title: Bladder inflammatory transcriptome in response to tachykinins 2

tag: All mice in this study were sensitized with 1 µg DNP4-human serum albumin (HSA) in 1 mg alum on days 0, 7, 14, and 21, intraperitoneally (i.p.). In normal mice, this protocol induces sustained levels of IgE antibodies up to 56 days post-sensitization (20). One week after the last sensitization, cystitis was induced. Briefly, sensitized WT and NK1R-/- mice were anesthetized (ketamine 40 mg/kg and xylazine 2.5 mg/kg, i.p.), then transurethrally catheterized (24 Ga.; 3/4 in; Angiocath, Becton Dickson, Sandy, Utah), and the urine was drained by applying slight digital pressure to the lower abdomen. The urinary bladders were instilled with 200 µl of pyrogen-free saline or DNP4-OVA (1 µg/ml). One, four, and twenty-four hours after instillation, mice were sacrificed with pentobarbital (100 mg/kg, i.p.) and bladders


title: M600vs time 0 of 14C shock

status: Public on Jul 12 2005

type: mixed

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32711.gif

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

organism: Streptomyces coelicolor

source_name: gDNA M600

tag: gDNA M600

molecule: total RNA

source_name: time zero 30-->14C shock

tag: time zero 30-->14C shock


title: Control 1 Cy5-labeled total RNA

status: Public on Jun 11 2005

type: RNA

city: Baltimore

first: Djikolngar

last: Maouyo

state: MD

institute: University of Maryland Baltimore

description: High quality spotted cDNA on glass slide microarrays were purchased from the Microarray Centre of the University Health Network (Toronto, Canada). These arrays contained PCR-generated cDNA inserts of all 15,264 sequence-verified mouse ESTs, from the National Institute of Aging collection. Duplicate 100-mm diameter cDNA spots are represented on GAPS II slides (Corning, Inc.). Spot cDNA identity is tracked by composed identifiers including clone identifier, description, and Unigene, and catalogued as “M15Kv1”.

hyb_protocol: The labeled cDNAs from the control and test samples were mixed and hybridized with the mouse cDNA arrays in humidified hybridization chambers at 60°C for 18 hours. After 3-step wash, cDNA arrays were then hybridized with Cy5-coupled dendrimers at 60°C for 4 hours. http://www.genisphere.com/array_detection_home.html.

scan_protocol: Slides were read using a laser confocal scanner, the GSI Lumonics ScanArray 5000 imaging system, at 10-µm resolution set up for excitation/emission at 649/670 nm, and for acquisition of Cy5-labeled spots respectively.

data_processing: Prior to data analysis, data were normalized so that total intensity of both channels was equal using an algorithm provided by TM4-MIDAS (www.tm4.org). Relative transcript abundance was deduced from the ratio of the background-subtracted and normalized Cy5/Cy3 fluorescence intensities at each target, the so-called expression ratio. Significantly up-regulated or down-regulated genes on individual arrays were identified from frequency-log expression ratio histogram as data points that were at least ± 1.5 X standard deviation from the mean expression ratio.

organism: Mus musculus

source_name: Cortical collecting duct M-1 cells

label_protocol: Five-microgram total RNA was reverse-transcribed using oligo-dT flanked at 5’ end with capture sequences specific to fluorescent Cy5-coupled dendrimer complexes.

growth_protocol: M-1 cells derived from mouse cortical collecting duct cells (57) were grown at 37C in 5% CO2 in complete PC-1 medium (BioWhittaker, Maryland) supplemented with 100 U/ml penicillin/100 mg/ml streptomycin and 2 mM glutamine. After cells reached confluence, the PC-1 medium was replaced with a medium nominally free of steroid hormones (DMEM/F12 medium containing 2 mM glutamine, 100 U/ml penicillin G/100 mg/ml streptomycin, 10% charcoal and dextran-treated fetal bovine serum) for 24 to 36 hours.

extract_protocol: RNA samples from dexamethasone-treated and control cells were extracted with Trizol reagent, and DNA-decontaminated using DNA-free kit, commercially available (Ambion, Austin, TX).

treatment_protocol: Cells were then treated with 100 nM hydrosoluble dexamethasone for 3 hours at 37°C with 5% CO2.

tag: Mouse cortical collecting duct cells

tag: M-1 Cell line

tag: Passage number

tag: Confluent and polarized cells


title: R5 M145 OD 1 vs gDNA M145

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33159.gif

source_name: gDNA M145

tag: gDNA M145


title: Gene expression profiling of patient No. 1 (B)

status: Public on Jul 05 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
An aliquot of 20-30 x106 leukemic bone marrow cells was used to prepare total RNA applying the Trizol (Invitrogen) purification method according to the manufacturers’ instructions.
Total RNA was retro-transcribed and labeled using a MICROMAX TSA Labeling Kit (PerkinElmer). Two μg of total RNA were used in each reaction but only half of the labeled cDNA was actually hybridized to the microarrays. Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer). . Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.

Keywords = human bone marrow
Keywords = childhood leukemia
Keywords = gene expression profiling

organism: Homo sapiens

source_name: normal human bone marrow (Reference)

source_name: leukemic bone marrow of patient No. 1 (Test)


title: gDNA M145 vs RNAM600 OD1 R5

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33514.gif

source_name: RNA M600 OD1 R5

tag: RNA M600 OD1 R5


title: Mouse synovial fibroblast vehicle

status: Public on May 20 2005

city: kyoto

first: tetsuya

last: honda

country: Japan

institute: kyoto university

description:
Synovial fibroblasts were extracted from knee joints of naïve mice(DBA/1J, male 8-12 week old), and passaged 3-4 times. Cells were plated at a concentration of 1 X 106 cells/dish in 60 mm dish in 5 ml of RPMI1640 medium with 1% heat-inactivated FCS at 37°C, 5% CO2.  Cells were treated vehicle or stimulated by IL-1beta. In IL-1beta(5ng/ml) stimulated groups, indomethacin (1 μM) and iloprost (1μM) were further added either alone or in combination. After 6 hour stimulation as described above, cells were isolated and frozen by liquid nitrogen, and stored at –80°C before use. Total RNA was extracted by RNAeasy Mini Kit. The  RNA sample was labeled for hybridization onto the genechip array according to the standard affymetrix protcols.
Keywords = arthritis prostacyclin

source_name: DBA/1J_synovial fibroblast


title: Gene expression profiling of patient No. 2 (A)

description:
An aliquot of 20-30 x106 leukemic bone marrow cells was used to prepare total RNA applying the Trizol (Invitrogen) purification method according to the manufacturers’ instructions.
Total RNA was retro-transcribed and labeled using a MICROMAX TSA Labeling Kit (PerkinElmer). Two μg of total RNA were used in each reaction but only half of the labeled cDNA was actually hybridized to the microarrays. Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer). . Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = human bone marrow
Keywords = childhood leukemia
Keywords = gene expression profiling

source_name: leukemic bone marrow of patient No. 2 (Test)


title: Sucrose Hypo 15 min R5

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34026.gif

source_name: time zero

tag: time zero

source_name: 15 min

tag: 15 min


title: Mouse synovial fibroblast IL-1beta


title: 30-->14C 15 min

description:
Simple annotation: Stress, Cold-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32714.gif


title: M600vs time 0 of 37C shock

description:
Simple annotation: Stress, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32712.gif

source_name: time zero 30-->37C shock

tag: time zero 30-->37C shock


title: Mouse synovial fibroblast IL-1beta+Indomethacin+Iloprost


title: Mouse synovial fibroblast IL-1beta+Indomethacin


title: gDNA M600 vs RNA OD1 R5

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33158.gif


title: RNA M145OD 1 R5 vs RNA M600 OD1 R5

description:
Simple annotation: Stress, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33513.gif

source_name: RNA M145OD 1 R5

tag: RNA M145OD 1 R5


title: Sucrose Hypo 30 min R5

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34027.gif

source_name: 30 min

tag: 30 min


title: Sucrose Hypo 45 min R5

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34028.gif

source_name: 45 min

tag: 45 min


title: Sucrose Hypo 60 min R5

description:
Simple annotation: Stress, osmotic
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34029.gif

source_name: tine zero

tag: tine zero

source_name: 60 min

tag: 60 min


title: rrp6trf4

status: Public on Apr 28 2005

city: Paris

first: Alain

last: Jacquier

country: France

institute: Institut Pasteur

description:
rrp6∆, trf4∆ (BMA64; Mat alpha).

Grown at 30°C to OD <0.6 in YPD.

organism: Saccharomyces cerevisiae

source_name: total RNA


title: Arrocillo leaves under supplemental UV-B-3

status: Public on May 17 2005

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Field treatments used different plastic filters to screen UV-B (UV-B exclusion) or UV-B lamps (UV-B supplementation).  Solar UV-B radiation was removed to produce the minus UV-B treatment using polyester filters (PE, 100 µm clear polyester plastic; Tap Plastics, Mountain View CA).  This PE filter absorbs UV-B without significantly affecting UV-A or visible radiation (Casati and Walbot 2003).  To control for differences in wind or humidity under plastic sheeting, cellulose acetate sheeting was placed over a control group (CA, 100 µm extra clear cellulose acetate plastic, Tap Plastics); the CA sheeting transmit most radiation from sunlight. Seeds from the six maize lines were planted during summers 2002 and 2003 outdoors at the Stanford Plant Growth Facility. Approximately 14 days after sowing and 7 days after germination, 1.5 m x 3.2 m of each plastic was draped over 1 m x 2.5 m wooden frames; the excess plastic was stapled to the sides of the frames to reduce light exposure. The N and S sides were left open to allow air circulation. However, 50 cm-long curtains with the same plastic were made on the E and W sides to avoid early morning and late afternoon UV exposure.  The frames were maintained about 30 cm above the plant canopy during the course of the experiments.  Temperature and humidity in the soil and in the leaves were recorded using an infrared thermometer (Model 210ALCS microcomputer based agri-term infrared thermometer, Everest Interscience Inc., Fullerton, CA) and a relative humidity hygrometer (Thermo-Hygro 800016, Sper Scientific, Scottsdale, AZ); there were no differences among the plots. Average canopy temperatures under the filters were always within 0.5 °C of each other, and in no case were consistent differences in temperature detected between filter treatments. The same was observed when humidity was recorded; differences were <25% between treatments.  Measurements of incoming solar radiation were obtained using an Optronics model 752 spectroradiometer (Optronics Laboratories, Orlando, FL) that was calibrated against a National Bureau of Standards certified radiation source before each use. The spectrum under each filter was recorded periodically with 1 nm resolution across the entire sunlight spectrum (290 to 800 nm) to check for changes in the transmittance of the filters. Under our conditions, there were no significant reductions in transmittance after 3 weeks of exposure to solar UV-B, equivalent to the duration of our experiments.  Consequently the filters were not replaced, but as they accumulate dust and could develop small tears, we cleaned them at least every fourth day and we replaced areas with small rips. Plants were grown under the specified conditions for 21 days, adult leaf samples from adult leaf 9 or 10 were collected for experiments at 4 PM in all treatments. The experiment was repeated using different replicate plots (with at least 10 plants of each genotype per plot) to control the field variables that might influence measurements.

