title: BG1-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69971.gif
Strain Name: BG1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1160, 6760; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 285131; Parameter Laser Power = 1.39; Parameter Scan Time = 17:19:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.57; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 650041; Parameter Laser Power = 2.21; Parameter Scan Time = 17:19:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.57; Performer: Boris,,Stambuk

tag: S288c  1 ug genomic DNA sonicated

source_name: BG-1 1 ug genomic DNA HaeIII cut

tag: BG-1 1 ug genomic DNA HaeIII cut


title: Tumor Sample 2

status: Public on Sep 24 2009

type: RNA

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer

scan_protocol: The resulting detection pictures were evaluated using the Geniom Wizard Software.

data_processing: For each array, the median signal intensity was extracted from the raw data file such that for each miRNA seven intensity values have been calculated corresponding to each replicate copy of miRBase on the array. Following background subtraction the seven replicate intensity values of each miRNA were summarized by their median value. To normalize the data across different arrays, quantile normalizatio  was applied.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood of tumor patient

label_protocol: Sample labeling with biotin has been carried out either by using the miRVANA™ miRNA Labeling Kit (Applied Biosystems Inc, Foster City, California USA) or by microfluidic-based enzymatic on-chip labeling of miRNAs (MPEA).

extract_protocol: It is a known fact that that gene expression in peripheral blood changes post-phlebotomically within a few minutes via transcript induction and degradation (Rainen, Oelmueller et al. 2002; Kruhoffer, Dyrskjot et al. 2007).  To counter this problem, the PAXgeneTM blood sample tubes have been developed. These tubes contain a solution that lyses blood cells and at the same time stabilizes the RNA. By that, the ex vivo changes of expression profiles are avoided. The RNA can be stabilized by PAXgene™ system can stabilize RNA for three days at 18-25°C, for five days at 2-8°C, and over a longer period (at least 6 months) at -20°C to -70°C. The PAXgene™ tubes contain 6,9 ml of RNA stabilizing solution and are suitable for the sampling of 2,5 ml blood per tube. Two tubes at 2,5 ml blood were sampled from each patient and healthy blood donor, which equals 5 ml per person. After 8-10fold reversal of the tubes, they were stored over night at 4°C. For a longer storage over several days tubes were frozen at -20°C. Before RNA isolation the blood was incubated for at least 2 hours at room temperature (RT).  2 Isolation of total RNA including miRNA    The contents of both blood sampling tubes of each patient and healthy donor was pooled and centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL  were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step  with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

tag: class label

value: lung tumor


title: Stumpy 297 Y 1

city: Seattle

first: Dhileep

last: Sivam

state: WA

address: 307 Westlake Ave N

department: Bioinformatics Core

country: USA

institute: Seattle Biomedical Research Institute

description: Cells were isolated from irradiated Wistar rats.  Analysis of procyclin expression four hours after cells were induced to differentiate with 6 mM cis aconitate indicates that 68% of the cells were stumpy

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data pair file (.txt) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trypanosoma brucei brucei TREU927

source_name: T. brucei strain TREU927/4 stumpy

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: In vivo cells were grown in irradiated Wistar rats.  In vitro cultured bloodform cells were grown in HMI-9 supplemented with 10% FCS. Procyclic cells were grown in SDM-79 with 15% FCS.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA).  RNA quality was determined by analysis with an Agilent 2100 bioanalyzer

tag: life cycle stage

value: In vivo stumpy form


title: Stumpy 299 B 1

description: Cells were isolated from irradiated Wistar rats.  Analysis of procyclin expression four hours after cells were induced to differentiate with 6 mM cis aconitate indicates that 88% of the cells were stumpy


title: Stumpy 299 G 1

description: Cells were isolated from irradiated Wistar rats.  Analysis of procyclin expression four hours after cells were induced to differentiate with 6 mM cis aconitate indicates that 89% of the cells were stumpy


title: PE2_1

type: genomic

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69976.gif
Strain Name: PE2

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 6040; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 290921; Parameter Laser Power = 1.32; Parameter Scan Time = 09:44:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.73; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 655831; Parameter Laser Power = 2.02; Parameter Scan Time = 09:44:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.73; Performer: Boris,,Stambuk

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

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S288c  1 ug genomic DNA sonicated

label_protocol: not provided

extract_protocol: not provided

source_name: PE2-1 1 ug genomic DNA HaeIII cut

tag: PE2-1 1 ug genomic DNA HaeIII cut


title: VR1-2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69980.gif
Strain Name: VR1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 5800; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 290471; Parameter Laser Power = 1.40; Parameter Scan Time = 16:50:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.07; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 655381; Parameter Laser Power = 2.11; Parameter Scan Time = 16:50:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.07; Performer: Boris,,Stambuk

source_name: VR1-2 1 ug genomic DNA HaeIII cut

tag: VR1-2 1 ug genomic DNA HaeIII cut


title: control

city: St Lucia

first: Rosemarie

middle: Lotte

last: Kryger

state: Qld

address: Sir Fred Schonell Drive

department: Biochemistry

country: Australia

institute: University of Queensland

description: Anti-sense RNA (aRNA) was synthesised by linear amplification of the total RNA extracted from all BLA samples as well as from the reference samples. Amino-allyl dUTP was incorporated to minimize dye bias.

hyb_protocol: Labelled sample plus 8μl 20xSSC, 20μl deionised formamide and 1μl 20% (w/v) SDS, 95oC for 5 min, then 45oC for 45 min, hybridised to a 19Kv4 human single spotted microarray slide (OCI, Ontario, Canada) for about 18 hr at 42oC

scan_protocol: Slides were scanned on a GSM 487 scanner. Since the scanner read the image in the opposite direction from the way the gene ID of the OCI chip listed it, the first step was to rotate the image through 180o, effectively reversing the gene ID.

data_processing:
ImaGene 5 software (Biodiscovery, El Segundo, CA, USA) was used to analyse the scanned images.  Analysis proceeded with GeneSpring 6.1 software (Silicon Genetics, Redwood, California, USA).
Per-spot per-chip intensity-dependent Lowess fit normalisation. Three filters were used: filter on expression level, filter on flags (present) and filter on error. The cross-gene error model gave a value for the average constant error of the spots and genes with a raw data value of less than this were filtered out. Three filters were used: filter on expression level, filter on flags (present) and filter on error. The resultant gene list was subjected to an ANOVA (p<0.05). The ANOVA list was submitted to the NIH annotation program “DAVID”
Normalisation description: a Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Values below 0.01 were set to 0.01

source_name: human basolateral amygdala

label_protocol: Amino-allyl dUTP was incorporated to minimize dye bias. aRNA (6μg) and 6μg random hexamer primer (Roche Diagnostics, Castle Hill, NSW, Australia) plus 0.5μl RNase inhibitor (Invitrogen, Melbourne, Australia) in a volume of 8.5μl, 70oC for 10 min, 5μl RT 5

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: mc1 age

tag: mc1 cause of death

value: Suicide by hanging. Asphyxia

tag: mc1 medical history

value: Asthma

tag: mc1 gender

value: male

tag: mc2 gender

tag: mc2 age

tag: mc2 cause of death

value: Pulmonary embolism

tag: mc2 medical history

value: heavy smoker & high cholesterol

tag: mc3 age

tag: mc3 cause of death

value: Cardiac coronary artery  atheroma

tag: mc3 medical history

value: Heavy smoker

tag: mc3 gender

tag: mc4 age

tag: mc4 cause of death

value: Coronary thrombosis

tag: mc4 medical history

value: Hyper cholesterolemia, heavy smoker

tag: mc4 gender

tag: mc5 age

tag: mc5 cause of death

value: Cardiac tamponade, ganglioneuroma

tag: mc5 medical history

value: No medical conditions

tag: mc5 gender

tag: mc6 age

tag: mc6 cause of death

value: Ischaemic heart disease

tag: mc6 medical history

value: Social smoker

tag: mc6 gender

source_name: Total RNA from pooled human motor cortex, pallidus/putamen, caudate and cerebellum (alcoholics as well as controls)

tag: reference


title: Tumor Sample 1

tag: class label


title: alcoholic

tag: ma1 age

tag: ma1 cause of death

value: Broncopneumonia & myocardial infarction

tag: ma1 medical history

value: Alcoholic liver disease 10 years, microvesicular steatosis, smoker

tag: ma1 gender

tag: ma2 age

tag: ma2 cause of death

value: Acute Alcohol poisoning

tag: ma2 medical history

value: Head injury, epilepsy, diabetes cirrhosis; fatty liver

tag: ma2 gender

tag: ma3 age

tag: ma3 cause of death

value: Bleeding oesophageal varices

tag: ma3 medical history

value: Alcoholic liver disease  Macrovesicular steatosis

tag: ma3 gender

tag: ma4 age

tag: ma4 cause of death

value: Cardiomyopathy

tag: ma4 medical history

value: Obese, ventolin macrovesicular steatosis, alcoholic steatohepatitis

tag: ma4 gender

tag: ma5 age

tag: ma5 cause of death

value: Alcohol Intoxication

tag: ma5 medical history

value: Alcoholic hepatitis, cirrhosis

tag: ma5 gender

tag: ma6 age

tag: ma6 cause of death

value: Ischaemic Disease and emphysema

tag: ma6 medical history

value: longterm homeless person, steatosis

tag: ma6 gender

value: Total RNA from pooled human motor cortex, pallidus/putamen, caudate and cerebellum (alcoholics as well as controls)


title: S288C self

description:
Simple annotation: control, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69284.gif
Strain Name: S288C

