title: BSE vs. Control Rep. 6

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 600 nano gram labeled DNA per channel were mixed probes were denatured for 3 min at 70 degree celcius hybridisation at 58 degree celcius SSPE washes as recommended

data_processing:
- dye swap design
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- variance homogenisation by division of each value with the standard deviation of the normalized log2-ratios
- as statistical software we use 'R'

label_protocol: 2 µg of the enriched miRNA preparation was polyudenylated using equal amounts of UTP and aminoallyl-UTP (Biozym, Hamburg, Germany) with poly(A) polymerase (Epicentre Biotechnologies, Madison, Wisconsin) for 2 h at 37°C. Polyudenylated miRNAs were recovered by Ethanol/NaAcetat precipitation and labeled with fluorescent dyes DY547 or DY647 (MoBiTec, Göttingen, Germany), respectively, in 100 mM NaCO_3 -buffer, pH 9.5 for 2 h in the dark. After an additional precipitation step, samples were resuspended in RNase-free ddH_2 O and were frozen at -20°C before further use.

source_name: BSE-infected monkeys

tag: Brain section (basis pontis) of BSE-infected monkeys


title: A0 6h2

status: Public on Jul 06 2009

type: RNA

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Cells  Treated with A0 for 6h

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina Human_RefSeq-8V2 BeadChips at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: HT1080 cells were grown in DMEM supplemented with 4mM glutamine, penicillin  streptomicyn, and 10%FBS (complete growth medium)

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: Cells were incubated in complete growth medium supplemented with cisplatin or A0, 25µM, for the indicated times.

tag: fibrosarcoma cell line


title: A0 12h1

description: Cells  Treated with A0 for 12h

data_processing: analyzed by Illumina's BeadStudio version 1.5.1.3


title: 24 hrs after the third OVA challenge Lung tissue Group3_4

city: Budapest

first: Gergely

last: Tolgyesi

address: Nagyvarad ter 4

country: Hungary

institute: Semmelweis University Budapest

description: This is the fourth sample of the four biological replicates, belonging to group3

hyb_protocol: Agilent dual color protocol version 5.5

scan_protocol: Agilent microarray scanner default setting for 4x44k dual color microarray

data_processing:
Data were normalised by Agilent Feature Extraction 7.5
Value is normalized log10Ratio, default Per Spot and Per Chip: Intensity dependent (Lowess) normalization

organism: Mus musculus

source_name: Placebo treated control pool (Cy3)

label_protocol:
Agilent dual color microarray protocol version 5.5
Data normalisation by Agilent Feature Extraction 7.5

extract_protocol:
Qiagen RNeasy kit
Quality controlled by Agilent bioanalyzer

tag: Balb/c mice  placebo challenged control lung tissue

molecule: polyA RNA

source_name: OVA challenged mice

tag: Balb/c mice treated and challenged with OVA lung tissue RNA

value: 24 hours after the third OVA allergen challenge (day31), after the AHR measurement


title: A0 6h1

description: Cells  Treated with A0 for 6h


title: A0 3h1

description: Cells  Treated with A0 for 3h


title: 4 hrs after the third OVA challenge Lung tissue Group2_4

description: This is the fourth sample of the four biological replicates, belonging to group2

value: 4 hours after the third OVA allergen challenge (day30)


title: Noninfected monkey brain Rep. 1

type: other

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = BSE miRNA

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 600 nano gram labeled DNA were denatured for 3 min at 70 degree celcius hybridisation at 58 degree celcius SSPE washes as recommended

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automic Imageprocessing for Microarrays' (for details: http://www.techfak.uni-bielefeld.de/ags/ai/projects/microarray/)

data_processing:
- Normalization of the log2(cy5)-values with quantile normalization
- as statistical software we use 'R'

molecule: other

organism: Macaca mulatta

source_name: non-infected monkeys

label_protocol: 2 µg of the enriched miRNA preparation was polyudenylated using equal amounts of UTP and aminoallyl-UTP (Biozym, Hamburg, Germany) with poly(A) polymerase (Epicentre Biotechnologies, Madison, Wisconsin) for 2 h at 37°C. Polyudenylated miRNAs were recovered by Ethanol/NaAcetat precipitation and labeled with fluorescent dye DY647 (MoBiTec, Göttingen, Germany), respectively, in 100 mM NaCO_3 -buffer, pH 9.5 for 2 h in the dark. After an additional precipitation step, samples were resuspended in RNase-free ddH_2 O and were frozen at -20°C before further use.

extract_protocol: small fraction RNA isolation (mirVana miRNA-isolation kit, Ambion) according to the manufactures standard protocol

tag: Brain section (basis pontis) of non-infected monkeys


title: 4 hrs after the third OVA challenge Lung tissue Group2_3

description: This is the third sample of the four biological replicates, belonging to group2


title: BSE vs. Control Rep. 5


title: BSE vs. Control Rep. 1


title: BSE vs. Control Rep. 4


title: FD19 lung, total RNA, biological replicate 1

status: Public on Jul 07 2009

city: Toronto

first: Gail

last: Otulakowski

state: ON

address: 555 University Ave

department: Physiology & Experimental Medicine

country: Canada

institute: Hospital for Sick Children Research Institute

description: steady-state expression data from canalicular lung

hyb_protocol: 15 ug of labeled cRNA were used for hybridization to Affymetrix RAE2302 chips using protocol EukGE-WS2v4

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000

data_processing: scaling target signal 150 using GCOS 1.4

organism: Rattus norvegicus

source_name: total RNA from FD19 rat lung

label_protocol: Biotinylated cRNA were prepared from 5 ug RNA using Enzo IVT kit for in vitro transcription

growth_protocol: fetuses and newborn rats from timed pregnant gestation.  Fetuses delivered by Cesarean section.  Newborns vaginally delivered.

extract_protocol: Total RNA by Trizol extraction according to the manufacturer's instructions.  Polysomal RNA from sucrose density gradient fractions where n> 7 ribosomes/mRNA, extracted by guanidine-HCl, phenol/CHCl3 extracted, and ethanol precipitated.  All further purified with Qiagen RNeasy according to the manufacturer's instructions.

