title: yellow experiment 3


title: yellow experiment 2

status: Public on Mar 01 2005

type: RNA

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 yellow 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 6h.  At this time cells were collected. Experiment was carried out hybridising the cDNA from the same RNA (from this culture) with both Cy3 and Cy5

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: BY4741 Strain (Control mRNA: no treatment)


title: Affy 2054M

city: Heidelberg

first: Joerg

last: Schlingemann

address: Technologiepark III, Im Neuenheimer Feld 280

department: Molecular Biology (B060)

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
the specimen contained > 80% tumor tissue and < 10% necrotic debris. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). Hybridization on an Affymetrix GeneChip HG-U133A array was carried out using standard Affymetrix protocols and equipment.
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = high density oligonucleotide array
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity

organism: Homo sapiens

source_name: lymph node metastasis corresponding to a primary HNSCC (oropharynx; grade 2) from a 49 year old male (sample 2056PT)


title: Human TK6 cells treated with three concentrations of BPDE or N-OH-AABP yielding 5%, 15% and 40% of toxicity

status: Public on Mar 02 2005

city: Seattle

first: Wen

last: Luo

state: WA

address: 1800 East Lake

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Material

Benzo[a]pyrene-r-7,t-8-dihydrodiol-t-9,10-epoxide(±)(anti) (BPDE) and N-hydroxy-4-acetylaminobiphenyl (N-OH-AABP) were purchased from National Cancer Institute Chemical Carcinogen Reference Standard Repository (Kansas City, MO).

Cell culture

Human lymphoblastoid line TK6 was derived from the parental human lymphoblastoid line HH4 and heterozygous for thymidine kinase (TK), an enzyme which phosphorylates thymidine and its toxic analogs in an ATP-dependent reaction. The cells were grown in spinner flasks to allow for gentle stirring.  Cells were maintained in exponential growth by daily dilution in RPMI 1640 medium supplemented with 5% donor horse serum and maintained in 37oC incubators with a 5% CO2 atmosphere.  Cell counts were taken daily using a Coulter Counter, and cultures were diluted to 4~5´105 cells/mL.  Detailed growth records were maintained and used to ascertain any effects of the treatment on growth rate.

Chemical treatment, mutagenesis and survival measurements
N-OH-AABP and BPDE stock solutions were prepared in anhydrous DMSO (99.997% purity) and used immediately. The final DMSO concentration in the culture was less than 0.1%.

Prior to mutagen treatment, the background HPRT mutant fraction was reduced. TK6 cells were first “CHAT” treated for three days, followed by two days recovery period in “THC”.  Cells were then treated with various concentrations of test chemicals such as BPDE or N-OH-AAB for up to 27 hours. Duplicate cultures were completed at each condition. Untreated cells were used as negative controls. At the end of the treatment, cells were sampled for measurement of the mutant fractions, DNA adducts level and gene expression. At 1, 9 or 27 hours after the treatment, cells were sampled for mutant fraction.  At sampling, a 100 ml aliquot from each culture was centrifuged, and cells were resuspended in fresh RPMI medium to remove test chemicals. After cells had been growing exponentially for 7 days to allow for phenotypic expression, cultures were plated to determine mutant fractions. To determine mutant fraction at HPRT or TK locus, cells were plated in the presence and absence of 6-thioguanine (6TG) or triflurothymidine (F3TdR), respectively. The mutant fraction is the ratio of the colony-forming efficiency under selective conditions to that of efficiency in the absence of selective conditions. Survival of treated cultures was calculated from back extrapolation of growth curves by comparison of the growth of treated cultures to control cultures. For analysis of gene expression and DNA adducts, two 100 ml aliquots of cells (about 5´105 cells/mL) were removed from each culture at 1, 9 or 27 hours after the treatment. Cells were collected by centrifugation, immediately frozen down in liquid nitrogen, and stored at -80oC.

DNA microarrays

Human cDNA arrays were generated in the Genomics Facility at Fred Hutchinson Cancer Research Center. Microarrays were constructed employing the first 17,569 clones from the sequence-verified ResGen Human Unigene Set comprising 31,105 clones (Research Genetics, Huntsville, AL - now Invitrogen). Although each clone was originally representative of a unique UniGene Cluster, members of these clusters have changed over time. Our review of the annotations for 521 clones indicated that redundancy of probes was approximately less than 2.5% (12/521). Clones are representative of over 20 different human tissues/organs.  The average length of the probe was 1200 ± 364 bases, with the minimum probe length being 251 bases and the maximum probe length being 2000+ bases.

For array construction, each clone insert was individually amplified using PCR. Each PCR product was then verified on the basis of size using gel electrophoresis, and purified using the Millipore Multiscreen-PCR filtration system. In some instances, re-sequencing was performed to verify the identity of clones. Purified PCR products in 3X SSC (450 mM sodium chloride and 45 mM sodium citrate, pH 7.0) were each mechanically “spotted” onto poly-lysine coated microscope slides using an OmniGrid high-precision robotic gridder (GeneMachines, San Carlo, CA).  Each clone was represented once per array.

Preparation and hybridization of cDNA probes labeled with Cy3 or Cy5

RNA was extracted using Qiagen RNeasyMaxi Kits according to the manufacturer’s instructions (Qiagen, Valencia, CA), followed by a quality test using Agilent BioAnalyzerächips. Synthesis of the labeled first strand cDNA was conducted using InVitrogen Superscript II reverse transcript system with starting material of 30 µg total RNA plus oligo-dT. The amino-allyl labeled dUTP was added to the reaction to generate amino-allyl labeled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using a Microcon–30 concentrator. Probe mixtures were evaporated in a vacuum centrifuge, and the cDNA pellet was resuspended in 4.5 µL of water. The dye coupling reactions were performed by mixing the cDNA samples with Cy3 or Cy5 dyes and incubating for 1 hour in the dark. After the reactions were quenched with hydroxylamine, Cy3 and Cy5 samples were combined for hybridization. To remove unincorporated/quenched Cy dye, a Qia-quick PCR purification kit (Qiagen) was used. The reactions were purified with Qiaquik PCR purification kits to remove the unincorporated/quenched dyes. The mixture of Cy3 and Cy5 labeled samples was dried down in a vacuum centrifuge and then brought to a volume of 20 µL with water. Millipore 0.45 µM spin columns were used to clean up after adding 20X SSC and Poly A to the mixture. Finally, the samples were stored at –20o C until ready for hybridization.

The labeled cDNAs were co-hybridized to cDNA microarrays in triplicate, including one dye swap. Slides were scanned on the GenePix 4000A Microarray Scanner at the optimal wavelength for the Cy3 and Cy5 using lasers. The fluorescence signals of each spot on the slide were analyzed and extracted with GenePix software to generate .gpr file, which was further formatted to plain .txt file for further data analysis. All the data mining steps including transformation, cleaning-up, normalization and hypothesis tests, were performed using the SAS statistical software.

Data Analysis
The mean log2 ratios of fluorescence intensities relative to untreated controls for each gene and each treatment were clustered using the J-Express Software (University of Bergen, Norway) unsupervised algorithm. Briefly, the fluorescence intensity of each spot was calculated using local median background subtraction. The relative fluorescent units (RFUs) were then normalized to the median signal (Cy3 and Cy5) for that slide. If both Cy3 and Cy5 signals were under the signal intensity of negative controls, genes were considered as not being expressed in either sample. The normalized microarray data were then analyzed at using two approaches, visualization and statistical analysis. The first of these involved a comparison of the normalized fluorescence intensity ratios, and was used only for the purpose of visualizing the data.  In this approach, the fold change in gene expression for each array feature was determined as a ratio of normalized fluorescence intensities relative to the reference sample (i.e, RFU treated/RFU untreated). We then selected a value of 2.0 in fold change in gene expression as the arbitrary cut-off for inclusion of data in clustering algorithms. The log2 gene expression ratios for all genes showing a 2-fold or greater change in gene expression at any concentration were used in unsupervised cluster analysis to generate the dendogram shown in Figure 3.  The data were also analyzed by multi-dimensional scaling using Self Organization Map techniques. The arbitrary 2-fold cut-off was selected because it is the most frequently used value for preliminary comparison of expression profiles. As illustrated in Figu

source_name: TK6 cells treated with 0.5 uM N-OH-AABP, 27 hours, cy5

source_name: wild type TK6 cells at 0 hours, cy3


title: yellow experiment 1


title: Operon 2054M vs. 2056PT (ID407)

description:
the tumor specimens contained > 80% tumor tissue and < 10% necrotic debris. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = spotted long oligonucleotide array
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity

source_name: primary HNSCC (oropharynx; grade 2) from a 49 year old male (sample 2056PT)

source_name: lymph node metastasis of the same patient (2054M)


title: Operon 2056PT vs. 2054M (ID406)


title: Operon 1732N vs. 1730PT (ID400)

description:
the tumor specimen contained > 80% tumor tissue and < 10% necrotic debris, the control specimen was surgically resected from healthy tissue surrounding the tumor. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = spotted long oligonucleotide array
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity

source_name: primary HNSCC (oropharynx; grade 2) from a 56 year old male (sample 1730PT)

source_name: healthy control tissue surrounding the tumor (sample 1732N)


title: Affy 1868PT

source_name: primary HNSCC (hypopharynx; grade 2) from a 47 year old female


title: Affy 1867N

description:
the specimen was surgically resected from healthy tissue surrounding the tumor. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). Hybridization on an Affymetrix GeneChip HG-U133A array was carried out using standard Affymetrix protocols and equipment.
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = high density oligonucleotide array
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity

source_name: normal tissue corresponding to a primary HNSCC (hypopharynx; grade 2) from a 47 year old female (sample 1868PT)


title: Operon 1868PT vs. 1867N (ID405)

source_name: healthy control tissue surrounding the tumor (sample 1867N)

source_name: primary HNSCC (hypopharynx; grade 2) from a 47 year old female (sample 1868PT)


title: Affy 2056PT

source_name: primary HNSCC (oropharynx; grade 2) from a 49 year old male


title: Operon 1710M vs. 1713PT (ID399)

source_name: primary HNSCC (hypopharynx; grade 2) from a 58 year old male (sample 1713PT)

source_name: lymph node metastasis of the same patient (1710M)


title: Operon 1805N vs. 1802PT (ID402)

source_name: primary HNSCC (hypopharynx; grade 2) from a 57 year old male (sample 1730PT)

source_name: healthy control tissue surrounding the tumor (sample 1805N)


title: Affy 1710M

source_name: lymph node metastasis corresponding to a primary HNSCC (hypopharynx; grade 2) from a 58 year old male (sample 1713PT)


title: Affy 1730PT

source_name: primary HNSCC (oropharynx; grade 2) from a 56 year old male


title: Affy 1805N

source_name: normal tissue corresponding to a primary HNSCC (hypopharynx; grade 2) from a 57 year old male (sample 1802PT)