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 840, 5960; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-07-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 700; Parameter Laser on time = 305454; Parameter Laser Power = 1.27; Parameter Scan Time = 13:17:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.82; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-07-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 670364; Parameter Laser Power = 2.06; Parameter Scan Time = 13:17:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.82; Performer: Barbara,,Dunn

source_name: S288C genomic DNA 1lg sonicated

tag: S288C genomic DNA 1lg sonicated


title: L6E9_rat_myoblast_cell_line_infected_with_Y T.cruzi_strain_rep1

status: Public on Sep 23 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
l6e9 rat myogenic neonatal cell line (nadal-ginard b. cell. 1978 15(3): 855-64). Infection: Trypanosoma cruzi, Brazil (TCI); Y, CL and Tulahuen (TC II) strains
Determine and compare the transcriptomic alteration induced by infection with various strains of the parasite T. cruzi

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 27k Operon rat oligonucleotides V3.0 (GPL9207). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_647

organism: Rattus norvegicus

label_protocol: 20ug total RNA extracted from the culture dish was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: The L6E9 rat myoblast cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin/Streptomycin at 37°C with 5% CO2 atmosphere. Cells were dissociated with Trypsin/EDTA solution (Gibco) and 1mil cells were plated in 100mm cell culture dishes. After 24 hours of plating, cells were washed with PBS containing Ca2+ and Mg2+ (Gibco) and infected with 2x106 trypomastigote forms of T. cruzi in DMEM.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: After 24 hours of plating in 100mm cell culture dishes, myoblasts were washed with PBS containing Ca2+ and Mg2+ (Gibco). 4 dishes were kept as control and 16 dishes were infected with 2mil trypomastigote forms of the Y, CL, Tulahuen or Brazil Trypanosoma cruzi strains (4 dishes for each strain). Forty eight hours post-infection cells were washed twice with Ca2+/Mg2+ PBS to remove free trypomastigotes in the supernatant and re-fed with fresh supplemented DMEM. Total RNA was harvested at 72 hours post infection using TRIZOL reagent (Invitrogen) following the protocol indicated by the manufacturer when at least 25% of the cultured cells were infected, presenting only intracellular amastigotes and no release of trypomastigotes (which would lead to reinfection of culture)

tag: cell line

value: l6e9 rat myogenic neonatal cell line (nadal-ginard b. cell. 1978 15(3):855-64).

tag: infection

value: Y strain


title: L6E9_rat_myoblast_cell_line_infected_with_Y T.cruzi_strain_rep3


title: L6E9_rat_myoblast_cell_line_infected_with_Y T.cruzi_strain_rep4

hyb_protocol: Alexa Fluor®_555-labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-labeled biological replica overnight at 50°C on a MO2 AECOM mouse oligonucleotide array spotted with 27k Operon rat oligonucleotides V3.0 (GPL9207). Hybridization design ("multiple yellow" strategy) described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from the culture dish was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: L6E9_rat_myoblast_cell_line_infected_with_Tulahuen T.cruzi_strain_rep2

value: Tulahuen strain


title: L6E9_rat_myoblast_cell_line_infected_with_Tulahuen T.cruzi_strain_rep4


title: L6E9_rat_myoblast_cell_line_infected_with_Tulahuen T.cruzi_strain_rep3


title: L6E9_rat_myoblast_cell_line_infected_with_CL T.cruzi_strain_rep4

value: CL strain


title: L6E9_rat_myoblast_cell_line_infected_with_Y T.cruzi_strain_rep2


title: L6E9_rat_myoblast_cell_line_infected_with_CL T.cruzi_strain_rep3


title: L6E9_rat_myoblast_cell_line_infected_with_CL T.cruzi_strain_rep2


title: L6E9_rat_myoblast_cell_line_infected_with_Brazil T.cruzi_strain_rep3

value: Brazil strain


title: L6E9_rat_myoblast_cell_line_infected_with_Brazil T.cruzi_strain_rep2


title: L6E9_rat_myoblast_cell_line_infected_with_CL T.cruzi_strain_rep1


title: Control_ L6E9_rat_myoblast_cell_line_rep4

source_name: Control_ L6E9_rat_myoblast_cell_line

value: control


title: Control_ L6E9_rat_myoblast_cell_line_rep3


title: L6E9_rat_myoblast_cell_line_infected_with_Brazil T.cruzi_strain_rep4


title: intermediolateral column motoneuron (IML), Transection, Set e2, Replicate 2

city: Atlanta

first: Dapeng

last: Cui

state: GA

address: 24 Peachtree Center Avenue

department: Biology

institute: Georgia State University

description: The study generated 30 chips from sham-operated control mice and 32 chips from spinalized (spinal cord transection) mice. The expression profiles from sham control animals have been uploaded to GEO website with accession number GSE2595

hyb_protocol: The high quality aRNA target was express mailed on dry ice to the Genomics Core Laboratory at the Medical College of Georgia, (Augusta, GA), whereupon it was fragmented and hybridized to Affymetrix oligonucleotide microarrays (Murine Genome Chip U74Av2) according to the manufacturer’s instructions.

scan_protocol: Per affymetrix protocol

data_processing: The digitized data were processed with Affymetrix MAS software and then normalized with RMA to generate a list of all the probe sets on the chip and their corresponding signal intensities.

organism: Mus musculus

label_protocol: A modification of Baugh et al., (2001) was used for aRNA amplification and labeling, in which the first IVT is followed by a second round of RT, SSS, and IVT. In the first round, RNA was primed with 4 pmol of the (dT)-T7 primer described above, and reverse transcribed in 2µl with 0.8 µg T4gp32 (USB, Cleveland, Ohio), 20U SuperScript II, 10mM DTT, 500µM dNTP in first-strand buffer at 42C for 1h. The reaction was inactivated at 65C for 15minutes. SSS was performed in 15µl with 200µM dNTP, 4U DNA polymerase I, 0.2 U RNase H and 1U E.coli DNA ligase. The resulting cDNA was polished with 2U T4 DNA polymerase and purified as described above. All of the cDNA was then used as the template in a 20µl IVT (Enzo kit) and the resulting aRNA was purified as described above. The aRNA was precipitated with 20µg of glycogen (Ambion) after measuring the absorbance (OD260/280 and yield were typically 1.9~2.1 and 100~500ng, respectively). The pellet was then re-dissolved in 2µl of water, and the second round RT was performed. The first round aRNA was primed at 70C for 4 minutes with 20 pmol random hexamer and 10pmol of TC primers [5’-TATCAACGCAGAGTCCC-3’, 5’-TATCAACGCAGAGTCGG-3’] (Ginsberg and Che, 2002). Next, the RT was performed in 5µl containing 1.6µg T4gp32, 40U SuperScript II, 20mM DTT, 500µM dNTP in first-strand buffer. The reaction was incubated for 20 minutes at 37C, then 20 minutes at 42C, followed by 10 minutes at 50C and finally 10 minutes at 55C. The reaction was inactivated at 65C for 10 minutes. First round aRNA was degraded by adding 0.5U RNase H and the reaction was incubated at 37C for 30 minutes. The first strand DNA was then denatured at 95C for 2 minutes. In preparation for the second round SSS, the first strand DNA was primed by adding 20pmol (dT)-T7 at 42C for 10 minutes. The second round SSS was then performed in 30µl containing 200µM dNTP, 8U E.Coli DNA polymerase I, 0.4U RNase H in second-strand buffer at 15C for 2h. cDNA was polished with 5U T4 DNA polymerase and purified as described above. The resulting cDNA was diluted to 50µl, 5µl were used for quantitative real time PCR (QRT-PCR; see below) and the remaining 45µl were precipitated and used as the template in a 40µl IVT. The resulting biotinylated aRNA was purified as described above. aRNA was only used as a target if it was of high quality (OD260/280 of 1.9~2.1, yield of 20µg, and a smear centered at around 1kb).

extract_protocol: Motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, total RNA was extracted from the 400 captures using an Arcturus picopure kit

tag: gender

value: male

tag: age

value: postnatal day 24

tag: tissue

value: spinal cord

tag: cell type


title: medial motoneuron (MMN), Transection, Set e2, Replicate 1

value: medial motoneuron (MMN)


title: intermediolateral column motoneuron (IML), Transection, Set e2, Replicate 1


title: medial motoneuron (MMN), Transection, Set e2, Replicate 2


title: L6E9_rat_myoblast_cell_line_infected_with_Brazil T.cruzi_strain_rep1


title: Control_ L6E9_rat_myoblast_cell_line_rep2


title: medial motoneuron (MMN), Transection, Set e1, Replicate 2


title: lateral motoneuron (LMN), Transection, Set e2, Replicate 2

value: lateral motoneuron (LMN)


title: lateral motoneuron (LMN), Transection, Set e1, Replicate 2


title: medial motoneuron (MMN), Transection, Set d, Replicate 2


title: intermediolateral column motoneuron (IML), Transection, Set e1, Replicate 1


title: intermediolateral column motoneuron (IML), Transection, Set e1, Replicate 2


title: lateral motoneuron (LMN), Transection, Set e1, Replicate 1


title: medial motoneuron (MMN), Transection, Set d, Replicate 1


title: intermediolateral column motoneuron (IML), Transection, Set d, Replicate 2


title: intermediolateral column motoneuron (IML), Transection, Set d, Replicate 1


title: medial motoneuron (MMN), Transection, Set e1, Replicate 1


title: lateral motoneuron (LMN), Transection, Set e2, Replicate 1


title: lateral motoneuron (LMN), Transection, Set d, Replicate 2


title: lateral motoneuron (LMN), Transection, Set d, Replicate 1


title: intermediolateral column motoneuron (IML), Transection, Set b, Replicate 2


title: lateral motoneuron (LMN), Transection, Set c, Replicate 2


title: lateral motoneuron (LMN), Transection, Set b, Replicate 2


title: intermediolateral column motoneuron (IML), Transection, Set b, Replicate 1


title: medial motoneuron (MMN), Transection, Set b, Replicate 2


title: L6E9_rat_myoblast_cell_line_infected_with_Tulahuen T.cruzi_strain_rep1


title: lateral motoneuron (LMN), Transection, Set b, Replicate 1


title: Expression Meiosis Time Course - Meiosis 9 hours Replicate 3

type: mixed

city: Chicago

first: Sean

middle: Erik

last: Hanlon

state: IL

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

institute: University of Chicago

hyb_protocol: Reverse transcribed total RNA samples and genomic DNA references were competitively hybridized to yeast whole genome PCR based spotted arrays (resolution ~1kb). Hybridizations were carried out overnight at 65 C.