treatment_protocol: lungs excised and snap-frozen in liquid nitrogen

tag: Strain

value: Wistar


title: muscle_wild_19

status: Public on Jul 03 2009

city: West Vancouver

first: Wendy

last: Tymchuk

state: BC

address: 4160 Marine Drive

department: Science

institute: Fisheries & Oceans Canada

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 68).  Fluorescence intensity data were extracted from TIF images using Spotfinder (TIGR).

data_processing: Data transformation (Lowess normalization) and analysis were performed in MeV (TIGR).  Spots with intensity less than the empty spot mean plus 2.5 times their standard deviation were excluded from the analysis.

organism: Oncorhynchus mykiss

source_name: muscle, wild, fish 19

label_protocol: Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

extract_protocol: Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions.

tag: tissue

value: muscle

tag: strain

value: Pennask Lake wild

tag: sample type

value: individual

source_name: muscle, wild, pool

value: reference pool


title: muscle_wild_16

source_name: muscle, wild, fish 16


title: CTRL1

description: Control cells


title: BSE vs. Control Rep. 2


title: BSE vs. Control Rep. 3


title: A0 1h2

description: Cells  Treated with A0 for 1h


title: A0 1h1

description: Cells  Treated with A0 for 1h


title: A0 3h2

description: Cells  Treated with A0 for 3h


title: 4 hrs after the first OVA challenge Lung tissue Group1_5

description: This is the fifth sample of the four biological replicates, belonging to group 1

tag: Group 1

value: 4 hours after the first OVA allergen challenge (day28)


title: 4 hrs after the first OVA challenge Lung tissue Group1_1

description: This is the first sample of the four biological replicates, belonging to group 1


title: 4 hrs after the first OVA challenge Lung tissue Group1_4

description: This is the third sample of the four biological replicates, belonging to group 1


title: 4 hrs after the third OVA challenge Lung tissue Group2_1

description: This is the first sample of the four biological replicates, belonging to group2


title: CTRL2

description: Control cells


title: muscle_dom_13

source_name: muscle, domestic, fish 13

value: Spring Valley domestic


title: muscle_dom_14

source_name: muscle, domestic, fish 14


title: 4 hrs after the first OVA challenge Lung tissue_Group1_2

description: This is the second sample of the four biological replicates, belonging to group 1

source_name: OVA challenged mice_Group1


title: muscle_dom_10

source_name: muscle, domestic, fish 10


title: 4 hrs after the third OVA challenge Lung tissue Group2_2

description: This is the second sample of the four biological replicates, belonging to group2


title: muscle_dom_9

source_name: muscle, domestic, fish 9


title: muscle_dom_2

source_name: muscle, domestic, fish 2


title: muscle_wild_3

source_name: muscle, wild, fish 3


title: liver_wild_3

source_name: liver, wild, pool

value: liver

source_name: liver, wild, fish 3


title: liver_dom_7

source_name: liver, domestic, fish 7


title: liver_wild_10

source_name: liver, wild, fish 10


title: liver_dom_3

source_name: liver, domestic, fish 3


title: muscle_wild_8

source_name: muscle, wild, fish 8


title: Control

status: Public on Jul 04 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Control RNA from leaves of the Musa cultivar 'Cachac' onto Rice array.

hyb_protocol: The cRNAs were randomly fragmented at 94oC for 35 min in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to generate molecules of approximately 35 to 200 bp. Affymetrix A. thaliana ATH1 Genome or Rice Genome Arrays were then hybridised with 15 ug of fragmented, labeled cRNA for 16 h at 45C as described in the Affymetrix Technical Analysis Manual. GeneChip arrays were stained with Streptavidin-Phycoerythrin solution as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com).

scan_protocol: GeneChip arrays were scanned with an Affymetrix G2500A GeneArray scanner, as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: The Microarray Analysis Suite (MAS Version 5.0; Affymetrix) was used to generate .cel files for each of the RNA hybridisations by scanning and computing summary intensities for each probe without the use of probe mask files. These .cel files were then loaded into the GeneSpring (Agilent Technologies) analysis software package using the Robust Multichip Average (RMA) pre-normalisation algorithm. During .cel file loading and pre-normalisation, .cel files were interpreted using the respective A. thaliana or rice .cdf files (i.e. with no probe-selection used), or (2) using .cdf files generated from the Musa genomic DNA .cel file with CDF values ranging from 0 to 1000. Following RMA pre-normalisation and masking of individual probes, each probeset signal value from treated (drought stressed) samples was standardised relative to the probeset signal value of its corresponding control, to give the relative gene expression ratios between the two conditions.

organism: Musa sp.

source_name: leaves, control

label_protocol: Approximately 5 ug of Musa total RNA was reverse transcribed at 42oC for 1 h to generate first strand cDNA using 100 pmol oligo dT(24) primer containing a 5'-T7 RNA polymerase promoter sequence, 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT), 10 mM dNTPs and 200 units SuperScript II reverse transcriptase (Invitrogen Life Technologies). Following first strand cDNA synthesis, second strand cDNA was synthesised using 10 units of Escherichia coli polymerase I, 10 units of E. coli DNA ligase and 2 units of RNase H in a reaction containing 25 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 10 mM (NH4)SO4, 0.15 mM beta-NAD+ and 10 mM dNTPs. This second strand synthesis reaction proceeded at 16oC for 2 h before 10 units of T4 DNA polymerase was added and the reaction allowed to proceed for a further 5 min. The reaction was terminated by adding 0.5 M EDTA. Double stranded cDNA products were purified using the GeneChip Sample Cleanup Module (Affymetrix). The synthesised cDNAs were transcribed in-vitro using T7 RNA polymerase (Enzo BioArray High Yield RNA Transcript Labelling Kit, Enzo Life Sciences Inc., Farmingdale, NY, USA) and biotinylated nucleotides to generate biotinylated complementary RNAs (cRNAs). The cRNAs were then purified using the Affymetrix Sample Cleanup Module (Affymetrix).