organism: Zea mays

source_name: leaves under supplemental UV-B

source_name: leaves under solar UV-B


title: Conico leaves under supplementary UV-B-3

source_name: leaves under supplementary UV-B


title: Mishca leaves under supplementary UV-B-3


title: Arrocillo leaves under solar UV-B-3

source_name: leaves under no UV-B


title: Mishca leaves under solar UV-B-3

description:
Field treatments used different plastic filters to screen UV-B (UV-B exclusion) or UV-B lamps (UV-B supplementation).  Solar UV-B radiation was removed to produce the minus UV-B treatment using polyester filters (PE, 100 µm clear polyester plastic; Tap Plastics, Mountain View CA).  This PE filter absorbs UV-B without significantly affecting UV-A or visible radiation (Casati and Walbot 2003).  To control for differences in wind or humidity under plastic sheeting, cellulose acetate sheeting was placed over a control group (CA, 100 µm extra clear cellulose acetate plastic, Tap Plastics); the CA sheeting transmit most radiation from sunlight. Seeds from the six maize lines were planted during summers 2002 and 2003 outdoors at the Stanford Plant Growth Facility. Approximately 14 days after sowing and 7 days after germination, 1.5 m x 3.2 m of each plastic was draped over 1 m x 2.5 m wooden frames; the excess plastic was stapled to the sides of the frames to reduce light exposure. The N and S sides were left open to allow air circulation. However, 50 cm-long curtains with the same plastic were made on the E and W sides to avoid early morning and late afternoon UV exposure.  The frames were maintained about 30 cm above the plant canopy during the course of the experiments.  Temperature and humidity in the soil and in the leaves were recorded using an infrared thermometer (Model 210ALCS microcomputer based agri-term infrared thermometer, Everest Interscience Inc., Fullerton, CA) and a relative humidity hygrometer (Thermo-Hygro 800016, Sper Scientific, Scottsdale, AZ); there were no differences among the plots. Average canopy temperatures under the filters were always within 0.5 °C of each other, and in no case were consistent differences in temperature detected between filter treatments. The same was observed when humidity was recorded; differences were <25% between treatments.  Measurements of incoming solar radiation were obtained using an Optronics model 752 spectroradiometer (Optronics Laboratories, Orlando, FL) that was calibrated against a National Bureau of Standards certified radiation source before each use. The spectrum under each filter was recorded periodically with 1 nm resolution across the entire sunlight spectrum (290 to 800 nm) to check for changes in the transmittance of the filters. Under our conditions, there were no significant reductions in transmittance after 3 weeks of exposure to solar UV-B, equivalent to the duration of our experiments.  Consequently the filters were not replaced, but as they accumulate dust and could develop small tears, we cleaned them at least every fourth day and we replaced areas with small rips. Plants were grown under the specified conditions for 21 days, adult leaf samples from adult leaf 9 or 10 were collected for experiments at 4 PM in all treatments. The experiment was repeated using different replicate plots (with at least 10 plants of each genotype per plot) to control the field variables that might influence measurements.
For experiments with supplemental UV-B radiation at the field, plants from the six lines were grown in the field for 4 weeks under natural sunlight conditions. After that, plants were illuminated by UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h, and leaf samples were collected at 4 PM immediately after the end of the light treatment; this simulates a 4-fold increase in UV-B at 305 nm compared to the Stanford field in August at noon. The bulbs were covered using CA filters to exclude wavelengths lower than 280 nm. As a control, plants were exposed for the same period of time under the same lamps covered with PE (no UV-B treatment).


title: Confite under solar UV-B-3


title: Cacahuacintle leaves under supplemental UV-B-3


title: Conico leaves under solar UV-B-3


title: Confite leaves under supplemental UV-B-3


title: W23 b,pl leaves under supplementary UV-B-3


title: W23 b,pl leaves under solar UV-B


title: control FDE

status: Public on Mar 31 2005

city: Davis

first: Farah

last: ESfandiari

institute: University of California davis

description: cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity value of less than 100. Genes whose expressions in livers from the folate deficient and ethanol fed groups were either increased or decreased by 2-fold or more (p<0.05) compared to those in livers from the control group were considered significantly changed. GeneChip cRNA probes used in GeneChip expressions were obtained by following a protocol from the manufacturer. First strand cDNA was synthesized by reverse transcription of 8 μg total RNA with superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7-oligo (dT) 24 primer (Genset Oligos, Boulder, CO), followed by second strand cDNA  synthesis. Biotin-labeled cRNA probes were generated by reverse transcription of double stranded cDNA using BioArray High yield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). The cRNA probes were purified from unincorporated nucleotides by RNeasy mini column (QIAGEN, Valencia, CA), fragmented and hybridized overnight at 680 C to the Human GeneChip array (HG U133A, Affymetrix). The hybridized probe array was stained with streptavidin phycoerythrin conjugate and scanned by the GeneArray scanner.

source_name: Pig liver


title: M4-GFP positive sorted cells sample #3

status: Public on Mar 05 2005

city: La Jolla

first: Nick

last: Reeves

address: 9500 Gilman Dr.

department: Section of Cellular and Developmental Biology

institute: University of California, San Diego

description:
Approximately 200 E(spl)m4-GFP wing imaginal discs were dissected from late third-instar larvae and collected in ice-cold PBS.  Discs were transferred to a 5-ml Falcon tube containing 1 ml of 9X trypsin-EDTA (Sigma)/1X PBS and dissociated at room temperature with gentle rocking for 2 hours and vigorous pipetting every 15 minutes for another hour.  Before sorting, the viability of the dissociated cells was confirmed by examining a small trypan blue-stained sample in a hemacytometer. The background fluorescence of wing imaginal disc cells was determined by analyzing w1118 disc cells using FACS.  All E(spl)m4-GFP wing disc cells with fluorescence greater than that of w1118 control cells (GFP-positive cells) and 100,000 cells with fluorescence below the w1118 control threshold (GFP-negative cells) were sorted directly into 600 μl of RLT lysis buffer (Qiagen).
Keywords = Proneural
Keywords = PNS
Keywords = PNC
Keywords = SOP
Lot batch = 2004163

organism: Drosophila melanogaster

source_name: M4-GFP wing disc cells


title: wild type 4 hours exposure to congo red 8 (cell wall chip)

status: Public on Mar 01 2005

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 Strain (4 hours Congo Red treatment)

source_name: BY4741 Strain (Control mRNA: no treatment)


title: M4-GFP positive sorted cells sample #2

description:
Approximately 200 E(spl)m4-GFP wing imaginal discs were dissected from late third-instar larvae and collected in ice-cold PBS.  Discs were transferred to a 5-ml Falcon tube containing 1 ml of 9X trypsin-EDTA (Sigma)/1X PBS and dissociated at room temperature with gentle rocking for 2 hours and vigorous pipetting every 15 minutes for another hour.  Before sorting, the viability of the dissociated cells was confirmed by examining a small trypan blue-stained sample in a hemacytometer. The background fluorescence of wing imaginal disc cells was determined by analyzing w1118 disc cells using FACS.  All E(spl)m4-GFP wing disc cells with fluorescence greater than that of w1118 control cells (GFP-positive cells) and 100,000 cells with fluorescence below the w1118 control threshold (GFP-negative cells) were sorted directly into 600 μl of RLT lysis buffer (Qiagen).
Keywords = Proneural
Keywords = PNS
Keywords = PNC
Keywords = SOP
Lot batch = 2002962


title: M4-GFP negative sorted cells sample #3


title: M4-GFP positive sorted cells sample #1

description:
Approximately 200 E(spl)m4-GFP wing imaginal discs were dissected from late third-instar larvae and collected in ice-cold PBS.  Discs were transferred to a 5-ml Falcon tube containing 1 ml of 9X trypsin-EDTA (Sigma)/1X PBS and dissociated at room temperature with gentle rocking for 2 hours and vigorous pipetting every 15 minutes for another hour.  Before sorting, the viability of the dissociated cells was confirmed by examining a small trypan blue-stained sample in a hemacytometer. The background fluorescence of wing imaginal disc cells was determined by analyzing w1118 disc cells using FACS.  All E(spl)m4-GFP wing disc cells with fluorescence greater than that of w1118 control cells (GFP-positive cells) and 100,000 cells with fluorescence below the w1118 control threshold (GFP-negative cells) were sorted directly into 600 μl of RLT lysis buffer (Qiagen).
Keywords = Proneural
Keywords = PNS
Keywords = PNC
Keywords = SOP
Lot batch = 2003497