scan_protocol: The arrays were scanned with an Axon 4000B scanner, and data was extracted using GenePix 6.0 software.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, with a background corrected sum of medians for both channels less than 500, or with fewer than 40 foreground pixels were excluded from analysis (flagged as bad in GenePix). Additionally, failed probes, probes representing intergenic regions, probes representing rRNA, probes representing telomeres and probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (Cy5/Cy3) for each probe was converted to a log2 ratio. These log2 ratios (Cy5/Cy3) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

organism: Saccharomyces cerevisiae SK1

source_name: Genomic DNA

label_protocol: Purified genomic DNA (4 micrograms) was labeled with Klenow (NEB) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy3 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8.

extract_protocol: 100 ml of vegetative cells (OD600 0.6-0.8) were pelleted and resuspended in 2 ml lysis buffer (10 mM Tris-Cl pH 8.0, 100 mM NaCl, 1 mM EDTA, 1% SDS, 2% Triton X-100). The cells were split into 4 tubes (500 ul each) and an equal volume of phenol:chloroform:isoamyl-alcohol was added to each tube. The cells were then lysed with glass beads. The samples were spun down for 5 minutes at top speed and the aqueous layers was transfered to fresh tubes. Nucleic acids were precipitated with 1 ml of 95% ethanol and resuspended in 200 ul of 1X TE + 30 ug RNAse and incubated at 30 C for 30 minutes. 5 M NaCl was added to a final concentration of 500 mM and the samples were precipitated with isopropanol. Pellets were washed 2X with 70% ethanol and dried at room temperature for 30 minutes. The resulting genomic DNA was resuspended in 10 mM Tris-Cl pH 7.4 and pooled and the concentration was determined with a spectrophotometer.

tag: strain

value: SK1 yeast strain SHy002

tag: growth condition

value: YPD

tag: molecule

value: Genomic DNA

source_name: RT cDNA from cells 9hr after transfer to sporulation media (SM) - Replicate 3

label_protocol: Total RNA (30 micrograms) was reverse-transcribed using SuperScript II Reverse Transcriptase (Invitrogen) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy5 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

growth_protocol: Synchronous sporulation was carried out by using YPD overnight cultures of wild-type cells to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm.

extract_protocol: Total RNA was isolated from frozen samples using hot acid-phenol as previously described (Ausubel 1997).

value: Meiosis 9 hours

value: reverse transcribed total RNA


title: Expression Meiosis Time Course - Meiosis 12 hours Replicate 1

source_name: RT cDNA from cells 12hr after transfer to sporulation media (SM) - Replicate 1

value: Meiosis 12 hours


title: medial motoneuron (MMN), Transection, Set b, Replicate 1


title: lateral motoneuron (LMN), Transection, Set c, Replicate 1


title: Expression Meiosis Time Course - Meiosis 12 hours Replicate 3

source_name: RT cDNA from cells 12hr after transfer to sporulation media (SM) - Replicate 3


title: Expression Meiosis Time Course - Meiosis 4.5 hours Replicate 1

source_name: RT cDNA from cells 4.5hr after transfer to sporulation media (SM) - Replicate 1

value: Meiosis 4.5 hours


title: Expression Meiosis Time Course - Meiosis 3 hours Replicate 3

source_name: RT cDNA  from cells 3hr after transfer to sporulation media (SM) - Replicate 3

value: Meiosis 3 hours


title: Expression Meiosis Time Course - Meiosis 6 hours Replicate 1

source_name: RT cDNA from cells 6hr after transfer to sporulation media (SM) - Replicate 1

value: Meiosis 6 hours


title: Expression Meiosis Time Course - Meiosis 3 hours Replicate 1

source_name: RT cDNA  from cells 3hr after transfer to sporulation media (SM) - Replicate 1


title: lateral motoneuron (LMN), Transection, Set a, Replicate 2


title: intermediolateral column motoneuron (IML), Transection, Set a, Replicate 2


title: Expression Meiosis Time Course - Meiosis 4.5 hours Replicate 3

source_name: RT cDNA from cells 4.5hr after transfer to sporulation media (SM) - Replicate 3


title: MC38 tumor CpG 1826 treated_183

city: Melbourne

first: Michael

middle: Henry

last: Kershaw

state: Victoria

address: 14 St. Andrews Place

department: Research

institute: Peter MacCallum Cancer Centre

description: MC38 tumor CpG 1826 treated

hyb_protocol: Hybridization was performed on Mouse Gene 1.0 ST arrays according to Affymetix instructions.

scan_protocol: Affymetrix platform, using a fluidics station FS450 for washing and staining the arrays and a single laser GS-7000 scanner with autoloader. Expression Console software (Affymetrix) is used for preliminary data analysis and quality control

data_processing: The data were analyzed with R 2.7.1 using the affy and limma packages.

source_name: MC38 tumor CpG 1826 treated

label_protocol: Labelling & amplification kit used is the Affyemtrix WT (whole transcriptome) labelling and amplification kit

growth_protocol: MC38 colon cancer cells were grown in C57BL/6 mice subcutaneously

extract_protocol: Total RNA was extracted using Qiagen RNAeasy kits

treatment_protocol: MC38 tumors in mice (~40 mm2) were injected with 50 micrograms of CpG1826 in 50 microliters PBS. Six hours later tumors were disected and frozen.

value: MC38 colon cancer cells

tag: mouse id number

tag: agent


title: Expression Meiosis Time Course - Meiosis 9 hours Replicate 1

source_name: RT cDNA from cells 9hr after transfer to sporulation media (SM) - Replicate 1


title: MC38 tumor PBS treated_592

description: MC38 tumor PBS treated

source_name: MC38 tumor PBS treated

value: PBS


title: MC38 tumor CpG 1826 treated_595

description: MC38 tumor CpG 1826 treated


title: medial motoneuron (MMN), Transection, Set a, Replicate 2


title: Expression Meiosis Time Course - Meiosis 0 hours Replicate 3

source_name: RT cDNA  from cells 0hr after transfer to sporulation media (SM) - Replicate 3

value: Meiosis 0 hours


title: Expression Meiosis Time Course - Meiosis 6 hours Replicate 3

source_name: RT cDNA from cells 6hr after transfer to sporulation media (SM) - Replicate 3


title: Expression Meiosis Time Course - Meiosis 1.5 hours Replicate 3

source_name: RT cDNA  from cells 1.5hr after transfer to sporulation media (SM) - Replicate 3

value: Meiosis 1.5 hours


title: PKRKO_mock 1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: 24 hr infection

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data were obtained and processed with the Agilent Feature Extraction Software (v9.5).  The resulting data were imported into Rosetta Resolver (v7.1) and log2 intensities were exported.

source_name: Mouse/ Lung, PKR deficient, viral-free media treated

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Trizol/Qiagen RNA clean up

value: Male

value: PKR-/-


title: medial motoneuron (MMN), Transection, Set a, Replicate 1

value: male

value: postnatal day 24

value: spinal cord

value: medial motoneuron (MMN)


title: Expression Meiosis Time Course - Meiosis 1.5 hours Replicate 1

value: SK1 yeast strain SHy002

value: YPD

value: Genomic DNA

source_name: RT cDNA  from cells 1.5hr after transfer to sporulation media (SM) - Replicate 1


title: MC38 tumor CpG 1826 treated_50

description: MC38 tumor CpG 1826 treated


title: Dicer KO replicate 3

city: San Francisco

first: Robert

last: Blelloch

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

description: Gene expression data from Dicer knockout ES cells

hyb_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).

data_processing: Data were normalized using the GCRMA algorithm.

source_name: Embryonic Stem Cells

growth_protocol: Wild-type, dgcr8 knockout, and dicer1 knockout ES cells were plated on 60-mm plates in triplicate.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: embryonic stem cells

tag: genetic modification

value: Dicer knockout


title: KO_RSV 1

description: 24 hr infection

source_name: Mouse/ Lung, PKR deficient, RSV treated


title: KO_RSV 2

description: 24 hr infection


title: KO_RSV 3

description: 24 hr infection


title: Expression Meiosis Time Course - Meiosis 0 hours Replicate 1

source_name: Genomic DNA

source_name: RT cDNA  from cells 0hr after transfer to sporulation media (SM) - Replicate 1

value: reverse transcribed total RNA


title: Expression Meiosis Time Course - YPA 8 hours Replicate 1

source_name: RT cDNA RT cDNA from cells in respiratory growth (YPA 8 hours) - Replicate 1

value: YPA 8 hours


title: MC38 tumor CpG 1826 treated_189

description: MC38 tumor CpG 1826 treated

value: MC38 colon cancer cells


title: MC38 tumor PBS treated_661

description: MC38 tumor PBS treated

value: PBS


title: intermediolateral column motoneuron (IML), Transection, Set a, Replicate 1


title: PKRKO_mock 3

description: 24 hr infection


title: Dicer KO replicate 1

scan_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).


title: Expression Meiosis Time Course - YPA 8 hours Replicate 3

source_name: RT cDNA RT cDNA from cells in respiratory growth (YPA 8 hours) - Replicate 3


title: lateral motoneuron (LMN), Transection, Set a, Replicate 1

value: lateral motoneuron (LMN)


title: Dicer KO replicate 2

label_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).