growth_protocol: Plants were grown at a density of 24 plants per table under a standardised light/dark regime of 12/12 h at 26/23oC respectively with a light intensity of around 10,000 lux (300 watts/m2) and a relative humidity of 75%. At the onset of the experiment, all plants were hand-watered until water drained freely from the base of the pots. The control plants were then watered once a day by flooding the tables with a fertigation solution and allowing the pots to stand for 30 min. Water-deficit (drought) conditions were imposed by withholding water supply for in total up to five weeks. Leaf samples consisted of a 5-8 cm wide strip (~3g fresh weight) removed from one side of the middle of the second, fully expanded leaf down from the top of the plant. Samples were snap frozen in liquid nitrogen and stored at -80oC until analysis. All sampling took place between 14:00 and 17:00 pm.

extract_protocol: RNA was extracted using a modified Tris-LiCl method, based on the work of Tattersall et al. The modifications involved a DNAse treatment and an additional phenol:chloroform cleanup step. RNA concentrations and purity were determined using a MultiScan Spectrum microtitre plate scanning UV-VIS spectrophotometer (Multiskan Spectrum, Thermolabsystems, Brussels, Belgium). For purity assessment, the AU 260/280 and AU 260/230 ratios were measured and samples with a ratio of ~2.0 were considered as 'pure'. One microgram of total RNA sample was also run on a 1% agarose gel containing ethidium bromide in TAE buffer to check for possible degradation. Gels were imaged using a GelDoc 1000 gel imaging system and Molecular Analyst v1.5 image analysis software version 4 (Bio-Rad, Hercules, CA).

value: leaf

tag: cultivar

value: 'Cachac'

tag: treatment

value: control


title: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells (Dataset 100040)

type: genomic

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

department: Biochemistry

country: USA

institute: UW-Madison

description: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells using monoclonal antibody NT73.

hyb_protocol: Samples were hybridized to arrays by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.
VALUE=log2(Cy5_signal/Cy3_signal)=log2(SIGNAL_RED/SIGNAL_GREEN)

molecule: genomic DNA

organism: Escherichia coli

source_name: RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells, untreated

label_protocol: Samples were labeled by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Strain MG1655 cells were grown in MOPS minimal medium supplemented with 0.2% glucose (www.genome.wisc.edu/resources/protocols/mopsminimal.htm).

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

treatment_protocol: Cells were grown with vigorous shaking at 37 °C to mid-log (light scattering at 600 nm equivalent to 0.4 OD). Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and shaking was continued for 5 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with agitation for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

tag: antibody

value: Monoclonal antibody for RNA polymerase Beta' subunit (NT73)

source_name: Genomic DNA control from E. coli K-12 MG1655 cells, untreated

tag: reference

value: input Genomic DNA control


title: muscle_dom_6

source_name: muscle, wild, pool

source_name: muscle, domestic, fish 6


title: muscle_wild_7

source_name: muscle, wild, fish 7


title: muscle_wild_4

source_name: muscle, wild, fish 4


title: liver_wild_6

source_name: liver, wild, fish 6


title: liver_dom_9

source_name: liver, domestic, fish 9


title: liver_dom_8

source_name: liver, domestic, fish 8


title: Musa_DNA_RICE

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: Musa DNA hybridized onto Rice array.

hyb_protocol: Genomic DNA hybridisation was carried out essentially as described by Hammond et al. In brief, labeled gDNA was hybridised to the Rice Genome Arrays for 16 h at 45oC, using standard Affymetrix hybridisation protocols. This was then followed by the Affymetrix eukaryotic wash protocol that included antibody staining. The GeneChip Genome Arrays were then hybridised with 0.5 ug of target Musa genomic DNA. GeneChip arrays were stained with Streptavidin-Phycoerythrin solution as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com). Only one genomic DNA hybridisation was performed, as replicate genomic DNA hybridisations all challenge the GeneChip arrays with the whole genome.

scan_protocol: Scanning done with G2500A GeneArray scanner as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: From these results a genomic DNA cell intensity file (.cel file) was generated using the Microarray Analysis Suite software (MAS, v5.0, Affymetrix). This .cel file contains the hybridisation intensities between Musa genomic DNA fragments and all the Rice GeneChip oligonucleotide probes. Probes showing a suitably strong cross-hybridisation signal were selected from the .cel file, using a .cel file parser script (Xspecies v 1.1, available with instructions at http://affymetrix.arabidopsis.info/xspecies/) written in the Perl programming language (http://www.perl.com). This Perl script creates a probe mask (.cdf) file, which is compatible with a range of microarray analysis software packages and provides the template for the generation of a signal across the probeset when analyzing the test (Musa) transcriptome (i.e. the RNA .cel files). Specifically it allows information to be extracted from the RNA .cel files for only those probe-pairs whose perfect-match (PM) probe genomic DNA hybridisation intensity value is above a user-defined hybridisation intensity threshold (CDF value). In practice the optimal genomic DNA CDF is determined systematically and empirically using probe masks created with CDF values of between 50 and 1000. A probeset is retained for analysis when it is represented by at least one PM probe-pair per probeset. Therefore one 25 bp probe, identical in sequence to a Musa genomic DNA fragment is the minimum requirement for inclusion of that probeset in the subsequent transcriptome analysis of the target Musa RNA.

source_name: Musa DNA

label_protocol: Musa genomic DNA was labeled using the Bioprime DNA hybridisation System (Invitrogen).

extract_protocol: Genomic DNA (gDNA) was isolated from young leaves which had been kept in the dark for 48 h to deplete starch and polysaccharide levels using a modified CTAB method essentially as according to Michiels et al. Contaminating RNA was removed by addition of 2.5 ul of a 10 ug/ml stock solution of RNase and incubation at 37oC for 30 min. To check the quality and quantity of DNA, 1 ul samples of isolated DNA were run on a 1% agarose gel in TAE buffer (0.04 M Tris-acetate; 1 mM EDTA, pH 8) as outlined by Sambrook et al. After staining of the gel with ethidium bromide for 15 min, DNA concentrations were visually estimated by comparison to different amounts of lambda-DNA run at the same time. genomic DNA quality was determined spectrophotometrically using the AU absorbance ratios at 260/280 nm. Samples with a 260/280 ratio of 1.9-2.0 were considered 'pure'.


title: Drought

description: Drought-stressed RNA from leaves of the Musa cultivar 'Cachac' onto Rice array.

