 plants for five time points (6, 12, 24, 48 and 72 h) and two treatments (inoculated and mock-inoculated controls). S. sclerotiorum isolate 321 generated from field canola plants were used throughout the experiment (Kohli and Kohn, 1995). When the plants were at the full flower stage, three sites of the main stem were inoculated at every other internodes with 8 mm plugs cut from the growing margin of a colony cultured on minimal salts-glucose agar (20.0 g glucose, 2.0 g NH4NO3, 1.0 g KH2PO4, 1.0 g NaOH, 0.1 g MgSO47H2O, 0.1 g malic acid and 20.0 g agar per 1000 ml distilled water) modified from (Cruickshank, 1983). Mock infected plants were inoculated with only an agar plug. Plugs were secured to the stem with Parafilm™. Each line yielded 180 inoculation sites per biological replicate or 540 sites in total. Epidermal stem tissues extending 10 mm beyond the inoculation site and 1 mm deep were harvested at 6, 12, 24, 48, and 72 h post inoculation (hpi) with a razor blade. The tissues from one biological replicate at each time point (six individual plants comprising 18 inoculation sites) were pooled as one sample. Harvested tissues were frozen immediately in liquid nitrogen and stored at -80°C.

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 24 hours after infection

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after infection with Scleotinia scleotiorum


title: Zhong You 821 stem-24 hour Control vs Infection-Replicate 1

description:
Biological replicate 1 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.


title: Zhong You 821 stem-6 hour Control vs Infection-Replicate 2

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 6 hours after infection

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 6 hours after infection

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after infection with Scleotinia scleotiorum


title: Zhong You 821 stem-6 hour Infection vs control-Replicate 3

description:
Biological replicate 3 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.


title: Zhong You 821 stem-6 hour Control vs Infection-Replicate 3


title: Zhong You 821 stem-6 hour Infection vs control-Replicate 2


title: Zhong You 821 stem-24 hour Infection vs control-Replicate 2


title: Zhong You 821 stem-6 hour Infection vs control-Replicate 1

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hours after infection with Sclerotinia sclerotiorum

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after mock infection with Scleotinia scleotiorum


title: Zhong You 821 stem-6 hour Control vs Infection-Replicate 1


title: Westar stem-72 hour Control vs Infection-Replicate 2

data_processing: Spot intensities from scanned slides were quantified using ArrayPro 4.0 (Bio-Rad Laboratories) and the data imported into the BioArray Software Environment (BASE version 1.0). Spots with intensities lower than the background were eliminated. Gene Spring 7.3 (Agilent Technologies, Inc.) was used to select spots with intensity values > 50 in at least half of the samples (slides) for further analysis.  Normalization was conducted using the per spot and per-chip Lowess normalization procedure with a smooth factor of 20.  A one-way ANOVA with a parametric test and variances not assumed to be equal was performed. A multiple test correction (Benjamini and Hochberg, 1995) was applied and a False Discovery Rate (FDR) of < 0.0001 was used.

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 72 hours after infection

label_protocol: 5 mg aRNA was coupled with either Cy3 or Cy5 dye. The coupling reaction mixture was incubated at 20°C for 30 min, quenched with 4 M hydroxylamine for 15 min and purified. Cy3/Cy5 labelled aRNA was completely dried in a vacuum, dissolved in 9 ml ddH2O and fragmented by adding 1 ml of fragmentation reagent followed by incubation at 70°C for 15 min.  The reaction was stopped with 1 ml of stop solution and 47 ml of hybridization solution was added.

growth_protocol: Seeds of ZY821 were sown in Redi-Earth soil mixture (Scotts Fertilizer Company) amended with coconut fibre to improve drainage and Osmocote 15-7-12 for controlled release of fertilizer. The plants were grown in a growth chamber under 200 mmol m-2 s-1 light with a 16 h photoperiod provided by fluorescent and incandescent light. The temperature was maintained at 20°C in the light and 16°C in the dark. Two seeds were planted in each of 36 cells and seedlings were thinned to one plant per cell eleven days after planting. Four week-old seedlings were vernalized in a cold room at 5 - 8°C for 4 weeks under an 8 h photoperiod and half of the previous light intensity. After vernalization, each plant was transplanted to a six-inch pot and returned to the growth chamber. Seeds of Westar were planted directly in six-inch pots and plants were grown under the same conditions as ZY821 except for the vernalization treatment.  Excess plants were grown and only those with uniform stem size and architecture were used. Plants were selected for inoculation and sampling using a randomized design with three biological replicates for each cultivar.

treatment_protocol: One replicate consisted of 60 plants for five time points (6, 12, 24, 48 and 72 h) and two treatments (inoculated and mock-inoculated controls).  S. sclerotiorum isolate 321 generated from field canola plants were used throughout the experiment (Kohli and Kohn, 1995). When the plants were at the full flower stage, three sites of the main stem were inoculated at every other internodes with 8 mm plugs cut from the growing margin of a colony cultured on minimal salts-glucose agar (20.0 g glucose, 2.0 g NH4NO3, 1.0 g KH2PO4, 1.0 g NaOH, 0.1 g MgSO47H2O, 0.1 g malic acid and 20.0 g agar per 1000 ml distilled water) modified from (Cruickshank, 1983). Mock infected plants were inoculated with only an agar plug. Plugs were secured to the stem with Parafilm™. Each line yielded 180 inoculation sites per biological replicate or 540 sites in total. Epidermal stem tissues extending 10 mm beyond the inoculation site and 1 mm deep were harvested at 6, 12, 24, 48, and 72 h post inoculation (hpi) with a razor blade. The tissues from one biological replicate at each time point (six individual plants comprising 18 inoculation sites) were pooled as one sample. Harvested tissues were frozen immediately in liquid nitrogen and stored at -80°C.

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 72 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 72 hours after infection

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 72 hrs after infection with Scleotinia scleotiorum


title: Westar stem-72 hour Control vs Infection-Replicate 3


title: Westar stem-72 hour Infection vs control-Replicate 3


title: Westar stem-72 hour Control vs Infection-Replicate 1


title: Westar stem-72 hour Infection vs control-Replicate 2


title: Zhong You 821 stem-24 hour Infection vs control-Replicate 3


title: Zhong You 821 stem-24 hour Infection vs control-Replicate 1


title: Westar stem-72 hour Infection vs control-Replicate 1


title: Westar stem-48 hour Infection vs control-Replicate 3

source_name: B. napus stem tissue, infected with Sclerotinia, 48 hours after infection

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 48 hrs after infection with Scleotinia scleotiorum

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 48 hours after infection

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 48 hrs after mock infection


title: Westar stem-48 hour Control vs Infection-Replicate 3


title: Westar stem-48 hour Control vs Infection-Replicate 2


title: Westar stem-24 hour Infection vs control-Replicate 2

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after infection with Scleotinia scleotiorum

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after mock infection


title: Westar stem-48 hour Infection vs control-Replicate 1


title: Westar stem-48 hour Infection vs control-Replicate 2


title: Westar stem-24 hour Control vs Infection-Replicate 2


title: Westar stem-24 hour Infection vs control-Replicate 3


title: Westar stem-24 hour Control vs Infection-Replicate 1


title: Westar stem-24 hour Control vs Infection-Replicate 3


title: Westar stem-12 hour Infection vs control-Replicate 1

source_name: B. napus stem tissue, infected with Sclerotinia, 12 hours after infection

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 12 hrs after infection with Scleotinia scleotiorum