title: Operon 1713PT vs. 1710M (ID398)


title: Operon 1867N vs. 1868PT (ID404)


title: Affy 1802PT

source_name: primary HNSCC (hypopharynx; grade 2) from a 57 year old male


title: Affy 1732N

source_name: normal tissue corresponding to a primary HNSCC (oropharynx; grade 2) from a 56 year old male (sample 1730PT)


title: Affy 1606PT

source_name: primary HNSCC (hypopharynx; grade 2) from a 48 year old male


title: Operon 1730PT vs. 1732N (ID401)

source_name: primary HNSCC (oropharynx; grade 2) from a 56 year old male (sample 1730PT)


title: Operon 1802PT vs. 1805N (ID403)


title: Affy 1713PT

source_name: primary HNSCC (hypopharynx; grade 2) from a 58 year old male


title: Operon 1607N vs. 1606PT (ID396)

source_name: primary HNSCC (hypopharynx; grade 2) from a 48 year old male (sample 1606PT)

source_name: healthy control tissue surrounding the tumor (sample 1607N)


title: Stationary Phase cells, time 0 seconds (Replicate 4)

status: Public on Feb 19 2005

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

description:
Yeast cells cultured for 7 days in YPD+A subsequently exposed to 50 uM menadione
Cells were collected every 10 seconds for 3 minutes with a final time point a 5 minutes. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixied 1:1. RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 30 µl of the hybridization solution.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were normalized to exogonus controls.
Keywords = Stationary phase yeast

source_name: Stationary Phase culture, 0 seconds

source_name: Stationary Phase and Exponental mix 1:1


title: T1.5_3DP1_BiolRep5

status: Public on Feb 25 2005

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

description: Gene expression profiling of human promyelocytic cells in response to infection with Anaplasma phagocytophilum.  Total RNA derived from 3DPI Anaplasma phagocytophilum-infected HL-60 cells labeled with A647 and Total RNA derived from 3DPI Mock-infected HL-60 cells labeled  with A546.  For each, 5 µg of total RNA was labeled using Genisphere Array900, Alexa Fluor dyes and SuperscriptII.   Slide scanned with ScanArray Express and images processed with GenePix Pro version 4.0.  Normalized log ratios VALUES determined using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) through the GenePix AutoProcessor (GPAP) website (P. Ayoubi, unpublished results).

source_name: 3DPI Anaplasma phagocytophilum-infected HL-60 cells (Biological Replicate 5)

source_name: 3DPI Mock-infected HL-60 cells (Biological Replicate 5)


title: Operon 1606PT vs. 1607N (ID397)


title: T1.4_3DP1_BiolRep4

description: Gene expression profiling of human promyelocytic cells in response to infection with Anaplasma phagocytophilum.  Total RNA derived from 3DPI Anaplasma phagocytophilum-infected HL-60 cells labeled with A647 and Total RNA derived from 3DPI Mock-infected HL-60 cells labeled  with A546.  For each, 5 µg of total RNA was labeled using Genisphere Array900, Alexa Fluor dyes and SuperscriptII.   Slide scanned with ScanArray Express and images processed with GenePix Pro version 4.0.  Normalized log ratios VALUES determined using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap) website (P. Ayoubi, unpublished results).

source_name: 3DPI Anaplasma phagocytophilum-infected HL-60 cells (Biological Replicate 4)

source_name: 3DPI Mock-infected HL-60 cells (Biological Replicate 4)


title: Stationary Phase cells, time 0 seconds (Replicate 2)


title: Stationary Phase cells, time 0 seconds (Replicate 3)


title: Stationary Phase cells, time 0 seconds (Replicate 5)


title: Affy 1607N

description:
the specimen was surgically resected  from healthy tissue surrounding the tumor. 30-50 µg of frozen tissue sample were combined with 1 µl Trizol (Invitrogen) and dispersed using an Ultra-Turrax T25 tissue homogenizer (IKA). Total RNA was extracted according to the recommendations given by the Trizol protocol and further purified on RNeasy Mini spin columns (QIAGEN). Hybridization on an Affymetrix GeneChip HG-U133A array was carried out using standard Affymetrix protocols and equipment.
Keywords = cancer
Keywords = HNSCC
Keywords = human
Keywords = high density oligonucleotide array
Keywords = comparative study
Keywords = statistics & numerical data
Keywords = sensitivity and specificity

source_name: normal tissue corresponding to a primary HNSCC (hypopharynx; grade 2) from a 48 year old male (sample 1606PT)


title: T1.2_3DP1_BiolRep2

source_name: 3DPI Anaplasma phagocytophilum-infected HL-60 cells (Biological Replicate 2)

source_name: 3DPI Mock-infected HL-60 cells (Biological Replicate 2)


title: T1.1_3DP1_BiolRep1

source_name: 3DPI Anaplasma phagocytophilum-infected HL-60 cells (Biological Replicate 1)

source_name: 3DPI Mock-infected HL-60 cells (Biological Replicate 1)


title: T1.3_3DP1_BiolRep3

source_name: 3DPI Anaplasma phagocytophilum-infected HL-60 cells (Biological Replicate 3)

source_name: 3DPI Mock-infected HL-60 cells (Biological Replicate 3)


title: Stationary Phase cells, time 160 seconds


title: Stationary Phase cells, time 0 seconds (Replicate 1)


title: Stationary Phase cells, time 170 seconds


title: Stationary Phase cells, time 110 seconds


title: Stationary Phase cells, time 120 seconds


title: Stationary Phase cells, time 150 seconds


title: Stationary Phase cells, time 300 seconds


title: Stationary Phase cells, time 60 seconds

source_name: Stationary Phase cells, time 60 seconds


title: Stationary Phase cells, time 140 seconds


title: Stationary Phase cells, time 10 seconds

source_name: Stationary Phase cells, time 10 seconds


title: Stationary Phase cells, time 30 seconds

source_name: Stationary Phase cells, time 30 seconds


title: Stationary Phase cells, time 90 seconds

source_name: Stationary Phase cells, time 90 seconds


title: Stationary Phase cells, time 80 seconds

source_name: Stationary Phase cells, time 80 seconds


title: lens250

status: Public on Feb 15 2005

city: Miami

first: Valery

middle: I.

last: Shestopalov

state: FL

department: Ophtalmology

institute: University of Miami

description:
Lenses were removed and immediately fixed using 4% paraformaldehide or methanol-based UMFIX reagent (Sakura Finetek USA, Inc.). To map the exact location of both elongating and maturing fibers on the lens slices, lenses were vibratome-sliced (Vibratome 1000, St. Louis, MO) as described previously and the GFP expression pattern was captured by confocal microscopy. For RNA extraction lens tissue was sliced into 5 micron-thick paraffin sections and microdissected using LCM (Leica Microsystems, Bannockburn, IL). The mid-saggital slices were used both for syncytium border measurements and for LCM. Control measurement (data not shown) confirmed that similar rates of shrinkage in paraformaldehyde- and UMFIX-fixed samples did not affect precision of LCM dissection.
Fiber cell samples were dissected out of 5 micron-thick slices. In one experiment we typically processed about 40 slices, which was sufficient to collect the minimum of 200 zone-specific cells pooled from P5 littermate lenses. This sample size provided a reliable representation of RNA species in experimental procedure originally designed and tested for just 1-10 cells.
Localization of the syncytium border characterized by the abrupt change of GFP labeling pattern was captured by confocal microscopy as described previously. In brief, GFP fluorescence was visualized using LSM510 instrument (Carl Zeiss, NY) equipped with an argon/krypton laser at 488 nm excitation and a 515-565 nm band pass emission filter. Physical parameters of the zones containing young and maturing fibers were measured in fixed lens slices using the morhphometric software provided by Zeiss.

Lenses were fixed in 4% paraformaldehyde/PBS and sectioned with a vibratome. Cells from elongating and maturing fiber regions were dissected out using the Leica DMLA laser capture microscope, (Leica Microsystems, Bannockburn, IL). The cut-out pieces containing captured cells were put directly into tubes containing the lysis buffer supplied in the Absolutely RNA® nanoprep kit (Stratagene, La Jolla, CA). Total RNA from the microdissected tissue sections was extracted and purified using the Absolutely RNA nanoprep kit according to the manufacturer's protocol. Caps briefly placed onto the section without laser activation were used as negative controls. Samples from several age-matched lenses were pooled together to obtain differentiation-specific samples for microarray analysis.
Target RNA amplification and labeling with Cy-3 or Cy-5 dyes from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer. Quality and size distribution of the targets were determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The Amino Allyl MessageAmp aRNA Kit is configured to incorporate the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) into the aRNA during in vitro transcription. Once purified and fragmented, the dye labeled aRNA was used for microarray hybridization.
Labeled amplified RNA was hybridized to the 22K Mouse Oligo microarrays (Agilent Technologies)) according to the manufacturer's instructions. After hybridization microarrays were washed and scanned using GenePix 4000A (Axon Instruments,Inc.).
Keywords = mouse
Keywords = lens
Keywords = eye
Keywords = fiber cells

organism: Mus musculus

source_name: Elongating fiber cells from the lens of mice (strain TgN(GFPU)5Nagy (Jackson Laboratory, Bar Harbor, ME))

source_name: Mature fiber cells from the lens of mice (strain TgN(GFPU)5Nagy (Jackson Laboratory, Bar Harbor, ME))


title: Stationary Phase cells, time 70 seconds

source_name: Stationary Phase cells, time 70 seconds

source_name: Stationary Phase and Exponental mix 1:1


title: lens249

description:
Lenses were removed and immediately fixed using 4% paraformaldehide or methanol-based UMFIX reagent (Sakura Finetek USA, Inc.). To map the exact location of both elongating and maturing fibers on the lens slices, lenses were vibratome-sliced (Vibratome 1000, St. Louis, MO) as described previously and the GFP expression pattern was captured by confocal microscopy. For RNA extraction lens tissue was sliced into 5 micron-thick paraffin sections and microdissected using LCM (Leica Microsystems, Bannockburn, IL). The mid-saggital slices were used both for syncytium border measurements and for LCM. Control measurement (data not shown) confirmed that similar rates of shrinkage in paraformaldehyde- and UMFIX-fixed samples did not affect precision of LCM dissection.
Fiber cell samples were dissected out of 5 micron-thick slices. In one experiment we typically processed about 40 slices, which was sufficient to collect the minimum of 200 zone-specific cells pooled from P5 littermate lenses. This sample size provided a reliable representation of RNA species in experimental procedure originally designed and tested for just 1-10 cells.
Localization of the syncytium border characterized by the abrupt change of GFP labeling pattern was captured by confocal microscopy as described previously. In brief, GFP fluorescence was visualized using LSM510 instrument (Carl Zeiss, NY) equipped with an argon/krypton laser at 488 nm excitation and a 515-565 nm band pass emission filter. Physical parameters of the zones containing young and maturing fibers were measured in fixed lens slices using the morhphometric software provided by Zeiss.

