title: D. pseudoobscura adult male heads 454

city: Chicago

first: Chung-I

last: Wu

state: IL

address: 1101 57th East

department: Ecology and Evoluation

institute: University of Chicago

description: small RNAs

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: after removing the flank adaptor sequences, the inserted sequences greater than 18nt were extracted

label: not applicable

organism: Drosophila pseudoobscura

source_name: Drosophila pseudoobscura adult male heads

label_protocol: not applicable

extract_protocol: total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH

tag: adult male heads


title: D. melanogaster adult male heads 454

status: Public on Feb 14 2008

type: other

country: USA

description: small RNAs

molecule: other

organism: Drosophila melanogaster

source_name: Drosophila melanogaster adult male heads


title: Aspergillus fumigatus treated with Amphotericin B replicate 2

type: RNA

city: San Jose

first: Jata

last: Shankar

state: CA

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

description: Biological 2 of 2. Dye swap

hyb_protocol: Labeled cDNAs in hybridization buffer were mixed and heated at 94 C for 5 min before loading onto the array slides. Slides were covered with a 2450 mm glass cover slip (Erie Scientific Company, Portsmouth, New Hampshire, US) and kept in hybridization chamber (Corning, Saint Louis, Missouri, US) at 42 C for 16-18 h to prevent evaporation (http://pfgrc.tigr.org/protocols).

scan_protocol: Scanned in both Cy3 and Cy5 channels with AXON Instruments Scanner 4200 with a 10 µm resolution. Each of the signals was converted into a resolution of 16 bits per pixel.

data_processing: TIFF images were analyzed using GenePix Pro 6.0 software. The signal intensity value of each spot was subtracted with local background for each spot. Intensity based normalization by means was used as previously described by Foster, W. R., and R. M. Huber.  2002. Current themes in microarray experimental design and analysis. Drug Discov Today. 7(5):290-2.

molecule: total RNA

organism: Aspergillus fumigatus

source_name: Aspergillus fumgatus grown for 24hrs in RPMI-1640 medium containing AmphotericinB

label_protocol: Total RNA (7µg) from Afu alone or Afu treated with AMB (MIC50) was reverse transcribed separately using fluorescein labeled dCTP and biotin labeled dCTP from MICROMAX TSA labeling kits (Perkin Elmer, Wellesley, Massachusetts, US). Labeled cDNA was purified by isopropanol precipitation method as described in the MICROMAX TSA labeling kit. Each of the purified labeled cDNA was dissolved in 20 µl of hybridization buffer; 50 % formamide, 5× sodium citrate-sodium cholride (SSC), 0.1 % sodium dodecyl sulphate (SDS) and 300 µg salmon sperm DNA.

growth_protocol: Aspergillus fumigatus were harvested from Afu culture (after 72 h) on SDA in 3-L haffkine flask using 100 ml phosphate-buffered saline (PBS) with 0.05 % Tween 20 (PBST) and centrifuged at 10,000 rpm for 10 min. at 4 °C and washed with 25 ml PBS twice. Conidia were then allowed to swell in PBS containing Ca2+ and Mg2+ for 1 h followed by a viability count on SDA plates by hemocytometer and CFU count/ml. Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) alone or with AMB (MIC50) followed by incubation at 37 °C for 24 h (Axygen, Union City, California, US).

extract_protocol: DNA free total RNA was isolated from Afu using RNeasy plant mini kits (Qiagen GmbH, Hilden, Germany). A fumigatus frozen in -70 °C were grinded using mortar and pestle in the presence of liquid nitrogen (1.5 g, wet weight). The cell powder was suspended in 2 ml of RLT lysis buffer provided with RNeasy plant mini kit and centrifuged at 10,000 rpm for 2 min followed by further steps for isolation of total RNA as described in the kit protocol. Examination of total RNA by gel electrophoresis revealed prominent intact 26S and 18S ribosomal bands and no genomic DNA contamination. RNA concentration was determined spectrophotometer by measuring absorption at 260 nm in a Lambda Bio 20 UV-visible spectrophotometer (Perkin Elmer, Wellesley, Massachusetts, US).

tag: Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) with Amphoterin B (MIC50= determined to be 0.125±0.008 µg/ml using MTT assay) followed by incubation at 37 °C for 24 h (Axygen, Union City, California, US). Afu treated with AMB were scraped from the culture flask and pelleted at 4 °C by centrifuging at 18,000 rpm for 15 min and kept at -70 °C.

source_name: Aspergillus fumgatus grown alone in RPMI-1640 medium for 24hrs

tag: Afu Spores (1×106/ ml) were inoculated in 100 ml of RPMI-1640 medium (with L-glutamine with sodium bicarbonate) (Sigma, Saint Louis, Missouri, US) in culture flasks (225 cm2) alone at 37 °C for 24 h (Axygen, Union City, California, US). Afu were scraped from the culture flask and pelleted at 4 °C by centrifuging at 18,000 rpm for 15 min and kept at -70 °C for microarray experiment.


title: ALI patient #1

status: Public on Feb 15 2008

city: Boston

first: Judie

middle: Ann

last: Howrylak

state: MA

address: 75 Francis Street

department: Pulmonary and Critical Care Medicine

institute: Brigham and Women's Hospital

description: patient with Acute Lung Injury

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GCRMA

label: biotin

organism: Homo sapiens

source_name: patient with Acute Lung Injury

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: plasma

tag: patient with Acute Lung Injury


title: Suc+GA_vs_GA_in_dark_3

status: Public on Feb 13 2008

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: The aim of this study is to analize the genes that are up or down-regulated in response to sprouting promoting effectors such as GAs and light, in order to elucidate the signalling cascades triggered during this process. Half sections of certified pathogen tested Spunta tubers were put into sterile MS-agar (0.7%) containing flasks at 16„aC and subjected to different treatments:  Dark controls: Tuber sections were incubated for 10 or 35 days in complete darkness. Light control: Tuber sections were incubated  for 10 days under continuous light conditions.   Treatments performed in complete darkness during 35 days: a) GA treatment: 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma) b) Sucrose treatment: 1% sucrose  c) GA & sucrose treatment: 5 uM GA3 (Sigma) + 1% sucrose  Treatments performed in light (10 days)d) GA treatment  : 5 uM GA3 (Sigma).   Three independent biological replicates of each condition (3 controls and 4 treatments) wereperformed. At the moment of harvest (10 or 35 days) sprout length was measured and photographs of the different samples were taken. Sprouts were excised and frozen in liquid Nitrogen. Total RNA was obtained using the Trizol reagent (Invitrogen) according to the manufacturer¡¦s instructions. RNAs were quantified by OD: 260/280 and checked in agarose gels.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Tuber half-sections were grown in complete darkness for 35 days at 16°C in MS-agar (0,7% ) with the addition of 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma) and 1 % sucrose

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: GA + Sucrose treatment in dark-3

tag: Solanum tuberosum, Tuber sprouts, Development

treatment_protocol: GA treatment in dark-3


title: GA_in_light_vs_Light_ctrl_3

growth_protocol: Tuber half-sections were grown under continuous light for 10 days at 16°C in MS-agar (0,7%) with the addition of  5M gibberellic acid (C19H22O6) = GA3 (Sigma)

treatment_protocol: GA treatment in light-3

treatment_protocol: Light control-3


title: Suc+GA_vs_Light_ctrl_3

growth_protocol: Tuber half-sections were grown under continuous light for 10 days at 16°C in MS-agar (0,7%)


title: Suc_in_dark_vs_dark_35d_2

growth_protocol: Tuber half-sections were grown in complete darkness for 35 days at 16°C in MS-agar (0,7% ) with the addition of 1% sucrose

treatment_protocol: Sucrose treatment in dark-2

growth_protocol: Tuber half-sections were grown in complete darkness for 35 days at 16°C in MS-agar (0,7%)

treatment_protocol: Dark control 35 days-2


title: GA_in_light_vs_GA_in_dark_3

growth_protocol: Tuber half-sections were grown in complete darkness for 35 days at 16°C in MS-agar (0,7% ) with the addition of 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma)


title: Suc+GA_vs_Light_ctrl_1

treatment_protocol: GA + Sucrose treatment in dark-1

treatment_protocol: Light control-1


title: Suc+GA_vs_Suc_in_dark_3

treatment_protocol: Sucrose treatment in dark-3


title: D. simulans adult male heads 454

description: small RNAs

organism: Drosophila simulans

source_name: Drosophila simulans adult male heads


title: GA_in_dark_vs_Suc_in_dark_1

treatment_protocol: GA treatment in dark-1

treatment_protocol: Sucrose treatment in dark-1


title: GA_in_light_vs_GA_in_dark_1

growth_protocol: Tuber half-sections were grown under continuous light for 10 days at 16°C in MS-agar (0,7%) with the addition of 5 uM gibberellic acid (C19H22O6) = GA3 (Sigma)