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 12 hours after infection

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 12 hrs after mock infection


title: Westar stem-12 hour Infection vs control-Replicate 3


title: Westar stem-48 hour Control vs Infection-Replicate 1


title: Westar stem-6 hour Control vs Infection-Replicate 3

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after mock infection

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after infection with Scleotinia scleotiorum


title: Westar stem-24 hour Infection vs control-Replicate 1


title: Westar stem-12 hour Infection vs control-Replicate 2


title: Westar stem-12 hour Control vs Infection-Replicate 3


title: Westar stem-12 hour Control vs Infection-Replicate 2


title: Westar stem-12 hour Control vs Infection-Replicate 1


title: Westar stem-6 hour Infection vs control-Replicate 3


title: Westar stem-6 hour Control vs Infection-Replicate 2


title: Westar stem-6 hour Infection vs control-Replicate 1

tag: B. napus (Westar), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hours after infection with Sclerotinia sclerotiorum

tag: B. napus (Westar), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 6 hrs after mock infection with Scleotinia scleotiorum


title: Westar stem-6 hour Infection vs control-Replicate 2


title: Westar stem-6 hour Control vs Infection-Replicate 1


title: Populus x canescens root hypoxia_rep_09

status: Public on Jan 31 2009

city: Freiburg

first: Juergen

last: Kreuzwieser

address: Georges-Koehler-Allee

department: Chair of Tree Physiology

country: Germany

institute: University of Freiburg

description: Roots of Grey poplar 168 h hypoxia

hyb_protocol: standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)

data_processing: GCOS1,4 (Affymetrix)

label: Biotin

organism: Populus tremula x Populus alba

source_name: poplar root tissue flooded up to 168h

label_protocol: Labelling of cRNA from 3.5 µg of root total RNA was performed exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol:
For total RNA extraction the Plant RNeasy kit (Qiagen) was used according to the manufacturer’s instructions with some minor modifications. Aliquots of 90 mg of frozen plant powder were added to 900 µl RLT buffer supplemented with 1% ß-mercaptoethanol, 1% PVPP and 2% (w/v) polyethylenglycol (PEG 10,000), and then incubated for 10 min at 58°C. The samples were further processed according to the manufacturer’s protocol. Total RNA was treated with DNase during (RNase free DNase kit, Qiagen) and after (DNA-free TM kit, Ambion) the extraction procedure.
The quality of the isolated total RNA was tested using an Agilent Bioanalyzer and spectrophotometric analysis (NanoDrop® ND-1000, NanoDrop Technologies) to determine the A260 to A280 ratio.

tag: Experiments were performed with 3-month-old hybrid poplar plants (Populus x canescens). At the beginning of the experiment, the shoots of the trees had a size of 20 to 25 cm. To induce root hypoxia 52 trees were transferred into large plastic containers. The containers were filled with tap water until the water level exceeded the soil surface by 2-3 cm. Shoots were exposed to ambient air.


title: Populus x canescens root hypoxia_rep_04

description: Roots of Grey poplar 24 h hypoxia

scan_protocol: standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)

source_name: poplar root tissue flooded up to 24h


title: Populus x canescens root control_rep_12

description: Roots of Grey poplar 168 h control

source_name: Untreated control poplar root tissue at 168h


title: Populus x canescens root control_rep_11

description: Roots of Grey poplar 168 h control


title: Populus x canescens root hypoxia_rep_08

description: Roots of Grey poplar 168 h hypoxia


title: Populus x canescens root control_rep_10

description: Roots of Grey poplar 168 h control


title: Populus x canescens root hypoxia_rep_05

description: Roots of Grey poplar 24 h hypoxia


title: Populus x canescens root control_rep_07

description: Roots of Grey poplar 24 h control

source_name: Untreated control poplar root tissue at 24h


title: Populus x canescens root hypoxia_rep_03

description: Roots of Grey poplar 5 h hypoxia

source_name: poplar root tissue flooded up to 5h


title: Populus x canescens root hypoxia_rep_02

description: Roots of Grey poplar 5 h hypoxia


title: Populus x canescens root control_rep_08

description: Roots of Grey poplar 24 h control


title: Populus x canescens root control_rep_02

description: Roots of Grey poplar 0 h control

source_name: Untreated control poplar root tissue at t=0


title: Populus x canescens root control_rep_09

description: Roots of Grey poplar 24 h control


title: Populus x canescens root control_rep_01

description: Roots of Grey poplar 0 h control


title: Populus x canescens root control_rep_03

description: Roots of Grey poplar 0 h control


title: Populus x canescens leaf hypoxia_rep_03

description: Source leaves of Grey poplar 168 h hypoxia treated

source_name: poplar leaf tissue flooded up to 168h

label_protocol: Labelling of cRNA from 5 µg of leaf total RNA was performed exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual.


title: Populus x canescens root control_rep_06

description: Roots of Grey poplar 5 h control

source_name: Untreated control poplar root tissue at 5h


title: Populus x canescens root hypoxia_rep_07

description: Roots of Grey poplar 168 h hypoxia


title: Populus x canescens root control_rep_04

description: Roots of Grey poplar 5 h control


title: Populus x canescens root hypoxia_rep_01

description: Roots of Grey poplar 5 h hypoxia


title: Populus x canescens root hypoxia_rep_06

description: Roots of Grey poplar 24 h hypoxia


title: Populus x canescens root control_rep_05

description: Roots of Grey poplar 5 h control


title: Populus x canescens leaf control_rep_06

description: Source leaves of Grey poplar Untreated control at t=168h

source_name: Untreated control poplar leaf tissue at time 168h


title: Populus x canescens leaf control_rep_02

description: Source leaves of Grey poplar Untreated control at t=0

source_name: Untreated control poplar leaf tissue at t=0


title: Populus x canescens leaf hypoxia_rep_01

description: Source leaves of Grey poplar 168 h hypoxia


title: Populus x canescens leaf control_rep_03


title: Populus x canescens leaf control_rep_01


title: AtT-20 cells 24h -/+ CRH replicate 4

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

institute: German Research Center for Environmental Health

hyb_protocol: The labeled aRNA samples were hybridized on Max-Planck Institute 24 k mouse cDNA arrays (Max-Planck-Institute of Psychiatry, Munich, Germany) as described at Deussing JM et al. J Cereb Blood Flow Metab. (2007), performing 3 technical replicates for each control/CRH treated dye coupling combination.

scan_protocol: Mircorarrays were scanned on a PerkinElmer Life Sciences ScanArray 4000 laser scanner.

data_processing: The microarray data analysis was accomplished by the fixed circle quantification method using QuantArray (PerkinElmer Life Sciences) and raw data was normalized using a nonlinear regression method (Yang YH et al., Nucleic Acids Res (2002)).

organism: Mus musculus

source_name: untreated AtT-20 cells 24h

label_protocol: aRNA synthesis and aRNA labelling was performed with the Amino Allyl MessageAmp™ aRNA Kit (Ambion) following the manufacturer’s protocol using 3 µg of total RNA.

growth_protocol: AtT-20 cells were plated in 10 cm cell culture dishes (Nunc) in DMEM medium (Invitrogen) including 10% FCS (Invitrogen) and antibiotics (Invitrogen) 48h before Crh treatment. With a confluency of approximately 50% cells were FCS-deprived 18h before Crh treatment.

extract_protocol: Total RNA of harvested AtT-20 cells was extracted using the TRIzol reagent (Invitrogen) according to manufacturer´s instruction. RNA qualitiy was analysed by gel electrophoresis.

treatment_protocol: Medium of all FCS-deprived cells was changed to DMEM pure without FCS and antibiotics. Crh treatment was performed by adding human/rat Crh (Bachem) to the medium with an end concentration of 100 nM. At indicated time points treated and control cells were harvested with TRIzol (Invitrogen).