title: M4-GFP negative sorted cells sample #1


title: M4-GFP negative sorted cells sample #2


title: MIN6-Sir2KD2 slide 4

status: Public on Apr 02 2005

city: St Louis

first: Andrew

middle: Alexander

last: Grimm

state: MO

address: 660 S Euclid Ave, Campus Box 8103

department: Molecular Biology and Pharmacology

institute: Washington University School of Medicine

description:
Cell culture and establishment of cell lines
The mouse pancreatic beta cell line MIN6 at passage 24 was obtained with permission from Dr. Jun-ichi Miyazaki at Osaka University (Miyazaki et al., 1990).  MIN6 cells were cultured as described previously (Miyazaki et al., 1990).  Two independent Sirt1-overexpressing MIN6 cell lines (MIN6-Sir2OE1 and Sir2OE2) were established by infection with the ecotropic pBabe-Sirt1 retrovirus carrying the mouse Sirt1 gene and a neomycin-resistant gene (Revollo et al., 2004) and selection in the presence of 280 micrograms/ml of G418 (Invitrogen).  Two control cell lines (MIN6-Neo1 and Neo2) were also established by infection with the pBabe-neo control retrovirus.  To establish Sirt1-knockdown MIN6 cell lines, small interfering RNAs (siRNAs) were designed against the Sirt1 gene, and each double-stranded siRNA template was cloned in the mU6pro vector (Yu et al., 2002, a gift from Dr. David L. Turner at University of Michigan, Ann Arbor).  Sirt1 siRNA sequences are available upon request.  Two independent Sirt1-knockdown MIN6 cell lines (MIN6-Sir2KD1 and KD2) were established by co-transfection with expression vectors carrying two different siRNAs and a neomycin-resistant marker plasmid and selection in the presence of 400 micrograms/ml G418.  A control cell line (MIN6-mU6pro) was also established using the mU6pro vector. All experimental and control cell lines were propagated carefully to ensure equivalent passage numbers and maintain healthy cellular morphology.

Microarray hybridizations and data collection
All cell lines were cultured in media containing 5 mM glucose for four days prior to RNA collection.  RNA samples were purified from two Sirt1-overexpressing (Sir2OE1 and Sir2OE2), two Sirt1-knockdown (Sir2KD1 and Sir2KD2), and three control (Neo1, Neo2 and mU6pro) MIN6 cell lines using Trizol (Sigma) according to the manufacturer’s protocol.  The quality of RNA was examined by capillary electrophoresis and denaturing agarose gel electrophoresis.  RNA from MIN6-Neo1 and Neo2 was combined prior to cDNA synthesis.  Eight micrograms of total RNA from each sample were converted to cDNA by using the 3DNA Array 350 Expression Array Detection Kit (Genisphere, PA) according to the manufacturer’s protocol.  Microarray hybridization was then conducted with Cy3- and Cy5-labeled dendrimers as described (Scearce et al., 2002) with the following modifications.  Hybridization was conducted at 42ºC for 18 h in MWG Coverslips Hybridization Buffer (MWG USA, NC), and all post-hybridization washes were carried out at 25ºC.  To increase the accuracy of the microarray analysis, we performed dye-swap experiments for each pair of cell lines (Sir2OE1 vs. Neo1+Neo2, Sir2OE2 vs. Neo1+Neo2, Sir2KD1 vs. mU6pro, and Sir2KD2 vs. mU6pro).  Microarray hybridizations were performed in duplicate for each pair with the exception that the Cy3-Cy5 labeling scheme was swapped between hybridizations, i.e., (control-Cy3, experimental-Cy5) and (experimental-Cy5, control-Cy3).  Including dye-swaps, four microarray slides were used for each pair-wise comparison.  A ScanArray Express HT scanner and accompanying software (PerkinElmer, MA) was used to scan the slides and analyze the raw data, including normalization according to the Lowess method (Yang et al., 2002).

Microarray analysis
Spots used for statistical analysis satisfied the following criteria on at least three of the slides for both sets of comparisons: (1) ScanArray Express flag = 3, (2) Signal to noise ratio (defined as (mean foreground - mean background)/(standard deviation of background)) ≥ 2 in both channels.  Spot-specific dye bias was calculated as the arithmetic mean of the log2 transform of the Lowess-normalized ratio of the medians (Yang et al., 2002) across dye-swapped pairs of hybridizations for the given set of experiments (either Sirt1 overexpression or knockdown).  The spot-specific dye bias was subtracted from the log2 transform of the Lowess-normalized median of ratios of the foreground pixels in the Cy5 and Cy3 channels to obtain the log2 transform of the “expression ratio”.  For up-regulated genes, fold changes are equivalent to the expression ratio.  For down-regulated genes, fold changes are the negative inverse of the expression ratio.  In either case, fold change = ±2^|log2(expression ratio)|.  To reduce the effect of multiple hypothesis testing, significant changes were demarcated by a difference of least 3 standard deviations (99.74% of normally distributed data) from the control.  In addition, only genes that differed by at least 1.8-fold from the control were considered.

References
Miyazaki, J.-I., Araki, K., Yamato, E., Ikegami, H., Asano, T., Shibasaki, Y., Oka, Y., and Yamamura, K. (1990). Establishment of a pancreatic beta cell line that retains glucose-inducible insulin secretion: special reference to expression of glucose transporter isoforms. Endocrinology 127, 126-132.

Revollo, J. R., Grimm, A. A., and Imai, S. (2004). The NAD biosynthesis pathway mediated by nicotinamide phosphoribosyltransferase regulates Sir2 activity in mammalian cells. J Biol Chem 279, 50754-50763.

Scearce, L. M., Brestelli, J. E., McWeeney, S. K., Lee, C. S., Mazzarelli, J., Pinney, D. F., Pizaro, A., Stoeckert Jr., C. J., Clifton, S. W., Permutt, M. A., et al. (2002). Functional genomics of the endocrine pancreas: The pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51, 1997-2004.

Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30, e15.

Yu, J.-Y., DeRuiter, S. L., and Turner, D. L. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci USA 99, 6047-6052.
Keywords = Sir2
Keywords = Sirt1
Keywords = Sir2[alpha]
Keywords = NAD-dependent deacetylase
Keywords = pancreatic ß cells
Keywords = BESTO
Keywords = beta cell-specific Sirt1-overexpressing transgenic mice
Keywords = transgenic
Keywords = glucose tolerance
Keywords = insulin secretion
Keywords = microarray
Keywords = gene expression profiling
Keywords = Ucp2
Keywords = ATP
Keywords = glucose sensitivity
Keywords = aging
Keywords = diabetes


title: Control 1

status: Public on Mar 02 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description:
Probiotics are live microorganisms known to have beneficial effects on the health of humans or animals. Although the use of probiotics has a long tradition in medicine, the molecular mechanisms behind the probiotic-host interaction remain unclear. We here report the results of a study, aimed to characterize the host gene expression program initiated by the probiotic E. coli strain Nissle 1917 (EcN) in human intestinal epithelial cells. Confluent Caco-2 cells were therefore cocultured with EcN and the E. coli K12 laboratory isolate MG1655 for 6 hours. Analysis of microarray data revealed selective expression of 126 genes after EcN treatment in comparison with the control strain. For further studies, 10 genes of major interest were chosen to confirm regulatory data by real-time RT-PCR and, if possible, by cytometric bead array (CBA) at protein level. Interestingly, treatment of Caco-2 cells with EcN significantly up-regulated genes encoding the proinflammatory molecules monocyte chemoattractant protein-1 ligand 2 (MCP-1), macrophage inflammatory protein-2 alpha (MIP-2α) and macrophage inflammatory protein-2 beta (MIP-2β), and led to expression of more than 300 pg/ml MCP-1 protein into tissue culture media. EcN-mediated gene expression of MCP-1 peaked at 6 hours. In Caco-2 cells protected from bacterial overgrowth with gentamycin, maximum gene expression of MIP-2α and MIP-2β was reached after 24 hours. We here describe a proinflammatory signaling of Caco-2 cells after EcN treatment which adds novel facts to the multifaceted probiotic-host interaction of EcN and will direct further research to fully elucidate the molecular basis of the probiotic nature of this strain.
Cell culture conditions. Caco-2 cells were maintained in IMDM cell culture medium (Invitrogen, Karlsruhe, Germany) containing 10 % fetal calf serum (PAA Laboratories, Cölbe, Germany) and 5 % penicillin/streptomycin at 37°C in a cell culture incubator. They were split twice a week at a ratio of 1:3. 4 x 105 cells per well were seeded in six well plates (Nunc, Wiesbaden, Germany) and cultured for approximately four days until confluence.

Preparation of bacteria. E. coli strain Nissle 1917 was cultured from a tablet of Mutaflor® (Ardeypharm, Herdecke, Germany), isolated from MacConkey plates (Oxoid, Wesel, Germany), serotyped and confirmed by EcN specific PCR (6). E. coli K12 MG1655 was kindly provided by Ulrich Dobrindt (Institute for Molecular Infection Biology, Würzburg, Germany). Both strains were grown overnight in Luria Bertani (LB) medium (Invitrogen) at 37 °C on a shaker. The cultures were then diluted 1:100 in 50 ml prewarmed IMDM medium with 10 % fetal calf serum and grown at 37 °C. Bacteria were harvested in late logarithmic phase, after about 5 hours at an OD600 = 1.

Cocultivation of Caco-2 cells with EcN. Confluent Caco-2 cells (~ 0.4 x 107 cells per well) were washed with phosphate buffered saline (PBS) and cultured in IMDM cell culture medium containing 10 % fetal calf serum at 37 °C in a cell culture incubator for 6 hours. Prior to RNA isolation Caco-2 cells were washed twice with PBS.

RT-PCR. RNA was extracted using TriFast FL (PEQLAB, Erlangen, Germany) according to the manufacturer’s protocol, following DNAse I digestion with DNA-free® (Ambion, Huntingdon Cambridgeshire, UK) and reversely transcribed with 200 U Superscript II® (Invitrogen) for 45 minutes at 42 °C in 20 µl assays containing 1 µl Oligo dT-primers and 10 mM deoxynucleoside triphosphates (dNTPs). Conventional PCR was performed with 250 U AmpliTaq Gold® DNA polymerase (Applied Biosystems, Darmstadt, Germany) in 20 µl assays containing 0.25 pmol primers and 0.5 mM dNTP using the following cycling conditions: activation of Taq polymerase for 10 minutes at 95 °C, followed by a first round of 10 cycles each consisting of a 30 second denaturing interval at 95 °C, a 90 second annealing step at the respective primer Tm and a primer extension at 72 °C for again 90 seconds. This first amplification step was followed by a second round of 27 cycles, consisting of 15 seconds denaturation, 45 seconds annealing and 90 seconds extension. PCR products were separated in 2 % agarose gels and visualized by ethidium-bromide staining.