treatment_protocol: GA treatment in light-1


title: Suc+GA_vs_GA_in_dark_1


title: GA_in_light_vs_Light_ctrl_2

treatment_protocol: GA treatment in light-2

treatment_protocol: Light control-2


title: GA_in_dark_vs_dark_35d_3


title: GA_in_light_vs_GA_in_dark_2

treatment_protocol: GA treatment in dark-2


title: GA_in_dark_vs_Suc_in_dark_3


title: GA_in_dark_vs_dark_35d_1

treatment_protocol: Dark control 35 days-1


title: Suc+GA_vs_Suc_in_dark_1


title: Suc_in_dark_vs_dark_35d_1


title: GA_in_dark_vs_dark_35d_2


title: Dark_35d_vs_dark_10d_3

treatment_protocol: Dark control 35 days-3

growth_protocol: Tuber half-sections were grown in complete darkness for 10 days at 16°C in MS-agar (0,7%)

treatment_protocol: Dark control 10 days-3


title: GA_in_light_vs_Light_ctrl_1


title: dark_vs_blue_flip_1

description: A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry.

molecule: polyA RNA

growth_protocol: Grown in tissue culture under continuous white fluorescent light at 21C

treatment_protocol: Blue light for 2 days after 3.5 weeks in darkness

tag: Solanum tuberosum, Stem and leaf, Development

treatment_protocol: Continuous darkness for 3 weeks, 4 days


title: Light_ctrl_vs_dark_ctrl_2

treatment_protocol: Dark control 10 days-2


title: dark_vs_blue_rep_1


title: Light_ctrl_vs_dark_ctrl_1

treatment_protocol: Dark control 10 days-1


title: Light_ctrl_vs_dark_ctrl_3

treatment_protocol: Light control-3


title: germinating_seed_v_berry

description: The purpose of this study is to survey gene expression of potato (solanum tuberosum gilroy) in a variety of tissues and life cycle timepoints.  Potato plants were grown from true seeds, planted in either soil or MS media, and grown in growth chambers.  Four biological replicates each of twenty different tissue samples were collected at the appropriate timepoints.  The samples were immediately frozen at -80.  The tissues were then ground into a powder in liquid nitrogen, and RNA was extracted using Qiagen's QiaShredder columns and Qiagen's Rneasy MinElute Kit.  The RNA was amplified using Arcturus' RiboAmp RNA Amplification Kit.  1ug of amplified RNA was used in TIGR's indirect labelleling procedure.  All hybridaztions were applied to TIGR's 10kV4 potato array.

growth_protocol: Grown in chamber (24h light, 25C) on 0.5X MS, 1% sucrose agar plate.

tag: Solanum tuberosum, Germinating seed, Development

growth_protocol: Grown in chamber (16h light/8hr darkness, 25C) in Pro-Mix BX general purpose growing medium.

tag: Solanum tuberosum, Berry, Development


title: dark_vs_blue_rep_3


title: dark_vs_blue_flip_2


title: root_v_berry

tag: Solanum tuberosum, Root, Development


title: Dark_35d_vs_dark_10d_1


title: germinating_seed_v_calyx

tag: Solanum tuberosum, Calyx, Development


title: dark_vs_blue_rep_2


title: berry_v_root


title: tuber_epidermis_v_root

tag: Solanum tuberosum, Tuber epidermis, Development


title: tuber_epidermis_v_calyx


title: berry_v_germinating_seed


title: dark_vs_blue_flip-3


title: Dark_35d_vs_dark_10d_2

treatment_protocol: Dark control 35 days-2


title: calyx_v_germinating_seed


title: microtuber10%_v_stolon(MS)

growth_protocol: Grown in Magenta box in chamber (24h light, 25C) on 1X MS, 10% sucrose agar.

tag: Solanum tuberosum, Microtuber, Development

growth_protocol: Grown in Magenta box in chamber (24h light, 25C) in liquid media of 1X MS, 10% sucrose

tag: Solanum tuberosum, Stolon, Development


title: stolon(MS)_v_microtuber10%


title: calyx_v_tuber_epidermis


title: stolon(soil)_v_microtuber1%

growth_protocol: Grown in Magenta box in chamber (24h light, 25C) on 0.5X MS, 1% sucrose agar.


title: stolon(MS)_v_tuber_cortex

tag: Solanum tuberosum, Tuber cortex, Development


title: flower_v_corolla

tag: Solanum tuberosum, Whole flower, Development

tag: Solanum tuberosum, Corolla, Development


title: corolla_v_flower


title: prox_leaf_pair_v_shoot

tag: Solanum tuberosum, Proximal leaflet pair, Development

tag: Solanum tuberosum, Shoot, Development


title: tuber_cortex_v_microtuber1%


title: flower_v_bud

tag: Solanum tuberosum, Bud, Development


title: microtuber1%_v_tuber_cortex


title: mictrotuber1%_v_stolon(soil)


title: petiole+rach_v_dist_leaf_pair

tag: Solanum tuberosum, Petiole + rachis, Development

tag: Solanum tuberosum, Distal leaflet pair, Development


title: microtuber10%_v_stolon(soil)


title: pistil_v_stamen

tag: Solanum tuberosum, Pistil, Development

tag: Solanum tuberosum, Stamen, Development


title: shoot_v_prox_leaf_pair


title: etiolated_sdlng_v_shoot

tag: Solanum tuberosum, Etiolated seedling, Development


title: stamen_v_pistil


title: bud_v_pistil


title: stamen_v_corolla


title: corolla_v_stamen


title: etiolated_sdlng_v_petiole+rach


title: petiole+rach_v_etiolated_sdlng


title: pistil_v_bud


title: bud_v_flower


title: distal_v_prox_leaflet_pairs


title: M_str_3_vs_WT_str_3

description: Pollen development is one of the most heat-sensitive developmental stages in a wide range of crops. Our longer-term goal is to understand the mechanism how starch metabolism in maturing pollen grains of the Solanaceae family contributes to maintaining higher pollen quality under heat-stress conditions. The specific aim of the suggested proposal is to characterize N. sylvestris WT and mutant (starch-deficient) transcriptomes during microgametogenesis under ambient and heat-stress conditions. Expression profiles of maturing microspores derived from flower buds at developmental stage of 4 to 2 days before flower opening will be obtained. Pollen was derived from WT and mutant plants exposed to either ambient or heat-stress conditions (exposing the plants to 45oC for 2.5 hours).

organism: Nicotiana sylvestris

growth_protocol: Growth for 45-60 days in green house at 25/18oC day/night temperatures

treatment_protocol: Challenged with 45oC for 2.5 hours

tag: Nicotiana sylvestris, Microspores, Abiotic stress


title: dist_leaf_pair_v_petiole+rach


title: M_ctrl_4_vs_M_str_4

treatment_protocol: Control


title: prox_v_distal_leaflet_pairs


title: WT_ctrl_3_vs_M_ctrl_3


title: WT_ctrl_4_vs_M_ctrl_4


title: M_str_4_vs_WT_str_4


title: WT_str_3_vs_WT_ctrl_3


title: M_ctrl_2_vs_WT_ctrl_2


title: WT_ctrl_1_vs_WT_str_1


title: mock_vs_pvy_systemic_6dpi_1.2

description: The goal of these studies is analysis of gene expression profiles in potato plants infected with potato virus Y (necrotic strain - PVYN). A prototypic plant pathogen interaction system used to study disease resistance is tobacco (Nicotiana tabacum) and tobacco mosaic virus (TMV). In tobacco, the resistance response comprises two phenomena, known as the hypersensitive response (HR) and systemic acquired resistance (SAR). HR is typically characterized by a local necrosis surrounding the site of viral entry leading to restriction of pathogen replication and spread. SAR is the enhanced ability of the plant to resist a secondary challenge by the same or a different pathogen inoculated elsewhere on the plant. The identity of the signal(s) that induces HR and SAR is still poorly understood. Plants of S. tuberosum cv. Rywal, resistant to all known (N, 0, NTN) PVY strains, were grown in growth chambers using 16 h period of light (22°C) and 8 h of darkness (18°C). For all experiments, 6-week-old plants were used. For inoculation with PVY, carborundum-dusted leaves were rubbed with water (mock control) or PVYN solution (1 µg ml-1). Two to four leaves were inoculated on each plant and harvested together at 1, 3, and 6 days post inoculation (dpi). Separately, noninoculated leaves were harvested at the same time points (upper leaves). The first time point (1 dpi) has been chosen to study the early stage of plant response before necrotic lesion formation. At 3 dpi necrotic lesions start to appear, and at 6 dpi necroses are fully developed which correlates with the maximum of salicylic acid increase in virus inoculated leaves.