Lenses were fixed in 4% paraformaldehyde/PBS and sectioned with a vibratome. Cells from elongating and maturing fiber regions were dissected out using the Leica DMLA laser capture microscope, (Leica Microsystems, Bannockburn, IL). The cut-out pieces containing captured cells were put directly into tubes containing the lysis buffer supplied in the Absolutely RNA® nanoprep kit (Stratagene, La Jolla, CA). Total RNA from the microdissected tissue sections was extracted and purified using the Absolutely RNA nanoprep kit according to the manufacturer's protocol. Caps briefly placed onto the section without laser activation were used as negative controls. Samples from several age-matched lenses were pooled together to obtain differentiation-specific samples for microarray analysis.
Target RNA amplification and labeling with Cy-3 or Cy-5 dyes from CyDye Post Labelling Reactive Dye Pack (Amersham, USA) was carried out in two rounds using the Amino Allyl MessageAmp™ aRNA Kit (Ambion, USA) as specified by the manufacturer. Quality and size distribution of the targets were determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The Amino Allyl MessageAmp aRNA Kit is configured to incorporate the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) into the aRNA during in vitro transcription. Once purified and fragmented, the dye labeled aRNA was used for microarray hybridization.
Labeled amplified RNA from three different biological experiments was hybridized to the 22K Mouse Oligo microarrays (Agilent Technologies)) according to the manufacturer's instructions. For each biological replicate we performed two technical subreplicates for dye-swap. After hybridization microarrays were washed and scanned using GenePix 4000A (Axon Instruments,Inc.).


title: Stationary Phase cells, time 130 seconds


title: Stationary Phase cells, time 40 seconds

source_name: Stationary Phase cells, time 40 seconds


title: Stationary Phase cells, time 0 seconds

source_name: Stationary Phase cells, time 0 seconds


title: Stationary Phase cells, time 20 seconds

source_name: Stationary Phase cells, time 20 seconds


title: AdLacZ+vehicle JMTM16

status: Public on Feb 09 2005

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

description: Gene expression changes caused by estrogen treatment of breast cancer cells that re-express ERalpha was investigated by infecting ER-negative MDA-MB-231 breast cancer cells for 24 h with recombinant adenovirus encoding full-length human ERalpha (Ad-ERalpha) or control vector (Ad-LacZ), and treating them with 0·01% ethanol (vehicle control) or 10-8 M 17beta-estradiol (E2). After 48 h of treatment, total RNA was isolated and used for transcript profiling on Affymetrix GeneChips. Three independent biological replicates of this experiment were carried out.


title: AdLacZ+E2-8 JMTM17


title: AdLacZ+vehicle JMTM1


title: AdLacZ+E2-8 JM6


title: AdLacZ+E2-8 JMTM2


title: AdERalpha+vehicle JM1


title: AdLacZ+vehicle JM4


title: AdERalpha+vehicle JMTM4


title: AdERalpha+vehicle JMTM18


title: AdERalpha+E2-8 JM3


title: HOXA5 E1_0hr

status: Public on Feb 05 2005

city: Baltimore

first: Hexin

last: Chen

state: MD

institute: Johns Hopkins University

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from uninduced cells (0hr) of experiment one.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 1

source_name: HOXA5-inducible breast cancer cell line Hs578T


title: HOXA5 E2_9hr

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from induced cells (9hr) of experiment two.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 2


title: AdERalpha+E2-8 JMTM19


title: HOXA5 E2_0hr

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from uninduced cells (0hr) of experiment two.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 2


title: HOXA5 E1_6hr

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from induced cells (6hr) of experiment one.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 1


title: HOXA5 E1_9hr

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from induced cells (9hr) of experiment one.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 1


title: DNGH-4

status: Public on Jan 22 2005

city: Rockville

first: Maryanne

last: Vahey

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

description:
HIV seropositive drug naïve group, viral load high
Keywords = HIV, Human, PBMC, in vivo

source_name: Human PBMC


title: BW0000004, low PMT

status: Public on Feb 04 2005

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description:
Adult B. malayi worms were isolated from the peritoneal cavity of infected jirds (Meriones unguiculatus) (Mongolian gerbils) obtained from the NIAID filariasis Repository (University of Georgia, Athens GA).  Male and female worms were carefully separated by size; broken worms were discarded.  The worms were washed and immediately frozen at –80o C.<P>

Worms were crushed under liquid nitrogen with a ceramic mortar and pestle and extracted in TRIzol reagent (Invitrogen, Carlsbad, CA) as previously described [11].  The accuracy of worm gender separation was assessed by PCR with B. malayi major sperm protein primers (BmMSP) and B. malayi embryo-associated fatty acid-binding protein primers (Bm-FAB-1) [10].  RNA quality was assessed with a model 2100 Bioanalyzer (Agilent, Palo Alto, CA).
cDNA was synthesized from 5-7 ug each of male and female total RNA samples using 3DNA capture sequence primers (3DNA Array 350 Detection system, Genisphere, Hatfield, PA) and SuperScript II Reverse Transcriptase (Gibco BRL, Gaithersburg, MD) for each probe according to standard protocols.  cDNA was concentrated by Microcon YM-30 filter (Millipore). cDNA was synthesized from two different male and female RNA samples (independently prepared as biologic replicates).

A two-step protocol was used for hybridization (3DNA Array 350 Detection system, Genisphere, Hatfield, PA).   First, oligo arrays were hybridized to the cDNA probes in formamide based-hybridization buffer (MWG’s “Coverslips Hybridization buffer”) at 42C overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each.   Fluorescent Cy3- and Cy5- capture reagents were combined in MWG’s “Coverslips hybridization buffer” and added to each array.  The arrays were incubated for 3 hours at 50C and washed as above.  Each experiment consisted of a pair wise competitive hybridization of cDNA samples from female and male worms and a reciprocal dye-flip replicate.   Since biological duplicates were tested, a total of four DNA microarrays were used for comparison of the two types of cDNA.

Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer, Boston, MA) to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively.  Laser power was kept constant for Cy3/Cy5 scans, and photomultiplier tube values were 69 and 60 volts, respectively. An additional scan was done for each slide with the PMT set for 54 and 46 volts.  Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer, Boston, MA).   Each spot was defined on a pixel-by-pixel basis, using a modified Mann-Whitney statistical test.

[10]	Michalski ML, Weil GJ. Gender-specific gene expression in Brugia malayi. Mol Biochem Parasitol 1999;104:247-57.
[11]	Li BW, Rush AC, Tan J, Weil GJ. Quantitative analysis of gender-regulated transcripts in the filarial nematode Brugia malayi by real-time RT-PCR. Mol Biochem Parasitol 2004;137:329-337.
Keywords = brugia malayi nematode worm parasite filaria filariasis
Lot batch = Brugia v.1 batch 1

organism: Brugia malayi

source_name: male worms sample#2

source_name: female worms sample#2


title: BW0000004


title: BW0000003


title: HOXA5 E2_6hr

description:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
This sample is mRNA from induced cells (6hr) of experiment two.
Keywords = HOXA5 breast cancer
Lot batch = Experiment 1


title: BW0000003, low PMT


title: DNGH-2


title: DNGM-10

description:
HIV seropositive drug naïve group, viral load medium
Keywords = HIV, Human, PBMC, in vivo


title: DNGM-12


title: BW0000001

source_name: female worms sample#1

source_name: male worms sample#1


title: DNGH-1


title: BW0000002

description:
Adult B. malayi worms were isolated from the peritoneal cavity of infected jirds (Meriones unguiculatus) (Mongolian gerbils) obtained from the NIAID filariasis Repository (University of Georgia, Athens GA). Male and female worms were carefully separated by size; broken worms were discarded. The worms were washed and immediately frozen at –80o C.

Worms were crushed under liquid nitrogen with a ceramic mortar and pestle and extracted in TRIzol reagent (Invitrogen, Carlsbad, CA) as previously described [11]. The accuracy of worm gender separation was assessed by PCR with B. malayi major sperm protein primers (BmMSP) and B. malayi embryo-associated fatty acid-binding protein primers (Bm-FAB-1) [10]. RNA quality was assessed with a model 2100 Bioanalyzer (Agilent, Palo Alto, CA).
cDNA was synthesized from 5-7 ug each of male and female total RNA samples using 3DNA capture sequence primers (3DNA Array 350 Detection system, Genisphere, Hatfield, PA) and SuperScript II Reverse Transcriptase (Gibco BRL, Gaithersburg, MD) for each probe according to standard protocols. cDNA was concentrated by Microcon YM-30 filter (Millipore). cDNA was synthesized from two different male and female RNA samples (independently prepared as biologic replicates).

A two-step protocol was used for hybridization (3DNA Array 350 Detection system, Genisphere, Hatfield, PA). First, oligo arrays were hybridized to the cDNA probes in formamide based-hybridization buffer (MWG’s “Coverslips Hybridization buffer”) at 42C overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each. Fluorescent Cy3- and Cy5- capture reagents were combined in MWG’s “Coverslips hybridization buffer” and added to each array. The arrays were incubated for 3 hours at 50C and washed as above. Each experiment consisted of a pair wise competitive hybridization of cDNA samples from female and male worms and a reciprocal dye-flip replicate. Since biological duplicates were tested, a total of four DNA microarrays were used for comparison of the two types of cDNA.

Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer, Boston, MA) to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power was kept constant for Cy3/Cy5 scans, and photomultiplier tube values were 69 and 60 volts, respectively. An additional scan was done for each slide with the PMT set for 54 and 46 volts. Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer, Boston, MA). Each spot was defined on a pixel-by-pixel basis, using a modified Mann-Whitney statistical test.

[10] Michalski ML, Weil GJ. Gender-specific gene expression in Brugia malayi. Mol Biochem Parasitol 1999;104:247-57.
[11] Li BW, Rush AC, Tan J, Weil GJ. Quantitative analysis of gender-regulated transcripts in the filarial nematode Brugia malayi by real-time RT-PCR. Mol Biochem Parasitol 2004;137:329-337.
Keywords = brugia malayi nematode worm parasite filaria filariasis
Lot batch = Brugia v.1 batch 1


title: DNGM-11


title: BW0000002, low PMT


title: DNGH-3


title: DNGM-14


title: BW0000001, low PMT

description:
Adult B. malayi worms were isolated from the peritoneal cavity of infected jirds (Meriones unguiculatus) (Mongolian gerbils) obtained from the NIAID filariasis Repository (University of Georgia, Athens GA).  Male and female worms were carefully separated by size; broken worms were discarded.  The worms were washed and immediately frozen at –80o C.