hyb_protocol: The cRNAs were randomly fragmented at 94oC for 35 min in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to generate molecules of approximately 35 to 200 bp. Affymetrix A. thaliana ATH1 Genome or Rice Genome Arrays were then hybridised with 15 ug of fragmented, labeled cRNA for 16 h at 45oC as described in the Affymetrix Technical Analysis Manual. GeneChip arrays were stained with Streptavidin-Phycoerythrin solution as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com).

source_name: leaves, drought

value: drought


title: liver_wild_9

source_name: liver, wild, pool

source_name: liver, wild, fish 9


title: liver_wild_4

source_name: liver, wild, fish 4


title: liver_dom_10

source_name: liver, domestic, fish 10


title: liver_wild_2

source_name: liver, wild, fish 2


title: liver_dom_6

source_name: liver, domestic, fish 6


title: liver_wild_1

source_name: liver, wild, fish 1


title: brain_wild_10

source_name: brain, wild, fish 10

value: brain

source_name: brain, wild, pool


title: liver_dom_4

source_name: liver, domestic, fish 4


title: brain_wild_9

source_name: brain, wild, fish 9


title: brain_dom_6

source_name: brain, domestic, fish 6


title: brain_wild_3

source_name: brain, wild, fish 3


title: brain_dom_9

source_name: brain, domestic, fish 9


title: brain_wild_4

source_name: brain, wild, fish 4


title: brain_dom_8

source_name: brain, domestic, fish 8


title: brain_dom_2

source_name: brain, domestic, fish 2


title: brain_wild_6

source_name: brain, wild, fish 6


title: brain_dom_3

source_name: brain, domestic, fish 3


title: brain_wild_7

source_name: brain, wild, fish 7


title: brain_dom_10

source_name: brain, domestic, fish 10


title: brain_dom_1

source_name: brain, domestic, fish 1


title: brain_dom_7

source_name: brain, domestic, fish 7


title: brain_wild_8

source_name: brain, wild, fish 8


title: brain_wild_1

source_name: brain, wild, fish 1


title: brain_wild_2

source_name: brain, wild, pool

source_name: brain, wild, fish 2


title: brain_dom_4

source_name: brain, domestic, fish 4


title: BM iPS#7

status: Public on Jul 02 2009

city: Machida-shi

first: Kenji

last: Nagao

state: Tokyo

address: 3-6-6, Asahi-machi,

department: Innovative Drug Research Laboratories

country: Japan

institute: Kyowa Hakko Kirin Co., Ltd.

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Agilent Gene Expression Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent).

source_name: BMMNCs derived iPS cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: ES and established iPS cells were cultured on irradiated MEF cells (purchased from Dainippon Sumitomo Pharma Co., Osaka, Japan) in ES medium（DMEM containing 20% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, beta-mercaptoethanol and nonessential amino acid.

extract_protocol: RNA was isolated from MEF depleted mouse ES line or BMiPS cell lines by preplating on gelatin, or BMMNCs using the RNeasy Mini Kit (Qiagen).

tag: cell type

value: BMMNC derived iPS cells

tag: genetic modification

value: Oct4-EGFP transgenic mice derived cells


title: AVT IT_cross-hybridization

city: Austin

first: Lin

last: Huffman

state: TX

address: 2400 Speedway, PAT 141

department: Institute for Cellular and Molecular Biology

institute: The University of Texas

description: Hybridization used DNA targets instead of more common RNA targets, so we used the same protocol as we have established for comparative genomic hybridizations.

hyb_protocol: Added Cot-1 DNA, yeast tRNA, SSC, SDS and DTT to samples. Competitively hybridized onto a glass cDNA microarray at 65C for 17 hours.

scan_protocol: Scanned on an Axon 4000B array scanner at PMT Gain of 750 (635nm) and 650 (532nm) using GenePix 6.0 software.

data_processing: Analyzed using R version 2.3.1 and LIMMA package version 2.7.3. Removed all features within 2 standard deviations of background intensity and performed minimal background correction on remaining features. Normalized single-channel intensities for both print-tip group and according to the Lowess method. Calculated M values from normalized single-channel intensities (log2(red/green)).

organism: Haplochromis burtoni

source_name: Arginine vasotocin fragment_PCR product_whole brain_male

label_protocol: Cy5-dCTP label (Amersham) incorporated using random primers and Klenow fragment from BioPrime DNA Labeling System (Invitrogen) and dNTP mix (Invitrogen) at 37C for 2 hours.

extract_protocol: Whole brain trizol-chloroform RNA extraction, reverse transcribed into cDNA, amplified via PCR using species-specific primers

tag: sex

value: male

tag: status

value: territorial

value: whole brain

source_name: Isotocin fragment_PCR product_whole brain_male

label_protocol: Cy3-dCTP label (Amersham) incorporated using random primers and Klenow fragment from BioPrime DNA Labeling System (Invitrogen) and dNTP mix (Invitrogen) at 37C for 2 hours.


title: Streptomyces avermitilis NRRL8165 day 10

city: Shanghai

first: Lei

last: Chen

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: This sample is of Streptomyces avermitilis NRRL8165, fermentation medium at day 10

hyb_protocol: Microarray assays including Labeling, microarray hybridization and washing, scanning and microarray data normalization were performed by Shanghai Biochip Co., Ltd (China), according to standard protocols suggested by the NimbleChipTM Expression Array User’s guide (Version 1.0, NimbleGen Systems, Inc.)

data_processing: The raw data (.pair file) 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: Streptomyces avermitilis

source_name: Streptomyces avermitilis NRRL8165

extract_protocol: RNA isolation was carried out with TrizolTM (Invitrogen, USA) following the procedures recommended by the manufacturer.

tag: genotype

value: Wild-type


title: Streptomyces avermitilis 8165ΔI day 10

description: This sample is of Streptomyces avermitilis 8165ΔI, fermentation medium at day 10

scan_protocol: Microarray assays including Labeling, microarray hybridization and washing, scanning and microarray data normalization were performed by Shanghai Biochip Co., Ltd (China), according to standard protocols suggested by the NimbleChipTM Expression Array User’s guide (Version 1.0, NimbleGen Systems, Inc.)

source_name: Streptomyces avermitilis 8165ΔI

value: aveI deletion mutant


title: Streptomyces avermitilis 8165ΔI day 7

description: This sample is of Streptomyces avermitilis 8165ΔI, fermentation medium at day 7

label_protocol: Microarray assays including Labeling, microarray hybridization and washing, scanning and microarray data normalization were performed by Shanghai Biochip Co., Ltd (China), according to standard protocols suggested by the NimbleChipTM Expression Array User’s guide (Version 1.0, NimbleGen Systems, Inc.)