growth_protocol: Grown in growth chambers using 16 h period of light (22°C) and 8 h of darkness (18°C), light intensity 5000 to 6000 lux, 65% humidity

treatment_protocol: Systemic leaves from PVY infected plants, 6dpi

tag: Solanum tuberosum, Leaflet, Biotic stress

treatment_protocol: Systemic leaves from water treated plants, 6dpi


title: M_str_1_vs_M_ctrl_1


title: mock_vs_pvy_systemic_3dpi_1_FD

treatment_protocol: Systemic leaves from PVY infected plants, 3dpi

treatment_protocol: Systemic leaves from water treated plants, 3dpi


title: mock_vs_pvy_systemic_1dpi_2.1

treatment_protocol: Systemic leaves from PVY infected plants, 1dpi

treatment_protocol: Systemic leaves from water treated plants, 1dpi


title: mock_vs_pvy_systemic_6dpi_1.1


title: mock_vs_pvy_systemic_3dpi_1.1


title: mock_vs_pvy_systemic_1dpi_2.2


title: mock_vs_pvy_systemic_3dpi_2.1


title: WT_str_4_vs_WT_ctrl_4


title: WT_str_2_vs_M_str_2


title: M_ctrl_3_vs_M_str_3


title: mock_vs_pvy_systemic_6dpi_2.2


title: mock_vs_pvy_systemic_3dpi_1.2


title: mock_vs_pvy_systemic_3dpi_2.2


title: mock_vs_pvy_systemic_6dpi_2.1


title: mock_vs_pvy_systemic_1dpi_1.1


title: mock_vs_pvy_systemic_1dpi_1.2


title: mock_vs_pvy_infected_6dpi_2.2

treatment_protocol: Carborundum-dusted leaves rubbed with PVYN strain Wilga solution (1 µg ml-1), 6dpi

treatment_protocol: Carborundum-dusted leaves rubbed with water, 6dpi


title: mock_vs_pvy_infected_6dpi_1.2


title: mock_vs_pvy_infected_6dpi_2.1


title: mock_vs_pvy_infected_6dpi_1.1


title: mock_vs_pvy_infected_3dpi_2.1

treatment_protocol: Carborundum-dusted leaves rubbed with PVYN strain Wilga solution (1 µg ml-1), 3dpi

treatment_protocol: Carborundum-dusted leaves rubbed with water, 3dpi


title: mock_vs_pvy_infected_1dpi_2.2

treatment_protocol: Carborundum-dusted leaves rubbed with PVYN strain Wilga solution (1 µg ml-1), 1dpi

treatment_protocol: Carborundum-dusted leaves rubbed with water, 1dpi


title: mock_vs_pvy_infected_3dpi_1.2


title: mock_vs_pvy_infected_3dpi_2.2


title: mock_vs_pvy_infected_1dpi_2.1


title: Light_96h_vs_0h_B2

description: Potato (cv. King Edward and Bintje) tubers were obtained from local suppliers, and synchronized by storage in darkness for 3 weeks at +4 C followed by +20 C for two days. Tubers were then stressed in a time-course experiment either by exposure to white light (0 to 96h) or wounded by sectioning into 5mm pieces (0 to 48h).

growth_protocol: 110 microE, 23 degrees C

treatment_protocol: Constant white light 96h

tag: Solanum tuberosum, Tuber, Abiotic stress

growth_protocol: Darkness, 23 degrees C

treatment_protocol: Light 0h (control)


title: mock_vs_pvy_infected_1dpi_1.1


title: mock_vs_pvy_infected_1dpi_1.2


title: Light_48h_vs_0h_B2

treatment_protocol: Constant white light 48h


title: Light_24h_vs_0h_B2

treatment_protocol: Constant white light 24h


title: Wounding_24h_vs_0h_B1

growth_protocol: Darkness, 23 degrees C, between moist filter papers

treatment_protocol: Wounded 24h

treatment_protocol: Wounded 0h (control)


title: Light_96h_vs_0h_B1


title: mock_vs_pvy_infected_3dpi_1.1


title: Light_24h_vs_0h_B1


title: Wounding_6h_vs_0h_B2

treatment_protocol: Wounded 6h


title: Wounding_12h_vs_0h_B1

treatment_protocol: Wounded 12h


title: Wounding_12h_vs_0h_B2


title: Wounding_6h_vs_0h_B1


title: Wounding_24h_vs_0h_B2


title: Light_48h_vs_0h_B1


title: Dark_ctrl_96h_vs_0h_KE2

treatment_protocol: Constant darkness 96h


title: Light_48h_vs_0h_KE2


title: Dark_ctrl_96h_vs_0h_KE1


title: Light_24h_vs_0h_KE2


title: Light_96h_vs_0h_KE2


title: Light_96h_vs_0h_KE1


title: Light_24h_vs_0h_KE1


title: Wounding_48h_vs_0h_KE2

treatment_protocol: Wounded 48h


title: Light_12h_vs_0h_KE1

treatment_protocol: Constant white light 12h


title: Light_12h_vs_0h_KE2


title: Light_48h_vs_0h_KE1


title: Wounding_6h_vs_0h_KE2


title: Wounding_48h_vs_0h_KE1


title: Wounding_24h_vs_0h_KE2


title: Wounding_6h_vs_0h_KE1


title: Wounding_12h_vs_0h_KE1


title: ctrl_vs_FR_RECEIVER_2

description: In plants, an increase in resource allocation to growth (primary metabolism) associated with the presence of neighbors is likely to reduce defense-related production (secondary metabolism), making plants more vulnerable to herbivory. Even though there is increasing evidence supporting this “trade-off hypothesis”, the underlying mechanisms are still unclear. Far red (FR) radiation reflected from plant tissues serves as an early warning signal of future competition, triggering a suite of plastic morphological adjustments that improve plant’s ability to compete for light in crowded populations. Recent evidence from our lab showed that, when competition signals are present, plant defenses are severely reduced. Besides direct effects of herbivory and competition signals on target plants, second order effects occurs on neighboring plants through plant volatiles (PVs) communication. PVs play a key role in plant-plant and plant-insect interactions, changing its content and composition in response to environmental conditions. To increase our understanding of the molecular mechanisms underlying those interacting signaling webs, we performed a field study with tomato plants (cv Moneymaker), in which plants of EMITTER plots (six plants plot-1) were subjected to herbivory (nine larvae of Spodoptera eridania plant-1) and competition signals (increased FR radiation) in a factorial design. Light treatment started 28 days after sowing (DAS), and herbivory treatment and volatiles conduction started 34 DAS. Volatiles were conducted from EMITTER to RECEIVER plots (five plants plot-1) using a 5 inch, 1.4 m long tube fitted with a computer-type fan. 40 and 45 DAS, larval performance was measured on EMITTER plots as well as naturally-occurring insect colonization on RECEIVER plots. Finally (46 DAS), samples for bulk phenolic content were taken on every plot, and plant material from 4th and 5th leaves was collected for microarray analysis. There were three real biological replicates.

organism: Solanum lycopersicum

growth_protocol: Grown 2 weeks in greenhouse, 1 aditional week in the field

treatment_protocol: Signals of competition

tag: Solanum lycopersicum, Leaves, Biotic stress

treatment_protocol: RECEIVER control


title: ctrl_vs_herb_RECEIVER_2

treatment_protocol: Herbivory


title: ctrl_vs_herb+FR_RECEIVER_2

treatment_protocol: Signals of competition + herbivory


title: ctrl_vs_herb+FR_RECEIVER_3


title: Wounding_12h_vs_0h_KE2


title: ctrl_vs_herb_RECEIVER_1


title: ctrl_vs_herb_RECEIVER_3


title: Wounding_24h_vs_0h_KE1


title: ctrl_vs_herb+FR_RECEIVER_1


title: ctrl_vs_herb+FR_EMITTER_3

treatment_protocol: EMITTER control


title: ctrl_vs_FR_RECEIVER_1


title: ctrl_vs_FR_EMITTER_3


title: ctrl_vs_herb+FR_EMITTER_2


title: ctrl_vs_herb_EMITTER_3


title: ctrl_vs_FR_EMITTER_2


title: ctrl_vs_FR_EMITTER_1


title: ctrl_vs_herb+FR_EMITTER_1


title: ctrl_vs_herb_EMITTER_1


title: mock_vs_pvy_infected_3dpi_1_FD

treatment_protocol: Carborundum-dusted leaves rubbed with PVYN strain Wilga solution (1 µg ml-1), 3dpi

treatment_protocol: Carborundum-dusted leaves rubbed with water, 3dpi


title: Mut_Inf_Cort_vs_Mut_Hth_Cort_c

description: Russet Nugget and the corresponding smooth skin mutant tubers harvested from disease and healthy filed plots. Tubers were washed with 10% Clorox and dried before harvesting tissue. Cortex and peel tissue was collected from healthy and infected regions of the mutant. Healthy peel and cortex tissue was collected from Russet Nugget (wild-type) potato tuber and snap-frozen in liquid nitrogen and stored at -80 °C. RNA was extracted from frozen tissues using a hot phenol method in triplicate from the different sets of tuber tissue. Extracted RNA was purified by Qiagen kits after treatment with DNAse. In all of these experiments RNA from Russet Nugget peel and cortex tissue will be used as reference samples where as mutant tissue will be used as query samples.