DNA microarray hybridization. Quality and integrity of the total RNA isolated from approximately 1 x 106 cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). For biotinylated target synthesis, RNA was labeled using standard protocols supplied by the manufacturer (Affymetrix, Santa Clara, CA). Briefly, 5 µg total RNA was converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec, Seraing, Belgium) containing a T7 promoter. The cDNA was then used directly in an in vitro transcription reaction in the presence of biotinylated nucleotides. The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 12.5 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix HG_U133A arrays for 16 hours. After hybridization, the GeneChips were washed, stained with strepavidin-phycoerythrin and read using an Affymetrix GeneChip fluidic station and scanner.

Data analysis. Analysis of microarray data was performed using Affymetrix Microarray Suite 5.0, Affymetrix MicroDB 3.0 and the Affymetrix Data Mining Tool 3.0. For normalization all array experiments were scaled to a target intensity of 150, otherwise using the default values of the Microarray Suite. Results were filtered as follows: genes are considered strongly regulated when their fold change is greater than or equal 2 or less than or equal – 2, the statistical parameter for a significant change is less than 0.01 (change p-Value for changes called increased (I)) or greater than 0.99 (change p-Value for changes called decreased (D)). Additionally, the signal difference of a certain gene should be greater than 100. Genes are considered as weakly regulated when their fold change is greater than or equal 1.5 or less than or equal – 1.5, the statistical parameter for a significant change is less than 0.001 or greater than 0.999 and the signal difference of a certain gene should be greater than 40.

source_name: colon adenocarcinoma cellline


title: Sir2OE1 slide 3

source_name: MIN6-Neo1 + MIN6-Neo2


title: wild type 4 hours exposure to congo red 7 (cell wall chip)


title: Sir2OE2 slide 3


title: Control 2


title: MIN6-Sir2KD1 slide 1


title: Sir2OE2 slide 1


title: wild type 4 hours exposure to congo red 12 (cell wall chip)


title: MIN6-Sir2KD1 slide 3


title: Coculture Nissle 6h_2

description:
Probiotics are live microorganisms known to have beneficial effects on the health of humans or animals. Although the use of probiotics has a long tradition in medicine, the molecular mechanisms behind the probiotic-host interaction remain unclear. We here report the results of a study, aimed to characterize the host gene expression program initiated by the probiotic E. coli strain Nissle 1917 (EcN) in human intestinal epithelial cells. Confluent Caco-2 cells were therefore cocultured with EcN and the E. coli K12 laboratory isolate MG1655 for 6 hours. Analysis of microarray data revealed selective expression of 126 genes after EcN treatment in comparison with the control strain. For further studies, 10 genes of major interest were chosen to confirm regulatory data by real-time RT-PCR and, if possible, by cytometric bead array (CBA) at protein level. Interestingly, treatment of Caco-2 cells with EcN significantly up-regulated genes encoding the proinflammatory molecules monocyte chemoattractant protein-1 ligand 2 (MCP-1), macrophage inflammatory protein-2 alpha (MIP-2α) and macrophage inflammatory protein-2 beta (MIP-2β), and led to expression of more than 300 pg/ml MCP-1 protein into tissue culture media. EcN-mediated gene expression of MCP-1 peaked at 6 hours. In Caco-2 cells protected from bacterial overgrowth with gentamycin, maximum gene expression of MIP-2α and MIP-2β was reached after 24 hours. We here describe a proinflammatory signaling of Caco-2 cells after EcN treatment which adds novel facts to the multifaceted probiotic-host interaction of EcN and will direct further research to fully elucidate the molecular basis of the probiotic nature of this strain.
Cell culture conditions. Caco-2 cells were maintained in IMDM cell culture medium (Invitrogen, Karlsruhe, Germany) containing 10 % fetal calf serum (PAA Laboratories, Cölbe, Germany) and 5 % penicillin/streptomycin at 37°C in a cell culture incubator. They were split twice a week at a ratio of 1:3. 4 x 105 cells per well were seeded in six well plates (Nunc, Wiesbaden, Germany) and cultured for approximately four days until confluence.

Preparation of bacteria. E. coli strain Nissle 1917 was cultured from a tablet of Mutaflor® (Ardeypharm, Herdecke, Germany), isolated from MacConkey plates (Oxoid, Wesel, Germany), serotyped and confirmed by EcN specific PCR (6). E. coli K12 MG1655 was kindly provided by Ulrich Dobrindt (Institute for Molecular Infection Biology, Würzburg, Germany). Both strains were grown overnight in Luria Bertani (LB) medium (Invitrogen) at 37 °C on a shaker. The cultures were then diluted 1:100 in 50 ml prewarmed IMDM medium with 10 % fetal calf serum and grown at 37 °C. Bacteria were harvested in late logarithmic phase, after about 5 hours at an OD600 = 1.

Cocultivation of Caco-2 cells with EcN. Confluent Caco-2 cells (~ 0.4 x 107 cells per well) were washed with phosphate buffered saline (PBS) and cocultured with a bacterial MOI (multiplicity of infection) of 1 in IMDM cell culture medium containing 10 % fetal calf serum at 37 °C in a cell culture incubator for 6 hours. Prior to RNA isolation Caco-2 cells were washed twice with PBS.

RT-PCR. RNA was extracted using TriFast FL (PEQLAB, Erlangen, Germany) according to the manufacturer’s protocol, following DNAse I digestion with DNA-free® (Ambion, Huntingdon Cambridgeshire, UK) and reversely transcribed with 200 U Superscript II® (Invitrogen) for 45 minutes at 42 °C in 20 µl assays containing 1 µl Oligo dT-primers and 10 mM deoxynucleoside triphosphates (dNTPs). Conventional PCR was performed with 250 U AmpliTaq Gold® DNA polymerase (Applied Biosystems, Darmstadt, Germany) in 20 µl assays containing 0.25 pmol primers and 0.5 mM dNTP using the following cycling conditions: activation of Taq polymerase for 10 minutes at 95 °C, followed by a first round of 10 cycles each consisting of a 30 second denaturing interval at 95 °C, a 90 second annealing step at the respective primer Tm and a primer extension at 72 °C for again 90 seconds. This first amplification step was followed by a second round of 27 cycles, consisting of 15 seconds denaturation, 45 seconds annealing and 90 seconds extension. PCR products were separated in 2 % agarose gels and visualized by ethidium-bromide staining.

DNA microarray hybridization. Quality and integrity of the total RNA isolated from approximately 1 x 106 cells was controlled by running all samples on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). For biotinylated target synthesis, RNA was labeled using standard protocols supplied by the manufacturer (Affymetrix, Santa Clara, CA). Briefly, 5 µg total RNA was converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec, Seraing, Belgium) containing a T7 promoter. The cDNA was then used directly in an in vitro transcription reaction in the presence of biotinylated nucleotides. The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 12.5 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix HG_U133A arrays for 16 hours. After hybridization, the GeneChips were washed, stained with strepavidin-phycoerythrin and read using an Affymetrix GeneChip fluidic station and scanner.

Data analysis. Analysis of microarray data was performed using Affymetrix Microarray Suite 5.0, Affymetrix MicroDB 3.0 and the Affymetrix Data Mining Tool 3.0. For normalization all array experiments were scaled to a target intensity of 150, otherwise using the default values of the Microarray Suite. Results were filtered as follows: genes are considered strongly regulated when their fold change is greater than or equal 2 or less than or equal – 2, the statistical parameter for a significant change is less than 0.01 (change p-Value for changes called increased (I)) or greater than 0.99 (change p-Value for changes called decreased (D)). Additionally, the signal difference of a certain gene should be greater than 100. Genes are considered as weakly regulated when their fold change is greater than or equal 1.5 or less than or equal – 1.5, the statistical parameter for a significant change is less than 0.001 or greater than 0.999 and the signal difference of a certain gene should be greater than 40.


title: Sir2OE2 slide 4


title: Tiling microarray analysis of rice japonica chromosome 10 forward strand ,stressed

status: Public on Apr 09 2005

city: New Haven

first: Xing-Wang

last: Deng

state: CT

address: 165 Prospect

department: MCD Biology

institute: Yale University

description:
The cDNA target was derived from pooled poly(A)+ RNA isolated from leaves of stress-treated japonica seedlings. For stress treatment, japonica seedlings were grown for seven days on MS medium under four different conditions: (i) MS medium deprived of nitrogen, (ii) MS medium deprived of phosphorus, or (iii) supplemented with 150 mM NaCl or (iv) 100 M CdSO4. For RNA isolation, plant materials were frozen in liquid nitrogen and homogenized. Total RNA and mRNA were isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen), respectively. First-strand cDNA was generated from 4 µg poly(A)+ RNA with SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA). The cDNAs were precipitated in ethanol:isopropanol (1:1 v/v) and resuspended in 0.1 M NaHCO3 to facilitate coupling of Alexa Fluor 555 NHS esters (Molecular Probes, Eugene, OR) to the reactive groups of the amino-allyl dUTPs and were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ). Microarrays were hybridized with 4 µg labeled cDNA in 300 µL hybridization buffer (50 mM MES, 0.5 M NaCl, 10 mM EDTA, and 0.005% (v/v) Tween-20) for 16 hours at 50°C in disposable adhesive chambers (Grace BioLabs, Bend, OR) in a hybridization oven with constant agitation. Hybridized arrays were washed on an orbital platform in non-stringent buffer (6× SSPE, 0.01% [v/v] Tween-20) for 10 minutes at room temperature, then in stringent buffer (100 mM MES, 0.1 M NaCl, 0.01% Tween-20) for 30 minutes at 45°C. This was followed by a 5-minute wash in non-stringent buffer and a 2-minute wash in 0.1X SSC. The arrays were dried with compressed nitrogen and scanned with an Axon 4000B laser scanner at 5 µm resolution. The fluorescence intensity data were extracted with the NimbleScan software (NimbleGen Systems, Madison, WI).
Keywords = Rice
Keywords = poly(A)+ RNA
Keywords = stress

organism: Oryza sativa

source_name: Poly(A)+ RNA derived from rice seedlings undergone mineral/nutrient disturbances.