Worms were crushed under liquid nitrogen with a ceramic mortar and pestle and extracted in TRIzol reagent (Invitrogen, Carlsbad, CA) as previously described [11].  The accuracy of worm gender separation was assessed by PCR with B. malayi major sperm protein primers (BmMSP) and B. malayi embryo-associated fatty acid-binding protein primers (Bm-FAB-1) [10].  RNA quality was assessed with a model 2100 Bioanalyzer (Agilent, Palo Alto, CA).
cDNA was synthesized from 5-7 ug each of male and female total RNA samples using 3DNA capture sequence primers (3DNA Array 350 Detection system, Genisphere, Hatfield, PA) and SuperScript II Reverse Transcriptase (Gibco BRL, Gaithersburg, MD) for each probe according to standard protocols.  cDNA was concentrated by Microcon YM-30 filter (Millipore). cDNA was synthesized from two different male and female RNA samples (independently prepared as biologic replicates).

A two-step protocol was used for hybridization (3DNA Array 350 Detection system, Genisphere, Hatfield, PA).   First, oligo arrays were hybridized to the cDNA probes in formamide based-hybridization buffer (MWG’s “Coverslips Hybridization buffer”) at 42C overnight and washed in a series of room temperature baths (2X SSC, 0.2% SDS; then 2X SSC, then 0.2X SSC) for 12 minutes each.   Fluorescent Cy3- and Cy5- capture reagents were combined in MWG’s “Coverslips hybridization buffer” and added to each array.  The arrays were incubated for 3 hours at 50C and washed as above.  Each experiment consisted of a pair wise competitive hybridization of cDNA samples from female and male worms and a reciprocal dye-flip replicate.   Since biological duplicates were tested, a total of four DNA microarrays were used for comparison of the two types of cDNA.

Slides were scanned immediately after hybridization on a ScanArray Express HT Scanner (Perkin Elmer, Boston, MA) to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively.  Laser power was kept constant for Cy3/Cy5 scans, and photomultiplier tube values were 69 and 60 volts, respectively. An additional scan was done for each slide with the PMT set for 54 and 46 volts.  Gridding and analysis of images was performed with ScanArray software Express V2.0 (Perkin Elmer, Boston, MA).   Each spot was defined on a pixel-by-pixel basis, using a modified Mann-Whitney statistical test.

[10]	Michalski ML, Weil GJ. Gender-specific gene expression in Brugia malayi. Mol Biochem Parasitol 1999;104:247-57.
[11]	Li BW, Rush AC, Tan J, Weil GJ. Quantitative analysis of gender-regulated transcripts in the filarial nematode Brugia malayi by real-time RT-PCR. Mol Biochem Parasitol 2004;137:329-337.
Keywords = brugia malayi nematode worm parasite filaria filariasis
Lot batch = Brugia v.1 batch 1


title: DNGM-8


title: DNGM-3


title: AdERalpha+E2-8 JMTM5


title: DNGM-7


title: DNGM-5


title: DNGM-4


title: DNGM-9


title: DNGM-2


title: DNGM-13


title: DNGM-6


title: DNGL-4

description:
HIV seropositive drug naïve group, viral load low
Keywords = HIV, Human, PBMC, in vivo


title: DNGL-2


title: 88-red200micE_4

status: Public on Jan 01 2005

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

description: Comparison of plants grown for 48 hours at 200µE red light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished

organism: Arabidopsis thaliana

source_name: WT, ecotype Landsberg, finally grown for 48 hours at 200µE red light


title: DNGL-1


title: DNGM-1


title: 88-white20micE_4

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to white light


title: 88-red200micE_3


title: 88-red200micE_2


title: DNGL-3


title: 88-red200micE_1


title: Non-Hardened Sample 2

status: Public on Jan 20 2005

first: Kelsi

last: Rotter

address: 4444 Forest Park Pkwy.

description:
Total RNA was prepared from 100 mg of wheat crown tissue collected from a single non-hardened (NH) five week old 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: 87-red20micE_4

description: Comparison of plants grown for 48 hours at 200µE red light versus plants exposed for 48 hours at 20µE to red light. E. Lopez, unpublished

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to red light


title: 87-red20micE_3


title: 88-white20micE_1


title: 87-red20micE_2


title: 87-red200micE_1


title: 7-HLrec_2d_6

description: Comparison of plants recovered for 48 h in normal light at 80 µE after 1 h of exposure to light stress at 1000 µE versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0, recovered for 48 h in normal light at 80 µE after exposure to light stress at 1000 µE for 1 h


title: Stationary Phase cells, time 100 seconds

description:
Yeast cells cultured for 7 days in YPD+A subsequently exposed to 50 uM menadione
Cells were collected every 10 seconds for 3 minutes with a final time point a 5 minutes. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixied 1:1. RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 30 µl of the hybridization solution.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were normalized to exogonus controls.
Keywords = Stationary phase yeast


title: 87-red200micE_4


title: Non-Hardened Sample 1

institute: Washington University School of Medicine


title: 87-red20micE_1


title: 87-red200micE_2


title: Stationary Phase cells, time 50 seconds

source_name: Stationary Phase cells, time 50 seconds


title: 7-0h_6

source_name: WT, ecotype Columbia 0, grown in light at 80 µE


title: 7-HLrec_2d_5


title: 7-HLrec_2d_4


title: 7-0h_5


title: 7-HLrec_2d_3


title: 88-white20micE_3


title: 7-0h_3


title: 7-0h_4


title: 7-0h_2


title: 7-HLrec_2d_1


title: 6-0h_6

description: Comparison of plants exposed to light stress at 1000 µE for 1 h versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498


title: 6-HL_1h_6

source_name: WT, ecotype Columbia 0, exposure to light at 1000 µE for 1 h


title: 7-0h_1


title: 7-HLrec_2d_2


title: 6-0h_3


title: 6-HL_1h_1


title: 6-HL_1h_2


title: 69-pete2_5

description: Comparison of the Arabidopsis pete2 mutant lacking one of the two isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.

source_name: Arabidopsis pete2 mutant, ecotype Columbia 0, grown on MS media


title: 6-0h_1


title: 6-0h_2


title: 69-pete2_6


title: 6-HL_1h_4


title: 6-0h_5


title: 6-HL_1h_3


title: 6-HL_1h_5


title: 69-WT_6

source_name: WT, ecotype Columbia 0, grown on MS media


title: 6-0h_4


title: 69-WT_5


title: 69-pete2_4


title: 69-WT_4


title: 69-pete2_3


title: 69-WT_2


title: 69-pete2_2


title: 69-WT_3


title: 69-pete2_1


title: 68-pete1_5

description: Comparison of the Arabidopsis pete1 mutant lacking one of the two isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.

source_name: Arabidopsis pete1 mutant, ecotype Columbia 0, grown on MS media


title: 69-WT_1


title: 68-WT_6


title: 68-pete1_4


title: 68-WT_5


title: 68-WT_3


title: 68-pete1_2


title: 68-WT_2


title: 68-WT_4


title: 68-pete1_3


title: 67-pete1_pete2_6

description: Comparison of the Arabidopsis pete1 pete2 doublemutant lacking both isoforms of plastocyanin versus WT. Both grown on MS media. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.

source_name: Arabidopsis pete1 pete2 doublemutant, ecotype Columbia 0, grown on MS media


title: 67-pete1_pete2_5


title: 68-WT_1


title: 68-pete1_1


title: 67-WT_5


title: 67-WT_6


title: 67-pete1_pete2_4


title: 67-WT_4


title: 67-pete1_pete2_3


title: 67-WT_3


title: 67-pete1_pete2_2


title: 65-WT_5

description: Comparison of the Arabidopsis pam48 mutant with altered photosynthesis and defective in an unknown protein versus WT. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0


title: 67-WT_2


title: 65-pam48_5

source_name: Arabidopsis pam48 mutant, ecotype Columbia 0


title: 67-pete1_pete2_1


title: 87-red200micE_3


title: 65-WT_6


title: 65-pam48_4


title: 67-WT_1


title: 65-WT_4


title: 65-pam48_3


title: 65-pam48_6


title: 65-WT_1


title: 65-WT_2


title: 65-pam48_1


title: 65-WT_3


title: 64-pam46_5

description: Comparison of the Arabidopsis pam46 mutant with altered photosynthesis and defective in an unknown protein versus WT. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: Arabidopsis pam46 mutant, ecotype Columbia 0


title: 65-pam48_2


title: 64-WT_6


title: 64-WT_5


title: 64-pam46_6


title: 64-pam46_4


title: 64-pam46_3


title: 64-WT_3


title: 64-WT_4


title: 64-pam46_2


title: 59-pStau_6

description: Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus treatment for 4 h with H2O followed by 4 h treatment with 25 mM Staurosporin (pH 5,5). A. Kandlbinder, K.J. Dietz, unpublished

source_name: WT, ecotype Columbia 0, treated for 4 h with H2O followed by 4 h treatment with 25 mM Staurosporin (pH 5,5)


title: 64-WT_2


title: 64-WT_1


title: 64-pam46_1


title: 59-pStaupAsc_5

source_name: WT, ecotype Columbia 0, treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5)


title: 59-pStau_3


title: 59-pStau_5


title: 59-pStaupAsc_3


title: 59-pStaupAsc_2


title: 59-pStaupAsc_1


title: 59-pStaupAsc_4


title: 59-pStaupAsc_6


title: 59-pStau_1


title: 68-pete1_6


title: 59-pStau_4


title: 58-pStaupAsc_6

description: Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus treatment for 4 h with H2O followed by treatment of 4 h with 25 mM Ascorbat (pH 5,5). A. Kandlbinder, K.J. Dietz, unpublished


title: 58-pAsc_4

source_name: WT, ecotype Columbia 0, treated for 4 h with H2O followed by treatment of 4 h with 25 mM Ascorbat (pH 5,5)


title: 58-pStaupAsc_3


title: 58-pAsc_3


title: 57-pStaupAsc_4

description: Comparison of plants treated for 4 h with 2µM Staurosporin followed by 4 h treatment with 4 h 25 mM Ascorbat (pH 5,5) versus 8 h treatment with H20. A. Kandlbinder, K.J. Dietz, unpublished


title: 57-H2O_6


title: 57-H2O_5


title: 57-pStaupAsc_5


title: 58-pStaupAsc_2


title: 57-pStaupAsc_3


title: 58-pAsc_5


title: 57-pStaupAsc_6


title: 57-H2O_1


title: 59-pStau_2


title: 58-pStaupAsc_5


title: 88-white20micE_2

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to white light


title: 58-pAsc_6


title: 58-pAsc_1


title: 57-pStaupAsc_1


title: 58-pStaupAsc_1


title: 57-H2O_3


title: 58-pStaupAsc_4


title: 57-H2O_2


title: 51-pPar_6

description: Comparison of plants treated with benzoquinone herbicide paraquat 30' after reexposure to light (after one 12h dark period) versus 30' after reexposure to light and treatment with H20 as control. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Landsberg, treated with 50 microM paraquat and reexposed for 30 min in light