growth_protocol: Field Grown

treatment_protocol: Mutant and Russet Nugget grown in diseased field plots

tag: Solanum tuberosum, Tuber Cortex, Biotic stress


title: Mut_Hth_Cort_vs_RN_Hth_Cort_b


title: Mut_Inf_Cort_vs_Mut_Hth_Cort_b


title: Mut_Inf_Peel_vs_Mut_Hth_Peel_c

tag: Solanum tuberosum, Tuber Peel, Biotic stress


title: Mut_Inf_Peel_vs_RN_Hth_Peel_b


title: Mut_Inf_Peel_vs_Mut_Hth_Peel_b


title: Mut_Inf_Peel_vs_RN_Hth_Peel_a


title: Mut_Hth_Cort_vs_RN_Hth_Cort_c


title: Mut_Inf_Peel_vs_RN_Hth_Peel_c


title: Mut_Inf_Cort_vs_Mut_Hth_Cort_a


title: ctrl_vs_herb_EMITTER_2


title: Mut_Hth_Peel_vs_RN_Hth_Peel_c


title: Mut_Hth_Cort_vs_RN_Hth_Cort_a


title: Mut_Hth_Peel_vs_RN_Hth_Peel_a


title: Mut_Hth_Peel_vs_RN_Hth_Peel_b


title: Mut_Inf_Peel_vs_Mut_Hth_Peel_a


title: ctrl_vs_FR_RECEIVER_3


title: Ref_vs_40_12wks_2

description: This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers.

growth_protocol: Commercial field, central Wisconsin sumer 2006

treatment_protocol: Held at 40 F to 12 weeks

treatment_protocol: Held at 48 F to 9 weeks, transferred to 40 F for 3 weeks


title: Ref_vs_48to40_12wks_2


title: Ref_vs_48to40_12wks_3


title: Ref_vs_48to40_12wks_1


title: Ref_vs_40_12wks_3


title: Ref_vs_40_12wks_1


title: Ref_vs_48_12wks_2

treatment_protocol: Held at 48 F to 12 weeks


title: Ref_vs_48_12wks_3


title: Ref_vs_48to40_9wks_2

treatment_protocol: Held at 48 F to 6 weeks, transferred to 40 F and held for 3 weeks


title: Ref_vs_48_12wks_1


title: Ref_vs_48to40_9wks_3


title: Ref_vs_40_9wks_1

treatment_protocol: Held at 40 F to 9 weeks


title: Ref_vs_48to40_9wks_1


title: Ref_vs_40_9wks_2


title: Ref_vs_48_9wks_3

treatment_protocol: Held at 48 F to 9 weeks


title: Ref_vs_40_9wks_3


title: Ref_vs_48_9wks_1


title: Ref_vs_48_9wks_2


title: Ref_vs_48_6wks_3

treatment_protocol: Held at 48 F to 6 weeks


title: Ref_vs_40_6wks_1

treatment_protocol: Held at 40 F to 6 weeks


title: Ref_vs_48_6wks_2


title: Ref_vs_40_3wks_3

treatment_protocol: Cooled to 41.5 F  over 3 weeks


title: Ref_vs_40_3wks_2


title: Ref_vs_40_6wks_3


title: Ref_vs_48_6wks_1


title: Ref_vs_40_3wks_1


title: Ref_vs_48_3wks_3

treatment_protocol: Cooled to 48 F and held over 3 weeks


title: Cont_vs_C+MG_6h_3

description: To study basal resistance we inoculated tobacco plants with Pseudomonas syringae pv. syringae 61 hrcC mutants (gift of A. Collmer). To compare the expression profiles of basal resistance to hypersensitive response, we used P. syringae pv. syringae 61. Gene activation triggered by the live compatible pathogen P. syringae pv. tabaci was compared to kanamycine-inactivated P. tabaci (10 min in 100 ug/ml KM, then washed 2x in H2O). Water-infiltrated control leaves were used. The aim of another set of experiments was to investigate the influence of various signal transduction pathways on basal resistance. Control plants were infiltrated with P. syringae pv syringae hrcC mutant bacteria. These were compared to treatments, in which the bacterial suspensions were supplemented with inhibitors that can block a specific type of signal transduction pathway. The inhibitors represented Ca2+ signaling, lipid derived signals generated by phospholipase C and A, protein phosphorilation (kinases) and protein degradation (degradation of transcription repressors or activators). The used inhibitors were LaCl3, neomycin, aristolochic acid, K252a and MG115 respectively. 2-2.5 months old tobacco plants (Nicotiana tabacum cv. Samsun nn) were grown in a greenhouse in soil with cca. 16/8 hr light/dark period at 20°C, then in a growth chamber 2 days before and during experiments, under identical conditions. A syringe was used for the injection of bacteria or chemical solutions into the tobacco leaves. At 6 or 48 hours post inoculation, leaf samples were taken, and frozen in liquid nitrogen.  Every experiment was carried out in 3 independent replicates. Total RNA was extracted using the Quiagen RNeasy Plant Mini kit and the Quiagen Rnase-free Dnase Set, then re-purified and concentrated on Microcon-30 (Millipore) columns. The concentration and quality of isolated RNA was estimated by measuring its absorbency at 260 and 280 nm and running on 1% agarose gel.

organism: Nicotiana tabacum

growth_protocol: Grown for 8 weeks in green house (16/8 h light/dark period, 20°C) in soil

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant + MG115

tag: Nicotiana tabacum, Leaf, Biotic stress


title: Ref_vs_48_3wks_1


title: Ref_vs_48_3wks_2


title: Cont_vs_C+AR_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant + aristolochic acid


title: Cont_vs_C+Nm_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant + neomycin


title: Cont_vs_C+MG_6h_2

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant


title: Cont_vs_C+La_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant + LaCl3


title: Cont_vs_C+AR_6h_2


title: Cont_vs_C+Nm_6h_2


title: Cont_vs_C+La_6h_2


title: Cont_vs_C+MG_6h_1


title: Cont_vs_C+K252_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae hrcC mutant + K252a


title: Cont_vs_C+K252a_6h_2


title: Cont_vs_C+La_6h_1


title: Cont_vs_C+AR_6h_1


title: wat_vs_PS61_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas syringae pv. syringae 61

treatment_protocol: Injected with sterile distilled water


title: Cont_vs_C+K252a_6h_1


title: wat_vs_HrcC_48h_3


title: Cont_vs_C+Nm_6h_1


title: wat_vs_TAB_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas tabaci


title: wat_vs_HrcC_6h_3


title: wat_vs_TAB_6h_2


title: wat_vs_HrcC_6h_2

growth_protocol: Green house grown, 16h light, 8h darkness

tag: Nicotiana langsdorffii x Nicotiana sanderae, Nectary, Biotic stress


title: wat_vs_PS61_6h_2

tag: Nicotiana langsdorffii x Nicotiana sanderae, Stigma, Biotic stress


title: wat_vs_HrcC_48h_2

organism: Nicotiana langsdorffii x Nicotiana sanderae


title: wat_vs_PS61_6h_1


title: wat_vs_HrcC_48h_1


title: wat_vs_TABKM_6h_3

treatment_protocol: Injected with 10^8 CFU/ml Pseudomonas tabaci inactivated with kanamycine