title: Sir2OE2 slide 2


title: Sir2OE1 slide 1

source_name: MIN6-NEO1 + MIN6-NEO2


title: Sir2OE1 slide 2


title: MIN6-Sir2KD2 slide 1


title: wild type 4 hours exposure to congo red 9 (cell wall chip)


title: MIN6-Sir2KD2 slide 3


title: wild type 4 hours exposure to congo red 6 (cell wall chip)


title: MIN6-Sir2KD2 slide 2


title: wild type 4 hours exposure to congo red 3 (cell wall chip)


title: wild type 4 hours exposure to congo red 11 (cell wall chip)


title: hog1 mutant 4 hours exposure to congo red 4

description: S. cerevisiae hog1Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 -hog1 Strain (4 hours Congo Red treatment)

source_name: BY4741 -hog1 Strain (Control mRNA: no treatment)


title: hog1 mutant 4 hours exposure to congo red 2


title: hog1 mutant 4 hours exposure to congo red 3


title: hog1 mutant 4 hours exposure to congo red 1


title: wild type 4 hours exposure to congo red 4 (cell wall chip)


title: wild type 4 hours exposure to congo red 10 (cell wall chip)


title: Tiling microarray analysis of rice japonica chromosome 10 reverse strand, stressed


title: MIN6-Sir2KD1 slide 2


title: Coculture Nissle 6h_1


title: wild type 4 hours exposure to congo red 2 (cell wall chip)


title: Cold-Hardened Sample 2

status: Public on Jan 20 2005

city: St. Louis

first: Kelsi

last: Rotter

address: 4444 Forest Park Pkwy.

department: Genetics

description:
Five week old non-hardened (NH) plants were cold-hardened (CH) at 3°C for three weeks. Total RNA was prepared from 100 mg of wheat crown tissue collected from a single plant. RNA was isolated using the Qiagen RNeasy Plant Mini Kit, DNA was degraded using the Qiagen RNase-Free DNase Set and RNA cleanup was performed with the RNeasy MinElute Cleanup Kit.

Hybridization probes were prepared according to Affymetrix protocols. In brief, cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) and T7(dT)24Primer (Operon) then purified with the GeneChip Sample Cleanup Module (Affymetrix). The Enzo BioArray HighYield RNA Transcript Labeling Kit was used to generate biotin-labeled cRNA target which was subsequently purified and fragmented with the Genechip Sample Cleanup module. Targets were transported to the Siteman Cancer Center Gene Chip Facility, Washington University School of Medicine, St. Louis, MO where 15 µg of target was hybridized, washed, stained and scanned on Affymetrix instruments following Affymetrix protocols.

Keywords = wheat
Keywords = crowns
Keywords = cold tolerance
Keywords = freezing resistance
Keywords = Triticum aestivum L. cv Jackson
Lot batch = 4002177

organism: Triticum aestivum

source_name: Crown


title: Cold-Hardened Sample 1


title: Subzero-Hardened Sample 1

description:
Five week old non-hardened (NH) plants were cold-hardened (CH) at 3°C for three weeks then subzero-hardened (SZH) at -3°C for three days. Total RNA was prepared from 100 mg of wheat crown tissue collected from a single plant. RNA was isolated using the Qiagen RNeasy Plant Mini Kit, DNA was degraded using the Qiagen RNase-Free DNase Set and RNA cleanup was performed with the RNeasy MinElute Cleanup Kit.

Hybridization probes were prepared according to Affymetrix protocols. In brief, cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen) and T7(dT)24Primer (Operon) then purified with the GeneChip Sample Cleanup Module (Affymetrix). The Enzo BioArray HighYield RNA Transcript Labeling Kit was used to generate biotin-labeled cRNA target which was subsequently purified and fragmented with the Genechip Sample Cleanup module. Targets were transported to the Siteman Cancer Center Gene Chip Facility, Washington University School of Medicine, St. Louis, MO where 15 µg of target was hybridized, washed, stained and scanned on Affymetrix instruments following Affymetrix protocols.

Keywords = wheat
Keywords = crowns
Keywords = cold tolerance
Keywords = freezing resistance
Keywords = Triticum aestivum L. cv Jackson
Lot batch = 4002177


title: Muscle after 20 weeks of endurance exercise-training Sample 3

status: Public on Feb 14 2005

city: Baton Rouge

first: Margarita

last: Teran-Garcia

state: LA

address: 6400 Perkins Rd

department: Human Genomics

institute: Pennington Biomedical Research Center

description:
source1 =  Pooled RNA samples correspond to 4 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 1.7±0.3 μU/ml/min.  These individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training, the average response was –0.8±1.7 μU/ml/min. Cy3 labeled.

source2 = Pooled RNA samples correspond to 3 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.9±0.5 μU/ml/min.  These individuals had high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training, their average response was +4.4±0.5 μU/ml/min.  Cy5 labeled.

Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-46

source_name: Pooled samples (4M, 4F) after exercise-training with no changes on insulin sensitivity response (LSIR)

source_name: Pooled samples (3M, 4F) after exercise-training with improved insulin sensitivity response (HSIR)


title: Muscle after 20 weeks of endurance exercise-training Sample 2

description:
source1 =  Pooled RNA samples correspond to 4 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 1.7±0.3 μU/ml/min.  These individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training, the average response was –0.8±1.7 μU/ml/min. Cy5 labeled.

source2 = Pooled RNA samples correspond to 3 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.9±0.5 μU/ml/min.  These individuals had high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training, their average response was +4.4±0.5 μU/ml/min.  Cy3 labeled.

Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-47


title: Muscle after 20 weeks of endurance exercise-training Sample1

description:
source1 =  Pooled RNA samples correspond to 4 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 1.7±0.3 μU/ml/min.  These individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training, the average response was –0.8±1.7 μU/ml/min. Cy3 labeled.

source2 = Pooled RNA samples correspond to 3 males and 4 females after 20 weeks of endurance exercise-training, with the following characteristics (mean±sd): age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.9±0.5 μU/ml/min.  These individuals had high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training, their average response was +4.4±0.5 μU/ml/min.  Cy5 labeled.

Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-49


title: Arrocillo leaves under supplementary UV-B-2

description: Field treatments used different plastic filters to screen UV-B (UV-B exclusion) or UV-B lamps (UV-B supplementation).  Solar UV-B radiation was removed to produce the minus UV-B treatment using polyester filters (PE, 100 µm clear polyester plastic; Tap Plastics, Mountain View CA).  This PE filter absorbs UV-B without significantly affecting UV-A or visible radiation (Casati and Walbot 2003).  To control for differences in wind or humidity under plastic sheeting, cellulose acetate sheeting was placed over a control group (CA, 100 µm extra clear cellulose acetate plastic, Tap Plastics); the CA sheeting transmit most radiation from sunlight. Seeds from the six maize lines were planted during summers 2002 and 2003 outdoors at the Stanford Plant Growth Facility. Approximately 14 days after sowing and 7 days after germination, 1.5 m x 3.2 m of each plastic was draped over 1 m x 2.5 m wooden frames; the excess plastic was stapled to the sides of the frames to reduce light exposure. The N and S sides were left open to allow air circulation. However, 50 cm-long curtains with the same plastic were made on the E and W sides to avoid early morning and late afternoon UV exposure.  The frames were maintained about 30 cm above the plant canopy during the course of the experiments.  Temperature and humidity in the soil and in the leaves were recorded using an infrared thermometer (Model 210ALCS microcomputer based agri-term infrared thermometer, Everest Interscience Inc., Fullerton, CA) and a relative humidity hygrometer (Thermo-Hygro 800016, Sper Scientific, Scottsdale, AZ); there were no differences among the plots. Average canopy temperatures under the filters were always within 0.5 °C of each other, and in no case were consistent differences in temperature detected between filter treatments. The same was observed when humidity was recorded; differences were <25% between treatments.  Measurements of incoming solar radiation were obtained using an Optronics model 752 spectroradiometer (Optronics Laboratories, Orlando, FL) that was calibrated against a National Bureau of Standards certified radiation source before each use. The spectrum under each filter was recorded periodically with 1 nm resolution across the entire sunlight spectrum (290 to 800 nm) to check for changes in the transmittance of the filters. Under our conditions, there were no significant reductions in transmittance after 3 weeks of exposure to solar UV-B, equivalent to the duration of our experiments.  Consequently the filters were not replaced, but as they accumulate dust and could develop small tears, we cleaned them at least every fourth day and we replaced areas with small rips. Plants were grown under the specified conditions for 21 days, adult leaf samples from adult leaf 9 or 10 were collected for experiments at 4 PM in all treatments. The experiment was repeated using different replicate plots (with at least 10 plants of each genotype per plot) to control the field variables that might influence measurements.


title: W23 b,pl leaves under supplemental UV-B-2

source_name: leaves under supplemental UV-B


title: Subzero-Hardened Sample 2


title: Mishca leaves under supplemental UV-B

source_name: leaves under solar UV-B


title: d4-A-1

status: Public on Jan 26 2005

city: Toronto

first: Daniel

last: Kirouac

state: Ontario

department: Biomaterials and Biomedical Engineering

country: Canada

institute: University of Toronto

description:
Umbilical cord blood was lineaqge depelted using a stemsep column and cultured in serum free liquid culture for 4 days with cytokines SCF, FL, and Tpo.  Total cellular mRNA was collected by lysing cells in 500 μl Trizol Reagent (Invitrogen, Groningen, The Netherlands) for 5 min followed by addition of 100 μl chloroform. After centrifugation at 12,000 g for 15 min, the aqueous phase was collected and mixed with isopropanol to precipitate the mRNA. The mRNA pellet was then obtained by centrifugation at 12,000 g for 10 min, washed in 70% ethanol and re-suspended in sterile water. mRNA concentration was then determined using a mQuant plate reader (Biotek Instruments, Winooski, VT).