title: 58-pAsc_2


title: 57-pStaupAsc_2


title: 57-H2O_4


title: 51-H2O_6

source_name: WT, ecotype Landsberg, treated with H20 and reexposed for 30 min in light


title: 51-H2O_5


title: 51-pPar_4


title: 51-pPar_5


title: 51-H2O_3


title: 51-pPar_3


title: 51-H2O_4


title: 48-0d_6

description: Comparison of plants  grown for 6 d at high-CO2 levels of (1 % (v/v) CO2) versus normal CO2 levels. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0, grown at normal CO2 levels


title: 51-pPar_2


title: 51-pPar_1


title: 50-pParL_6

description: Comparison of plants treated with benzoquinone herbicide paraquat 30' after reexposure to light (after one 12h dark period) versus treatment with paraquat and incubation for 12h in darkness. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498


title: 50-pParD_6

source_name: WT, ecotype Landsberg, treated with 50 microM paraquat and dark adapted for 12 h


title: 51-H2O_2


title: 51-H2O_1


title: 48-pCO2_6d_5

source_name: WT, ecotype Columbia 0, finally grown for 6 d at high-CO2 (1 % (v/v) CO2)


title: 50-pParL_5


title: 50-pParL_4


title: 50-pParD_3


title: 48-pCO2_6d_6


title: 48-0d_4


title: 50-pParD_5


title: 50-pParL_2


title: 50-pParD_2


title: 50-pParD_4


title: 50-pParL_1


title: 50-pParL_3


title: 48-0d_5


title: 48-pCO2_6d_4


title: 50-pParD_1


title: 48-0d_3


title: 48-0d_2


title: 48-pCO2_6d_3


title: 48-0d_1


title: 47-0d_4

description: Comparison of plants  grown for 1 d at high-CO2 levels of (1 % (v/v) CO2) versus normal CO2 levels. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498


title: 48-pCO2_6d_1


title: 47-pCO2_1d_4

source_name: WT, ecotype Columbia 0, finally grown for 1 d at high-CO2 levels (1 % (v/v) CO2)


title: 48-pCO2_6d_2


title: 47-0d_3


title: 46-0d_2

description: Comparison of plants  grown for 10 d at high-CO2 (1 % (v/v) CO2) versus normal CO2 levels.  E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498


title: 46-pCO2_10d_4

source_name: WT, ecotype Columbia 0, finally grown for 10 d at high-CO2 (1 % (v/v) CO2)


title: 47-0d_2


title: 46-pCO2_10d_2


title: 46-pCO2_10d_3


title: 46-0d_4


title: 47-pCO2_1d_3


title: 47-0d_1


title: 45-pCK_6

description: Comparison of cytokinin-treated (2 h) cell culture versus untreated cell culture. T. Schmüllig, unpublished

source_name: WT cell culture, ecotype Columbia 0, treated with cytokinin


title: 45-pCK_5


title: 47-pCO2_1d_2


title: 45-H2O_6

source_name: WT cell culture, ecotype Columbia 0, treated with H20


title: 46-pCO2_10d_1


title: 47-pCO2_1d_1


title: 46-0d_3


title: 46-0d_1


title: 45-H2O_5


title: 45-pCK_4


title: 45-H2O_3


title: 45-pCK_2


title: 45-H2O_2


title: 45-pCK_3


title: 45-pCK_1


title: 45-H2O_4


title: 45-H2O_1


title: 44-H2O_2

description: Comparison of plants treated with nitrile herbicide bromoxynil 30' after reexposure to light (after one 12h dark period) versus 30' after reexposure to light and treatment with H20 as control. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498


title: 44-H2O_5


title: 44-pBro_2

source_name: WT, ecotype Landsberg, treated with 500 microM bromoxynil and reexposed for 30 min in light


title: 44-pBro_3


title: 44-pBro_6


title: 44-pBro_5


title: 43-pBroD_6

description: Comparison of plants treated with nitrile herbicide bromoxynil 30' after reexposure to light (after one 12h dark period) versus treatment with bromoxynil and incubation for 12h in darkness. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Landsberg, treated with 500 microM bromoxynil and dark adapted for 12 h


title: 43-pBroD_5


title: 44-pBro_1


title: 44-H2O_3


title: 43-pBroL_5


title: 44-H2O_6


title: 43-pBroL_6


title: 44-pBro_4


title: 44-H2O_1


title: 43-pBroL_4


title: 43-pBroL_3


title: 43-pBroD_4


title: 43-pBroD_2


title: 43-pBroD_1


title: 43-pBroL_2


title: 43-pBroL_1


title: 43-pBroD_3


title: 39-mCO2_4d_10

description: Comparison of plants grown for 96 h at low-CO2 (0.003 % (v/v) CO2) versus plants grown at normal CO2 level. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0, finally grown for 96 h at low-CO2 stress of 0.003 % (v/v) CO2


title: 39-0d_10

source_name: WT, ecotype Columbia 0, grown at normal CO2 level


title: 39-mCO2_4d_9


title: 39-0d_8


title: 39-0d_9


title: 39-0d_7


title: 39-mCO2_4d_8


title: 39-0d_6


title: 39-mCO2_4d_5


title: 39-mCO2_4d_6


title: 39-mCO2_4d_7


title: 39-mCO2_4d_4


title: 39-0d_4


title: 39-0d_5


title: 39-mCO2_4d_2


title: 39-mCO2_4d_3


title: 39-0d_3


title: 38-mCO2_2d_6

description: Comparison of plants grown for 48 h at low-CO2 (0.003 % (v/v) CO2) versus plants grown at normal CO2 level. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0, finally grown for 48 h at low-CO2 stress of 0.003 % (v/v) CO2


title: 39-mCO2_4d_1


title: 39-0d_2


title: 39-0d_1


title: 38-mCO2_2d_4


title: 38-0d_6


title: 38-mCO2_2d_5


title: 38-0d_5


title: 38-0d_4


title: 38-0d_1


title: 38-mCO2_2d_1


title: 38-mCO2_2d_3


title: 27-white20micE_8

description: Comparison of plants  grown for 48 hours at 20µE blue light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished


title: 38-0d_2


title: 38-0d_3


title: 38-mCO2_2d_2


title: 27-blue20micE_7

source_name: WT, ecotype Landsberg, finally grown for 48 hours at 20µE blue light


title: 27-white20micE_7


title: 27-white20micE_6


title: 27-blue20micE_6


title: 27-blue20micE_8


title: 27-blue20micE_5


title: 27-blue20micE_2


title: 27-white20micE_2


title: 27-blue20micE_4


title: 27-blue20micE_3


title: 27-white20micE_4


title: 27-white20micE_5


title: 27-white20micE_3


title: 26-white20micE_6

description: Comparison of plants  grown for 48 hours at 200µE blue light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished


title: 26-blue200micE_6

source_name: WT, ecotype Landsberg, finally grown for 48 hours at 200µE blue light


title: 27-white20micE_1

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to white light


title: 27-blue20micE_1


title: 26-blue200micE_4


title: 26-white20micE_4


title: 26-white20micE_3


title: 26-blue200micE_5


title: 26-blue200micE_2


title: 26-white20micE_5


title: 26-blue200micE_3


title: 26-white20micE_2


title: 25-blue20micE_6

description: Comparison of plants  grown for 48 hours at 200µE blue light versus plants exposed for 48 hours at 20µE to blue light. E. Lopez, unpublished

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to blue light


title: 25-blue200micE_5


title: 26-blue200micE_1


title: 25-blue20micE_5


title: 25-blue200micE_1


title: 26-white20micE_1


title: 25-blue20micE_2


title: 25-blue200micE_6


title: 25-blue200micE_4


title: 25-blue200micE_2


title: 25-blue200micE_3


title: 25-blue20micE_4


title: 19-WT_6

description: Comparison of the Arabidopsis pete2 mutant grown on soil and lacking one of the two plastocyanin protein isoforms versus WT. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.

source_name: WT, ecotype Columbia 0, grown on soil


title: 19-pete2_soil_5

source_name: Arabidopsis pete2 mutant, ecotype Columbia 0, grown on soil


title: 25-blue20micE_3


title: 44-H2O_4

source_name: WT, ecotype Landsberg, treated with H20 and reexposed for 30 min in light


title: 25-blue20micE_1


title: 19-pete2_soil_6


title: 19-pete2_soil_3


title: 19-pete2_soil_4


title: 19-pete2_soil_2


title: 19-WT_5


title: 18-WT_8

description: Comparison of the Arabidopsis pete1 mutant grown on soil and lacking one of the two plastocyanin protein isoforms versus WT. M. Weigel et al., J. Biol. Chem. 278 (2003), pp. 31286–31289.


title: 19-pete2_soil_1


title: 19-WT_2


title: 18-pete1_soil_8

source_name: Arabidopsis pete1 mutant, ecotype Columbia 0, grown on soil


title: 19-WT_1


title: 19-WT_4


title: 18-pete1_soil_7


title: 18-WT_7


title: 18-pete1_soil_6


title: 18-WT_2


title: 18-pete1_soil_5


title: 18-WT_4


title: 18-WT_5


title: 18-pete1_soil_4


title: 18-pete1_soil_3


title: 18-WT_6


title: 18-WT_3


title: 18-WT_1


title: 18-pete1_soil_2


title: 16-PSII_5

description: Comparison of plants grown under PSII-specific light versus plants grown under PSI-specific light. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype C24, grown under PSII-specific light


title: 16-PSI_5

source_name: WT, ecotype C24, grown under PSI-specific light


title: 16-PSI_4


title: 16-PSII_4


title: 16-PSI_2


title: 16-PSI_3


title: 16-PSII_2


title: 18-pete1_soil_1


title: 16-PSII_6


title: 19-WT_3


title: 16-PSII_1


title: 16-PSII_3


title: 16-PSI_6


title: 16-PSI_1


title: 13-ML_20C_3

description: Comparison of plants exposed to photoinhibitory conditions of medium light at 4 °C for 24 h versus plants grown under medium light at 20 °C. A. Haldrup, unpublished

source_name: WT>>>WT, ecotype Columbia 0, grown under medium light at 20 °C


title: 13-ML_20C_1


title: 12-ML4c_rec_24h_6

description: Comparison of plants recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to photoinhibitory conditions in medium light at 4 °C  versus plants exposed to photoinhibitory conditions of medium light at 4 °C for 24 h. A. Haldrup, unpublished

source_name: WT, ecotype Columbia 0, recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to medium light at 4 °C