title: wat_vs_TABKM_6h_2


title: wat_vs_TAB_6h_1


title: wat_vs_TABKM_6h_1


title: Solanum2_ctrl_vs_drought_10_1

description: The aim of the present work is to apply microarrays to identify candidate genes associated with the strategies adopted by different Solanum wild species to maintain their metabolism and limit the harm under water stress conditions. Wild genotypes are a rich source of novel genes for introduction into cultivated species to enhance stress tolerance. The mechanisms in which genes act can involve different pathways inside the cell, resulting in the expression of stress responsive genes. We will identify genes whose expression change in the leaves of potato plants subjected to drought stress. We will analyze different Solanum genotypes in six moments of water stress (0,1,3,5,7 & 10 days after initiation of stress). We will selected 4 time-points (days 0,5,7 & 10) and 2 genotypes (with divergence behavior) for microarrays analysis. The candidate genes obtained with this approach will be validated by semi-quantitative northern blot analysis (Typhoon scanner) and/or RT-PCR in each time-point of treatment and with all wild genotypes in study. This will help us to get a better understanding respect the dynamics of expression of a great number of genes in response to stress, as well as to establish functional relations between the involved genes. Research Plan: 5-weeks-old Solanum wild species plants were randomly sorted in 2 groups (25 plants per group). One group was submitted to non-irrigated conditions, withholding water and the other was normally watered. For microarray analysis, leaflets tissue from 4 plants per group of 4 time-points (days 0,5,7, & 10) were pooled, frozen in liquid nitrogen and stored at –80°C.RNA of the pool was extracted following TRIZOL method (Invitrogen). RNA integrity was verified on agarose gel. Hybridizations were performed with n genotypes,t time-points and r repeats. The hybridizations proposed in this experiment to enhance statistical robustness of data will be: 32 slides = n*t*r ; (2 genotypes; 4 time-points; 4 repeats (dye-swap).

growth_protocol: Plants were grown 5 weeks in greenhouse (16/8h light/darkness, 65% Humidity and 25ºC) in terra nature substrate suplied by Bas Van Buuren (Holland)

treatment_protocol: To induce water stress,Solanum wild plants were randomly sorted in 2 groups. A group was submitted to non-irrigated conditions (withholding water) and the other was normally watered. Samples were collected at 0,5,7 & 10 days after the initiation of stress

tag: Solanum tuberosum, Leaves, Abiotic stress


title: wat_vs_HrcC_6h_1


title: Solanum2_ctrl_vs_drought_10_2


title: Solanum2_ctrl_vs_drought_10_3


title: Solanum2_ctrl_vs_drought_7_4


title: Solanum2_ctrl_vs_drought_5_2


title: Solanum2_ctrl_vs_drought_7_3


title: Solanum2_ctrl_vs_drought_0_1


title: Solanum2_ctrl_vs_drought_7_1


title: Solanum2_ctrl_vs_drought_0_4


title: Solanum2_ctrl_vs_drought_5_4


title: Solanum2_ctrl_vs_drought_10_4


title: Solanum2_ctrl_vs_drought_5_3


title: Solanum2_ctrl_vs_drought_0_2


title: Solanum1_ctrl_vs_drought_10_3


title: Solanum1_ctrl_vs_drought_10_1


title: Solanum2_ctrl_vs_drought_0_3


title: Solanum1_ctrl_vs_drought_7_4


title: Solanum1_ctrl_vs_drought_10_2


title: Solanum1_ctrl_vs_drought_5_3


title: Solanum1_ctrl_vs_drought_7_2


title: Solanum1_ctrl_vs_drought_5_2


title: Solanum1_ctrl_vs_drought_7_3


title: Solanum2_ctrl_vs_drought_5_1


title: Solanum2_ctrl_vs_drought_7_2


title: Solanum1_ctrl_vs_drought_10_4


title: Solanum1_ctrl_vs_drought_7_1


title: Solanum1_ctrl_vs_drought_5_4


title: Solanum1_ctrl_vs_drought_0_2


title: Solanum1_ctrl_vs_drought_0_1


title: L-IL HCC-ope9

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

hyb_protocol: HitachiSoft AceGene

scan_protocol: ScanArray G, DNASIS array v2.6

data_processing: Global Normalization

label: L-IL HCC-ope9

source_name: L-IL HCC-ope9

label_protocol: Amino Allyl MessageAmp aRNA kit (Ambion)

extract_protocol: Micro RNA isolation kit (Stratagene)

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.9

label: reference

source_name: reference

tag: peripheral blood mononuclear cells of healthy volunteer


title: Solanum1_ctrl_vs_drought_0_3


title: L-IL HCC-ope13

label: L-IL HCC-ope13

source_name: L-IL HCC-ope13

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.13


title: L-IL HCC-ope12

label: L-IL HCC-ope12

source_name: L-IL HCC-ope12

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.12


title: L-IL HCC-ope11

label: L-IL HCC-ope11

source_name: L-IL HCC-ope11

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.11


title: Solanum1_ctrl_vs_drought_0_4


title: Solanum1_ctrl_vs_drought_5_1


title: L-IL HCC-ope6

label: L-IL HCC-ope6

source_name: L-IL HCC-ope6

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.6


title: L-IL HCC-ope5

label: L-IL HCC-ope5

source_name: L-IL HCC-ope5

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.5


title: L-IL HCC-ope1

label: L-IL HCC-ope1

source_name: L-IL HCC-ope1

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.1


title: L-IL HCC-ope10

label: L-IL HCC-ope10

source_name: L-IL HCC-ope10

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.10


title: L-IL HCC-ope7

label: L-IL HCC-ope7

source_name: L-IL HCC-ope7

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.7


title: L-IL HCC-ope2

label: L-IL HCC-ope2

source_name: L-IL HCC-ope2

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.2


title: L-IL HCC-ope3

label: L-IL HCC-ope3

source_name: L-IL HCC-ope3

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.3


title: HCC-IL HCC-ope13

label: HCC-IL HCC-ope13

source_name: HCC-IL HCC-ope13

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.13


title: HCC-IL HCC-ope10

label: HCC-IL HCC-ope10

source_name: HCC-IL HCC-ope10

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.10


title: HCC-IL HCC-ope12

label: HCC-IL HCC-ope12

source_name: HCC-IL HCC-ope12

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.12


title: L-IL HCC-ope4

label: L-IL HCC-ope4

source_name: L-IL HCC-ope4

tag: Non-cancerous Liver-infiltrating Lymphocytes of HCC-ope No.4


title: HCC-IL HCC-ope11

label: HCC-IL HCC-ope11

source_name: HCC-IL HCC-ope11

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.11


title: HCC-IL HCC-ope7

label: HCC-IL HCC-ope7

source_name: HCC-IL HCC-ope7

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.7


title: HCC-IL HCC-ope6

label: HCC-IL HCC-ope6

source_name: HCC-IL HCC-ope6

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.6

label: reference

source_name: reference

tag: peripheral blood mononuclear cells of healthy volunteer


title: HCC-IL HCC-ope2

label: HCC-IL HCC-ope2

source_name: HCC-IL HCC-ope2

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.2


title: HCC28

description: Expression profile of peripheral blood mononuclear cells obtained from type C cirrhotic patients

tag: peripheral blood mononuclear cells from type C LC with HCC No.28


title: HCC-IL HCC-ope1

label: HCC-IL HCC-ope1

source_name: HCC-IL HCC-ope1

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.1


title: HCC25

tag: peripheral blood mononuclear cells from type C LC with HCC No.25


title: HCC-IL HCC-ope9

label: HCC-IL HCC-ope9

source_name: HCC-IL HCC-ope9

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.9


title: HCC-IL HCC-ope3

label: HCC-IL HCC-ope3

source_name: HCC-IL HCC-ope3

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.3


title: HCC-IL HCC-ope4

label: HCC-IL HCC-ope4

source_name: HCC-IL HCC-ope4

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.4


title: HCC24

tag: peripheral blood mononuclear cells from type C LC with HCC No.24


title: HCC29

tag: peripheral blood mononuclear cells from type C LC with HCC No.29


title: HCC-IL HCC-ope5

label: HCC-IL HCC-ope5

source_name: HCC-IL HCC-ope5

tag: Hepatocellular Carcinoma-infiltrating Lymphocytes of HCC-ope No.5


title: HCC27

tag: peripheral blood mononuclear cells from type C LC with HCC No.27


title: L.reuteri_sourdough_rep3_dyeswap2

city: Stuttgart

first: Eric

last: Huefner

address: Garbenstrasse 28

department: Food Microbiology

country: Germany

institute: University of Hohenheim

description: A comparison of Lactobacillus reuteri cells grown in chemically defined medium (CDML) and sourdough helped uncover pathways involved in the adaptation of L. reuteri to the ecological niche of sourdough.

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer.  Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight. Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC.