Subsequent sample preparation and hybridization was conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). Because of the limited numbers of cells that could be collected from each experiment, the Two-Cycle Target Labeling technique was used which first translates RNA into cDNA using a T7-oligo(dT) polymerase primer. The cDNA was then subjected to in vitro transcription during which biotin labeled nucleotides are incorporated into the resultant cRNA. The cRNA was then fragmented and hybridized to the Affymetrix HU133 chip set. All samples were obtained in triplicate and sent to the Ontario Genomics Innovation Centre (Ottawa Health Research Institute, Ottawa, Canada) for analysis.

replicate sample 1 of 3

source_name: cultured cord blood progenitors


title: Cacahuacintle leaves under supplemenatary UV-B-2

source_name: leaves under supplemenatary UV-B


title: Muscle at sedentary state sample 1

description:
source1 =  Pooled RNA samples (4 males, 4 females) before exercise-training.  Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 2.0±0.5 μU/ml/min.  Individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training (response average –0.8±1.7 μU/ml/min).
source2 = Pooled RNA samples (3 males, 5 females) before exercise-training. Age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.0±0.2 μU/ml/min.  Individuals with high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training (average response +4.4±0.5 μU/ml/min).
Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-72

source_name: Pooled samples (4M, 4F) sedentary state, with no changes on insulin sensitivity response (LSIR) after exercise-training

source_name: Pooled samples (3M, 5F) sedentary state, improved insulin sensitivity response (HSIR) after exercise-training


title: Arrocillo leaves under supplemental UV-B


title: Confite leaves under supplementary UV-B

source_name: leaves under supplementary UV-B


title: Muscle at sedentary state sample 2

description:
source1 =  Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 2.0±0.5 μU/ml/min.  Individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training (response average –0.8±1.7 μU/ml/min). Cy5 labeled.  Source2 = Age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.0±0.2 μU/ml/min.  Individuals with high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training (average response +4.4±0.5 μU/ml/min). Cy3 labeled.
Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-73


title: Muscle at sedentary state sample 3

description:
source1 =  Age 29.2 ±14.7 yrs, BMI  24.6 ±5.0 kg/m2, insulin sensitivity 2.0±0.5 μU/ml/min.  Individuals had no changes or lower their insulin sensitivity response (LSIR) after 20 wk of endurance exercise-training (response average –0.8±1.7 μU/ml/min). Cy5 labeled.  Source2 = Age 29.2 ±12.9 yrs, BMI  23.2 ±2.5 kg/m2,  insulin sensitivity 2.0±0.2 μU/ml/min.  Individuals with high insulin sensitivity response (HSIR) after 20 wk of endurance exercise-training (average response +4.4±0.5 μU/ml/min). Cy3 labeled.
Muscle biopsies were taken from the middle of the vastus lateralis by the percutaneous needle biopsy technique.  Frozen tissue samples were crushed in liquid nitrogen, and total RNA was extracted using the TRI Reagent followed by purification in Qiagen columns from the RNeasy kit.  Equal amounts from the individual RNA samples were used to generate RNA pools for this experiments using the HSIR (1) and LSIR (2) sources.  Pool RNA samples (2 µg, each pool) was reverse-transcribed into cDNA with reagents provided by the MICROMAX Human cDNA Microarray System.  These RNA pools were used for the biotin or fluorescein labeling to generate the cDNAs analyzed in the microarrays.  The differentially fluorescent-labeled first-strand cDNA from each source was suspended in 22 µl of hybridization solution containing 5µl of poly-A (5mg/ml), 12.5µl of 20x SSC, 0.5µl 10% SDS and 12.5µl deionized formamide, combined and hybridized to the arrays for 30-36 hrs.  The signals from specifically hybridized biotin- and fluorescein-labeled cDNAs were amplified either with streptavidin–horseradish peroxidase (HRP) and Cy5–tyramide or antifluorescein–HRP and Cy3–tyramide, respectively.  Fluorescent array images were collected with a GSI Lumonics ScanArray 5000 fluorescent scanner (Packard Biochip Technologies; Meriden, CT) and image intensity data were extracted and analyzed using the provided QuantArray V. 3.0 software (Packard Bioscience; Meriden, CT).  A uniform scale factor was applied to normalize signal intensities between Cy5 and Cy3.  LOWESS normalization was applied to account for dye variation across and between slides, and for signal intensity effects.  An in-house software program was used to perform this analysis (Details of the algorithm can be found at http://bioinfo.pbrc.edu).  Fluorescent intensities below 500 were removed, and the expression ratios were lowess transformed to obtain the log base 2 values given in the data table.
Keywords = skeletal muscle
Keywords = vastus lateralis
Keywords = healthy individuals
Lot batch = PBRC series H3-49


title: Mishca leaves under supplemental UV-B-2


title: W23 leaves under solar UV-B-2

source_name: leaves under no UV-B


title: Conico leaves under supplemental UV-B-2


title: W23 leaves under supplementary UV-B


title: Mishca leaves under solar UV-B-2


title: Confite leaves after solar UV-B-2


title: Confite leaves under supplementary UV-B-2


title: Arrocillo leaves under solar UV-B-2


title: Conico leaves under supplemental UV-B


title: Conico leaves under solar UV-B


title: Cacahuacintle leaves under solar UV-B-2


title: Cacahuacintle leaves under supplemental UV-B


title: wild type 4 hours exposure to congo red 5 (cell wall chip)

description: S. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.

source_name: BY4741 Strain (Control mRNA: no treatment)

source_name: BY4741 Strain (4 hours Congo Red treatment)


title: Conico leaves after solar UV-B


title: c64

status: Public on Dec 22 2004

description: cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity value of less than 100. Genes whose expressions in livers from the folate deficient and ethanol fed groups were either increased or decreased by 2-fold or more (p<0.05) compared to those in livers from the control group were considered significantly changed. GeneChip cRNA probes used in GeneChip expressions were obtained by following a protocol from the manufacturer. First strand cDNA was synthesized by reverse transcription of 8 μg total RNA with superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7-oligo (dT) 24 primer (Genset Oligos, Boulder, CO), followed by second strand cDNA  synthesis. Biotin-labeled cRNA probes were generated by reverse transcription of double stranded cDNA using BioArray High yield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). The cRNA probes were purified from unincorporated nucleotides by RNeasy mini column (QIAGEN, Valencia, CA), fragmented and hybridized overnight at 680 C to the Human GeneChip array (HG U133A, Affymetrix).

source_name: pig rna


title: A63

source_name: pig liver


title: Cacahuacintle leaves under solar UV-B


title: YSS89, T=40, c

status: Public on Nov 06 2004

city: Geneva

first: Stephan

middle: B.

last: Schawalder

address: Quai Ansermet 30

department: Departement of Molecular biology

country: Switzerland

institute: University of Geneva

description:
Experiment Design:
•Type of experiment: time course after GAL (galactose) induction
•Experimental factor: time, genotype
•Number of hybridizations performed in the experiment: 24 (eight conditions with three biological replicates each)

Samples used, extract preparation and labeling:
•The origin of the biological sample:
Species: S. cerevisiae
Cell type:
wild-type (YSS37, IFH1-13myc-TRP1, MATa)
UASIFH1::HIS3-UASGAL1 (YSS89, UASGAL1-IFH1-13myc-TRP1, MATa)
•Growth conditions: log phase (2x107/mL) at 30°C in YPLG medium, then addition of Galactose to 2%
•Treatments: all cells were harvested by rapid centrifugation at 4°C then flash frozen in liquid nitrogen.
•RNA extraction: RNeasy Protect mini kit (Quiagen)
•Labeling protocol(s):
cDNA synthesis using Invitrogen reagents according to Affymetrix protocol (5 µg of total RNA)
GeneChip IVT labeling kit (Affymetrix)
•External controls (spikes): according to the Affymetrix protocols
Hybridization controls
Poly-A spike controls