title: 13-ML_4C_1

source_name: WT>>>WT, ecotype Columbia 0, exposed for 24 h to medium light at 4 °C


title: 12-ML_4C_6

source_name: WT, ecotype Columbia 0, exposed for 24 h to medium light at 4 °C


title: 13-ML_4C_3


title: 13-ML_4C_4


title: 13-ML_4C_6


title: 12-ML_4C_5


title: 13-ML_20C_4


title: 13-ML_20C_5


title: 13-ML_20C_6


title: 13-ML_20C_2


title: 12-ML_4C_2


title: 13-ML_4C_5


title: 12-ML4c_rec_24h_5


title: 12-ML_4C_1


title: 12-ML4c_rec_24h_2


title: 12-ML_4C_3


title: 13-ML_4C_2


title: 12-ML4c_rec_24h_3


title: 12-ML_4C_4


title: 11-ML4c_rec_24h_6

description: Comparison of plants recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to photoinhibitory conditions in medium light at 4 °C  versus plants grown under medium light at 20 °C. A. Haldrup, unpublished


title: 12-ML4c_rec_24h_1


title: 11-ML4c_rec_24h_2


title: 11-ML_20C_2

source_name: WT, ecotype Columbia 0, grown under medium light at 20 °C


title: 9-0h_5

description: Comparison of plants exposed to light for 30 min after a 12 h dark period versus 12 h dark adapted plants. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Landsberg, 12 h dark adapted


title: 11-ML4c_rec_24h_1


title: 9-0h_6


title: 9-0h_4


title: 11-ML4c_rec_24h_5


title: 11-ML_20C_3


title: 9-L30min_3

source_name: WT, ecotype Landsberg, exposed to light for 30 min after a 12 h dark period


title: 11-ML_20C_4


title: 11-ML4c_rec_24h_3


title: 9-L30min_6


title: 11-ML_20C_5


title: 9-L30min_4


title: 9-0h_2


title: 11-ML_20C_1


title: 8-HLrec_2h_6

description: Comparison of plants recovered for 2 h in normal light at 80 µE after 1 h of exposure to light stress at 1000 µE versus plants grown under normal light conditions of 80 µE. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498

source_name: WT, ecotype Columbia 0, recovered for 1 h in normal light at 80 µE after exposure to light stress at 1000 µE for 1 h


title: 9-0h_3


title: 9-L30min_1


title: 9-0h_1


title: 8-0h_5

source_name: >WT, ecotype Columbia 0, grown in light at 80 µE


title: 9-L30min_2


title: 11-ML_20C_6


title: 11-ML4c_rec_24h_4


title: 8-0h_6


title: 8-HLrec_2h_4


title: 8-0h_3


title: 89-red20micE_3

description: Comparison of plants grown for 48 hours at 20µE red light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished

source_name: WT, ecotype Landsberg, finally grown for 48 hours at 20µE red light


title: 89-white20micE_4

source_name: WT, ecotype Landsberg, exposed for 48 hours at 20µE to white light


title: 89-white20micE_3


title: 8-HLrec_2h_5


title: 89-red20micE_4


title: 8-HLrec_2h_3


title: 8-0h_4


title: 8-HLrec_2h_1


title: 88-red200micE_6

description: Comparison of plants grown for 48 hours at 200µE red light versus plants exposed for 48 hours at 20µE to white light. E. Lopez, unpublished

source_name: WT, ecotype Landsberg, finally grown for 48 hours at 200µE red light


title: 89-red20micE_1


title: 8-HLrec_2h_2


title: 89-white20micE_2


title: 88-red200micE_5


title: 89-red20micE_2


title: 8-0h_2


title: 89-white20micE_1


title: 88-white20micE_6


title: 88-white20micE_5


title: M JH 8 h 122312

status: Public on Dec 31 2004

city: Reno

first: Christopher

middle: Ian

last: Keeling

state: NV

address: 1664 North Virginia Street

department: Department of Biochemistry/Mail Stop 330

institute: University of Nevada, Reno

description:
Tissue: Logging slash of Jeffrey pine (Pinus jeffreyi Grev. & Balf.) infested with Ips pini were obtained from the Sierra Nevada in CA and NV and placed in a greenhouse to allow emergence of adult beetles (Browne, J. Econ. Entomol. 65, 1499-1501, 1972). Upon emergence, beetles were typed and sexed and kept at 4°C on moist paper towels. For the JH III treatments, beetles were immobilized by chilling and then treated topically on the ventral surface of the abdomen with either 10 µg (±) juvenile hormone III (Sigma) in 0.5 µL acetone or acetone (control). They were then incubated in the dark at room temperature in groups of 15 in 60 mL plastic containers (Dixie) for specified times. For the feeding experiments, holes (3 mm dia.) were drilled into the phloem of an un-infested Jeffrey pine bolt (15-20 cm dia. X 100 cm). One male beetle was placed head first into each hole and held in with metal screening. The bolt was then placed vertically at room temperature for specified times. At the same time, unfed beetles were kept at room temperature in the dark in 60 mL plastic containers, 15 beetles per container. At the end of the incubation, the bark was removed to recover each fed beetle. Beetles were immersed in water and the anterior midguts excised under a stereo microscope. Midguts were gently purged of their contents and then immediately frozen in liquid nitrogen and stored at -80°C. Each treatment/control time point pair was replicated four times and each replicate contained tissue from 60 midguts (30 each for treatment and control). Treatment and control beetles were cohorts for a replicate pair and were incubated simultaneously. Beetles in different replicate pairs and time points were not always cohorts.
Hybridizations: Hybridizations were done in quadruplicate, each with tissue from different groups of beetles. Total RNA was extracted using QIAshredder and RNeasy Mini kits (Qiagen) and quantified spectrophotometrically. Total RNA (approx. 40 µg) was reverse transcribed with oligo(dT)15 (Promega), Superscript II RT- (Invitrogen), and dNTPs (Promega) containing aminoallyl-dUTP (Sigma, aminoallyl-dUTP to dTTP ratio of 2 to 3). After alkaline hydrolysis of the RNA, clean up with a Microcon-30 (Millipore), and lyophilization, the aminoallyl-dUTP cDNA was reacted with Cy3 or Cy5 monofunctional reactive dyes (Amersham). Cy3 and Cy5 dyes were swapped equally between treatment and control samples among replicates (see source info for dye used for each target). After 60 min, unreacted dyes were removed from the labeled cDNA by a QIAquick spin column (Qiagen). The fluorescently labeled cDNAs from treatment and control samples were combined together with 20 µg herring sperm DNA (Promega) and 20 µg polydA (Amersham), lyophilized, and then resuspended in 15 µL hybridization buffer (50% formamide, 5x SSC, and 0.1% SDS). The hybridization mixture was denatured at 95°C for 5 min, centrifuged at 16,000 g for 5 min, and then immediately applied to the microarray preheated to 42°C. The microarray had previously been incubated for 60 min at 42°C in pre-hybridization buffer (5x SSC, 0.1% SDS, and 1% BSA), washed 2 min in water, 2 min in 2-propanol, and dried by centrifugation. The hybridization mixture was covered with a HybriSlip (22 x 22 mm, Sigma) and then the microarray was immediately placed into a preheated, humidified hybridization chamber and placed in a 42°C oven for 16-20 h. Microarrays were removed from the hybridization chamber and immediately washed with agitation at room temperature for 2 min each in 2x SSC with 0.03% SDS, 1x SSC, and 0.2x SSC, and then dried by centrifugation.
Analysis: Arrays were scanned at 5 µm resolution with a Packard Bioscience ScanArray 4000 array scanner and analyzed with ScanArray and QuantArray software (versions 3.1 and 3.0 respectively). Median signal (adaptive spot algorithm) and background intensities were obtained for both dyes for each element. Data were background subtracted, globally normalized, log transformed (base 2), converted to mean log (intensities) and log (ratios), and then locally normalized across element signal intensity (span=0.7, trim=0.1) using online SNOMAD tools (Colantuoni et al., Bioinformatics 18, 1540-1, 2002). To account for outliers, the duplicate elements on the 4 replicated arrays were treated as unique measurements and a Q-test (99% confidence, Dean and Dixon, Anal. Chem. 23, 636-8, 1951) was performed on the 8 measurements. If a measurement tested as an outlier, its VALUE was replaced with the VALUE of the duplicate spot on the same array.  At most, only 1 of the 8 measurements was excluded.
Keywords = North American pine engraver beetle, anterior midgut, juvenile hormone, pheromone biosynthesis, Coleoptera, Scolytidae

organism: Ips pini

source_name: Anterior midguts from acetone treated males, 8 hours (Cy3)

source_name: Anterior midguts from juvenile hormone III treated males, 8 hours (Cy5)


title: M JH 8 h 122307

source_name: Anterior midguts from acetone treated males, 8 hours (Cy5)

source_name: Anterior midguts from juvenile hormone III treated males, 8 hours (Cy3)


title: M JH 4 h 122321

source_name: Anterior midguts from acetone treated males, 4 hours (Cy3)

source_name: Anterior midguts from juvenile hormone III treated males, 4 hours (Cy5)


title: M JH 4 h 122322

source_name: Anterior midguts from acetone treated males, 4 hours (Cy5)

source_name: Anterior midguts from juvenile hormone III treated males, 4 hours (Cy3)


title: M JH 8 h 122305


title: M JH 4 h 122320


title: M JH 8 h 122306


title: 9-L30min_5


title: M JH 4 h 122319


title: M JH 2 h 122326

source_name: Anterior midguts from acetone treated males, 2 hours (Cy5)

source_name: Anterior midguts from juvenile hormone III treated males, 2 hours (Cy3)


title: M JH 16 h 122329

source_name: Anterior midguts from acetone treated males, 16 hours (Cy5)

source_name: Anterior midguts from juvenile hormone III treated males, 16 hours (Cy3)


title: M Fed 24 h 122310

source_name: Anterior midguts from unfed males, 24 hours (Cy3)

source_name: Anterior midguts from fed males, 24 hours (Cy5)


title: M JH 2 h 122323

source_name: Anterior midguts from acetone treated males, 2 hours (Cy3)

source_name: Anterior midguts from juvenile hormone III treated males, 2 hours (Cy5)


title: M JH 16 h 121833


title: M Fed 24 h 122311

source_name: Anterior midguts from unfed males, 24 hours (Cy5)

source_name: Anterior midguts from fed males, 24 hours (Cy3)


title: M JH 16 h 122327

source_name: Anterior midguts from acetone treated males, 16 hours (Cy3)

source_name: Anterior midguts from juvenile hormone III treated males, 16 hours (Cy5)


title: M JH 2 h 122324


title: M JH 16 h 121831


title: M JH 2 h 122325


title: F JH 8 h 122315

source_name: Anterior midguts from acetone treated females, 8 hours (Cy3)