tag: mouse, pituitary, corticotroph AtT-20 cells

source_name: 100 nM Crh AtT-20 cells 24h

treatment_protocol: Cells were treated 18h after FCS deprication in DMEM pure with 100 nM human/rat Crh for 24h.


title: AtT-20 cells 12h -/+ CRH replicate 6

source_name: untreated AtT-20 cells 12h

source_name: 100 nM Crh AtT-20 cells 12h

treatment_protocol: Cells were treated 18h after FCS deprication in DMEM pure with 100 nM human/rat Crh for 12h.


title: Populus x canescens leaf hypoxia_rep_02


title: Populus x canescens leaf control_rep_05


title: Populus x canescens leaf control_rep_04


title: AtT-20 cells 24h -/+ CRH replicate 3


title: AtT-20 cells 24h -/+ CRH replicate 5


title: AtT-20 cells 24h -/+ CRH replicate 6


title: AtT-20 cells 24h -/+ CRH replicate 2


title: AtT-20 cells 24h -/+ CRH replicate 1


title: AtT-20 cells 6h -/+ CRH replicate 5

source_name: untreated AtT-20 cells 6h

source_name: 100 nM Crh AtT-20 cells 6h

treatment_protocol: Cells were treated 18h after FCS deprication in DMEM pure with 100 nM human/rat Crh for 6h.


title: AtT-20 cells 6h -/+ CRH replicate 6


title: AtT-20 cells 6h -/+ CRH replicate 4


title: AtT-20 cells 12h -/+ CRH replicate 4


title: AtT-20 cells 12h -/+ CRH replicate 1


title: AtT-20 cells 12h -/+ CRH replicate 5


title: AtT-20 cells 3h -/+ CRH replicate 5

source_name: untreated AtT-20 cells 3h

source_name: 100 nM Crh AtT-20 cells 3h

treatment_protocol: Cells were treated 18h after FCS deprication in DMEM pure with 100 nM human/rat Crh for 3h.


title: AtT-20 cells 3h -/+ CRH replicate 6


title: AtT-20 cells 12h -/+ CRH replicate 2


title: AtT-20 cells 12h -/+ CRH replicate 3


title: AtT-20 cells 6h -/+ CRH replicate 2


title: AtT-20 cells 3h -/+ CRH replicate 3


title: AtT-20 cells 3h -/+ CRH replicate 4


title: AtT-20 cells 6h -/+ CRH replicate 3


title: AtT-20 cells 6h -/+ CRH replicate 1


title: AtT-20 cells 3h -/+ CRH replicate 2


title: AtT-20 cells 1h -/+ CRH replicate 6

source_name: untreated AtT-20 cells 1h

source_name: 100 nM Crh AtT-20 cells 1h

treatment_protocol: Cells were treated 18h after FCS deprication in DMEM pure with 100 nM human/rat Crh for 1h.


title: AtT-20 cells 1h -/+ CRH replicate 4


title: AtT-20 cells 1h -/+ CRH replicate 5


title: AtT-20 cells 3h -/+ CRH replicate 1

growth_protocol: AtT-20 cells were plated in 10 cm cell culture dishes (Nunc) in DMEM medium (Invitrogen) including 10% FCS (Invitrogen) and antibiotics (Invitrogen) 48h before Crh treatment. With a conlfuency of approximately 50% cells were FCS-deprived 18h before Crh treatment.


title: AtT-20 cells 1h -/+ CRH replicate 2


title: AtT-20 cells 1h -/+ CRH replicate 1


title: mPFC_14d_saline_5

status: Public on Jan 30 2009

city: Hershey

first: Kent

middle: E.

last: Vrana

state: PA

address: 500 University Drive

department: Pharmacology

country: USA

institute: Penn State College of Medicine

description: brain, saline, 14 days abstinence

hyb_protocol: 1.65 μg from each sample was fragmented, denatured, and then hybridized to Agilent 4x44 rat whole genome microarray slides for 17 hours at 65°C.  Slides were then washed according to protocol.

scan_protocol: Microarrays were scanned with an Axon 4000B scanner with GenePix4 v4.0 software at a 5 μm resolution and 635 nm with laser power at 100%, PMT voltage at 600 V, focus position 0 μm, and lines to average = 1.  Images were then imported into Agilent Feature Extraction Software.  Initial quality control (positive and negative controls), exclusion of manufacturing defects (MSR spots), background subtraction was then performed and the results exported to GeneSpring GX 7.3 (Agilent Technologies).

data_processing: Microarray data were normalized following import into GeneSpring GX 7.3 (Agilent Technologies) by transforming signal values less than 5.0 to an intensity of 5.0.  Normalization was done per chip to the 50th percentile, and per gene to the median. Values were then normalized on a per gene basis to the control group.

organism: Rattus norvegicus

source_name: brain, saline, 14 days abstinence

label_protocol: Following the manufacturer’s protocol of the Low Input Fluorescent Linear Amplification Kit (Agilent, Santa Clara, CA), 500ng RNA with the addition of One-Color Spike Mix was denatured and incubated with T7 Promoter primer.  Synthesis of cDNA followed with the addition of First-Strand buffer, DTT, dNTP mix, MMLV-RT and RNase Out and incubation at 40°C for 2 hours.  Transcription of the product incorporated the Cyanine 3-CTP in the Master Mix which includes Transcription buffer, DTT, NTPs, PEG, RNase Out, pyrophosphatases and T7 RNA Polymerase, with incubation for 2 hours at 40°C.

extract_protocol: Rats were anesthetized with Propofol and brains removed from skulls.  The section from Bregma +4.2 to 2.2mm was cut along the forceps minor and the cortex medial to this cut was collected.  Samples were immediately frozen on dry ice and stored at -80 C until RNA was extracted.  Total RNA was extracted using Tri-Tri Reagent (Molecular Research Center Inc., Cincinnati, OH).  Isolated RNA was further purified using an RNeasy Mini Kit for RNA clean-up (QIAGEN Sciences, Maryland).  RNA quantity and quality were assessed using the RNA 6000 Nano Assay with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: Gender

value: male

tag: Age

value: 4 months


title: mPFC_14d_heroin_5

description: brain, heroin, 14 days abstinence

source_name: brain, heroin, 14 days abstinence


title: AtT-20 cells 1h -/+ CRH replicate 3


title: mPFC_14d_saline_4

description: brain, saline, 14 days abstinence


title: mPFC_14d_heroin_4

description: brain, heroin, 14 days abstinence


title: mPFC_14d_saline_3

description: brain, saline, 14 days abstinence


title: mPFC_14d_saline_6

description: brain, saline, 14 days abstinence


title: mPFC_14d_heroin_6

description: brain, heroin, 14 days abstinence


title: 13690888 - YFP-2 vs YFP-2-Ind

status: Public on Jan 23 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: VIP1 early targets

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

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

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

growth_protocol: whole plant - Media MS(1/2) hygrometry sealed petridishes Temperature 22°C Light 8h

extract_protocol:
YFP-2-Ind:80ug.
Trizol

treatment_protocol: Name:estradiol induction - compound based treatment - compound addition,estradiol:quantity 0.04mM time 3hour . 11d-old-seedlings grown on MS(1/2) plates. transfer into 6-well-plates filled with 3ml 0.01%silwet,0.2%EtOH or 0.01%silwet,40µMestradiol(from 500xstock in EtOH), seedlings gently transferred with forceps, placed into the wells. Most leaves are submerged. No further handling. freeze after 3h.