title: E14 mESCs

source_name: mouse embryonic stem cells

value: ES cells


title: Streptomyces avermitilis 8165ΔI day 5

description: This sample is of Streptomyces avermitilis 8165ΔI, fermentation medium at day 5


title: Streptomyces avermitilis NRRL8165 day 5

description: This sample is of Streptomyces avermitilis NRRL8165, fermentation medium at day 5


title: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin (Dataset 94828)

description: RNA polymerase (Beta') ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin using monoclonal antibody NT73.

source_name: RNA polymerase (Beta') ChIP in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin

source_name: Genomic DNA control from E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin


title: Streptomyces avermitilis NRRL8165 day 7

description: This sample is of Streptomyces avermitilis NRRL8165, fermentation medium at day 7


title: Primary adrenocortical cancer replicate 3

status: Public on Jul 01 2009

first: Zsófia

last: Tömböl

address: Szentkirályi u. 46.

department: 2nd Department of Medicine

institute: Semmelweis University

hyb_protocol: 825 ng of cyanine 5-CTP-labeled cRNA per sample was mixed with an equal amount of cyanine 3-CTP-labeled uniform reference cRNA, and hybridized to 4x44 K Whole Human Genome Microarrays (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Array scan was performed with Agilent DNA Microarray Scanner G2565BA.

data_processing: Agilent Feature Extraction Software 8.5 was used for feature extraction and array normalization with default normalization scenario for Agilent 4x44 K two-colour array platforms.

source_name: adrenal cortex, primary adrenocortical carcinoma tissue

label_protocol: 1 µg of total RNA mixed with RNA Spike-In-Kit (Agilent Tech. Inc., Santa Clara, CA) was reverse transcribed and Cyanine 5 or Cyanine 3-CTP-labeled (Perkin-Elmer, Waltham, Massachusetts, MA, USA) complementary RNA (cRNA) was synthetized using the Low RNA Input Linear Amplification Kit (Agilent Tech. Inc., Santa Clara, CA) according to the manufacturer’s Dual Color Expression Microarray Protocol version 5.5. Successful labeling, cRNA yield and purity were controlled on a Nanodrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

extract_protocol: Total RNA was extracted from homogenized tissue samples using Rneasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions.

treatment_protocol: After surgical removal tissue samples were immediately snap frozen in liquid nitrogen and stored at -80○ until RNA isolation. Histological diagnoses were confirmed in each cases.

value: adrenal cortex

tag: gender

value: female

tag: age at the time of surgery

value: 48.67 years

tag: hormonal status

value: Cushing-syndrome

source_name: Uniform reference RNA pooled from total RNA of all 16 tissues examined.


title: BM iPS#13


title: Primary adrenocortical cancer replicate 4

value: 71.33 years


title: Primary adrenocortical cancer replicate 1

value: 61.53 years


title: Cortisol-secreting adenoma tissue replicate4

source_name: adrenal cortex, cortisol-secreting adenoma tissue

value: 30.68 years


title: control sample

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix.  The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing:
Preprocessing of microarray raw data including probe-specific background correction, summarization of probe set values, and normalization was carried out using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (Rainer et al., 2006).
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z (2006). CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 34:W498–W503

organism: Caenorhabditis elegans

source_name: C.elegans control exposure

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM  Premier RNA Amplification Kit (Ambion) for microarray analysis.  aRNA cleanup was achieved using magnetic beads (Ambion).

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

tag: age

value: larvae (L1)

value: whole animal

value: N2 (Bristol)


title: BM MNCs

source_name: mouse bone marrow derived mononuclear cells

value: BMMNCs


title: Cortisol-secreting adenoma tissue replicate2

tag: tissue

value: 23.95 years


title: Cortisol-secreting adenoma tissue replicate3

value: 46.82 years


title: Primary adrenocortical cancer replicate 2

value: 61.46 years


title: positive control (heat shock)

source_name: C.elegans heat shock exposure

tag: strain

tag: protocol

value: treated at 30 degC for 24 hrs to induce heat shock


title: bio-electrosprayed sample

source_name: C.elegans subjected to bio-electrospray

value: maintained as control nematodes but passed with an applied voltage (bio-electrosprayed).  Bio-electrospraying was carried out with a stainless steel needle with an internal and external bore diameter of ~6 and ~8mm respectively. The mid-section of the needle, held firmly in resin, was connected to a high voltage power supply (FP-30, Glassman Europe Ltd, Tadley, UK) capable of providing a voltage of up to ±30kV with a drawing current of ~4mA with high resolution. The inlet of the needle was connected to medical grade silicone tubing with a similar internal bore diameter. The inlet end of the silicone tube was connected to a reservoir of M9 buffer containing age synchronous C. elegans larvae (L1s). The flow of suspended nematodes was controlled by way of gravitational flow and could be varied from ~10-5-10-8m3s-1.


title: Cortisol-secreting adenoma tissue replicate1

value: 36.07 years


title: Inactive adenoma tissue replicate 2

source_name: adrenal cortex, inactive adenoma tissue

value: adrenal cortex

value: 45.88 years

value: normal hormonal status


title: Inactive adenoma tissue replicate 4

value: female

value: 45.52 years


title: Inactive adenoma tissue replicate 3

value: 50.81 years


title: Inactive adenoma tissue replicate 1

value: 61.16 years


title: Normal adrenal cortex replicate4

source_name: adrenal cortex, normal cortex tissue

value: 51.71 years


title: Normal adrenal cortex replicate1

value: male

value: 52.19 years


title: Normal adrenal cortex replicate3

value: 58.29 years


title: Normal adrenal cortex replicate2

value: 67.39 years


title: IMR90_control_rep2

status: Public on Dec 29 2008

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression after 4hr in un-irradiated human lung fibroblasts

hyb_protocol: 1.5 mg of cRNA (>9 pmol Cy3 per mg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent

scan_protocol: Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent)

data_processing: Background corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Non-uniform outliers or features not significantly above background intensity in 20% or more of the hybridizations were filtered out.