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner. Images were processed using GenePix Pro software (version 4.1)

data_processing: Only spots with >= 40% of pixels with fluorescence value > 1 standard deviation above the local background in at least one of the channels were considered valid. Normalization: Total fluorescence normalization. Calculation of expression ratios: fluorescence values of sourdough samples/values of CDML samples. Only genes that displayed valid values in at least two of the three biological replicates were used for further analysis. The geometric mean of the expression ratios and standard deviations were calculated and log2-transformed. For each gene, the ratio was generated using the average of three independent experiments (independently grown and prepared samples) with two replicate hybridizations. Genes with M-values (mean log2 ratio RNAdough / RNACDML) smaller than –1 (<0.5-fold expression) were considered repressed and values greater that +1 (>2-fold expression) were considered induced in sourdough as compared to CDML medium. To determine which genes differed statistically from the mean, we utilized iterative outlier analysis (Britton et al., 2002), in which three successive rounds of analysis are done to find genes with M-values greater than 2.5 standard deviations from the mean. Confidence limits of the data were calculated, including a standard error factor (distance from gene's average value to the nearest 2.5 standard deviation cut-off) and the number of standard deviations separating the spot from the 2.5 standard deviation cut-off. The M-values of outliers ranged from 5.08 (33.7-fold change) to -3.75 (0.07-fold change). Furthermore, all genes belonging to a putative operon were considered for analysis if at least one gene of the operon showed significant changes in the expression, and the remaining genes showed trends toward that expression.

organism: Limosilactobacillus reuteri

source_name: L.reuteri, exponential phase, sourdough

label_protocol: 10 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes.  Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP.  After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned.  cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Chemically defined medium CDML and sourdough (both containing 10µg/g erythromycin) were inoculated with over night cultures of L. reuteri: 1% inoculation of ripe dough and 1:100 inoculation of CDML culture, respectively. Both media were then incubated at 40°C for 3.5 h (sourdough) and to an OD600 value of 0.3 (CDML).

extract_protocol: Total RNA from L. reuteri was isolated using the Gentra Purescript RNA Isolation Kit (Gentra Systems) with modifications. L. reuteri cells (approximately 1 x 10^9 cells) were resuspended in 200 µL TE buffer containing 20 mg/ml lysozyme (SERVA) and 500 U/ml mutanolysin (Sigma-Aldrich) and incubated for 30 minutes at 37 °C. The cell suspensions were transferred to 2.0 ml screw cap tubes containing 50 mg of 0.1-mm zirconia beads (Carl Roth), and 200 µL Cell Lysis Solution (Gentra) was added. The cells were disrupted at 5,000 rpm for 5 min using the Mini-Beadbeater (BioSpec Products). 100 µL DNA/Protein Precipitation Solution (Gentra Systems) was added to the lysate and the mixture was incubated at 65 °C for 5 min. After centrifugation, the clear supernatant containing the RNA was added to 300 µL isopropanol and total RNA was harvested by centrifugation. After two washes with 70% ethanol the RNA was resuspended in RNAse-free deionized water and storage at –85 °C. The samples were treated with DNAse I (Roche Applied Science) and subsequently purified with RNeasy Mini Kit (Qiagen), both according to the manufacturers' instructions. The concentration and purity of RNA samples were determined by standard spectrophotometer measurements and agarose gel electrophoresis.

treatment_protocol: L. reuteri was grown in sourdough and CDML until exponential growth phase.

tag: strain ATCC 55730

source_name: L.reuteri, exponential phase, CDML


title: HCC26

tag: peripheral blood mononuclear cells from type C LC with HCC No.26


title: HCC22

tag: peripheral blood mononuclear cells from type C LC with HCC No.22


title: HCC18

tag: peripheral blood mononuclear cells from type C LC with HCC No.18


title: HCC30

tag: peripheral blood mononuclear cells from type C LC with HCC No.30


title: HCC21

tag: peripheral blood mononuclear cells from type C LC with HCC No.21

tag: peripheral blood mononuclear cells of healthy volunteer


title: HCC14

tag: peripheral blood mononuclear cells from type C LC with HCC No.14


title: L.reuteri_sourdough_rep2_dyeswap2


title: HCC17

tag: peripheral blood mononuclear cells from type C LC with HCC No.17


title: HCC7

tag: peripheral blood mononuclear cells from type C LC with HCC No.7


title: HCC13

tag: peripheral blood mononuclear cells from type C LC with HCC No.13


title: HCC10

tag: peripheral blood mononuclear cells from type C LC with HCC No.10


title: HCC19

tag: peripheral blood mononuclear cells from type C LC with HCC No.19


title: HCC8

tag: peripheral blood mononuclear cells from type C LC with HCC No.8


title: HCC12

tag: peripheral blood mononuclear cells from type C LC with HCC No.12


title: HCC11

tag: peripheral blood mononuclear cells from type C LC with HCC No.11


title: HCC20

tag: peripheral blood mononuclear cells from type C LC with HCC No.20


title: L.reuteri_sourdough_rep3_dyeswap1

tag: strain ATCC 55730


title: HCC23

tag: peripheral blood mononuclear cells from type C LC with HCC No.23


title: HCC15

tag: peripheral blood mononuclear cells from type C LC with HCC No.15


title: HCC16

tag: peripheral blood mononuclear cells from type C LC with HCC No.16


title: CD8+ cells 4 days with IL-21, 4 hours restim without cytokine, replicate 3

city: Bethesda

first: Keith

last: Kerstann

department: Surgery Branch

institute: National Institutes of Health

description: Biological replicate 3 of 3.  Untreated CD8+ used as control.

hyb_protocol: NCI Oligo Microarray Hybridization

scan_protocol: Scanned with Axon GenePix 4000B, images and spot values acquired with GenePix Pro 5.1.0.19

data_processing: Signal calculation: Mean Intensity minus Median Background, Normalization method: Precalculated 50th Percentile (Median), any spots designated as controls excluded

label: Cyanine 3

organism: Mus musculus

source_name: Total RNA from murine CD8+ t-cells incubated without cytokine for 4 days, restimulated without cytokine for 4 hours

label_protocol: 500ng of total RNA was used with Amino Allyl MessageAmp II reagents obtained from Ambion, Inc. following manufacture's protocols.

extract_protocol: Total RNA extracted using Trizol reagent following manufacture's protocol, followed by RNeasy column purification following manufacture's protocol.

tag: control

label: Cyanine 5

source_name: Total RNA from murine CD8+ t-cells incubated with 10ng/ml IL-21 for 4 days, restimulated without cytokine for 4 hours

tag: experimental


title: L.reuteri_sourdough_rep2_dyeswap1


title: HCC9

tag: peripheral blood mononuclear cells from type C LC with HCC No.9

tag: peripheral blood mononuclear cells of healthy volunteer


title: L.reuteri_sourdough_rep1_dyeswap2


title: HCC6

tag: peripheral blood mononuclear cells from type C LC with HCC No.6


title: HCC5

tag: peripheral blood mononuclear cells from type C LC with HCC No.5


title: CD8+ cells 4 days with IL-15, 4 hours restim without cytokine, replicate 3

source_name: Total RNA from murine CD8+ t-cells incubated with 10ng/ml IL-15 for 4 days, restimulated without cytokine for 4 hours


title: CD8+ cells 4 days with IL-2, 4 hours restim without cytokine, replicate 3

source_name: Total RNA from murine CD8+ t-cells incubated with 10ng/ml IL-2 for 4 days, restimulated without cytokine for 4 hours


title: L.reuteri_sourdough_rep1_dyeswap1


title: CD8+ cells 4 days with IL-21, 4 hours restim without cytokine, replicate 2

description: Biological replicate 2 of 3.  Untreated CD8+ used as control.


title: HCC4

tag: peripheral blood mononuclear cells from type C LC with HCC No.4


title: CD8+ cells 4 days with IL-15, 4 hours restim without cytokine, replicate 2


title: HCC3

tag: peripheral blood mononuclear cells from type C LC with HCC No.3


title: HSC#8, chip HG-U133B

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S163
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_123
Short description:			RNA extracted from whole blood cord cells of primary human hematopoietic cells.
Estimated purity:				>99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

label: Biotin

source_name: Whole blood cord cells of primary human hematopoietic cells

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

extract_protocol:
RNA prep method:				TRIzol and RNeasy
Amplification method:			T7-based
Cell purification method:			FACS-sorting
Method for estimating purity:		FACS

tag: Strain:


title: HCC1

tag: peripheral blood mononuclear cells from type C LC with HCC No.1


title: CD8+ cells 4 days with IL-2, 4 hours restim without cytokine, replicate 2


title: LC19

tag: peripheral blood mononuclear cells from type C LC No.19


title: CD8+ cells 4 days with IL-2, 4 hours restim without cytokine, replicate 1

description: Biological replicate 1 of 3.  Untreated CD8+ used as control.