source_name: Anterior midguts from juvenile hormone III treated females, 8 hours (Cy5)


title: CENPK113.7D N-lim3

status: Public on Dec 17 2004

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: The S. cerevisiae strains used in this study was the haploid, prototrophic strain CEN.PK113-7D (MATa LEU3). Strains were grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in van den Berg et al.. Cultures were fed with defined synthetic media based on the medium described by Verduyn et al . For nitrogen-limited growth the medium contained the following: (NH4)2SO4, 1.0 g·l-1; K2SO4, 5.3 g·l-1;  KH2PO4, 3.0 g·l-1; MgSO4·7H2O, 0.5 g·l-1; vitamins and trace elements. Glucose concentrations in the feed were designed to obtain approximately 17 g·l-1 residual glucose in the culture broth and thus to avoid transcriptional responses as a result of different degrees of glucose repression. Feed concentrations were 59 g·l-1 glucose (reference strain) and 53 g·l-1 glucose (leu3D strain). The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples were taken between 10 and 14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction

source_name: chemostat sampled cells


title: F JH 8 h 122317


title: F JH 8 h 122318

source_name: Anterior midguts from acetone treated females, 8 hours (Cy5)

source_name: Anterior midguts from juvenile hormone III treated females, 8 hours (Cy3)


title: M Fed 24 h 122309


title: 12-ML4c_rec_24h_4

source_name: WT, ecotype Columbia 0, recovered for 24 h in medium light at 20 °C after a period of 24 h of exposure to medium light at 4 °C


title: CENPK113.7D N-lim2


title: CENPK113.7D N-lim1


title: CENPK 113.7D C-lim1

description: The S. cerevisiae strains used in this study was the haploid, prototrophic strain CEN.PK113-7D (MATa LEU3). Strains were grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in van den Berg et al.. Cultures were fed with defined synthetic media based on the medium described by Verduyn et al . For carbon-limited growth the medium contained the following: (NH4)2SO4, 5.0 g·l-1; KH2PO4, 3.0 g·l-1; MgSO4·7H2O, 0.5 g·l-1; ethanol, 6.0 g·l-1; vitamins and trace elements. The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples were taken between 10 and 14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.


title: leu3 delta N-lim3

description: The S. cerevisiae strains used in this study were the haploid, prototrophic LEU3 deletion strain CEN.PK540-3A (MATa leu3(41,2621)::loxP-Kan-loxP). Strains were grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in van den Berg et al. . Cultures were fed with defined synthetic media based on the medium described by Verduyn et al . For nitrogen-limited growth the medium contained the following: (NH4)2SO4, 1.0 g·l-1; K2SO4, 5.3 g·l-1;  KH2PO4, 3.0 g·l-1; MgSO4·7H2O, 0.5 g·l-1; vitamins and trace elements. Glucose concentrations in the feed were designed to obtain approximately 17 g·l-1 residual glucose in the culture broth and thus to avoid transcriptional responses as a result of different degrees of glucose repression. Feed concentrations were 59 g·l-1 glucose (reference strain) and 53 g·l-1 glucose (leu3D strain). The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples were taken between 10 and 14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.


title: F JH 8 h 122316


title: CENPK113.7D C-lim2

source_name: Chemostat sampled cells


title: leu3 delta N-lim2


title: leu3 delta C-lim3

description: The S. cerevisiae strains used in this study were the haploid, prototrophic LEU3 deletion strain CEN.PK540-3A (MATa leu3(41,2621)::loxP-Kan-loxP). Strains were grown at 30 °C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter as described in van den Berg et al. . Cultures were fed with defined synthetic media based on the medium described by Verduyn et al . For carbon-limited growth the medium contained the following: (NH4)2SO4, 5.0 g·l-1; KH2PO4, 3.0 g·l-1; MgSO4·7H2O, 0.5 g·l-1; ethanol, 6.0 g·l-1; vitamins and trace elements. The dilution rate was set at 0.10 h-1. The pH was measured online and kept constant at 5.0 by the automatic addition of 2 M KOH with the use of an Applikon ADI 1030 biocontroller. Stirrer speed was 800 rpm and the airflow was 0.5 l.min-1. Dissolved oxygen tension was measured online with an Ingold model 34 100 3002 probe, and was above 50% air saturation. A condenser connected to a cryostat set at 2 °C cooled the off-gas, and oxygen and carbon dioxide were measured off-line. Steady-state samples were taken between 10 and 14 volume changes to avoid strain adaptation due to long term cultivation. Dry weight, metabolite-, and gas profiles were constant over at least 3 volume changes prior to sampling for RNA extraction.


title: leu3 delta C-lim2


title: leu3 delta C-lim1


title: leu3 delta N-lim1


title: CENPK113.7D C-lim3


title: M Fed 24 h 122314


title: virgin females

status: Public on Dec 09 2004

city: Ithaca

first: Lisa

middle: A.

last: McGraw

state: NY

address: 421 Biotechnology Bldg.

department: Molecular Biology and Genetics

institute: Cornell University

description:
Drosophila stocks and crosses.
Virgin female flies originated from a highly inbred, wild-type Canton S stock.

Flies were reared on standard yeast/glucose medium at 25oC under a 12:12 hour light:dark cycle, collected as virgins and aged three to four days prior to experimental use. Within three hours of the beginning of their light cycle, single virgin females were paired with single virgin males of the appropriate genotype and allowed to mate.  Mated female flies were flash-frozen in liquid nitrogen between one and three hours after the completion of mating and stored at -80oC until extraction of total RNA.

Sample preparation.
Frozen flies from replicate treatments were pooled to minimize potential variation in gene expression from time and/or day of mating. From each pooled batch, 50 flies were randomly chosen and separated into two equal batches for RNA extraction. Total RNA was prepared using Trizol (Invitrogen, Inc.) extraction and purified with RNeasy Mini kit (Qiagen). According to the manufacturer’s instructions, cDNA was prepared from the samples and hybridized to Drosophila Affymetrix GeneChips (Affymetrix, Santa Clara, CA) by the University of Kentucky Microarray Core Facility (Lexington, KY). Each experimental treatment consisted of two independent RNA extractions each replicated twice, for a total of four chips per treatment.

Hybridization conditions:
Rotating for 16 hours at 45 degrees C.

Hybridization cocktail components:
20ug labeled cRNA,
control Oligonucleotide B2 (3nM)  5ul,
20X Eukaryotic Hybridization controls 15ul,
Herring sperm DNA (10 mg/ml)  3ul,
Acetylated BSA (50mg/ml)  3ul,
2X Hybridization buffer  150ul,
dddH20   84ul;

final volume is 300 ul and 200 ul is loaded on the chip

organism: Drosophila melanogaster

source_name: virgin females


title: DTA-E

description:
Drosophila stocks and crosses.
Female flies originated from a highly inbred, wild-type Canton S stock. These females wer mated to males that do not produce sperm or accessory gland proteins (Acps). Males deficient in the production of sperm and Acps (DTA-E) were derived from a transgenic stock with a Canton S background. DTA-E males do not produce sperm and do not make Acps from the main cells of their accessory glands (96% of the secretory cells of this tissue).

Flies were reared on standard yeast/glucose medium at 25oC under a 12:12 hour light:dark cycle, collected as virgins and aged three to four days prior to experimental use. Within three hours of the beginning of their light cycle, single virgin females were paired with single virgin males of the appropriate genotype and allowed to mate.  Mated female flies were flash-frozen in liquid nitrogen between one and three hours after the completion of mating and stored at -80oC until extraction of total RNA.

Sample preparation.
Frozen flies from replicate treatments were pooled to minimize potential variation in gene expression from time and/or day of mating. From each pooled batch, 50 flies were randomly chosen and separated into two equal batches for RNA extraction. Total RNA was prepared using Trizol (Invitrogen, Inc.) extraction and purified with RNeasy Mini kit (Qiagen). According to the manufacturer’s instructions, cDNA was prepared from the samples and hybridized to Drosophila Affymetrix GeneChips (Affymetrix, Santa Clara, CA) by the University of Kentucky Microarray Core Facility (Lexington, KY). Each experimental treatment consisted of two independent RNA extractions each replicated twice, for a total of four chips per treatment.

Hybridization conditions:
Rotating for 16 hours at 45 degrees C.

Hybridization cocktail components:
20ug labeled cRNA,
control Oligonucleotide B2 (3nM)  5ul,
20X Eukaryotic Hybridization controls 15ul,
Herring sperm DNA (10 mg/ml)  3ul,
Acetylated BSA (50mg/ml)  3ul,
2X Hybridization buffer  150ul,
dddH20   84ul;

final volume is 300 ul and 200 ul is loaded on the chip

source_name: females mated to DTA-E males


title: Mated females

description:
Drosophila stocks and crosses.
Female flies originated from a highly inbred, wild-type Canton S stock. These females wer mated to wild type (Canton S) males.
Flies were reared on standard yeast/glucose medium at 25oC under a 12:12 hour light:dark cycle, collected as virgins and aged three to four days prior to experimental use. Within three hours of the beginning of their light cycle, single virgin females were paired with single virgin males of the appropriate genotype and allowed to mate.  Mated female flies were flash-frozen in liquid nitrogen between one and three hours after the completion of mating and stored at -80oC until extraction of total RNA.

Sample preparation.
Frozen flies from replicate treatments were pooled to minimize potential variation in gene expression from time and/or day of mating. From each pooled batch, 50 flies were randomly chosen and separated into two equal batches for RNA extraction. Total RNA was prepared using Trizol (Invitrogen, Inc.) extraction and purified with RNeasy Mini kit (Qiagen). According to the manufacturer’s instructions, cDNA was prepared from the samples and hybridized to Drosophila Affymetrix GeneChips (Affymetrix, Santa Clara, CA) by the University of Kentucky Microarray Core Facility (Lexington, KY). Each experimental treatment consisted of two independent RNA extractions each replicated twice, for a total of four chips per treatment.

Hybridization conditions:
Rotating for 16 hours at 45 degrees C.

Hybridization cocktail components:
20ug labeled cRNA,
control Oligonucleotide B2 (3nM)  5ul,
20X Eukaryotic Hybridization controls 15ul,
Herring sperm DNA (10 mg/ml)  3ul,
Acetylated BSA (50mg/ml)  3ul,
2X Hybridization buffer  150ul,
dddH20   84ul;

final volume is 300 ul and 200 ul is loaded on the chip

source_name: Canton S females mated to wild-type males


title: mated to sons of tudor males

description:
Drosophila stocks and crosses.
Female flies originated from a highly inbred, wild-type Canton S stock. These females were mated to males that do not produce sperm Spermless (sons of tudor) males are sons of Canton S males mated to bw sp tud1 females. These males have intact accessory glands and produce Acps that are transmitted in the ejaculate.
Flies were reared on standard yeast/glucose medium at 25oC under a 12:12 hour light:dark cycle, collected as virgins and aged three to four days prior to experimental use. Within three hours of the beginning of their light cycle, single virgin females were paired with single virgin males of the appropriate genotype and allowed to mate.  Mated female flies were flash-frozen in liquid nitrogen between one and three hours after the completion of mating and stored at -80oC until extraction of total RNA.