source_name: Lung fibroblast_control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 g RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions

growth_protocol: Early passage human lung fibroblast cell strain IMR-90 (Coriell repository, NJ) was sub-cultured in Dulbecco’s modified Eagle’s medium (Gibco) and Ham’s F10 medium in a 1:1 mixture plus 15% fetal bovine serum. Young fibroblasts at population doubling <35 were used in all experiments.

extract_protocol: RNA was isolated using Ribopure (Ambion, Applied Biosytems), according to the manufacturer’s instructions

treatment_protocol: Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator

tag: primary lung fibroblastTotal RNA


title: IMR90_alpha_rep2

description: Gene expression after 4hr in 0.5Gy-irradiated human lung fibroblasts

source_name: Lung fibroblast_irradiated


title: IMR90_bystander_rep2

description: Gene expression after 4hr in bystanders to 0.5Gy-irradiated human lung fibroblasts

source_name: Lung fibroblast_bystander


title: IMR90_control_rep1


title: IMR90_alpha_rep3


title: IMR90_alpha_rep4


title: IMR90_control_rep3


title: IMR90_bystander_rep1


title: IMR90_control_rep4


title: IMR90_bystander_rep4


title: IMR90_alpha_rep1


title: IMR90_bystander_rep3


title: H 36.txt

status: Public on Aug 11 2008

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: A male subject who is healthy where age 7 yrs, when sample taken.

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

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.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy Mini

tag: Age

value: 7 yrs, when sample taken.

tag: Gender

value: M

tag: Ethnicity

value: Not Hispanic or Latino

tag: Race

value: White

tag: Illness

value: Healthy


title: 5d-seed

status: Public on Jun 30 2007

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

description: Gene expression data from rice stigma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS software (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.

organism: Oryza sativa

source_name: Rice 5 day seed after pollination

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: Rice were grown in season beginning from May to October, in the experimental farm of the Institute of Genetics and Developmental biology, Beijing.

extract_protocol:
remove lemma and palea,grains were collected 5 days after flowering
total RNA was isolated and  purified by Qiagen RNeasy kit

value: Japonica Nipponbare

value: Rice 5 day seed after pollination


title: B16F1_untreated_rep1.2

status: Public on Sep 27 2006

city: Chicago

first: Assel

last: Biyasheva

state: IL

address: 303 East Chicago Ave., Ward 8-063

department: Cell and Molecular Biology

institute: Northwestern University

description: Gene expression data from control untreated B16F1 mouse melanoma cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse  Genome Array MG_U74Av2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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 100.

source_name: B16F1 mouse melanoma cells cultured at regular conditions.

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

growth_protocol: Dulbecco's modified Eagle's medium (DMEM) with L-glutamine, 4,5 g/L D-glucose, without sodium piruvate (Invitrogen Cat# 11965-092) supplemented with 10% fetal bovine serum. Temperature 37oC, CO2 10%. Passages every 3-4 days. Before RNA isolation, cells were detached from culture flask by trypsinization.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit (Cat # 74104) according to the manufacturer's instructions.

treatment_protocol: untreated control

tag: Cells were cultured to reach 95-99% confluency before lysis and RNA isolation

tag: B16F1 mouse melanoma cells were a gift from C. Ballestrem (Weizmann Institute of Science) and cultured as described previously (Ballestrem et al., 1998, J Cell Sci 111 ( Pt 12), 1649-1658).


title: Root

description: Gene expression data from rice stigma

source_name: Rice root

growth_protocol: Rice (O. sativa L. cv. Nipponbare) seeds were germinated and grown in a growth container for two weeks (28 degree, 16 h light, 8 h dark, photo intensity 240 ¦Ìm photos m-2s-1).

extract_protocol:
the seedling root were cutted and harvested from two-week seeding
total RNA was isolated and  purified by Qiagen RNeasy kit

value: two-week old rice root


title: B16F1_untreated_rep1.1

tag: Cells were cultured to reach 95-99% confluency before lysis and RNA isolation.


title: Endosperm

description: Gene expression data from rice stigma

source_name: Rice 10-day-old Endosperm

extract_protocol:
remove lemma and palea,endosperm were dissected from grains 10 days after flowering
total RNA was isolated and  purified by Qiagen RNeasy kit

tag: genotype

value: Rice 10-day-old endosperm after pollination


title: B16F1_untreated_rep1.3

growth_protocol: Dulbecco's modified Eagle's medium (DMEM) with L-glutamine, 4,5 g/L D-glucose, without sodium piruvate (Invitrogen Cat# 11965-092) supplemented with 10% fetal bovine serum. Temperature 37oC, CO2 10%. Passage every 3-4 days. Before RNA isolation, cells were detached from culture flask by trypsinization.


title: H 28.txt

description: A female subject who is healthy where age 12 yrs, when sample taken.

value: 12 yrs, when sample taken.

value: F

value: Hispanic or Latino

value: (Race Not Reported)


title: Anther

description: Gene expression data from rice stigma

source_name: mature anther

extract_protocol:
remove lemma and palea from floret,the anther is extracted and removed the filament
total RNA was isolated and  purified by Qiagen RNeasy kit

value: stage 1¨C2 days before floret flowering

tag: age:


title: Ovary 3, biological rep 3

description: Gene expression data from rice stigma

source_name: mature ovary

growth_protocol: natural conditions,growing season begins from December to next April, in an experimental farm in Hainan, China.