tag: Arabidopsis thaliana (col-0)  mutant (pER8::YFP) - age:11daydev.stage (Boyes et al. Plant Cell 2001):boyes

extract_protocol:
YFP-2:80ug.
Trizol

treatment_protocol: no treatment


title: mPFC_14d_heroin_2

description: brain, heroin, 14 days abstinence


title: mPFC_14d_saline_2

description: brain, saline, 14 days abstinence


title: 13690777 - YFP-1-Ind vs VIP1Da-1-Ind

description: VIP1 early targets

hyb_protocol: VIP1Da-1-Ind Cy5 / YFP-1-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,680V,laser power 33%, Cy5:635nm,pmt voltage 680V,laser power 33%

extract_protocol:
VIP1Da-1-Ind:80ug.
Trizol

tag: Arabidopsis thaliana (col-0)  mutant (pER8::VIP1_D-YFP) - age:11daydev.stage (Boyes et al. Plant Cell 2001):boyes 1.02

extract_protocol:
YFP-1-Ind:80ug.
Trizol

tag: Arabidopsis thaliana (col-0)  mutant (pER8::YFP) - age:11daydev.stage (Boyes et al. Plant Cell 2001):boyes 1.02


title: 13690779 - VIP1Da-1-Ind vs YFP-1-Ind

description: VIP1 early targets

hyb_protocol: YFP-1-Ind Cy5 / VIP1Da-1-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690246 - VIP1Da-2-Ind vs VIP1Da-2

description: VIP1 early targets

hyb_protocol: VIP1Da-2 Cy5 / VIP1Da-2-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol:
VIP1Da-2:80ug.
Trizol

extract_protocol:
VIP1Da-2-Ind:80ug.
Trizol


title: 13690773 - VIP1Da-1 vs YFP-1

description: VIP1 early targets

hyb_protocol: YFP-1 Cy5 / VIP1Da-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol:
YFP-1:80ug.
Trizol

extract_protocol:
VIP1Da-1:80ug.
Trizol


title: 13690887 - YFP-2-Ind vs YFP-2

description: VIP1 early targets

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


title: mPFC_14d_heroin_3

description: brain, heroin, 14 days abstinence


title: 13690258 - VIP1a-1 vs VIP1a-1-Ind

description: VIP1 early targets

hyb_protocol: VIP1a-1-Ind Cy5 / VIP1a-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol:
VIP1a-1--Ind:80ug.
Trizol

tag: Arabidopsis thaliana (col-0)  mutant (pER8::VIP1-YFP) - age:11daydev.stage (Boyes et al. Plant Cell 2001):boyes 1.02

extract_protocol:
VIP1a-1:80ug.
Trizol


title: 13690771 - YFP-1 vs VIP1Da-1

description: VIP1 early targets

hyb_protocol: VIP1Da-1 Cy5 / YFP-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: mPFC_14d_heroin_1

description: brain, heroin, 14 days abstinence


title: 13690364 - VIP1Da-1 vs VIP1Da-1-Ind

description: VIP1 early targets

hyb_protocol: VIP1Da-1-Ind Cy5 / VIP1Da-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690247 - VIP1Da-2 vs VIP1Da-2-Ind

description: VIP1 early targets

hyb_protocol: VIP1Da-2-Ind Cy5 / VIP1Da-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690255 - VIP1a-2-Ind vs VIP1a-2

description: VIP1 early targets

hyb_protocol: VIP1a-2 Cy5 / VIP1a-2-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol:
VIP1a-2:80ug.
Trizol

extract_protocol:
VIP1a-2-Ind:80ug.
Trizol


title: 13690363 - VIP1Da-1-Ind vs VIP1Da-1

description: VIP1 early targets

hyb_protocol: VIP1Da-1 Cy5 / VIP1Da-1-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690256 - VIP1a-2 vs VIP1a-2-Ind

description: VIP1 early targets

hyb_protocol: VIP1a-2-Ind Cy5 / VIP1a-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Normal prostate vs. 44816CC (young-car crash trauma)

status: Public on Jan 11 2009

type: other

city: Research Triangle Park

first: Michael

middle: D.

last: Mattie

state: NC

address: Five Moore Drive

department: Genomics Research

institute: GlaxoSmithKline

description: Quantitations are based on the images (ratios of median fluorescence intensity were the primary study measurements). Genepix 3.0 produces both feature and background intensity and ratio measurements for the Cy3 and Cy5 channels and notes if data are flagged by the analyst.

hyb_protocol: Briefly, 200 ng of enriched miRNA was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene). Arrays were washed as follows: Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge. The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius. Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius

scan_protocol: Images were acquired using an Axon 4000b confocal laser scanner with Genepix 3.0 software (Axon, Foster City, CA).

data_processing: Only Genepix median ratios for non-flagged spots were used for the analysis. Genepix data was uploaded to the NOMAD relational database (http://derisilab.ucsf.edu), median ratio information was downloaded after linear normalization of Cy3 and Cy5 signals (equal average intensity of each fluorescent channel). Data were formatted for the Cluster (http://rana.lbl.gov) algorithm, which was used after log base 2 transformation of ratios, and filtering to exclude genes flagged in more than 20% of the arrays.

molecule: other

organism: Homo sapiens

source_name: Normal prostate

label_protocol: Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere.

extract_protocol: MicroRNA was isolated from the tissue sample using the mirVana miRNA isolation kit from Ambion.

tag: Normal prostate reference control. RNA was isolated from prostate tissue of a 70 year old male without prostate cancer and enriched for the microRNA fraction.

source_name: 44816CC (young-car crash trauma)

tag: Normal prostate tissue from a young individual that died as a result of trauma (car crash). Prostate tissue was obtained through organ donation. RNA was isolated and enriched for the microRNA fraction.


title: 13690257 - VIP1a-1-Ind vs VIP1a-1

description: VIP1 early targets

hyb_protocol: VIP1a-1 Cy5 / VIP1a-1-Ind Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Normal prostate vs. 39927CC (young-car crash trauma)

hyb_protocol: Briefly, 200 ng of enriched miRNA was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene). Arrays were washed as follows: Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge. The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius. Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius.

source_name: 39927CC (young-car crash trauma)


title: Normal prostate vs. PR957T (prostate tumor)

source_name: PR957T (prostate tumor)

tag: Prostate tumor. RNA was isolated from a radical prostatectomy specimen and enriched for the microRNA fraction.


title: Normal prostate vs. 40248CC (young-car crash trauma)

source_name: 40248CC (young-car crash trauma)


title: Normal prostate vs. 39108CC (young-car crash trauma)

source_name: 39108CC (young-car crash trauma)


title: Normal prostate vs. 51349CC (young-car crash trauma)

source_name: 51349CC (young-car crash trauma)


title: Normal prostate vs. PR957N (normal adjacent to tumor)

source_name: PR957N (normal adjacent to tumor)

tag: Normal adjacent to tumor prostatic tissue from radical prostatectomy specimen.  Sample was enriched for the miRNA fraction.