title: Dgcr8 KO replicate 3

description: Gene expression data from Dgcr8 knockout ES cells

value: Dgcr8 knockout


title: MC38 tumor PBS treated_26

description: MC38 tumor PBS treated


title: Expression Meiosis Time Course - YPD Replicate 1

source_name: RT cDNA from cells growing logarithmically (YPD) - Replicate 1


title: Dgcr8 KO replicate 2


title: WT_RSV 3

description: 24 hr infection

source_name: Mouse/ Lung, WT, RSV treated

value: Male


title: MC38 tumor PBS treated_29

description: MC38 tumor PBS treated


title: Dgcr8 KO replicate 1


title: WT_RSV 1

description: 24 hr infection


title: WT_mock 2

description: 24 hr infection

source_name: Mouse/ Lung, WT, viral-free media treated


title: MC38 tumor CpG 1826 treated_58

description: MC38 tumor CpG 1826 treated

source_name: MC38 tumor CpG 1826 treated


title: MC38 tumor PBS treated_482

description: MC38 tumor PBS treated


title: PKRKO_mock 2

description: 24 hr infection

value: PKR-/-


title: WT3_mock

description: 24 hr infection


title: WT replicate 1

description: Gene expression data from WT ES cells

value: WT


title: WT replicate 2

description: Gene expression data from WT ES cells


title: WT_RSV 2

description: 24 hr infection


title: WT_mock 1

description: 24 hr infection


title: 24 hour phosphate starvation replicate 3

status: Public on Sep 22 2009

city: Baltimore

first: Petros

last: Karakousis

state: MD

address: 1550 Orleans street

department: Medicine

institute: John Hopkins University school of medicine

description: These data represent genes which were expressed in 24 hour phosphate-starved culture versus log phase phosphate-replete cultures.

hyb_protocol: PolyA, yeast tRNA, bovine rRNA human COT1 DNA was added to combined labeled cDNA samples as a blocker. Samples were added to hybridization buffer (10XSSC, 30% formamide, 0.2% SDS), denatured at 95°C for 3 minutes, and snap cooled on ice. Samples were loaded onto the slide by capillary action under a Corning lifter slip and sealed into a corning hybridization chamber with 30µl water at each as a humidifier. Samples were hybridized to the slides for 18 hours at 55°C in a hybridization oven. Hybridized slides were washed for 10 minutes at room temperature in each of 2XSSC, 0.1%SDS; 1XSSC, 0.1%SDS; 1XSSC; 0.5XSSC; and rinsed for 10 seconds in distilled water.

scan_protocol: Fluorescence intensity data were collected with a GenePix 4000B scanner (Axon Instruments) with GenePix Pro 4.0 software. Photomultiplier tube gains were set empirically for each channel to optomize intensity and to equalize intensities for control spots on each channel.

data_processing: Collected microarray data were normalized as follows: the sum total measured intensity of all genes from the sample channel (24 hrs) was divided by that of the control channel, and each gene's intensity value from the control channel then was multiplied by this ratio (global normalization). Globally normalized expression values were log2-transformed in order to calculate mean log intensity and log ratios between sample and control values. Local mean normalization was performed using Stata 10 software (StataCorp LP, College Station, TX) across the range of expression levels. The "residuals" from this regression fit (i.e., the distance between observed data and the regression fit,) were used as corrected log ratio values and further analyzed using SAM (Significance Analysis of Microarrays, version 3.01) software to obtain q-values (false discovery rate).

organism: Mycobacterium tuberculosis CDC1551

source_name: Log phase culture

label_protocol: Fluorescently-labeled cDNA was generated using Superscript III (Biorad) and fluorescent dyes Cy5 (Amersham).

extract_protocol: Log phase culture was centrifuged at 3500 rpm for 10 minutes at 4˚C. The supernatants were removed and the pellets resuspended in 1 ml TriZOL reagent (GIBCO/BRL). Mycobacterial membranes were disrupted using 0.1 mm zirconia/silica beads in a Bio-Spec bead beater (8 cycles x 30 sec/cycle). Mycobacterial RNA was recovered by centrifugation, chloroform extraction, and isopropyl alcohol precipitation. Prior to reverse transcription, RNA was treated with RNase-free DNase (Ambion) and subjected to 40 cycles of PCR to assure that all DNA had been removed, as assessed by ethidium bromide-stained agarose gel analysis.

tag: Mycobacterium tuberculosis CDC1551 was grown in modified Middlebrook broth containing 25mM phosphate until log phase (OD600 ~0.4).

source_name: 24 hour phosphate-starved culture

extract_protocol: 24 hour phosphate-starved culture was centrifuged at 3500 rpm for 10 minutes at 4˚C. The supernatants were removed and the pellets resuspended in 1 ml TriZOL reagent (GIBCO/BRL). Mycobacterial membranes were disrupted using 0.1 mm zirconia/silica beads in a Bio-Spec bead beater (8 cycles x 30 sec/cycle). Mycobacterial RNA was recovered by centrifugation, chloroform extraction, and isopropyl alcohol precipitation. Prior to reverse transcription, RNA was treated with RNase-free DNase (Ambion) and subjected to 40 cycles of PCR to assure that all DNA had been removed, as assessed by ethidium bromide-stained agarose gel analysis.

tag: Mycobacterium tuberculosis CDC1551 was grown in modified Middlebrook broth containing 25 mM phosphate until log phase (OD600 ~0.4). Then culture was pelleted, washed twice in modified Middlebrook phosphate-free broth by centrifugation at 3000 rpm for 5 min and resuspended in an equal volume of phosphate-free broth. Phosphate-starved cultures were incubated for 24 hours in a shaker at 37 °C.


title: 72 hour phosphate starvation replicate 1

description: These data represent genes which were expressed in 72 hour phosphate-starved culture versus log phase phosphate-replete cultures.

data_processing: Collected microarray data were normalized as follows: the sum total measured intensity of all genes from the sample channel (72 hrs) was divided by that of the control channel, and each gene's intensity value from the control channel then was multiplied by this ratio (global normalization). Globally normalized expression values were log2-transformed in order to calculate mean log intensity and log ratios between sample and control values. Local mean normalization was performed using Stata 10 software (StataCorp LP, College Station, TX) across the range of expression levels. The "residuals" from this regression fit (i.e., the distance between observed data and the regression fit,) were used as corrected log ratio values and further analyzed using SAM (Significance Analysis of Microarrays, version 3.01) software to obtain q-values (false discovery rate).

source_name: 72 hour phosphate-starved culture

extract_protocol: 72 hour phosphate-starved culture was centrifuged at 3500 rpm for 10 minutes at 4˚C. The supernatants were removed and the pellets resuspended in 1 ml TriZOL reagent (GIBCO/BRL). Mycobacterial membranes were disrupted using 0.1 mm zirconia/silica beads in a Bio-Spec bead beater (8 cycles x 30 sec/cycle). Mycobacterial RNA was recovered by centrifugation, chloroform extraction, and isopropyl alcohol precipitation. Prior to reverse transcription, RNA was treated with RNase-free DNase (Ambion) and subjected to 40 cycles of PCR to assure that all DNA had been removed, as assessed by ethidium bromide-stained agarose gel analysis.

tag: Mycobacterium tuberculosis CDC1551 was grown in modified Middlebrook broth containing 25 mM phosphate until log phase (OD600 ~0.4). Then culture was pelleted, washed twice in modified Middlebrook phosphate-free broth by centrifugation at 3000 rpm for 5 min and resuspended in an equal volume of phosphate-free broth. Phosphate-starved cultures were incubated for 72 hours in a shaker at 37 °C.


title: 72 hour phosphate starvation replicate 3


title: 72 hour phosphate starvation replicate 2


title: 24 hour phosphate starvation replicate 1

description: These data represent genes which were expressed  in 24 hour phosphate-starved culture versus log phase phosphate-replete cultures.

hyb_protocol: PolyA, yeast tRNA, bovine rRNA human COT1 DNA was added to combined labeled cDNA samples as a blocker. Samples were added to hybridization buffer (10XSSC, 30% formamide, 0.2% SDS), denatured at  95°C for 3 minutes, and snap cooled on ice. Samples were loaded onto the slide by capillary action under a Corning lifter slip and sealed into a corning hybridization chamber with 30µl water at each as a humidifier. Samples were hybridized to the slides for 18 hours at 55°C in a hybridization oven. Hybridized slides were washed for 10 minutes at room temperature in each of 2XSSC, 0.1%SDS; 1XSSC, 0.1%SDS; 1XSSC; 0.5XSSC; and rinsed for 10 seconds in distilled water.


title: m1_CD44lo

first: Mark

last: Klinger

address: 513 Parnassus Avenue, Box0414

department: Microbiology and Immunology

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 5

hyb_protocol: Equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). This procedure was carried out using the Bioconductor package limma (http://www.bioconductor.org). No background subtraction was performed.

source_name: Sorted CD4+ T cells, CD44lo

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturer’s protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE).

growth_protocol: Primary cells.

extract_protocol: Total RNA was purified with the RNEasy mini kit (Qiagen) with on-column DNAse treatment according to manufacturer's instructions.  Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto).

treatment_protocol: Sorted lymphocytes.