extract_protocol:
remove lemma and palea from floret, the stigma is extracted from pistil, the remainder of the pistil containing the style is used as the ovary samples.
total RNA was isolated and  purified by Qiagen RNeasy kit

value: ovaries at anthesis

value: rice ovary before pollination


title: Ovary 1, biological rep 1

description: Gene expression data from rice stigma

extract_protocol:
remove lemma and palea from floret, the stigma is extracted from pistil, the remainder of the pistil containing the style were used as the ovary samples.
total RNA was isolated and  purified by Qiagen RNeasy kit


title: Shoot

description: Gene expression data from rice stigma

source_name: Rice shoot

extract_protocol:
the shoot were cutted and harvested from two-week seeding
total RNA was isolated and  purified by Qiagen RNeasy kit

value: two-week old rice shoot


title: stigma 2, biological rep 2

description: Gene expression data from rice stigma

source_name: mature stigmas

extract_protocol:
remove lemma and palea from floret, the stigma is extracted  by cutting the pistil just below the base of the plumose stigma
total RNA was isolated and  purified by Qiagen RNeasy kit

value: unpollinated stigmas at anthesis

value: rice stigma before pollination


title: stigma 3, biological rep 2

description: Gene expression data from rice stigma


title: Embryo

description: Gene expression data from rice stigma

source_name: Rice 10-day-old embryo

extract_protocol:
remove lemma and palea,embryos were dissected from grains 10 days after flowering
total RNA was isolated and  purified by Qiagen RNeasy kit

value: Rice 10-day-old embryo after pollination


title: Ovary 2, biological rep 2

description: Gene expression data from rice stigma


title: stigma 1, biological rep1

description: Gene expression data from rice stigma

extract_protocol:
remove lemma and palea from floret, the stigma is collected  by cutting the pistil just below the base of the plumose stigma
total RNA was isolated and  purified by Qiagen RNeasy kit


title: HeLa mock-b vs. HeLa VHL-2651-AS_pos2_modified-b

status: Public on Sep 07 2006

city: Carlsbad

first: Aimee

last: Jackson

state: CA

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: For details please see: Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Kvorova A, and Linsley PS. RNA (2006) 12(7):1197-1205

data_processing: Local background correction

source_name: HeLa

tag: cell line

value: HeLa

tag: conditions

value: mock-b


title: HeLa mock-b vs. HeLa VHL-2651-b


title: HeLa mock-b vs. HeLa VHL-2652-AS_pos2_modified-b


title: HeLa mock-b vs. HeLa VHL-2652-b


title: HeLa mock-b vs. HeLa SOS1-1582-AS_pos2_modified-b


title: HeLa mock-b vs. HeLa SOS1-1582-b


title: HeLa mock-b vs. HeLa PRKCE-1295-b


title: 468GFP-LN biorep2

first: Ann

last: Chambers

state: Ontario

address: 790 Commissioner's Road E

department: Victoria research labs

institute: London Regional Cancer program

description: Human SNP 6.0 array data (affymetrix) from Parental Cell line 468GFP-LN, second biological replicate

hyb_protocol: Genomic DNA was hybridized as per standard affymetrix protocols for Human SNP6.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. .CEL files thus produced were imported into Partek Genomics Suite software and background subtracted using the RMA algorithm.

label: Biotin/SAPE

label_protocol: Genomic DNA was labeled was labeled as per Affymetrix standard protocol for Human SNP6.0 arrays

growth_protocol: Cells were grown out to three passages in alpha-MEM containing 10% FBS in 5% CO2 to 70 % confluency

extract_protocol: Genomic DNA was extracted using Sigma GeneElute kit using the Manufacturer's protocol,

treatment_protocol: No treatment


title: HeLa mock-b vs. HeLa PIK3CA-2629-AS_pos2_modified-b


title: HeLa mock-b vs. HeLa MPHOSPH1-2692-b


title: HeLa mock-b vs. HeLa PRKCE-1295-AS_pos2_modified-b


title: HeLa mock-a vs. HeLa VHL-2652-AS_pos2_modified-a

value: mock-a


title: 468GFP-LN biorep1

description: Human SNP 6.0 array data (affymetrix) from Parental Cell line 468GFP-LN, first biological replicate


title: HeLa mock-a vs. HeLa VHL-2652-a


title: HeLa mock-a vs. HeLa SOS1-1582-AS_pos2_modified-a


title: HeLa mock-a vs. HeLa PRKCE-1295-a


title: Suspension cell

description: Gene expression data from rice stigma

source_name: Rice suspension cell

growth_protocol: Rice calli were cultured in N6 liquid medium containing 2,4-D (1 mg/l) in a rotary shaker at 150 rpm at 25 degree for 4 weeks with the medium refreshed every week.

extract_protocol:
the suspension cultured cell were collected by centrifuge
total RNA was isolated and  purified by Qiagen RNeasy kit

value: Japonica Nipponbare

tag: 4 weeks suspension cultured cell


title: HeLa mock-a vs. HeLa VHL-2651-AS_pos2_modified-a


title: HeLa mock-a vs. HeLa VHL-2651-a


title: HeLa, mock, 24hr vs. HeLa, MPHOSPH1-202, AS_pos1+2_modified, 10nM, 24 hr

value: mock, 24hr


title: HeLa, mock, 24hr vs. HeLa, MPHOSPH1-202, AS_pos1+2_modified, 100nM, 24 hr


title: HeLa mock-a vs. HeLa MPHOSPH1-2692-AS_pos2_modified-a


title: HeLa mock-a vs. HeLa PIK3CA-2629-AS_pos2_modified-a


title: HeLa mock-a vs. HeLa PRKCE-1295-AS_pos2_modified-a


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, unmodified, 10nM, 24 hr

value: MAPK14-193, unmodified, 10nM, 24 hr


title: HeLa mock-a vs. HeLa SOS1-1582-a


title: RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells (Dataset 3427302)

status: Public on Jun 23 2009

description: RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells using monoclonal antibody W0002.

source_name: RNA polymerase (Beta) ChIP in E. coli K-12 MG1655 cells, untreated

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: antibody

value: Monoclonal antibody for RNA polymerase Beta subunit (W0002)

source_name: Genomic DNA control from E. coli K-12 MG1655 cells, untreated

tag: reference

value: input Genomic DNA control


title: HeLa mock-a vs. HeLa PIK3CA-2629-a


title: HeLa mock-a vs. HeLa MPHOSPH1-2692-a


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, AS_pos1+2_modified, 10nM, 24 hr


title: HeLa, mock, 24hr vs. HeLa, MPHOSPH1-202, unmodified, 10nM, 24 hr

value: MPHOSPH1-202, unmodified, 10nM, 24 hr


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, AS_pos1+2_modified, 100nM, 24 hr


title: 468GFP biorep2

description: Human SNP 6.0 array data (affymetrix) from Parental Cell line 468GFP, second biological replicate


title: HeLa, mock, 24hr vs. HeLa, MPHOSPH1-202, unmodified, 100nM, 24 hr

value: MPHOSPH1-202, unmodified, 100nM, 24 hr


title: RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin (Dataset 3428302)

description: RNA polymerase (Beta) ChIP-chip in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin using monoclonal antibody W0002.