title: Normal prostate vs. 39775CC (young-car crash trauma)

source_name: 39775CC (young-car crash trauma)


title: Normal prostate vs. 44451CC (young-car crash trauma)

source_name: 44451CC (young-car crash trauma)


title: 13690254 - YFP-1 vs YFP-1-Ind

description: VIP1 early targets

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


title: 13690250 - YFP-1-Ind vs YFP-1

description: VIP1 early targets

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


title: Normal prostate vs. PR884T (prostate tumor)

source_name: PR884T (prostate tumor)


title: Normal prostate vs. PR780T (prostate tumor)

source_name: PR780T (prostate tumor)


title: Normal prostate vs. PR764T

source_name: PR764T (prostate tumor)


title: Normal prostate vs. PR729N (normal adjacent to tumor)


title: Normal prostate vs. PR851T (prostate tumor)

source_name: PR851T (prostate tumor)


title: Normal prostate vs. PR951T (prostate tumor)

source_name: PR951T (prostate tumor)


title: Normal prostate vs. PR914N (normal adjacent to tumor)

source_name: Normal breast

source_name: PR914N (normal adjacent to tumor)


title: Normal prostate vs. PR729T (prostate tumor)

source_name: Normal prostate

tag: Prostate tumor. RNA was isolated from a radical prostatectomy specimen and enriched for the microRNA fraction


title: Normal prostate vs. PR863T (prostate tumor)

source_name: PR863T (prostate tumor)


title: Normal prostate vs. PR502T

extract_protocol: MicroRNA was isolated from the tissue sample using the mirVana miRNA isolation kit from Ambion

source_name: PR502T (prostate tumor)


title: Normal prostate vs. PR563T (prostate tumor)

source_name: PR563T (prostate tumor)


title: Normal prostate vs. PR458T (prostate tumor)

source_name: PR458T (prostate tumor)


title: Normal prostate vs. PR521T (prostate tumor)

source_name: PR521T (prostate tumor)


title: Normal prostate vs. PR434T

source_name: PR434T (prostate tumor)


title: Normal prostate vs. PR441T (prostate tumor)


title: Normal prostate vs. PR300T (prostate tumor)

source_name: PR300T (prostate tumor)


title: Normal prostate vs. PR379T

source_name: PR379T (prostate tumor)


title: Normal prostate vs. PR381T

source_name: PR381T (prostate tumor)


title: Normal prostate vs. PR399T (prostate tumor)

source_name: PR399T (prostate tumor)


title: Normal prostate vs. PR395T

source_name: PR395T (prostate tumor)


title: Normal prostate vs. 43613CC (young-car crash trauma)

source_name: 43613CC (young-car crash trauma)


title: Normal prostate vs. PR88T (prostate tumor)

source_name: PR88T (prostate tumor)


title: Normal prostate vs. 52160CC (young-car crash trauma)

source_name: 52160CC (young-car crash trauma)


title: Normal prostate vs. PR1127N (normal adjacent to tumor)

source_name: PR1127N (normal adjacent to tumor)


title: Normal prostate vs. 25071N (normal adjacent to tumor)

label_protocol: Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc.

extract_protocol: MicroRNA was isolated from the untreated SKBr3 cells using the mirVana microRNA isolation kit from Ambion

tag: Normal prostate reference control.  RNA was isolated from prostate tissue of a 70 year old male without prostate cancer and enriched for the microRNA fraction.

source_name: 25071N (normal adjacent to tumor)

tag: Normal adjacent to tumor.  RNA was isolated from a radical prostatectomy specimen and enriched for the microRNA fraction.


title: Normal prostate vs. 24871N (normal adjacent to tumor)

source_name: Normal prostate

tag: Normal prostate reference control.  RNA was isolated from the prostate of a 70 year old male without prostate cancer and enriched for the microRNA fraction.

source_name: 24871N (normal adjacent to tumor)


title: Normal prostate vs. 44243CC (young-car crash trauma)

source_name: 44243CC (young-car crash trauma)


title: Normal prostate vs. 40716CC (young-car crash trauma)

tag: Normal prostate reference control.  RNA was isolated from prostate tissue of a 70 year old male without prostate cancer and was enriched for the microRNA fraction.

source_name: 40716CC (young-car crash trauma)

tag: Young male that died of trauma (car crash).  Sample obtained through organ donation.  RNA was isolated from prostate tissue and enriched for the microRNA fraction.


title: Normal prostate vs. 44133CC (young-car crash trauma)

source_name: 44133CC (young-car crash trauma)


title: Normal prostate vs. 44652CC (young-car crash trauma)

source_name: 44652CC (young-car crash trauma)


title: Normal prostate vs. 24858T (prostate tumor)

tag: Normal prostate reference control.  RNA was isolated from prostate tissue from a 70 year old male without prostate cancer.  RNA was enriched for the microRNA fraction.

source_name: 24858T (prostate tumor)

tag: Prostate tumor.  RNA was isolated from a radical prostatectomy specimen and enriched for the microRNA fraction.


title: Normal prostate vs. 42209CC (young-car crash trauma)

source_name: 42209CC (young-car crash trauma)

tag: Normal prostate tissue from a young individual that died as a result of trauma (car crash).  Prostate tissue was obtained through organ donation.  RNA was isolated and enriched for the microRNA fraction.


title: Normal prostate vs. 24670N (normal adjacent to tumor)

source_name: Normal prostate reference control

extract_protocol: MicroRNA was isolated from the tissue sample using the mirVana microRNA isolation kit from Ambion.

tag: Normal prostate tissue from 70 year old male.  Sample was enriched for microRNA fraction.

source_name: Prostate normal adjacent to tumor, sample 24670N

tag: Normal adjacent to tumor prostatic tissue from radical prostatectomy specimen.  Sample was enriched for the microRNA fraction.


title: Normal prostate vs. 24880N (normal adjacent to tumor)

source_name: 24880N (normal adjacent to tumor)


title: Normal prostate vs. Pooled Normal

hyb_protocol: Briefly, 10 ng of enriched miRNA was amplified using a modification of the SenseAmp Plus protocol from Genisphere.  A total of 750 ng of amplified material was labeled and hybridized in the supplied 2X SDS based hybridization buffer to the arrays at 46 degrees Celsius for 16 hours in a Hybex hybridization oven (SciGene). Arrays were washed as follows: Cover slips were floated off in wash 1 (2X SSC, 0.2% SDS pre-warmed to 42 degrees Celsius), arrays were then washed in pre-warmed wash #1 for 15 minutes, rinsed in wash #2 (2X SSC) for 10 minutes at room temperature, and rinsed in wash #3 (0.2X SSC) for 10 minutes at room temperature. Slides were then dried in a centrifuge. The 3DNA Capture Reagent was then hybridized to the arrays for 4 hours at 60 degrees Celsius. Washes were performed as above with the exception that wash #1 was pre-warmed to 60 degrees Celsius.

label_protocol: Samples were labeled using the Array900 miRNA RT kit protocol from Genisphere Inc.  A total of 750 ng of amplified material was labeled.

extract_protocol: MicroRNA was isolated from the prostate tissue by Ambion (mirVana Isolation kit)

tag: Commercially obtained RNA from prostate of 79 year old male

source_name: Pooled Normal

extract_protocol: MicroRNA was isolated from the needle core biopsies using the mirVana microRNA isolation kit from Ambion

tag: Pooled normal prostate tissue from 10 needle core biopsies from 10 separate patients.


title: Normal prostate vs. 24711T (prostate tumor)

extract_protocol: MicroRNA was isolated using the mirVana microRNA isolation kit from Ambion.

tag: Normal prostate from 70 year old male.  Sample was enriched for microRNA fraction.

label: Cy 5

source_name: Prostate tumor, sample 24711

tag: Prostate tumor from radical prostatectomy specimen.


title: Normal prostate vs. PR571T (prostate tumor)

tag: Normal prostate reference control. RNA was isolated from prostate tissue of a 70 year old male without prostate cancer and enriched for the microRNA fraction.

tag: Prostate tumor. RNA was isolated from a radical prostatectomy specimen and enriched for the microRNA fraction.


title: Normal prostate vs. 24822N (normal adjacent to tumor)

tag: Normal prostate reference control.  RNA isolated from prostate of a 70 year old male without prostate cancer.  Sample was enriched for the microRNA fraction.