tag: Strain

tag: Gender

value: male

tag: Age

value: 15 weeks

tag: Tissue

value: pooled spleen and lymph nodes


title: m2_CD44hi

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 8

source_name: Sorted CD4+ T cells, CD44hi


title: 24 hour phosphate starvation replicate 2


title: m1_Treg

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 4

source_name: Sorted CD4+ T cells, Treg


title: m2_Tnaive

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 1

source_name: Sorted CD4+ T cells, naïve


title: m1_Tnaive

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 6


title: m2_Treg

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 7


title: m1_CD44hi

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 2


title: m2_CD44lo

description:
Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 3


title: Expression Meiosis Time Course - YPD Replicate 3

value: SK1 yeast strain SHy002

source_name: RT cDNA from cells growing logarithmically (YPD) - Replicate 3


title: WT replicate 3

description: Gene expression data from WT ES cells

source_name: Embryonic Stem Cells


title: M.lck6.vs.wt5 dye swap

description: Amplified total RNA was hybridized to MEEBO arrays

hyb_protocol: Hybridizations to Mouse Exonic Evidence Based Oligonucleotide (MEEBO) spotted microarrays were performed at 55˚C for 48 hours in Slide Hybridization buffer (Ambion).  A total of 16 arrays were used to analyze regulatory and memory subsets from eight mice (two arrays per littermate pair, including dye swaps, were used for each comparison).

scan_protocol: After hybridization, the arrays were washed and scanned using an Axon 4000B laser scanner (Molecular Devices).  Image analysis was performed using Spotreader (Niles Scientific).

data_processing: The ‘print-tip loess’ normalization was used to correct for within-array dye and spatial effects and single channel quantile normalization was used to facilitate comparison between arrays.  Functions in the library marray Norm of the R/Bioconductor package were used to perform these normalizations.

source_name: lck-deficient memory T cells

label_protocol: AminoAllyl-modified amplified RNA (aRNA) was prepared from approximately 1μg of total RNA using the AminoAllyl Message Amp II kit (Ambion).  15μg of this aRNA in 0.05 M sodium bicarbonate pH9.0 were then coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 dyes (CyScribe, Amersham Biosciences) for 90 minutes in the dark.  The labelled aRNA was neutralized with 100mM sodium acetate pH5.5 and purified using the RNA clean-up kit-25 (Zymo Research).  Immediately prior to hybridization, labelled aRNA samples were fragmented (Ambion Fragmentation buffer, Ambion) and denatured at 95ºC for 10 minutes.

growth_protocol: primary cells

extract_protocol: Total RNA was purified with the RNEasy mini kit (Qiagen) with on-column DNAse treatment according to manufacturer's instructions.  Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto)

treatment_protocol: sorted lymphocytes

value: female

value: 16 weeks

source_name: wt memory T cells


title: M.lck8.vs.wt7 dye swap


title: M.lck6.vs.wt5


title: M.lck8.vs.wt7


title: M.lck2.vs.wt1 dye swap

value: 12 weeks


title: M.lck2.vs.wt1


title: M.lck4.vs.wt3


title: R.lck6.vs.wt5 dye swap

source_name: lck-deficient regulatory T cells

source_name: wt regulatory T cells


title: R.lck6.vs.wt5


title: R.lck8.vs.wt7


title: R.lck8.vs.wt7 dye swap


title: Expression Meiosis Time Course - Meiosis 6 hours Replicate 2

source_name: RT cDNA from cells 6hr after transfer to sporulation media (SM) - Replicate 2

label_protocol: Total RNA (30 micrograms) was reverse-transcribed using SuperScript II Reverse Transcriptase (Invitrogen) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy3 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

value: Meiosis 6 hours

source_name: Genomic DNA

label_protocol: Purified genomic DNA (4 micrograms) was labeled with Klenow (NEB) incorporating amino-allyl dUTP (Sigma) at a ratio of 3:2 with dTTP. Reactive Cy5 (Amersham) was coupled to the amino-allyl of the resulting DNA fragments in the presence of sodium bicarbonate.

value: YPD

value: Genomic DNA


title: Expression Meiosis Time Course - Meiosis 1.5 hours Replicate 2

source_name: RT cDNA  from cells 1.5hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 1.5 hours

value: reverse transcribed total RNA


title: Expression Meiosis Time Course - Meiosis 12 hours Replicate 2

source_name: RT cDNA from cells 12hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 12 hours


title: Expression Meiosis Time Course - Meiosis 0 hours Replicate 2

source_name: RT cDNA  from cells 0hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 0 hours


title: Expression Meiosis Time Course - Meiosis 4.5 hours Replicate 2

source_name: RT cDNA from cells 4.5hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 4.5 hours


title: R.lck4.vs.wt3


title: Expression Meiosis Time Course - YPA 8 hours Replicate 2

source_name: RT cDNA RT cDNA from cells in respiratory growth (YPA 8 hours) - Replicate 2

value: YPA 8 hours


title: R.lck2.vs.wt1 dye swap


title: Expression Meiosis Time Course - Meiosis 9 hours Replicate 2

source_name: RT cDNA from cells 9hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 9 hours


title: Expression Meiosis Time Course - Meiosis 3 hours Replicate 2

source_name: RT cDNA  from cells 3hr after transfer to sporulation media (SM) - Replicate 2

value: Meiosis 3 hours

source_name: genomic DNA


title: R.lck2.vs.wt1

value: male


title: Avastin dosed, biological rep2

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

description: Gene expression data from biopsy of human tumor xenograph grown in mouse dosed with bevacizumab

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133 2.0+ Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Tumor xenograph from mouse dosed with bevacizumab (avastin)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: 5,000,000 Hec50co cells (human endometrial cancer derived cell line) were injected into an athymic mouse and solid tumors were allowed to grow.

extract_protocol: Qiagen RNeasy used for total RNA extraction and was performed according to manufacture's instructions.

treatment_protocol: Mice were injected with saline (undosed) or bevacizumab (avastin) at 0.2 mg/mouse through intraperitoneal injection twice a week, starting the day of cancer cell injection

value: avastin

tag: biological replicate

value: solid tumor grown from Hec50co cell line


title: 071019_Undosed control, biological rep2

description: Gene expression data from biopsy of human tumor xenograph grown in mouse

source_name: Tumor xenograph from undosed mouse

value: saline, control


title: Expression Meiosis Time Course - YPD Replicate 2

source_name: RT cDNA from cells growing logarithmically (YPD) - Replicate 2

value: SK1 yeast strain SHy002


title: R.lck4.vs.wt3 dye swap

value: female

value: 12 weeks

value: pooled spleen and lymph nodes


title: Avastin dosed, biological rep1


title: 071019_Undosed control, biological rep1


title: M.lck4.vs.wt3 dye swap

source_name: lck-deficient memory T cells


title: liver_M_SPF_2_11

city: Singapore

first: Martin

middle: Lloyd

last: Hibberd

address: 60 Biopolis Street, #02-01, Genome

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Labeled cDNA were re-suspended in DIG EasyHyb (Roche, Switzerland) buffer and hybridized overnight (14-16h) in the MAUI Hybridization chamber (BioMicro, USA).

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 6.1 image analysis software (Axon Instruments, USA).

data_processing: The data were Lowess normalized. Normalized ratio of means defined by CH1/CH2

label: Cy3, Cy5

source_name: Mouse liver tissue

label_protocol: For fluorescence labeling, 3 µg of total RNA from the reference or experimental samples were amplified using Ambion Amino Allyl MessageAmp aRNA Kit (Anbion) and reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled aRNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Adult NMRI mice were reared germ-free or specific pathogen free

extract_protocol: Total RNA of tissue samples were extracted using RNAeasy mini kit (Qiagen) according to the manufacturers instructions.

treatment_protocol: Direct comparison between germ-free and specific pathogen free mice without treatment

value: liver

tag: growth protocol

value: specific pathogen free

source_name: Universal mouse reference RNA (Stratagene CAT#740100-41, LOT#0610751)

tag: sample

value: Universal mouse reference RNA


title: C1, 6x st_wash, 1st series

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

institute: University Leipzig

description:
identical RNA hybridised to three arrays (A, B, C), different stringent wash cycles
staining protocol:  3 rounds total composed of staining with streptavidin phycoerythrin (SAPE) in two rounds which are  intermitted by a round of anti-SAPE antibody staining

hyb_protocol: Following fragmentation, 25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2.0. An Affymetrix Fluidics Station 400 was used for washing and staining.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChipScanner 3000 with the 7G upgrade.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: C1, 6x st_wash, 1st series

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: FTC133 cells were cultured under standard conditions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by a column purification with Qiagen RNeasy kit.

treatment_protocol: The cells were untreated.

tag: stringent wash cycles (total)

tag: initial stringent wash cycles before first staining (first series)

tag: additional stringent wash cycles after first staining (first series)

tag: initial stringent wash cycles before second staining (second series)

tag: additional stringent wash cycles after second staining (second series)

tag: staining (first series)

value: 3 rounds

tag: staining (second series)

tag: cell line


title: liver_M_GF_2_38

tag: tissue

value: germ-free


title: liver_M_SPF_2_8


title: liver_M_SPF_2_10


title: liver_M_GF_2_39


title: C2, 12x st_wash, 2nd series

source_name: C2, 12x st_wash, 2nd series


title: B7, 28x st_wash, 2nd series

source_name: B7, 28x st_wash, 2nd series


title: B6 23x st_wash, 2nd series

source_name: B6 23x st_wash, 2nd series


title: B5, 21x st_wash, 2nd series

source_name: B5, 21x st_wash, 2nd series


title: liver_M_GF_2_36


title: liver_M_SPF_2_9


title: B8, 38x st_wash, 2nd series

source_name: B8, 38x st_wash, 2nd series


title: B3, 9x st_wash, 1st series

source_name: B3, 9x st_wash, 1st series


title: liver_M_GF_2_37


title: B1, 2x st_wash, 1st series

source_name: B1, 2x st_wash, 1st series


title: LC from biological replicate C57BL/6_2

city: Dusseldorf

first: Charlotte

last: Esser

address: Auf´m Hennekamp 50

department: Molecular Immunology

institute: IUF

description: For cell culturing of epidermal cells, an additional digestion with DNAse I (15 min, 130 U/ml) was included. The resulting single cell suspension was cultured in complete medium for 16 hours at a density of 1.5x106 cells/ml in 6-well plates. For sorting, epidermal cells were centrifuged on dense BSA or OptiPrep® (Sigma). The low-density fraction contained 20-35 % LC, which were enriched by FACS sorting of vital MHC-II+ cells using a FACSCalibur (Becton Dickinson, Heidelberg, Germany) to a purity >95 %. Sort purity was verified by re-analysis of samples.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The resulting cel files were analyzed with the bioconductor affy package using the RMA (robust microarray analysis) algorithm.