Keywords = IFH1
Keywords = Transcriptional control of RP genes

source_name: Yeast


title: A72


title: C61


title: FGF2 stimulation in cortical neuron culture sample 2

status: Public on Dec 15 2004

city: Glasgow

first: Tomoko

last: Iwata

address: Beatson Laboratories, Garscube Estate, Switchback Road, Bearsden

department: Division of Cancer Sciences & Molecular Pathology

country: United Kingdom

institute: Faculty of Medicine, University of Glasgow

description:
We have performed the hybridisation in triplicate using total RNA samples pooled from three independent batches of primary cortical neuron culture derived from E14.5 CD1 mouse brains on one day in vitro (1DIV). We stimulated the cells with 50 ng/ml FGF2 in the presence of 10 μg/ml heparin for 4 hours, and the expression of genes were compared to those in the absence of FGF2. The data were obtained from the three experiments with the best possible conditions and strict measures were applied for the purpose of quality control. Seventeen features representing housekeeping genes in the array (GAPDH, HPRT and S16, S9, and S8 ribosomal proteins) gave average value of Ratio of Medians (ROM), 1.20 ± 0.28, which was confirmed to be acceptable. Total RNA was extracted from cells in the growing phase by using RNA Clean (Hybaid) according to the manufacturer’s instruction and further purified with RNeasy mini kit (Qiagen). Direct labelling of 20 µg of total RNA primed with Oligo(dT) was performed in the presence of Cy-5 and Cy-3-dUTP (Amersham Pharmacia Biotech) using SuperScript II (Invitrogen). The Cy5- and Cy3-labelled cDNA samples were then mixed and purified with GFX DNA purification kit (Amersham Pharmacia Biotech). The samples were added with 1.2 µg of salmon sperm DNA and 5 µg of Poly(dA) and dried in SpeedVac at 60°C. The high-density glass microarray chips were prepared at the EMBL core facility by spotting the PCR products prepared from the NIA 15k cDNA mouse clone set. Array slides were pre-hybridized in 6x SSC, 0.5% SDS, 1% BSA at 42°C for 1 hour and incubated in a boiled water for 2 min shortly prior to hybridisation. The cDNA samples were resuspended in 15 µl of hybridisation buffer (50% formamide, 6x SSC, 0.5% SDS and 5% Denhardt’s) and denatured by incubating at 95°C for 2 min. Hybridisation was at 42oC for 16 hours. The slides were washed for 10 min each with 2 x SSC, then with 0.5 x SSC, 0.1%SDS, followed by 0.1 x SSC, 0.1%SDS, at room temperature. Scanning was performed with GenePix 4000B (Axon). Quality control was performed, firstly by eye, to confirm scanner alignment and absence of significant bubbles and scratches. Scatter plots were further used to eliminate the unacceptable hybridisation data. The multiple spike-in controls RNA template were added to the sample upon direct labelling, and the successful labelling and hybridisation was confirmed in each hybridisations. GenePix Pro grogram calculates the Normalisation Factor of each hybridisation, based on the premise that the arithmetic mean of the ratios from every feature on the given array should be equal to 1. Normalisation was therefore performed by multiplying the Factor to Ratio of Medians (ROM) in each gene. The program also identifies features that did not give good alignment to the expected spotted area as “flagged” spots, indicative of the impaired-quality hybridisation of the specific genes.
Keywords = NIA mouse 15k
Keywords = cortical neuron
Keywords = FGF

source_name: cortical neuron culture from E14.5 mouse brains treated with FGF2 and heparin

source_name: cortical neuron culture from E14.5 mouse brains treated with heparin only


title: A74

source_name: pig RNA


title: YSS89, T=60, c

description:
Experiment Design:
•Type of experiment: time course after GAL (galactose) induction
•Experimental factor: time, genotype
•Number of hybridizations performed in the experiment: 24 (eight conditions with three biological replicates each)

Samples used, extract preparation and labeling:
•The origin of the biological sample:
Species: S. cerevisiae
Cell type:
wild-type (YSS37, IFH1-13myc-TRP1, MATa)
UASIFH1::HIS3-UASGAL1 (YSS89, UASGAL1-IFH1-13myc-TRP1, MATa)
•Growth conditions: log phase (2x107/mL) at 30°C in YPLG medium, then addition of Galactose to 2%
•Treatments: all cells were harvested by rapid centrifugation at 4°C then flash frozen in liquid nitrogen.
•RNA extraction: RNeasy Protect mini kit (Quiagen)
•Labeling protocol(s):
cDNA synthesis using Invitrogen reagents according to Affymetrix protocol (5 µg of total RNA)
GeneChip IVT labeling kit (Affymetrix)
•External controls (spikes): according to the Affymetrix protocols
Hybridization controls
Poly-A spike controls
Keywords = IFH1
Keywords = Transcriptional control of RP genes


title: FGF2 stimulation in cortical neuron culture sample 1


title: YSS89, T=20, c


title: Confite leaves after solar UV-B

source_name: leaf samples without UV-B

source_name: leaf samples under solar UV-B


title: Mishca leaves solar UV-B

source_name: leaves under solar UV-B


title: YSS89, T=0, b


title: YSS89, T=30, c


title: W23b,pl leaf solar UV-B

source_name: W23b,pl leaf solar UV-B (CA)

source_name: W23b,pl leaf no UV-B (PE)


title: Arrocillo leaves under solar UV-B


title: YSS89, T=60


title: YSS89, T=0, c


title: YSS89, T=20


title: YSS89, T=30


title: YSS89, T=60, b


title: c75


title: YSS89, T=0


title: FGF2 stimulation in cortical neuron culture sample 3


title: YSS89, T=40


title: YSS89, T=40, b


title: YSS89, T=20, b


title: YSS37, T=0


title: YSS37, T=30


title: TESS181

status: Public on Jul 31 2004

city: Naples

first: Massimo

last: Zollo

state: Naples

address: Via Pietro Castellino,111

department: TIGEM/ZOLLO

institute: TIGEM (Telethon Institute of genetics and Medicine)

description: Total RNA templates ranging from 15 to 20 µg were labeled using the Amersham CyScribe First Strand cDNA Labeling Kit with the following modifications. Reverse transcription time was increased to 3 hours at 42°C. The probe was then digested with Rnase-H for 25 minutes at 37oC. To eliminate the residual RNA the reaction was then incubated with 0.25 M NaOH for 15 minutes and then neutralized with 10 μl HEPES free acid. The total cDNA synthesized was purified by Qiagen PCR purification Kit (Qiagen) according to the manufacturer instructions. After purification the amount of incorporated Cy-dyes was calculated for both Cy5 and Cy3. Labeled Cy3 and Cy5 targets were coupled in equal amounts and hybridized onto the slides. Probes with less of 50 pmoles of incorporated Cy-dyes were not used for hybridizations. The reaction of hybridization was carried in a final volume of 50 μl containing the Cy3 and Cy5 labeled cDNA probes mixed with 50% Formamide, 25% Microarray Hybridization Buffer (Amersham CyScribe First Strand cDNA Labeling Kit), 50ng/μl Poly d(A) (Sigma) and 25% H2O Rnase free. After denaturation at 92°C for 2 minutes, the probe was added to the array, covered with a coverslip, and placed in a sealed chamber to prevent evaporation. After hybridization for 48h at 42°C, the arrays were washed in solutions of decreasing ionic strength (a washing for 10 minutes at 55°C in 1.0XSSC and 0.2% SDS, two washing for 10 minutes at 55°C in 0.1XSSC and 0.2% SDS, two washing for 1 minute in 0.1XSSC and a washing for 1 minute in deionized H2O milliQ). Three independent set of experiments have been performed for every data point of cellular induction.

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) not treated

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) Retinoic Acid treated for 72 hours


title: TESS185

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) Retinoic Acid treated for 7 days


title: YSS37, T=60, b


title: TESS182


title: TESS184


title: TESSF400-2

source_name: RNA from Mouse Adult Forebrain

source_name: RNA from Mouse Telencephalon at E14.5


title: TESS180

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) Retinoic Acid treated for 96 hours


title: YSS37, T=0, c


title: TESSF395


title: YSS37, T=0, b


title: YSS37, T=60, c


title: YSS37, T=60


title: TESSF394

source_name: NSCs differenziated

source_name: NSCs undifferentiated


title: TESS183


title: YSS37, T=30, c

source_name: Yeast


title: TESS039

description: Total RNA templates ranging from 15 to 20 µg were labeled using the Amersham CyScribe First Strand cDNA Labeling Kit with the following modifications. Reverse transcription time was increased to 3 hours at 42°C. The probe was then digested with Rnase-H for 25 minutes at 37oC. To eliminate the residual RNA the reaction was then incubated with 0.25 M NaOH for 15 minutes and then neutralized with 10 μl HEPES free acid. The total cDNA synthesized was purified by Qiagen PCR purification Kit (Qiagen) according to the manufacturer instructions. After purification the amount of incorporated Cy-dyes was calculated for both Cy5 and Cy3. Labeled Cy3 and Cy5 targets were coupled in equal amounts and hybridized onto the slides. Probes with less of 50 pmoles of incorporated Cy-dyes were not used for hybridizations. The reaction of hybridization was carried in a final volume of 50 μl  containing the Cy3 and Cy5 labeled cDNA probes mixed with 50% Formamide, 25% Microarray Hybridization Buffer  (Amersham CyScribe First Strand cDNA Labeling Kit), 50ng/μl Poly d(A) (Sigma) and 25% H2O Rnase free. After denaturation at 92°C for 2 minutes, the probe was added to the array, covered with a coverslip, and placed in a sealed chamber to prevent evaporation. After hybridization for 48h at 42°C, the arrays were washed in solutions of decreasing ionic strength (a washing for 10 minutes at 55°C in 1.0XSSC and 0.2% SDS, two washing for 10 minutes at 55°C in 0.1XSSC and 0.2% SDS, two washing for 1 minute in 0.1XSSC and a washing for 1 minute in deionized H2O milliQ). Three independent set of experiments have been performed for every data point of cellular induction.

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) Retinoic Acid treated for 24 hours


title: Estradiol_LPS_1

status: Public on Aug 18 2004

city: San Antonio

first: Phillip

last: Bowman

state: TX

address: 3400 Rawley E. Chambers Ave

institute: Institute of Surgical Research

description:
Pooled first passage cryopreserved, human umbilical vein endothelial cells (HUVEC) were obtained from Cascade Biologics (Portland, OR), thawed, and cultured according to the supplier’s recommendations in Medium 200. After thawing, cells were seeded onto 0.2% gelatin coated tissue culture plates and cultivated under 95% air, 5% CO2 at 37 oC.
Confluent cells were cultured in steroids-depleted medium for 96 hrs before the addition of 17β-estradiol (17βE) or hydrocortisone (H) to 1 µM for 5 hrs. For Lipopolysaccharide (LPS) or cytokine mix (CM)-treatments, cells or pretreated with vehicle (0.1% ethanol), 1µM 17βE, or H for 1 hr were exposed to 100 ng/ml LPS or a mixture of proinflammatory cytokines (CM, 500 U/ml IL-1b, 2500 U/ml TNF-α, and 1250 U/ml IFN-γ) for 4 hours. All treatments were done in quadruplicates. At the end of treatment, total cellular RNA was isolated.