source_name: 24822N (normal adjacent to tumor)

tag: Normal adjacent to tumor from a radical prostatectomy specimen.  RNA was isolated and enriched for the microRNA fraction.


title: BHI vs BHI koromicin 13622890

status: Public on Jan 06 2009

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae serotype 1 strain CM5 RNA extracted after growth in BHI broth and cDNA generated from the same condition but with a A. pleuropneumoniae serotype 1 strain CM5 mutant in gene malT

scan_protocol: Arrays were scanned with a Perkins Elmer ScanArray, and data was acquired using SpotFinder v3.1.1.

data_processing:
NORMALIZATION WITH MIDAS :
- One Bad Channel Tolerance Policy parameter on how to deal with one-bad-channel spots = Generous
- Net intensities were normalized using Lowess algorithm (MIDAS). Mode = block, smoothing parameter = 0.33, reference = Cy3
- In slide replicate analysis to merge data with same unique identifier

organism: Actinobacillus pleuropneumoniae

source_name: wt BHI D6

label_protocol:
RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

extract_protocol: RNA was extracted using Trizol reagent as prescribed.

tag: serotype 1 strain CM5

tag: bacteria grown in BHI broth to OD600 of 0.7

source_name: wt BHI-koro Q3

tag: bacteria grown in BHI-koromicin broth to OD600 of 0.7


title: BHI vs BHI koromicin 13626592

hyb_protocol: Complete protocol is described in : Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

source_name: wt BHI D7

source_name: wt BHI-koro Q5


title: wtBHI vs mutBALF 13623207

source_name: wt BHI J2

tag: bacteria grown in BHI broth to OD600 of 0.7 followed by subsequent incubation in fresh BHI broth for 30 min.

source_name: mut BALF J6

tag: serotype 1 strain CM5 malT mutant

tag: bacteria grown in BHI broth to OD600 of 0.7 followed by 30 min. incubation in warmed BALF


title: wtBHI vs mutBALF 13626792

source_name: wt BHI J4

source_name: mut BALF J7


title: BHI vs BHI koromicin 13626489

source_name: wt BHI-koro Q7

source_name: wt BHI D10


title: wtBHI vs mutBALF 13622824

source_name: wt BHI I4

source_name: mut BALF I5


title: wtBHI vs mutBALF 13622626

source_name: wt BHI K2

source_name: mut BALF K7


title: wtBHi vs wt BALF, 13623209

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae serotype 1 strain CM5 RNA extracted after growth in BHI broth and subsequent incubation in either fresh BHi broth or BALF.

source_name: wt BHI E2

source_name: wt BLALF E5


title: wtBHi vs mutBHI, 13622874

source_name: wt BHI F2

source_name: mut BHI F5


title: wtBHi vs mutBHI, 13623119

source_name: wt BHI F4

source_name: mut BHI F6


title: wtBHi vs mutBHI, 13623061

source_name: wt BHI G3

source_name: mut BHI G6


title: wtBHi vs wt BALF, 13623128

source_name: wt BHI B2.2

source_name: wt BALF B5.2


title: wtBHi vs wt BALF, 13623129

source_name: wt BHI B2.1

source_name: wt BALF B5.1


title: wtBHi vs wt BALF, 13626494

source_name: wt BHI E4

source_name: wt BALF E6


title: Merkel cell carcinoma tumor L13T

status: Public on Jan 01 2009

type: genomic

city: Seattle

first: Bianca

middle: Durando

last: Lemos

state: WA

address: 815 Mercer St.

department: Medicine/Dermatology

institute: University of Washington

hyb_protocol: 150 microliters of labeled target were added to 50 microliters Cot-1 DNA, 50 microliters blocking agent.  250 microliters of 2X Hybridization Buffer was then added followed by a quick spin. The hybridization mix was denatured by placing in 98 °C heat block for 3 min. Then samples were transfered to 37 °C heat block and incubated for 30 min, followed by centrifugation for 1 min at ~18,000 g. The hybridization chambers and gasket were assembled and the entire 500 microliters were transferred for hybridization to a slide-size array. The slide was then placed at 65 °C in a rotating hybridization oven for 40 h at 20 rpm.

scan_protocol: The arrays were scanned using the Agilent scanner and feature extraction software.

data_processing: The raw data were log-transformed and mode-centered.

molecule: genomic DNA

source_name: nodal merkel cell carcinoma

label_protocol: DNA with was random-prime labeled using the Klenow DNA polymerase, random primers, and cyanine-labeled nucleotides. Test DNA with was labeled with cyanine-3 (Cy3) and the reference DNA was labeled with cyanine-5 (Cy5).

extract_protocol: 15 micrograms of genomic DNA were digested with AluI and RsaI (New England Biolabs, Ipswich, MA) and purified using the QIAquick PCR Purification Kit (Qiagen).  DNA was eluted in water and diluted to 100 nanograms/microliter.

tag: Site of Primary

value: head/neck

tag: Size of Primary Tumor (cm)

tag: Survival

value: No relapse at >36 months

tag: AGE

tag: SEX

value: F

tag: Other


title: wtBHi vs mutBHI, 13610523

source_name: wt BHI H4

source_name: mut BHI H6

tag: serotype 1 strain CM5 mutant malT


title: Merkel cell carcinoma tumor 16

source_name: primary merkel cell carcinoma

value: upper limb

value: No relapse at 10 months

value: M

value: Also has bladder cancer


title: Merkel cell carcinoma tumor L16T

source_name: recurrence of merkel cell carcinoma

value: unknown


title: Merkel cell carcinoma tumor L5T

value: Died of disease at 26 months


title: Merkel cell carcinoma tumor L12T

value: Died of disease at 9 months


title: BHI vs BHI koromicin 13626490

source_name: wt BHI D9

source_name: wt BHI-koro Q6


title: Merkel cell carcinoma tumor LSm


title: Merkel cell carcinoma tumor 15

value: chest

value: No relapse at 5 months


title: wtBHi vs wt BALF, 13623126

source_name: wt BHI C2

source_name: wt BALF C5


title: Merkel cell carcinoma tumor L21T

value: lower limb

value: Alive with disease at 33 months


title: Merkel cell carcinoma tumor L1T

value: Died of disease at 14 months


title: Merkel cell carcinoma tumor L3T


title: Merkel cell carcinoma tumor 14

value: Alive with disease at 5 months; still alive at 24 months


title: Merkel cell carcinoma tumor 11

value: Collision tumor with squamous cell carcinoma


title: Merkel cell carcinoma tumor 12

value: Died disease free at 16 months

value: Also had renal cancer


title: Merkel cell carcinoma tumor 9

value: F


title: Merkel cell carcinoma tumor 10

value: flank

value: Patient on immunosuppressives


title: Merkel cell carcinoma tumor 8

value: head/neck


title: Merkel cell carcinoma tumor 13

source_name: metastasis merkel cell carcinoma

value: Alive with disease at 6 months; NED at 30 months (regression)

value: M


title: Merkel cell carcinoma tumor L4T

value: unknown

value: Died of disease at 40 months


title: Merkel cell carcinoma tumor 1p


title: Merkel cell carcinoma tumor 7

value: upper limb

value: No relapse at >36 months


title: Merkel cell carcinoma tumor 6

value: lower limb


title: Merkel cell carcinoma tumor 3p

value: buttock

value: Died of disease at 22 months

value: HIV positive


title: Merkel cell carcinoma tumor 3m


title: Merkel cell carcinoma tumor 5

value: No relapse at 14 months


title: primary mouth vcg-3

city: Cambridge

first: Amanda

middle: Jane Graham

last: Dickinson

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: ventral and cement gland tissue dissected st.26

hyb_protocol: Standard Affymetrix hybridization (small sample)

scan_protocol: Standard Affymetrix scan protocol

data_processing: Standard Affymetrix normalization method (MAS5)

label: biotin

organism: Xenopus laevis

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using Lithium chloride solution (Ambion) ppt following manufacturer's protocol.