source_name: purified Langerhans cells from ear epidermis, isolated after 16 hours of ex vivo cultivation

label_protocol: RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK))

growth_protocol: epidermal sheets, cultivated for 16 hours, then isolation of LC by BSA gradient and FACS sorting

extract_protocol: Total RNA was isolated with Trizol™ (Invitrogen) according to the manufacturers’ instructions. For microarray analysis mRNA was amplified prior to chip-hybridization using the MessageAmp™ Kit of Ambion (Woodward St. Austin, USA)

treatment_protocol: no treatment of mice

tag: C57BL/6 mice, 6-8 week old female mice


title: A8, 34x st_wash, 2nd series

source_name: A8, 34x st_wash, 2nd series


title: B2, 4x st_wash, 1st series

source_name: B2, 4x st_wash, 1st series


title: B4, 19x st_wash, 1st series

source_name: B4, 19x st_wash, 1st series


title: LC from biological replicate AhR ko_1

tag: strain C67BL/6 AhR -/- exon2 deleted, 6-8 week old female mice


title: LC from biological replicate C57BL/6_1


title: LC from biological replicate AhR ko_2


title: A6, 19x st_wash, 2nd series

source_name: A6, 19x st_wash, 2nd series


title: A7, 24x st_wash, 2nd series

source_name: A7, 24x st_wash, 2nd series


title: A4, 17x st_wash, 1st series

source_name: A4, 17x st_wash, 1st series


title: A5, 17x st_wash, 2nd series

source_name: A5, 17x st_wash, 2nd series


title: A3, 7x st_wash, 1st series

source_name: A3, 7x st_wash, 1st series


title: Endometrium-d2-3-not pregnant rep 4

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

description: Gene expression of morphological more advanced endometria, assessed buy Noyes' criteria, (n=3) was compared with matched less advanced endometria (n=4).

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing: Affymetrix GeneChip Operating (GCOS) 1.2 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval, dated as d2 or d3 of the luteal phase by Noyes' criteria, not pregnant

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix)

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer' s protocol

treatment_protocol: GnRH-antagonist/rec-FSH stimulated IVF cycle

tag: Endometrial dating d2-3, non-pregnant


title: Endometrium-d2-3-not pregnant rep 3


title: Endometrium-d2-3-not pregnant rep 1


title: Endometrium-d2-3-not pregnant rep 2


title: Endometrium-d4-not pregnant rep 3

source_name: Endometrium on day of oocyte retrieval, dated as d4 of the luteal phase by Noyes' criteria, not pregnant

tag: Endometrial dating d4, non-pregnant


title: A1, 0x st_wash, 1st series

source_name: A1, 0x st_wash, 1st series


title: Endometrium-d4-not pregnant rep 1


title: fru P1-GAL4; uas-EcRA RNAi 0-24 hr adult - CNS - replicate 2

status: Public on Sep 21 2009

city: Los Angeles

first: Matthew

middle: S

last: Lebo

address: 1040 Child's Way

department: Molecular and Copmutational Biology

institute: University of Southern California

description: adult_FruGal_Cy3_FruGalEcRARi_Cy5_R4.gpr

hyb_protocol: cRNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO). Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA). Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

scan_protocol: All arrays were scanned using the GenePix 4100A scanner and GenePix Pro 5.0 software from Axon Instruments (Molecular Diagnostics, Sunnyvale, CA).

data_processing: Visual inspection of the microarray images filtered out florescence most likely not due to labeled cDNA binding; the data from these array elements was discarded. Array elements were only considered for further analysis if at least one channel (Cy3 or Cy5) had greater than 75% of the pixels with intensity values one standard deviation above background levels. All microarray normalization and statistical analyses were performed using the limma package of BioConductor in the program R.

organism: Drosophila melanogaster

source_name: Exp male 0-24 hr adult

label_protocol: cRNA probes were made and Cy-labeled from RNA derived from CNS tissue using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).  The cRNA samples were then purified (Gel-Purification Kit, Qiagen, Valencia, CA).

extract_protocol: RNA was isolated from ~20 dissected brains by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA) and resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: Experimental and Control male flies were collected as 0-24 hour adults between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C.  Flies were lightly anesthetized using ether and CNS tissue was dissected in 1X PBS, and immediately placed in TRIzol®.

tag: Strain

value: fru P1-GAL4; uas-EcRA RNAi

tag: Gender

value: Male

tag: Age

value: 0-24 hr adult

tag: Tissue

value: brain

source_name: Cont male 0-24 hr adult

value: fru P1-GAL4; +


title: fru P1-GAL4; uas-EcRA RNAi 48 hr APF pupae - CNS - replicate 2

description: 48hr_FruGal_Cy3_FruGalEcRARi_Cy5_P12.gpr

source_name: Exp male 48 hr APF pupae

treatment_protocol: Experimental and Control male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours.  CNS tissue was dissected in 1X PBS, and immediately placed in TRIzol®.

value: 48 hr APF

source_name: Cont male 48 hr APF pupae


title: A2, 2x st_wash, 1st series

source_name: A2, 2x st_wash, 1st series

tag: stringent wash cycles (total)


title: fru P1-GAL4; uas-EcRA RNAi 48 hr APF pupae - CNS - replicate 1

description: 48hr_FruGal_Cy3_FruGalEcRARi_Cy5_P10.gpr


title: fru P1 48 hr APF pupae - CNS - replicate 2

description: slide_13_berlin_male_Cy3_fruw12_Cy5_700_590_second.gpr

source_name: fru P1 male 48 hr APF pupae

extract_protocol: RNA was isolated from ~20 dissected brains and VNCs by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA) and resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: fru P1 and wt male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours.  CNS tissue was dissected in 1X PBS, and immediately placed in TRIzol®.

value: w; fru-w12/fru-ChaM5

value: CNS

source_name: Wild type male 48 hr APF pupae

value: w; Berlin


title: fru P1 48 hr APF pupae - whole body - replicate 8

description: slide_52_fruw12_Cy3_vs_w_wt_berlin_Cy5_950_750.gpr

hyb_protocol: cDNA samples were then dried and resuspended in formamide (56%), sodium citrate buffer (SSC, 3.37×), SDS (1.12%), Denhardts (5.62×), and Polyadenylic acid potassium salt (0.9 mg/ml; Sigma-Aldrich, St. Louis, MO). Samples were boiled for 2 minutes and then applied to microarray slides underneath a LifterSlip (Erie Scientific, Portsmouth, PA). Microarrays were hybridized at 42◦C for 14-18 hours, then washed in a solution of 1.5% SDS and 1X SSC for 5 minutes, a solution of 0.20X SSC for 5 minutes, and two solutions of 0.05X SSC for 10 minutes each.

label_protocol: cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 30µg of total RNA was used as a starting template. The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL). The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM). After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA).

extract_protocol: RNA was isolated from ~30 pupae by homogenization and extraction using the TRIzol® protocol (Invitrogen, Carlsbad, CA) and resuspended in 20µL diethylpyrocarbonate (DEPC)-treated H2O.

treatment_protocol: fru P1 and wt male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours and then snap frozen in liquid nitrogen.

value: Whole Body


title: fru P1-GAL4; uas-EcRA RNAi 0 hr APF pupae - CNS - replicate 3

description: wpp_FruGal_Cy5_FruGalEcRARi_Cy3_G6_Sec.gpr

source_name: Cont male 0 hr APF pupae

treatment_protocol: Experimental and Control male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4.  CNS tissue was dissected in 1X PBS, and immediately placed in TRIzol®.

value: 0 hr APF

source_name: Exp male 0 hr APF pupae


title: fru P1-GAL4; uas-EcRA RNAi 0 hr APF pupae - CNS - replicate 4


title: wild type 48 hr APF pupae - CNS - replicate 4

description: slide_8_female_Cy3_vs_male_Cy5_second_scan_690_530.gpr

treatment_protocol: Wild type female and male flies were collected at the white pre-pupal stage between Zeitgeber time (ZT) 1 and ZT 4, aged at 25◦C for 48 hours.  CNS tissue was dissected in 1X PBS, and immediately placed in TRIzol®.