title: HCC2

tag: peripheral blood mononuclear cells from type C LC with HCC No.2


title: HSC#12, chip HG-U133B


title: CD8+ cells 4 days with IL-15, 4 hours restim without cytokine, replicate 1


title: CD8+ cells 4 days with IL-21, 4 hours restim without cytokine, replicate 1


title: HSC#11, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S162
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_122
Short description:			RNA extracted from progenitor cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: Progenitor cell fraction of primary human hematopoietic cells, Cord blood

tag: Defining markers:				CD34+, CD38+


title: LC20

tag: peripheral blood mononuclear cells from type C LC No.20


title: LC18

tag: peripheral blood mononuclear cells from type C LC No.18


title: HSC#6, chip HG-U133B


title: HSC#7, chip HG-U133B


title: 12825897 - WS_stress-2 vs T8_stress-2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What is the role of the mitochondrial formate dehydrogenase in the response to drought?

hyb_protocol: T8_stress-2 Cy5 / WS_stress-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: mutant T8_stress-2

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

growth_protocol: leaf - Media = soil Hygrometry = 60% Temperature = 20°C Light = 160 microE

treatment_protocol: Name:secheress - abiotic stress - hydrometry,water:. Day 1- Stop watering the plants.The pots are weighed and the rosette diameters measured. The pot weight is checked every 2-3 days to control the water loss which must not exceed 50%. Day 8, 11 AM - the rosette diameters are measured, the pots weighed and the plants are harvested and frozen in liquid nitrogen.

tag: Arabidopsis thaliana (wassilewskija) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: wild type WS_stress-2

tag: Arabidopsis thaliana (wassilewskija)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: HSC#10, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S161
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_121
Short description:			RNA extracted from second stem cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: Second stem cell fraction of primary human hematopoietic cells, Cord blood

tag: Defining markers:				CD34+, CD38-, CD36-


title: 12836308 - T8_stress-2 vs WS_stress-2

hyb_protocol: WS_stress-2 Cy5 / T8_stress-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: HSC#3, chip HG-U133B


title: LC17

tag: peripheral blood mononuclear cells from type C LC No.17

source_name: reference


title: LC16

tag: peripheral blood mononuclear cells from type C LC No.16


title: 12836307 - WS_stress-1 vs T8_stress-1

hyb_protocol: T8_stress-1 Cy5 / WS_stress-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.

source_name: mutant T8_stress-1

source_name: wild type WS_stress-1


title: 13302328 - S19_stress-3 vs col-stress-3

hyb_protocol: col-stress-3 Cy5 / S19_stress-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

source_name: wild type col-stress-3

growth_protocol: leaf - Media : soil	 hygrometry : 60%	 Temperature : 20°C	 Light : 160 microE

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

source_name: mutant S19_stress-3

tag: Arabidopsis thaliana (columbia) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: LC14

tag: peripheral blood mononuclear cells from type C LC No.14

tag: peripheral blood mononuclear cells of healthy volunteer


title: HSC#5, chip HG-U133B


title: 12836305 - WS-1 vs T8-1

hyb_protocol: T8-1 Cy5 / WS-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.

source_name: mutant T8-1

treatment_protocol: no treatment

source_name: wild type wild type WS-1


title: 12836306 - T8_stress-1 vs WS_stress-1

hyb_protocol: WS_stress-1 Cy5 / T8_stress-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: LC15

tag: peripheral blood mononuclear cells from type C LC No.15


title: HSC#2, chip HG-U133B

tag: Strain:


title: LC12

tag: peripheral blood mononuclear cells from type C LC No.12


title: HSC#9, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S160
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_120
Short description:			RNA extracted from first stem cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: First stem cell fraction of primary human hematopoietic cells, Cord blood

tag: Defining markers:				CD34+, CD38-, Lin-


title: HSC#1, chip HG-U133B


title: 12836304 - T8-1 vs WS-1

hyb_protocol: WS-1 Cy5 / T8-1 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: HSC#4, chip HG-U133B


title: HeLa (2.5) template ds-cDNA, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S64
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_48
Short description:			HeLa (2.5) template ds-cDNA: T7 based RNA amplification from 40 ng of total RNA, and then template ds-cDNA was generated from amplified RNA.
RNA concentration:			2.0 ug/ul
Sample volume:				5.0 ul

source_name: HeLa ds-cDNA, Cervical epithelium

extract_protocol: RNA prep method:				TRIzol extraction, RNeasy purification


title: LC11

tag: peripheral blood mononuclear cells from type C LC No.11


title: LC13

tag: peripheral blood mononuclear cells from type C LC No.13


title: 13302326 - S19-3 vs col-3

hyb_protocol: col-3 Cy5 / S19-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wild type wild type col-3

source_name: mutant mutant S19-3


title: 13302327 - col-stress-3 vs S19_stress-3

hyb_protocol: S19_stress-3 Cy5 / col-stress-3 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: HeLa (1.5) template ds-cDNA, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S63
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_47
Short description:			T7-based RNA amplification from 1.0 ug of total RNA followed by the generation of template ds-cDNA from amplified RNA.
RNA concentration:			5.0 ug/ul
Sample volume:				5.0 ul


title: 13302324 - col-3 vs S19-3

hyb_protocol: S19-3 Cy5 / col-3 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: 13302323 - T8_stress-3 vs WS_stress-3

hyb_protocol: WS_stress-3 Cy5 / T8_stress-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wild type WS_stress-3

source_name: mutant T8_stress-3


title: LC10

tag: peripheral blood mononuclear cells from type C LC No.10


title: 13302066 - WS-3 vs T8-3

hyb_protocol: T8-3 Cy5 / WS-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mutant mutant T8-3

source_name: wild type wild type WS-3


title: 13302321 - WS_stress-3 vs T8_stress-3

hyb_protocol: T8_stress-3 Cy5 / WS_stress-3 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: LC7

hyb_protocol: HitachiSoft AceGene

tag: peripheral blood mononuclear cells from type C LC No.7


title: 13302067 - T8-3 vs WS-3

hyb_protocol: WS-3 Cy5 / T8-3 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.

tag: Arabidopsis thaliana (wassilewskija) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: LC9

tag: peripheral blood mononuclear cells from type C LC No.9


title: LC5

tag: peripheral blood mononuclear cells from type C LC No.5


title: LC8

tag: peripheral blood mononuclear cells from type C LC No.8


title: 3JM 3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S273
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_245
Short description:			Human myoblast differentiated 4 days.
RNA concentration:			200ng/uL
Sample volume:				15uL

source_name: differentiated myoblast/myotube, muscle

growth_protocol: Growth medium:				Differentation Media, DMEM + 2.5% horse serum

extract_protocol: RNA prep method:				Protocol not specified

tag: Gender:					Male


title: 3JM 1, chip HG-U133B


title: 3JM 2, chip HG-U133B


title: LC6

tag: peripheral blood mononuclear cells from type C LC No.6


title: HeLa total RNA, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S6
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_5
Short description:			HeLa total RNA
RNA concentration:			7.0 ug/ul
Sample volume:				10 ul

source_name: HeLa total RNA, Cervix epithelium


title: LC4

tag: peripheral blood mononuclear cells from type C LC No.4

source_name: reference


title: 2JM#3, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S268
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_244
Short description:			Undifferentiated FM95-14 human embryonic myoblasts contain myogenic stem/progenitor cells. Gene expression analysis and comparison to FM95-14 cells that have been allowed to differentiate will allow the ascertainment of genes that are implicated in myogenic lineage commitment.
Cell line clone ID:			FM95-14
RNA concentration:			200 ng/uL
Num cells for RNA prep:			2.5 x 10^6 cells
Sample volume:				10uL

source_name: Undifferentiated FM95-14 myoblast, muscle

growth_protocol:
Growth medium:				SKBM-2 (cambrex)
Media supplements:			dexamethasone, glutamine, FBS 10%, hEGF

extract_protocol: RNA prep method:				RNeasy


title: Nitrosomonas europaea_exposure to 20 uM Toluene_60min_biological rep2

city: Corvallis

first: Tyler

middle: Steven

last: Radniecki

state: OR

address: 101 Gleeson Hall

department: CBEE

institute: Oregon State University

description: the activity of nitrosomonas europaea was inhibited 50% by 20 uM toluene.

hyb_protocol: 0.16 ug/ul of six cDNA samples (three controls and three treatments) were hybridized at 60 rpm for 16 h

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 at 570 nm.