treatment_protocol: tissues were dissected in 0.1XMBS and immediately placed into Trizol and stored at -80C until extraction.

tag: Xenopus laevis st. 26


title: Merkel cell carcinoma tumor 1m

value: Died of disease at 14 months


title: primary mouth pmo-1a

description: primary mouth tissue dissected st.26

source_name: primary mouth tissue dissected st.26


title: primary mouth ad-2

description: anterior dorsal tissue dissected st.26

source_name: anterior dorsal tissue dissected st.26


title: primary mouth vcg-2

source_name: ventral and cement gland tissue dissected st.26


title: primary mouth pmo-3

description: primary mouth tissue dissected st.26


title: primary mouth vcg-1


title: primary mouth ad-3

description: anterior dorsal tissue dissected st.26


title: mRNA profile of Chandipura virus infected RAW 264.7 cells (Dye swap)

city: Pune

first: Dr. AnuKumar

last: Bala Krishnan

address: Dr. Ambedkar Road

department: Dept of Immunology

country: India

institute: NATIONAL INSTITUTE OF VIROLOGY(ICMR)

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The fragmented cRNA were mixed with 55ul of 2x Hybridization Buffer (Agilent). About 110ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using Gene Spring GX v7.3. Per spot per chip lowess normalization was done.A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

source_name: Treated sample from RAW cells

label_protocol: 825ng of each Cyanine 3 or Cyanine 5 labeled cRNA in a volume of 41.8ul were combined with 11ul of 10x Blocking agent and 2.2ul of 25x Fragmentation buffer (Agilent), and incubated at 60deg C for 30 minutes in dark.

growth_protocol: The RAW 264.7 cell was grown in DMEM medium with 10% fetal bovine serum. After treatment the cells were maintained in DMEM without serum.

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: The RAW 264.7 cells infected with 10 MOI of Chandipura virus. The cells were incubated one hour for virus adsorption at 37oC. Post adsorption cells were washed and added fresh serum free DMEM medium. At six hour post infection the total RNA was isolated form infected cells. The isolated RNA was used for labeling and hybridization

tag: Chandipura virus infected RAW cells derived from Mus musculus

source_name: Control sample from RAW cells

treatment_protocol: The RAW 264.7 cells were grown in DMEM medium with 10% fetal bovine serum. on the day of experiment the medium was changed and added serum free medium. At six hour post media change, the total RNA was isolated. The isolated RNA was used for labeling and hybridization

tag: Chandipura virus uninfected RAW cells derived from Mus musculus


title: primary mouth ad-1

description: anterior dorsal tissue dissected st.26


title: mRNA profile of Chandipura virus infected RAW264.7 cells

tag: Chandipura virus uninfected  RAW cells  derived from Mus musculus

source_name: Treated samples from RAW cells

growth_protocol: The RAW 264.7 cell was maintained in DMEM medium with 10% fetal bovine serum

treatment_protocol: The RAW 264.7 cells infected with 10 MOI of Chandipura virus. The infected cells were incubated one hour for adsorption of virus at 37oC. Post adsorption the cells were washed and added fresh serum free DMEM medium. At six hour post infection the total RNA was isolated form infected cells. The isolated RNA was used for labeling and hybridization


title: primary mouth pmo-2

description: primary mouth tissue dissected st.26


title: Beta_cells_1

status: Public on Dec 31 2008

first: Burak

last: Kutlu

address: 1441 North 34th Street

institute: Institute for Systems Biology

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were GCRMA normalized using R/Bioconductor

label_protocol: Affymetrix

growth_protocol: INS-1 cells were cultured in complete medium and collected for analysis after 48h. Primary rat beta-cells (>87% beta-cells) and non-beta-cells (<3% beta cells, mostly alpha) were isolated by FACS mediated purification of two different rat islet preparations.

extract_protocol: Qiagen Rneasy

tag: beta cells purity >87%

tag: FACS-purified rat beta cells


title: INS_cells_1

tag: clonal INS cells

tag: Cultured insulinoma cell lines


title: Alpha_cells_1

tag: non-beta cells containing <3% beta cells

tag: FACS-purified rat non-beta cells


title: Beta_cells_2


title: INS_cells_2


title: Alpha_cells_2


title: Lova 24h3

status: Public on Dec 22 2008

city: shanghai

first: Zhang

last: Qinghua

address: 151# libing road

country: China

institute: Shanghai shbiochip co

description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42?  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Green signal/processed Red signal

source_name: HepG2 cells treated with Lovastatin, 24h

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each Lovastatin treated HepG2 cells was labeled with Cy3.

extract_protocol: Total RNA was prepared from HepG2 cells using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

tag: HepG2 cells were cultured in 2%FBS MEM media for 24 hours with the addition of Lovastatin 0.5 uM. The RNA were collected for transcript profiling analysis

source_name: HepG2 control sample, 24h

tag: HepG2 cells were cultured in 2%FBS media with the solvent DMSO as control for the same time periods. The RNA were collected for transcript profiling analysis


title: Lova 24h1


title: Lova 24h2


title: Lova 12h3

source_name: HepG2 cells treated with Lovastatin, 12h

tag: HepG2 cells were cultured in 2%FBS MEM media for 12 hours with the addition of Lovastatin 0.5 uM. The RNA were collected for transcript profiling analysis

source_name: HepG2 control sample, 12h


title: Lova 6h2

source_name: HepG2 cells treated with Lovastatin, 6h

tag: HepG2 cells were cultured in 2%FBS MEM media for 6 hours with the addition of Lovastatin 0.5 uM. The RNA were collected for transcript profiling analysis

source_name: HepG2 control sample, 6h


title: Lova 12h1


title: Lova 12h2


title: Lova 6h1


title: Lova 2h3

source_name: HepG2 cells treated with Lovastatin, 2h

tag: HepG2 cells were cultured in 2%FBS MEM media for 2 hours with the addition of Lovastatin 0.5 uM. The RNA were collected for transcript profiling analysis

source_name: HepG2 control sample, 2h


title: HEK293-PITX2_vs_Ctrl_Std-rep1

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: PITX2 overexpressed HEK293 cells vs control (mock transfected HEK293 cells). Standard (control on channel 2), biological replicate 1 of 4.

hyb_protocol: 825 ng of each Cy3- and Cy5-labeled cRNA in Agilent Hi RPM hybridization solution; 17 hours at 65 degree Celcius

scan_protocol: Scanned on an Agilent DNA Microarray scanner Quantification using Agilent Feature Extraction v. 9.5.

data_processing: Lowess normalized, background subtracted log2 of sample signal / control signal. Agilent Feature Extraction software was used.

source_name: HEK293 transfected with pEGFP-NFLAG-PITX2c

label_protocol: Agilent QuickAmp labeling protocol with Cy5-CTP from Perkin Elmer

growth_protocol: Hek293 cells grown in DMEM media

extract_protocol: Total RNA isolated using TRI Reagent (Ambion)

treatment_protocol: Transient transfection of Pitx2

tag: Cell line

tag: Transfected with pEGFP-NFLAG-PITX2c

source_name: HEK293 transfected with pEGFP-N1

label_protocol: Agilent QuickAmp labeling protocol with Cy3-CTP from Perkin Elmer

tag: Transfected with pEGFP-N1


title: Lova 2h2


title: Lova 6h3


title: HEK293-PITX2_vs_Ctrl_Std-rep3

description: PITX2 overexpressed HEK293 cells vs control (mock transfected HEK293 cells). Standard (control on channel 2), biological replicate 3 of 4.