source_name: HUVEC pretreated with 1 µM 17β-estradiol for 1 hr and then 100 ng/ml LPS for 4 hrs

source_name: Human universal reference RNA (Stratagene, La Jolla, CA)


title: TESS179


title: TESS051

source_name: Murine neuroblastoma cell line Neuro2a (ATCC CCL-131) Retinoic Acid treated for 48 hours


title: TESS049


title: TESS052


title: TESS043


title: TESS041


title: Vehicle_CM_2

status: Public on Jun 19 2004

source_name: HUVEC Vehicle (0.1% ethanol) pretreatment for 1 hr and then cytokines mix for 4 hrs


title: Vehicle_CM_3


title: Vehicle_CM_1


title: TESSF393


title: Estradiol_Ctl_1

source_name: HUVEC treated with 1 µM 17β-estradiol only for 5 hrs


title: Vehicle_LPS_1

source_name: HUVEC Vehicle (0.1% ethanol) pretreatment for 1 hr and 100 ng/ml LPS for 4 hrs


title: Vehicle_LPS_4


title: 3AJZ02072561_OlfactoryBulb

status: Public on Mar 19 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: OlfactoryBulb

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

scan_protocol: standard Affymetrix procedures

label: biotin

label_protocol: Five micrograms of total RNA was used to synthesize cDNA that was then used as a template to generate biotinylated cRNA using Enzo kits.

extract_protocol: Human tissue samples were obtained from several sources: Clinomics Biosciences (Pittsfield, MA), Clontech, AllCells (Berkeley, CA), Clonetics/BioWhittaker (Walk-ersville, MD), AMS Biotechnology (Abingdon, Oxfordshire, U.K.), and the University of California at San Diego. When samples from four or more subjects were available, equal numbers of male and female subjects were used to make two independent pools; when fewer than four samples were available, RNA samples were pooled, and duplicate amplifications were performed for each pool (detailed annotation for human samples is on our web site, http:\\symatlas.gnf.org)  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).


title: Vehicle_LPS_2


title: Vehicle_CM_4


title: Vehicle_LPS_3


title: 3AJZ02060514_OlfactoryBulb

description: OlfactoryBulb


title: Vehicle_Ctl_4

source_name: HUVEC Vehicle control only (0.1% ethanol) for 5 hrs


title: 3AJZ02083089a_Uterus_Corpus


title: 3AJZ02082987A_TONGUE

description: TONGUE


title: 3AJZ02082987B_TONGUE

description: TONGUE


title: Vehicle_Ctl_3


title: 3AJZ02083092b_Skeletal_Muscle_Psoas


title: 3AJZ02083089b_Uterus_Corpus


title: Vehicle_Ctl_1

status: Public on May 14 2004


title: 3AJZ02083092a_Skeletal_Muscle_Psoas


title: 3ARS02080736e_DRG

description: DRG


title: 3AJZ02081478a_Superior_Cervical_Ganglion


title: 3AJZ02081478b_Superior_Cervical_Ganglion


title: 3AJZ02030476_pituitary

description: pituitary


title: 3AJZ02081483b_Trigeminal_Ganglion


title: 3ARS02080736f_DRG

description: DRG


title: Vehicle_Ctl_2


title: 3AJZ02022867_Pituitary

description: Pituitary


title: 3AJZ02081483a_Trigeminal_Ganglion


title: 3ARS02080772a_atrioventricular_node


title: 3ARS02080773a_ciliary_ganglion


title: 3ARS02080776a_skin

description: skin


title: 3ARS02080776b_skin

description: skin


title: WT_TC_A_30(M)d_N=2

status: Public on Sep 10 2005

city: Stanford

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Development, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16429.gif

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: WT TC reference

tag: WT TC reference

source_name: 30(M)d Adult N=2

tag: 30(M)d Adult N=2


title: 3AJZ02052302_Ovary

description: Ovary


title: 3AJZ02081482a_Appendix

description: Appendix


title: 3AJZ02041226_salivarygland

description: salivarygland


title: 3AJZ02081482b_Appendix

description: Appendix


title: 3AJZ02040823_salivarygland

description: salivarygland


title: 3AJZ02050806_Ovary

description: Ovary


title: 3AJZ02051002_AdrenalCortex

description: AdrenalCortex


title: 3ARS02080773b_ciliary_ganglion


title: 3AJZ02050802_AdrenalCortex

description: AdrenalCortex


title: 3AJZ02052108_Testi-GermCell

description: Testi-GermCell


title: 3AJZ02052305_TestiIntersitial

description: TestiIntersitial


title: 3AJZ02051707_Testi_GermCell


title: 3AJZ02052112_TestiLeydigCell

description: TestiLeydigCell


title: 3AJZ02072570_HUMANCULTUREDADIPOCYTE

description: HUMANCULTUREDADIPOCYTE


title: 3AJZ02052114_TestiSeminiferousTubule

description: TestiSeminiferousTubule


title: 3AJZ02022756_trachea

description: trachea


title: 3AJZ02060417_IsletCell

description: IsletCell


title: 3AJZ02051711_Testi_LeydigCell


title: 3AJZ02060502_Pancreas

description: Pancreas


title: 3ARS02080772b_atrioventricular_node


title: 3AJZ02022639_trachea

description: trachea


title: 3AJZ02051709_Testi_Intersitial


title: 3AJZ02060401_Pancreas

description: Pancreas


title: 3AJZ02053101_HBEC

description: HBEC


title: 3AJZ02060603_SmoothMuscle

description: SmoothMuscle


title: 3AJZ02052312_HUMANCULTUREDADIPOCYTE

description: HUMANCULTUREDADIPOCYTE


title: 3AJZ02051713_Testi_SeminiferousTubule


title: 3AJZ02052309_Islet

description: Islet


title: 3AJZ02060604_CardiacMyocytes

description: CardiacMyocytes


title: 3AJZ02053107_CardiacMyocytes

description: CardiacMyocytes


title: 3AJZ02053105_SmoothMuscle

description: SmoothMuscle


title: 3ARS0207263HB_PLACENTA

description: PLACENTA


title: 3AJZ02022872_ fetal lung

description: fetal lung

source_name: 3AJZ02022872_ fetal lung

tag: 3AJZ02022872_ fetal lung


title: 3AJZ02052323_FETALTHYROID

description: FETALTHYROID


title: 3AJZ02052217_fetalThyroid

description: fetalThyroid


title: 3AMH02030703_Uterus

description: Uterus


title: 3AMH02022604_Thyroid

description: Thyroid


title: 3AMH02030704_Prostate

description: Prostate


title: 3AJZ02021913_ UTERUS

description: UTERUS


title: 3AMH02030706_Liver

description: Liver


title: 3AJZ02021915_ LIVER

description: LIVER


title: 3AMH02030705_Lung

description: Lung


title: 3AMH02022204_Thyroid

description: Thyroid


title: 3AJZ02022643_kidney

description: kidney


title: 3AJZ02053103_HBEC

description: HBEC


title: 3AJZ02021911_ PROSTATE

description: PROSTATE

source_name: 3AJZ02021911_ PROSTATE

tag: 3AJZ02021911_ PROSTATE


title: 3ARS0207253IA_PLACENTA

description: PLACENTA


title: 3AJZ02022762_adrenal gland

description: adrenal gland

source_name: 3AJZ02022762_adrenal gland

tag: 3AJZ02022762_adrenal gland


title: 3AMH02030702_Heart

description: Heart


title: 3AJW02021805_lung

description: lung


title: 3AJZ02022224_  spinal cord

description: spinal cord

source_name: 3AJZ02022224_  spinal cord

tag: 3AJZ02022224_  spinal cord


title: 3AJZ02021909_HEART

description: HEART


title: 3AJZ02031304_fetallung

description: fetallung


title: 3AJZ02060508_CingulateCortex

description: CingulateCortex


title: 3AJZ02081480a_Pons

description: Pons


title: 3ARS02080777b_subthalamic_nucleus


title: 3AJZ02022107_  spinal cord

description: spinal cord

source_name: 3AJZ02022107_  spinal cord

tag: 3AJZ02022107_  spinal cord


title: 3AJZ02081480b_Pons

description: Pons


title: 3AJZ02022760_kidney

description: kidney


title: 3AJZ02022111_ fetal brain

description: fetal brain

source_name: 3AJZ02022111_ fetal brain

tag: 3AJZ02022111_ fetal brain


title: 3ARS02080777a_subthalamic_nucleus


title: 3AJZ02022645_adrenal gland

description: adrenal gland

source_name: 3AJZ02022645_adrenal gland

tag: 3AJZ02022645_adrenal gland


title: 3AJZ02060407_CingulateCortex

description: CingulateCortex


title: 3AJZ02061907_Hypothalamus

description: Hypothalamus


title: 3AJZ02060506_Hypothalamus

description: Hypothalamus


title: 3AJZ02031306_brainThalamus

description: brainThalamus


title: 3AJZ02052306_OccipitalLobe

description: OccipitalLobe


title: 3AJZ02022228_ fetal brain

description: fetal brain

source_name: 3AJZ02022228_ fetal brain

tag: 3AJZ02022228_ fetal brain


title: 3AJZ02062605_OccipitalLobe

description: OccipitalLobe


title: 3AJZ02053109_PrefrontalCortex

description: PrefrontalCortex


title: 3AJZ02053111_PrefrontalCortex

description: PrefrontalCortex


title: 3AJZ02040819_brainThalamus

description: brainThalamus


title: 3AJZ02081479a_Medulla_Oblongata


title: 3AJZ02031410_wholebrain

description: wholebrain


title: 3AMH02022605_Brain Amygdala

description: Brain Amygdala

source_name: 3AMH02022605_Brain Amygdala

tag: 3AMH02022605_Brain Amygdala


title: 3AJZ02022764_cerebellum

description: cerebellum


title: 3AJZ02081479b_Medulla_Oblongata


title: 3AJZ02061902_CerebellumPeduncles

description: CerebellumPeduncles


title: 3AJZ02022226_  brain, caudate nucleus

description: brain, caudate nucleus

source_name: 3AJZ02022226_  brain, caudate nucleus

tag: 3AJZ02022226_  brain, caudate nucleus


title: 3AMH02030701_Whole Brain

description: Whole Brain

source_name: 3AMH02030701_Whole Brain

tag: 3AMH02030701_Whole Brain


title: 3AJZ02051606_ParietalLobe

description: ParietalLobe