data_processing: The data was analyzed with single array analysis in GeneChip Operating Software (GCOS)

label: biotin

organism: Nitrosomonas europaea

source_name: N. europaea cultured in Batch reactor with minimal growth media containing 5 mM total ammonia and trace metals, 60 min exposure to 20 uM toluene

label_protocol: The 3’termini of the cDNA fragmentation were labeled with 7.5 mM GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: (NH4)2SO4 (5 mM) in 30 mM KH2PO4 buffer with trace metals, 700rpm, in gas-tight 2 L reactor vessels, injection of 20 uM toluene

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.

treatment_protocol: Injection of 20 uM toluene, 60min

tag: N. europaea cells cultured in 25 mM (NH4)2SO4 (50 mM of total NH4+) were harvested in mid to late exponential phase. The cells (OD600=0.07) were washed twice with 40 mM NaHPO4 (pH 7.8) to remove residual ammonia and were resuspended in 1000 ml of 50 mM HEPES buffer. The cells (500 ml) were then placed in gas-tight 1.67 L reactor vessels (Wheaton Double-sidearm Cell stir). (NH4)2SO4 (5 mM) was injected in the reactor vessels and the cultures were stirred with a magnetic stirring bar. Once the cell reached pseudo-steady state in Batch-reactor, the 1 uM CdCl2 was injected into just treatment reactor.


title: Nitrosomonas europaea_exposure to 20 uM Toluene_60min_biological rep3

source_name: N. europaea cultured in Batch reactor with minimal growth media containing 5 mM total ammonia and trace metals, 60 min exposure to 20 uM toluene.


title: 2JM#2, chip HG-U133B

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).


title: 2JM#1, chip HG-U133B


title: LC2

tag: peripheral blood mononuclear cells from type C LC No.2

tag: peripheral blood mononuclear cells of healthy volunteer


title: Nitrosomonas europaea_no toluene_control condition_60min_biological rep3

description: showed 100 % activity of nitrosomonas europaea, control condition(no inhibition), Quasi-steady state

source_name: N. europaea cultured in Batch reactor with minimal growth media containing 5 mM total ammonia and trace metals, 60 min

growth_protocol: (NH4)2SO4 (5 mM) in 30 mM KH2PO4 buffer with trace metals, 700rpm, in gas-tight 2 L reactor vessels, no injection of toluene

treatment_protocol: No injection of toluene, 60min


title: LC3

description: Expression profile of peripheral blood mononuclear cells obtained from type C cirrhotic patients

tag: peripheral blood mononuclear cells from type C LC No.3


title: Nitrosomonas europaea_exposure to 20 uM Toluene_60min_biological rep1

source_name: N. europaea cultured in Batch reactor with minimal growth media containing 5 mM total ammonia and trace metals, 60 min exposure to 20 uM benzene


title: Nitrosomonas europaea_no toluene_control condition_60min_biological rep2


title: LC1

tag: peripheral blood mononuclear cells from type C LC No.1


title: Nitrosomonas europaea_no toluene_control condition_60min_biological rep1

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was then purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.


title: Nitrosomonas europaea_no benzene_control condition_60min_biological rep3

growth_protocol: (NH4)2SO4 (5 mM) in 30 mM KH2PO4 buffer with trace metals, 700rpm, in gas-tight 2 L reactor vessels, no injection of benzene

treatment_protocol: No Injection of benzene, 60min


title: Nitrosomonas europaea_exposure to 40 uM Benzene_60min_biological rep3

description: the activity of nitrosomonas europaea was inhibited 50% by 40 uM benzene.

source_name: N. europaea cultured in Batch reactor with minimal growth media containing 5 mM total ammonia and trace metals, 60 min exposure to 40 uM benzene

growth_protocol: (NH4)2SO4 (5 mM) in 30 mM KH2PO4 buffer with trace metals, 700rpm, in gas-tight 2 L reactor vessels, injection of 40 uM benzene

treatment_protocol: Injection of 40 uM benzene, 60min


title: Nitrosomonas europaea_exposure to 40 uM Benzene_60min_biological rep2


title: LC28

tag: peripheral blood mononuclear cells from type C LC No.28


title: 1JM#2, chip HG-U133B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S267
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_243
Short description:			293FT-human embryonal kidney, To be used as human control cell line for human myoblast study.
RNA concentration:			200 ng/uL
Num cells for RNA prep:			2 x 10^6 cells
Sample volume:				5 uL

source_name: 293FT, kidney

growth_protocol:
Growth medium:				DMEM (high glucose)
Media supplements:			10% pen/strep , 10%FBS , G418 500 ug/uL

tag: Strain:


title: 1JM#3, chip HG-U133B


title: LC30

tag: peripheral blood mononuclear cells from type C LC No.30


title: Nitrosomonas europaea_exposure to 40 uM Benzene_60min_biological rep1


title: Nitrosomonas europaea_no benzene_control condition_60min_biological rep2

treatment_protocol: No injection of benzene, 60min


title: LC31

tag: peripheral blood mononuclear cells from type C LC No.31


title: LC32

tag: peripheral blood mononuclear cells from type C LC No.32


title: LC29

tag: peripheral blood mononuclear cells from type C LC No.29


title: 1JM#1, chip HG-U133B


title: Nitrosomonas europaea_no benzene_control condition_60min_biological rep1


title: LC26

tag: peripheral blood mononuclear cells from type C LC No.26


title: LC27

tag: peripheral blood mononuclear cells from type C LC No.27


title: LC24

tag: peripheral blood mononuclear cells from type C LC No.24


title: Primary Myotube MCK-cre Rb flox L, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S326
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_373
Short description:			Primary MCK-cre Rb flox myotube RNA. Day 6 in low serum differenciation conditions. Samples are ffrom 3 independent cell lines.
Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			3-6x 10^6
Sample volume:				5 ul

source_name: MCK-cre Rb flox Primary Myotube, Skeletal muscle

growth_protocol:
Growth medium:				5% horse serum DMEM
Media supplements:			2% pen/strep
Culture conditions:			37 0C, 5% Co2

extract_protocol:
RNA prep method:				Qiagen Mini
Cell purification method:			Tissue dissociation, selective plating, marker staining
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Desmin, MyoD staining

treatment_protocol: Assays to confirm viability:		Staining and TUNEL

tag: Strain:					Balb/C

tag: Gender:					Female

tag: Karyotype:				Diploid

tag: Defining markers:				MHC, muscle creatine kinase, myosine light chain


title: HSC#12, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S163
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_123
Short description:			RNA extracted from whole blood cord cells of primary human hematopoietic cells.
Estimated purity:				>99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: Whole blood cord cells of primary human hematopoietic cells


title: LC25

tag: peripheral blood mononuclear cells from type C LC No.25


title: Primary Myotube WT I, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S325
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_372
Short description:			Primary wild type myotube RNA. Day 6 in low serum differenciation conditions. Samples are ffrom 3 independent cell lines.
Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			3-6x 10^6
Sample volume:				5 ul

source_name: Wild Type Primary Myotube, Skeletal muscle


title: LC22

tag: peripheral blood mononuclear cells from type C LC No.22

tag: peripheral blood mononuclear cells of healthy volunteer


title: HSC#7, chip HG-U133A


title: LC23

tag: peripheral blood mononuclear cells from type C LC No.23


title: Primary Myoblast Rb(-) E, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S324
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_371
Short description:			Satellite cell derived primary myoblasts. Myoblasts lacking retinoblastoma gene product. Differentiation defective. Biological triplicates, !Sample_description = Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			2-3 x 10^6
Sample volume:				5 ul

source_name: pRb Null Primary Myoblasts, Skeletal muscle

growth_protocol:
Growth medium:				Hams F-10 20% FBS
Media supplements:			bFGF
Culture conditions:			37 0C, 5% Co2

extract_protocol:
RNA prep method:				Qiagen Mini
Cell purification method:			Cultured homogenous populations
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Desmin, MyoD staining

treatment_protocol: Assays to confirm viability:		Staining and trypan blue exclusion

tag: Defining markers:				MyoD, Pax7


title: HSC#11, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S162
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_122
Short description:			RNA extracted from progenitor cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: Progenitor cell fraction of primary human hematopoietic cells, Cord blood

tag: Strain:

tag: Defining markers:				CD34+, CD38+


title: HSC#8, chip HG-U133A


title: Primary Myoblast Rb(-) F, chip MOE430B


title: LC21

tag: peripheral blood mononuclear cells from type C LC No.21


title: Primary Myotube MCK-cre Rb flox K, chip MOE430B


title: Primary Myotube MCK-cre Rb flox J, chip MOE430B


title: HSC#6, chip HG-U133A


title: Primary Myotube WT G, chip MOE430B


title: HSC#3, chip HG-U133A