title: Lova 2h1


title: GBE24h3

source_name: HepG2 cells treated with ginkgo biloba extract GBE50, 24h

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65C for 10 min, then reversed transcribed at 40C for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each GBE treated HepG2 cells was labeled with Cy3.

tag: HepG2 cells were cultured in 2%FBS MEM media for 24 hours with the addition of 200μg/mL ginkgo biloba extract GBE50. The RNA were collected for transcript profiling analysis


title: GBE24h2


title: GBE24h1


title: HEK293-PITX2_vs_Ctrl_Flip-rep2

description: PITX2 overexpressed HEK293 cells vs control (mock transfected HEK293 cells). Flip (control on channel 1), biological replicate 2 of 4.


title: Renal Clear Cell Carcinoma_TB3825

status: Public on Dec 27 2008

city: Philadelphia

first: Bradley

last: Wubbenhorst

address: 421 Curie Blvd

institute: University of Pennsylvannia

description: Array CGH data from Human RCC sample

hyb_protocol: Hybridization was done according to Illumina's standard protocol

scan_protocol: The chips were scanned using Illuminaa's standard scanner.

data_processing: The data were extracted using Illumina's Bead Studio software and analyzed in Partek as described in the paper Gordan et al. Cancer Cell (2008).

label: Illumina standard protocol

source_name: DNA from Renal Clear Cell Carcinoma

label_protocol: Labelling was done according to Illumina's standard protocol

extract_protocol:
Frozen RCCs were obtained through the Collaborative Human Tissue Network
H&E staining was performed on each sample, and they were confirmed to have clear cell morphology, and be more than 70% tumor
The Wizard® Genomic DNA Purification Kit from Promega was used to extract genomic DNA from the tumors

tag: Group

tag: Gender

tag: Age

tag: Fuhrman

tag: M


title: GBE12h2

source_name: HepG2 cells treated with ginkgo biloba extract GBE50, 12h

tag: HepG2 cells were cultured in 2%FBS MEM media for 12 hours with the addition of 200μg/mL ginkgo biloba extract GBE50. The RNA were collected for transcript profiling analysis


title: GBE12h1


title: GBE2h3

source_name: HepG2 cells treated with ginkgo biloba extract GBE50, 2h

tag: HepG2 cells were cultured in 2%FBS MEM media for 2 hours with the addition of 200μg/mL ginkgo biloba extract GBE50. The RNA were collected for transcript profiling analysis


title: GBE6h1

source_name: HepG2 cells treated with ginkgo biloba extract GBE50, 6h

tag: HepG2 cells were cultured in 2%FBS MEM media for 6 hours with the addition of 200μg/mL ginkgo biloba extract GBE50. The RNA were collected for transcript profiling analysis


title: GBE6h2


title: Renal Clear Cell Carcinoma_TB3940

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3823

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3901

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3817

description: Array CGH data from Human RCC sample


title: GBE6h3


title: Renal Clear Cell Carcinoma_TB3812

description: Array CGH data from Human RCC sample


title: GBE2h1


title: GBE2h2


title: Renal Clear Cell Carcinoma_TB3852

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3826

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3809

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3844

description: Array CGH data from Human RCC sample


title: 12997263 - Leaves_18-02-05 vs Meiocytes_18-02-05

status: Public on Dec 07 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description: What are the gene expressed during meiosis pathway in Arabidopsis thalina.

hyb_protocol: Meiocytes_18-02-05 Cy5 / Leaves_18-02-05 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,700V,laser power 100%, Cy5:635nm,pmt voltage 650V,laser power 100%

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

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):isolated male meoocytes

growth_protocol: leaf - Seeds were germinated on sand and plants were transfered to a half strength MS hydroponic solution and cultivated in a controlled environment: 8 h daylight at 300 umol.m-2.s-1, 22°C and 70% relative humidity.

tag: Arabidopsis thaliana (columbia)  - age:4week


title: Renal Clear Cell Carcinoma_TB3806

description: Array CGH data from Human RCC sample


title: 12997259 - Meiocytes_18-02-05 vs Leaves_18-02-05

hyb_protocol: Leaves_18-02-05 Cy5 / Meiocytes_18-02-05 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HEK293-PITX2_vs_Ctrl_Flip-rep4

description: PITX2 overexpressed HEK293 cells vs control (mock transfected HEK293 cells). Flip (control on channel 1), biological replicate 4 of 4.


title: Renal Clear Cell Carcinoma_TB4084

description: Array CGH data from Human RCC sample


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, miR-192, 25nM, 10hr

first: Sara

last: Georges

address: 401 Terry Ave N

institute: Rosetta Inpharmatics, LLC

description: Transfection_of_miR192_miR215_into_HCT116_Dicerex5_profiled_at_10h_and_24h_post_transfection.CancerResearch.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: HCT116 Dicer-/- #2, mock


title: Renal Clear Cell Carcinoma_TB4016

description: Array CGH data from Human RCC sample


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, luc, 25nM, 10hr

tag: HCT116 Dicer-/- #2, luc, 25nM, 10hr


title: GBE12h3

tag: HepG2 cells were cultured in 2%FBS media with the solvent DMSO as control for the same time periods. The RNA were collected for transcript profiling analysis


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, miR-192, 25nM, 24hr


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, miR-215, 25nM, 24hr


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, miR-215, 25nM, 10hr


title: Renal Clear Cell Carcinoma_TB4040

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB4105

description: Array CGH data from Human RCC sample


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, luc, 25nM, 24hr

tag: HCT116 Dicer-/- #2, luc, 25nM, 24hr


title: Renal Clear Cell Carcinoma_TB3939

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3822

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3908

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3821

description: Array CGH data from Human RCC sample


title: Renal Clear Cell Carcinoma_TB3903

description: Array CGH data from Human RCC sample


title: Mycobacterium bovis BCG_Sodium Hypochlorite_20min_replicate3

status: Public on Dec 01 2008

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: No treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated M. bovis cultures at 37°C with shaking at 250 rpm using sterilized Middlebrook 7H9 broth for 5days, (ii) Mycobacteria were harvested, washed and resuspended in sterilized Lurria-Bertani (LB) broth with 0.1% (v/v) Tween 80. Then the cultures were incubated for further 24 hours shaking at 37°C. To see the efficacy of an antimicrobial against mycobacteria, several concentrations of sodium hypochlorite were added to the cells.

extract_protocol: Total RNA was isolated after 10 and 20 min incubation with and without (control) sodium hypochlorite using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX)[16]. The mycobacterial cells treated with hydrogen peroxide and untreated cells as controls were harvested and resuspended in PBS buffer. For stabilize of RNA, we used for breaking the micobaterium cell, we used bead beater, 5 times for 1min beating and 2min on ice.

treatment_protocol: 2.5mM Sodium Hypochlorite

tag: strain Pasteur 1173P2 Wild type


title: Mycobacterium bovis BCG_Sodium Hypochlorite_20min_replicate1

description: No treatment


title: Mycobacterium bovis BCG_Sodium Hypochlorite_20min_replicate2

description: No treatment


title: Mycobacterium bovis BCG_Sodium Hypochlorite_10min_replicate2

description: No treatment


title: Mycobacterium bovis BCG_Sodium Hypochlorite_10min_replicate3

description: No treatment


title: Renal Clear Cell Carcinoma_TB3816

description: Array CGH data from Human RCC sample


title: Mycobacterium bovis BCG_Sodium Hypochlorite_10min_replicate1

description: No treatment