value: Canton S

source_name: Wild type female 48 hr APF pupae

value: Female


title: fru P1 48 hr APF pupae - CNS - replicate 1

description: slide_12_berlin_male_Cy3_fruw12_Cy5_700_580_first.gpr


title: wild type 48 hr APF pupae - CNS - replicate 1

description: slide_5_male_Cy3_vs_female_Cy5_second_scan__rewash__690_530.gpr


title: fru P1-GAL4; uas-EcRA RNAi 0 hr APF pupae - CNS - replicate 1


title: fru P1 48 hr APF pupae - whole body - replicate 7

description: slide_28_fruw12_Cy3_vs_w_wt_berlin_Cy5_second_scan__960_790_.gpr

label_protocol: cDNAs were directly labeled with Cy5 or Cy3 during the reverse transcription reaction; 30µg of total RNA was used as a starting template. The reverse transcription reaction was performed for two hours at 42◦C using the following reagents (values in parentheses are final molarity or final concentration): oligo dT primer (Operon, 3.75 μM), dithiothreitol (Invitrogen, 10 mM), First Strand Buffer (Invitrogen, 1×), dNTPs minus dTTP (Invitrogen, 0.5 mM), dTTP (Invitrogen, 50 μM), Cy-labeled dUTP (Perkin-Elmer, 0.625 nM), and Superscript II reverse transcriptase (Invitrogen, 10 U/μL). The reaction was stopped and RNA was hydrolyzed by a 20 minute incubation at 65◦C with NaOH (167 mM) and EDTA (83 mM). After neutralizing by adding HEPES buffer (pH8.0; 294 mM) and sodium acetate (pH5.2; 228 mM), cDNA samples were purified (Gel-Purification Kit, Qiagen, Valencia, CA)


title: fru P1-GAL4; uas-EcRA RNAi 0-24 hr adult - CNS - replicate 1

description: adult_FruGal_Cy3_FruGalEcRARi_Cy5_R2_Sec.gpr


title: fru P1-GAL4; uas-EcRA RNAi 0-24 hr adult - CNS - replicate 4

description: adult_FruGal_Cy5_FruGalEcRARi_Cy3_R5.gpr


title: fru P1-GAL4; uas-EcRA RNAi 0 hr APF pupae - CNS - replicate 2


title: fru P1 48 hr APF pupae - whole body - replicate 4

description: slide_68_fru_Cy3_vs_csM_Cy5_fourth_scan__rewash___1000_770_.gpr


title: Cold-stressed, ambient to 0 °C for 4h, BA June-cold 4 6h recovery (slide-185-118-1206.G)

city: Tiburon

first: Jonathon

middle: H

last: Stillman

address: 3152 Paradise Drive

department: Romberg Tiburon Center

institute: San Francisco State University

description:
cold-stressed (ramp from ambient to 0 °C for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 6h recovery

hyb_protocol: 50% deoinized formamide, 5XSSC, 0.1% SDS, 30µg PolyA RNA,  in a final volume of 48µl.  This volume heat denatured at 100°C for 2 min, cooled to room temperature, and pipetted underneath an Erie LifterSlip placed on the microarray slide and incubated in a Genetix hybridization chamber for 16-18 h at 42°C.

scan_protocol: 10 µm resolution (Axon Instruments, GenePix Personal 4000B; Axon GenePix Pro v.6.0) using the automatic PMT adjustment function.

data_processing: the data were log2 transformed, Lowess normalized, and statistically analyzed using R/maanova using a fixed model and the Fs statistic

organism: Petrolisthes cinctipes

source_name: BA_June_cold_4 pooled total RNA

label_protocol: Cy dye labeled amino-allyl cDNA was generated by RT from 3.475µg aRNA using amino-allyl dUTP with subsequent labeling by addition of Cy dye in DMSO.

growth_protocol: samples were immediatley dissected into RNAlater tissue protect and stored at -20°C

extract_protocol: Qiagen’s RNeasy Mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: crabs were collected at Bamfield, British Columbia, immediately returned to the laboratory and were either heat stressed (ambient to 31°C) or cold stressed (ambient to 0°C). Thermal ramps were performed with linear temperature change at 0.1°C per minute over a span of 4 hours. Controls were held at ambient temperature throughout the experiments.

value: heart


title: Endometrium-d4-not pregnant rep 2


title: fru P1 48 hr APF pupae - CNS - replicate 3

description: slide_14_berlin_male_Cy3_fruw12_Cy5_700_590_first.gpr


title: fru P1 48 hr APF pupae - whole body - replicate 3

description: slide_66_fru_Cy3_vs_csM_Cy5_third_scan__rewash___980_800_.gpr


title: fru P1-GAL4; uas-EcRA RNAi 48 hr APF pupae - CNS - replicate 4

description: 48hr_FruGal_Cy5_FruGalEcRARi_Cy3_P13.gpr


title: Control, held at ambient temperature for 4h, MR June-control 4 6h recovery (slide-183-116-1206.G)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 6h recovery

source_name: MR_June_control_4 pooled total RNA

treatment_protocol: crabs were collected at Monterey, California, immediately returned to the laboratory and were either heat stressed (ambient to 31°C) or cold stressed (ambient to 0°C). Thermal ramps were performed with linear temperature change at 0.1°C per minute over a span of 4 hours. Controls were held at ambient temperature throughout the experiments.


title: fru P1-GAL4; uas-EcRA RNAi 48 hr APF pupae - CNS - replicate 3

description: 48hr_FruGal_Cy5_FruGalEcRARi_Cy3_P11.gpr


title: fru P1 48 hr APF pupae - CNS - replicate 4

description: slide_9_fru_440_Cy3_cs_male_Cy5_700_580first.gpr


title: Control, held at ambient temperature for 4h, BA June-control 2 6h recovery (slide-183-116-1206.R)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data control individual at 6h recovery

source_name: BA_June_control_2 pooled total RNA


title: wild type 48 hr APF pupae - CNS - replicate 2

description: slide_6_male_Cy3_vs_female_Cy5_first_scan_690_530.gpr


title: fru P1 48 hr APF pupae - CNS - replicate 5

description: slide_10_fru_440_Cy3_cs_male_Cy5_700_580second.gpr


title: fru P1 48 hr APF pupae - CNS - replicate 6

description: slide_11_fru_440_Cy3_cs_male_Cy5_710_520_2nd_wash.gpr


title: Control, held at ambient temperature for 4h, BA June-control 4 6h recovery (slide-184-117-1206.G)

source_name: BA_June_control_4 pooled total RNA


title: fru P1-GAL4; uas-EcRA RNAi 0-24 hr adult - CNS - replicate 3

description: adult_FruGal_Cy5_FruGalEcRARi_Cy3_R3.gpr


title: fru P1 48 hr APF pupae - whole body - replicate 5

description: slide_29_w_wt_Berlin_Cy3_vs_fruw12_Cy5_second_scan__1040_810_.gpr


title: wild type 48 hr APF pupae - CNS - replicate 3

description: slide_7_female_Cy3_vs_male_Cy5_second_scan_690_550.gpr


title: Control, held at ambient temperature for 4h, BA June-control 3 6h recovery (slide-185-118-1206.R)

source_name: BA_June_control_3 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, MR June-heat 4 6h recovery (slide-179-112-1206.R)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data control individual at 4h recovery

source_name: MR_June_heat_4 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, BA June-heat 3 6h recovery (slide-180-113-1206.G)

source_name: BA_June_heat_3 pooled total RNA


title: fru P1 48 hr APF pupae - whole body - replicate 2

description: slide_67_csM_Cy3_vs_fru_Cy5_fourth_scan__rewash___990_760_.gpr


title: Heat-stressed, ambient to 31°C over 4h, CA June-heat 4 6h recovery (slide-181-114-1206.R)

source_name: CA_June_heat_4 pooled total RNA

treatment_protocol: crabs were collected at Cape Arago, Oregon, immediately returned to the laboratory and were either heat stressed (ambient to 31°C) or cold stressed (ambient to 0°C). Thermal ramps were performed with linear temperature change at 0.1°C per minute over a span of 4 hours. Controls were held at ambient temperature throughout the experiments.


title: Heat-stressed, ambient to 31°C over 4h, BA June-heat 4 6h recovery (slide-181-114-1206.G)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 2h recovery

source_name: BA_June_heat_4 pooled total RNA


title: Control, held at ambient temperature for 4h, CA June-control 4 6h recovery (slide-184-117-1206.R)

source_name: CA_June_control_4 pooled total RNA


title: Control, held at ambient temperature for 4h, MR June-control 2 6h recovery (slide-178-111-1206.R)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 4h recovery

source_name: MR_June_control_2 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, BA June-heat 2 6h recovery (slide-179-112-1206.G)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 4h recovery

source_name: BA_June_heat_2 pooled total RNA


title: Control, held at ambient temperature for 4h, BA June-control 1 6h recovery (slide-180-113-1206.R)

source_name: BA_June_control_1 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, MR June-heat 2 6h recovery (slide-172-109-1206.R)

source_name: MR_June_heat_2 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, CA June-heat 2 6h recovery (slide-172-109-1206.G)

source_name: CA_June_heat_2 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, BA June-heat 1 6h recovery (slide-171-108-1206.G)

source_name: BA_June_heat_1 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, CA June-heat 3 6h recovery (slide-173-110-1206.R)

source_name: CA_June_heat_3 pooled total RNA


title: fru P1 48 hr APF pupae - whole body - replicate 1

description: slide_60_csM_Cy3_vs_fru_Cy5_first_scan__920_720_.gpr

source_name: fru P1 male 48 hr APF pupae

source_name: Wild type male 48 hr APF pupae


title: Control, held at ambient temperature for 4h, CA June-control 2 6h recovery (slide-173-110-1206.G)

source_name: CA_June_control_2 pooled total RNA


title: Control, held at ambient temperature for 4h, MR June-control 3 6h recovery (slide-182-115-1206.G)

source_name: MR_June_control_3 pooled total RNA


title: Control, held at ambient temperature for 4h, CA June-control 3 6h recovery (slide-182-115-1206.R)

source_name: CA_June_control_3 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, MR June-heat 3 6h recovery (slide-178-111-1206.G)

source_name: MR_June_heat_3 pooled total RNA


title: fru P1 48 hr APF pupae - whole body - replicate 6

description: slide_30_w_wt_Berlin_Cy3_vs_fruw12_Cy5_second_scan__1000_810_.gpr


title: Cold-stressed, ambient to 0 °C for 4h, BA June-cold 3 6h recovery (slide-171-108-1206.R)

description:
cold-stressed (ramp from ambient to 0 °C for 4h)
3.475 µg aRNA
gene expression data control individual at 2h recovery

source_name: BA_June_cold_3 pooled total RNA


title: Control, held at ambient temperature for 4h, MR June-control 1 6h recovery (slide-170-107-1206.R)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 2h recovery