Sample preparation.
Frozen flies from replicate treatments were pooled to minimize potential variation in gene expression from time and/or day of mating. From each pooled batch, 50 flies were randomly chosen and separated into two equal batches for RNA extraction. Total RNA was prepared using Trizol (Invitrogen, Inc.) extraction and purified with RNeasy Mini kit (Qiagen). According to the manufacturer’s instructions, cDNA was prepared from the samples and hybridized to Drosophila Affymetrix GeneChips (Affymetrix, Santa Clara, CA) by the University of Kentucky Microarray Core Facility (Lexington, KY). Each experimental treatment consisted of two independent RNA extractions each replicated twice, for a total of four chips per treatment.

Hybridization conditions:
Rotating for 16 hours at 45 degrees C.

Hybridization cocktail components:
20ug labeled cRNA,
control Oligonucleotide B2 (3nM)  5ul,
20X Eukaryotic Hybridization controls 15ul,
Herring sperm DNA (10 mg/ml)  3ul,
Acetylated BSA (50mg/ml)  3ul,
2X Hybridization buffer  150ul,
dddH20   84ul;

final volume is 300 ul and 200 ul is loaded on the chip

source_name: females mated to sons of tudor males


title: S.l. animal 5, summer awake, reverse, liver

status: Public on Dec 03 2004

city: Pacific Grove

first: Andrew

last: Gracey

state: CA

institute: Stanford University

description:
Squirrel liver tissue was rapidly dissected and frozen on liquid nitrogen.
For each tissue sample total RNA was extracted from tissues using Trizol (Invitrogen). Fluorescently labelled cDNA was synthesized using amino-allyl adducts coupled to Cy3 and Cy5 fluors (www.microarrays.org) and compared to a reference RNA by hybridization to two arrays with reversal of the labeled fluorophores.  The reference RNA pool was prepared for each tissue by pooling RNA samples isolated from animals sampled under all conditions.  Microarrays were hybridized overnight at 65Ž°C, washed, scanned, and the images scanned and quantified (GenePix 4000A, Axon Instruments, CA).
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 3000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. Without background correction, the log base 10 expression ratios of the median pixel intensities were established, and the spatial and intensity based trends in the data were removed by Lowess normalization (GeneSpring, Silicon Genetics).
Data for each pair of fluor-reversed slides were combined by averaging the ratios derived from the two measurements.  The expression of each cDNA was then normalized to the median ratio observed for that transcript in the summer animals.

organism: Callospermophilus lateralis

source_name: Spermophilus lateralis liver reference RNA

source_name: Animal 5, summer awake, reverse, liver


title: S.l. animal 108, summer awake, reverse, liver

source_name: Animal 108, summer awake, reverse, liver


title: S.l. animal 84, late torpor, forward, liver

source_name: Animal 84, late torpor, forward, liver


title: S.l. animal 6, summer awake, forward, liver

source_name: Animal 6, summer awake, forward, liver


title: S.l. animal 84, late torpor, reverse, liver

source_name: Animal 84, late torpor, reverse, liver


title: S.l. animal 69, late torpor, forward, liver

source_name: Animal 69, late torpor, forward, liver


title: S.l. animal 108, summer awake, forward, liver

source_name: Animal 108, summer awake, forward, liver


title: S.l. animal 6, summer awake, reverse, liver

source_name: Animal 6, summer awake, reverse, liver


title: S.l. animal 3, summer awake, reverse, liver

source_name: Animal 3, summer awake, reverse, liver


title: S.l. animal 5, summer awake, forward, liver

source_name: Animal 5, summer awake, forward, liver


title: 8-0h_1

source_name: >WT, ecotype Columbia 0, grown in light at 80 µE


title: S.l. animal 16, late torpor, forward, liver

source_name: Animal 16, late torpor, forward, liver


title: S.l. animal 16, late torpor, reverse, liver

source_name: Animal 16, late torpor, reverse, liver


title: S.l. animal 162, late torpor, reverse, liver

source_name: Animal 162, late torpor, reverse, liver


title: S.l. animal 69, late torpor, reverse, liver

source_name: Animal 69, late torpor, reverse, liver


title: S.l. animal 89, interbout arousal, forward, liver

source_name: Animal 89, interbout arousal, forward, liver


title: S.l. animal 41, interbout arousal, forward, liver

source_name: Animal 41, interbout arousal, forward, liver

source_name: Spermophilus lateralis liver reference RNA


title: S.l. animal 97, interbout arousal, reverse, liver

source_name: Animal 97, interbout arousal, reverse, liver


title: S.l. animal 97, interbout arousal, forward, liver

source_name: Animal 97, interbout arousal, forward, liver


title: S.l. animal 89, interbout arousal, reverse, liver

source_name: Animal 89, interbout arousal, reverse, liver


title: S.l. animal 41, interbout arousal, reverse, liver

source_name: Animal 41, interbout arousal, reverse, liver


title: S.l. animal 93, interbout arousal, forward, liver

source_name: Animal 93, interbout arousal, forward, liver


title: S.l. animal 85, interbout arousal, reverse, liver

source_name: Animal 85, interbout arousal, reverse, liver


title: S.l. animal 93, interbout arousal, reverse, liver

source_name: Animal 93, interbout arousal, reverse, liver


title: S.l. animal 85, interbout arousal, forward, liver

source_name: Animal 85, interbout arousal, forward, liver


title: S.l. animal 103, summer awake, reverse, liver

source_name: Animal 103, summer awake, reverse, liver


title: S.l. animal 34, late torpor, reverse, liver

source_name: Animal 34, late torpor, reverse, liver


title: S.l. animal 93, interbout arousal, forward, heart

description:
Squirrel tissues were rapidly dissected and frozen on liquid nitrogen.
For each tissue sample total RNA was extracted using Trizol (Invitrogen). Fluorescently labelled cDNA was synthesized using amino-allyl adducts coupled to Cy3 and Cy5 fluors (www.microarrays.org) and compared to a reference RNA by hybridization to two arrays with reversal of the labeled fluorophores.  The reference RNA pool was prepared for each tissue by pooling RNA samples isolated from animals sampled under all conditions.  Microarrays were hybridized overnight at 65ŽÝC, washed, scanned, and the images scanned and quantified (GenePix 4000A, Axon Instruments, CA).
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 3000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. Without background correction, the log base 10 expression ratios of the median pixel intensities were established, and the spatial and intensity based trends in the data were removed by Lowess normalization (GeneSpring, Silicon Genetics).
Data for each pair of fluor-reversed slides were combined by averaging the ratios derived from the two measurements.  The expression of each cDNA was then normalized to the median ratio observed for that transcript in the summer animals.

source_name: Animal 93, interbout arousal, forward, heart

source_name: Spermophilus lateralis heart reference RNA


title: S.l. animal 34, late torpor, forward, liver

source_name: Animal 34, late torpor, forward, liver


title: S.l. animal 19, late torpor, forward, liver

source_name: Animal 19, late torpor, forward, liver


title: S.l. animal 19, late torpor, reverse, liver

source_name: Animal 19, late torpor, reverse, liver


title: S.l. animal 89, interbout arousal, reverse, heart

source_name: Animal 89, interbout arousal, reverse, heart


title: S.l. animal 103, summer awake, forward, liver

source_name: Animal 103, summer awake, forward, liver

source_name: Spermophilus lateralis liver reference RNA


title: S.l. animal 4, summer awake, forward, liver

source_name: Animal 4, summer awake, forward, liver


title: S.l. animal 4, summer awake, reverse, liver

source_name: Animal 4, summer awake, reverse, liver


title: S.l. animal 93, interbout arousal, reverse, heart

source_name: Animal 93, interbout arousal, reverse, heart


title: S.l. animal 84, late torpor, reverse, heart

source_name: Animal 84, late torpor, reverse, heart


title: S.l. animal 90, late torpor, forward, heart

source_name: Animal 90, late torpor, forward, heart


title: S.l. animal 1, summer awake, reverse, liver

source_name: Animal 1, summer awake, reverse, liver


title: S.l. animal 90, late torpor, reverse, heart

source_name: Animal 90, late torpor, reverse, heart


title: S.l. animal 1, summer awake, forward, liver

source_name: Animal 1, summer awake, forward, liver


title: S.l. animal 84, late torpor, forward, heart

source_name: Animal 84, late torpor, forward, heart


title: S.l. animal 78, interbout arousal, reverse, heart

source_name: Animal 78, interbout arousal, reverse, heart


title: S.l. animal 89, interbout arousal, forward, heart

source_name: Animal 89, interbout arousal, forward, heart

source_name: Spermophilus lateralis heart reference RNA


title: S.l. animal 78, interbout arousal, forward, heart

source_name: Animal 78, interbout arousal, forward, heart


title: S.l. animal 52, interbout arousal, reverse, heart

source_name: Animal 52, interbout arousal, reverse, heart


title: S.l. animal 52, interbout arousal, forward, heart

source_name: Animal 52, interbout arousal, forward, heart


title: S.l. animal 34, late torpor, forward, heart

source_name: Animal 34, late torpor, forward, heart


title: S.l. animal 5, summer awake, reverse, heart

source_name: Animal 5, summer awake, reverse, heart


title: S.l. animal 29, summer awake, forward, heart

source_name: Animal 29, summer awake, forward, heart


title: S.l. animal 29, summer awake, reverse, heart

source_name: Animal 29, summer awake, reverse, heart


title: S.l. animal 30, summer awake, reverse, heart

source_name: Animal 30, summer awake, reverse, heart


title: S.l. animal 34, late torpor, reverse, heart

source_name: Animal 34, late torpor, reverse, heart


title: S.l. animal 30, summer awake, forward, heart

source_name: Animal 30, summer awake, forward, heart


title: S.l. animal 3, summer awake, forward, heart

source_name: Animal 3, summer awake, forward, heart


title: S.l. animal 19, late torpor, reverse, heart

source_name: Animal 19, late torpor, reverse, heart


title: S.l. animal 2, summer awake, forward, heart

source_name: Animal 2, summer awake, forward, heart


title: S.l. animal 19, late torpor, forward, heart

source_name: Animal 19, late torpor, forward, heart


title: S.l. animal 130, interbout arousal, reverse, heart

source_name: Animal 130, interbout arousal, reverse, heart


title: S.l. animal 3, summer awake, reverse, heart

source_name: Animal 3, summer awake, reverse, heart