source_name: MR_June_control_1 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, MR June-cold 3 6h recovery (slide-169-106-1206.G)

description:
cold-stressed (ramp from ambient to 0 °C for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 2h recovery

source_name: MR_June_cold_3 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, MR June-cold 4 6h recovery (slide-170-107-1206.G)

source_name: MR_June_cold_4 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, BA June-cold 2 6h recovery (slide-169-106-1206.R)

source_name: BA_June_cold_2 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, MR June-cold 2 6h recovery (slide-167-105-1206.G)

source_name: MR_June_cold_2 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, MR June-cold 1 6h recovery (slide-164-102_1205.G)

source_name: MR_June_cold_1 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, MR June-heat 1 6h recovery (slide-167-105-1206.R)

source_name: MR_June_heat_1 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, CA June-cold 3 6h recovery (slide-165-103-1206.R)

source_name: CA_June_cold_3 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, BA June-cold 1 6h recovery (slide-165-103-1206.G)

source_name: BA_June_cold_1 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, CA June-cold 1 6h recovery (slide-163-101_1205.G)

source_name: CA_June_cold_1 pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, CA June-cold 2 6h recovery (slide-164-102_1205.R)

source_name: CA_June_cold_2 pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, Dec-heat 6h recovery (slide-159-15-1206.G)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data control individual at 1h recovery

source_name: Dec-Heat pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, CA June-heat 1 6h recovery (slide-163-101_1205.R)

source_name: CA_June_heat_1 pooled total RNA


title: Control, held at ambient temperature for 4h, CA June-control 1 6h recovery (slide-166-104-1206.R)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data control individual at 2h recovery

source_name: CA_June_control_1 pooled total RNA


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-162-18-1206.G)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 1h recovery

source_name: Dec-Control pooled total RNA


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-162-18-1206.R)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data control individual at 1h recovery

source_name: June-Control pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, Dec-cold 6h recovery (slide-158-14-1206.R)

description:
cold-stressed (ramp from ambient to 0 °C for 4h)
3.475 µg aRNA
gene expression data control individual at 6h recovery

source_name: Dec-Cold pooled total RNA


title: Heat-stressed, ambient to 31°C over 4h, Dec-heat 6h recovery (slide-160-16-1206.R)

source_name: Dec-heat pooled total RNA


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-160-16-1206.G)


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-158-14-1206.G)

description:
control (held at ambient temperature  for 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 6h recovery


title: Cold-stressed, ambient to 0 °C for 4h, CA June-cold 4 6h recovery (slide-166-104-1206.G)

source_name: CA_June_cold_4 pooled total RNA


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-161-17-1206.G)


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-159-15-1206.R)


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-161-17-1206.R)


title: Cold-stressed, ambient to 0 °C for 4h, Dec-cold 6h recovery (slide-157-13-1206.G)


title: Heat-stressed, ambient to 31°C over 4h, Dec-heat 6h recovery (slide-155-11-1206.R)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data from heat stressed individual at 6h recovery


title: Cold-stressed, ambient to 0 °C for 4h, Dec-cold 6h recovery (slide-156-12-1206.R)


title: Cold-stressed, ambient to 0 °C for 4h, Dec-cold 6h recovery (slide-155-11-1206.G)


title: Heat-stressed, ambient to 31°C over 4h, Dec-heat 6h recovery (slide-156-12-1206.G)


title: Heat-stressed, ambient to 31°C over 4h, June-heat 6h recovery (slide-154-10-1206.R)

description:
heat-stressed (ramp from ambient to 31°C over 4h)
3.475 µg aRNA
gene expression data control individual at 6h recovery

source_name: June-Heat pooled total RNA


title: Control, held at ambient temperature for 4h, Dec-control 6h recovery (slide-157-13-1206.R)


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-154-10-1206.G)


title: Cold-stressed, ambient to 0 °C for 4h, June-cold 6h recovery (slide-151-7_1206.G)

source_name: June-Cold pooled total RNA


title: Cold-stressed, ambient to 0 °C for 4h, June-cold 6h recovery (slide-152-8_1206.R)


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-151-7_1206.R)


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-153-9_1206.R)


title: Control, held at ambient temperature for 4h, June-control 6h recovery (slide-152-8_1206.G)


title: Heat-stressed, ambient to 31°C over 4h, June-heat 6h recovery (slide-153-9_1206.G)


title: Heat-stressed, ambient to 31°C over 4h, June-heat 6h recovery (slide-142-5_1206.R)

growth_protocol: samples  were immediatley dissected into RNAlater tissue protect and stored at -20°C


title: Cold-stressed, ambient to 0 °C for 4h, June-cold 6h recovery (slide-150-6_1206.R)


title: Heat-stressed, ambient to 31°C over 4h, June-heat 6h recovery (slide-150-6_1206.G)


title: Cold-stressed, ambient to 0 °C for 4h, June-cold 6h recovery (slide-142-5_1206.G)


title: Normal Lung_NL21

city: Brisbane

first: Santiyagu

middle: Mary

last: Savarimuthu Francis

state: Queensland

address: Level 1, Clinical Sciences Building, The Prince Charles Hospital, Rode Road

department: School of Medicine

institute: The University of Queensland

description: After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays.

hyb_protocol: Amersham hybridization protocol was used

scan_protocol: GMS418 confocal scanner was used according to manufacturer’s instructions

data_processing: Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 50% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.

source_name: Universal Reference RNA

label_protocol: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA.  Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (Normal Lung) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.

extract_protocol: Total RNA was extracted using TRizol following manufacturer's instructions

tag: sample type

value: Human Universal Reference RNA (Stratagene)

source_name: Normal Lung Sample 21

tag: gender

value: M

tag: % predicted fev1

tag: % predicted kco

tag: age

tag: pack years

tag: age quit smoking


title: Normal Lung_NL24

source_name: Normal Lung Sample 24


title: Normal Lung_NL30

source_name: Normal Lung Sample 30


title: Normal Lung_NL29

source_name: Normal Lung Sample 29


title: Normal Lung_NL27

source_name: Normal Lung Sample 27


title: Normal Lung_NL25

source_name: Normal Lung Sample 25


title: Normal Lung_NL22

source_name: Normal Lung Sample 22

value: F


title: Normal Lung_NL20

source_name: Normal Lung Sample 20


title: Normal Lung_NL16

source_name: Normal Lung Sample 16


title: Normal Lung_NL23

source_name: Normal Lung Sample 23


title: Normal Lung_NL18

source_name: Normal Lung Sample 18


title: Normal Lung_NL12

source_name: Normal Lung Sample 12


title: Normal Lung_NL19

source_name: Normal Lung Sample 19


title: Normal Lung_NL13

source_name: Normal Lung Sample 13


title: Normal Lung_NL9

source_name: Normal Lung Sample 9


title: Normal Lung_NL15

source_name: Normal Lung Sample 15


title: Normal Lung_NL28

source_name: Universal Reference RNA

source_name: Normal Lung Sample 28


title: Normal Lung_NL17

source_name: Normal Lung Sample 17


title: Normal Lung_NL8

source_name: Normal Lung Sample 8


title: Normal Lung_NL26

source_name: Normal Lung Sample 26


title: Normal Lung_NL10

source_name: Normal Lung Sample 10


title: Normal Lung_NL11

source_name: Normal Lung Sample 11


title: Normal Lung_NL7

source_name: Normal Lung Sample 7


title: Normal Lung_NL3

source_name: Normal Lung Sample 3


title: L428 T/IP

city: Groningen

first: Lu Ping

last: Tan

address: Hanzeplein 1

department: Department of Pathology

country: Netherlands

institute: University Medical Center Groningen

description: dye swap of GSM360096

hyb_protocol: Equal amounts of Cy3 or Cy5 labeled cRNA samples derived from the Ago2 immunoprecipitated or flow through fraction and from the total cell lysate fraction were mixed and hybridized in a dye swap design at 65°C overnight on Agilent 44k 60mer Human Whole Genome Oligo Microarray.

scan_protocol: On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).

data_processing: Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 9.1. Probes with no expression (ie. signal intensity similar to background) were filtered out in all tested RNA Samples.

source_name: RNA from total cell lysate fraction

label_protocol: First strand cDNA was synthesized from 200ng RNA, followed by cRNA amplification and labeling with Cy3 or Cy5 according to manufacturer's protocol (Agilent). Purification of Cy3 or Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.

growth_protocol: Both Hodgkin lymphoma cell lines, L428 and L1236 were cultured in RPMI 1640 supplemented with ultraglutamine, 100 U/mL penicillin/streptomycin, and 5% or 10% fetal bovine serum (Cambrex Biosciences, Walkersville, USA), respectively. Cells were diluted 1:2 on the day prior to Ago2 immnunoprecipitation.

extract_protocol: RNA was isolated using Trizol and glycogen (Invitrogen) as a carrier in the ethanol precipitation step.

tag: cell line

tag: cell type

value: Hodgkin lymphoma cell line

source_name: Ago2 coimmunoprecipitated RNA


title: Normal Lung_NL14

source_name: Normal Lung Sample 14


title: L1236 T/FT

description: dye swap of GSM360092

source_name: RNA from flow through fraction


title: Normal Lung_NL6

source_name: Normal Lung Sample 6


title: L1236 T/IP

description: dye swap of GSM360093


title: L1236 FT/T

description: L1236 flow through fraction compared against total cell lysate fraction


title: Normal Lung_NL4

source_name: Normal Lung Sample 4


title: Normal Lung_NL1

source_name: Normal Lung Sample 1


title: L428 IP/T

description: L428 Ago2 immunoprecipitated fraction compared against total cell lysate fraction


title: Normal Lung_NL2

source_name: Normal Lung Sample 2