source_name: RNA polymerase (Beta) ChIP in E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin

source_name: Genomic DNA control from E. coli K-12 MG1655 cells treated with 20ug/ml bicyclomycin


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, unmodified, 100nM, 24 hr

value: MAPK14-193, unmodified, 100nM, 24 hr


title: HeLa mock-b vs. HeLa MPHOSPH1-2692-AS_pos2_modified-b


title: 468GFP biorep1

description: Human SNP 6.0 array data (affymetrix) from Parental Cell line 468GFP, first biological replicate


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, unmodified, 24hr

value: MAPK14-193, unmodified, 24hr


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, AS_pos1+2_modified, 24hr

value: MAPK14-193, AS_pos1+2_modified, 24hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos1_modified-b, 18hr

value: mock, 18hr

value: MAPK14-193, AS_pos1_modified-b, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos1_modified, 18hr

value: MAPK14-193, AS_pos1_modified, 18hr


title: HeLa, mock, 20 hr vs. HeLa, 193-MAPK14, unmodified, 20 hr

value: mock, 20 hr

value: 193-MAPK14, unmodified, 20 hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos5+6_modified, 18hr

value: HeLa

value: MAPK14-193, AS_pos5+6_modified, 18hr


title: HeLa, mock, 18 hr vs. HeLa, MPHOSPH1-202, AS_pos1+2_modified, 10nM, 18 hr

value: mock, 18 hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos10+11_modified, 18hr

value: MAPK14-193, AS_pos10+11_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos8+9_modified, 18hr

value: MAPK14-193, AS_pos8+9_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos8+9_modified-b, 18hr

value: MAPK14-193, AS_pos8+9_modified-b, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos7+8_modified, 18hr

value: MAPK14-193, AS_pos7+8_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos9+10_modified, 18hr

value: MAPK14-193, AS_pos9+10_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos4+5_modified, 18hr

value: MAPK14-193, AS_pos4+5_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos2+3_modified, 18hr

value: MAPK14-193, AS_pos2+3_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos2_modified, 18hr

value: MAPK14-193, AS_pos2_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos6+7_modified, 18hr

value: MAPK14-193, AS_pos6+7_modified, 18hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos1+2_modified, 18hr

value: mock, 18hr

value: MAPK14-193, AS_pos1+2_modified, 18hr


title: HeLa, mock, 18 hr vs. HeLa, MPHOSPH1-202, unmodified, 100nM, 18 hr

value: MPHOSPH1-202, unmodified, 100nM, 18 hr


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos3+4_modified, 18hr

value: MAPK14-193, AS_pos3+4_modified, 18hr


title: Hela, mock, 24 hr vs. HeLa, 193-MAPK14, 24 hr, unmodified

value: mock, 24 hr

value: 193-MAPK14, 24 hr, unmodified


title: HeLa, mock, 18 hr vs. HeLa, MPHOSPH1-202, unmodified, 10nM, 18 hr

value: HeLa

value: MPHOSPH1-202, unmodified, 10nM, 18 hr


title: HeLa, mock, 18 hr vs. HeLa, MAPK14-193, unmodified, 100nM, 18 hr

value: mock, 18 hr

value: MAPK14-193, unmodified, 100nM, 18 hr


title: HeLa, mock, 18 hr vs. HeLa, MPHOSPH1-202, AS_pos1+2_modified, 100nM, 18 hr


title: cornea Sprague1

status: Public on Jan 27 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
cornea Sprague1
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley cornea
file:R3RS01112801


title: Hela, mock, 18hr vs. Hela, MAPK14-193, AS_pos11+12_modified, 18hr

value: MAPK14-193, AS_pos11+12_modified, 18hr


title: primary cortical neurons sprague1

description:
primary cortical neurons sprague1
pool of several animals, 16 days gestation, unknown gender
Sprague Dawley primary cortical neurons
file:R3RS01062111


title: cornea Sprague2

description:
cornea Sprague2
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley cornea
file:R3RS01112802


title: primary cortical neurons sprague2

description:
primary cortical neurons sprague2
pool of several animals, 16 days gestation, unknown gender
Sprague Dawley primary cortical neurons
file:R3RS01062216


title: prefrontal cortex sprague2

description:
prefrontal cortex sprague2
whole tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley prefrontal cortex
file:R3MH02052402


title: locus coeruleus sprague2

description:
locus coeruleus sprague2
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley locus coeruleus
file:R3MH02051602


title: prefrontal cortex sprague1

description:
prefrontal cortex sprague1
whole tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley prefrontal cortex
file:R3MH02052401


title: nucleus accumbens_shell sprague2

description:
nucleus accumbens_shell sprague2
Half-moon-shaped NAc shell samples were obtained with a 12 gauge punch of the remaining ventromedial shell tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley nucleus accumbens shell
file:R3MH01112101


title: MMRC_8w_MB1_T1

status: Public on Oct 18 2005

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description:
Strain: B6
Sex: M
Age: 8 Wk
Tissue: Brain
Biological Replicate: 1
Technical Replicate: 1
Dye: Cy5

source_name: Universal Mouse Reference RNA (Stratagene)

source_name: Mouse Brain


title: nucleus accumbens_shell sprague1

description:
nucleus accumbens_shell sprague1
Half-moon-shaped NAc shell samples were obtained with a 12 gauge punch of the remaining ventromedial shell tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley nucleus accumbens shell
file:R3MH01110601


title: hypothalamus sprague2

description:
hypothalamus sprague2
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley hypothalamus
file:R3MH02061201


title: hypothalamus sprague1

description:
hypothalamus sprague1
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley hypothalamus
file:R3MH02061102


title: endothelial cells sprague1

description:
endothelial cells sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley endothelial cells
file:R3JW02103021


title: dorsal striatum sprague 3978

description:
dorsal striatum sprague 3978
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley dorsal striatum
file:R3MH01022301


title: endothelial cells sprague2

description:
endothelial cells sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley endothelial cells
file:R3JW02103022


title: dorsal striatum sprague 3981

description:
dorsal striatum sprague 3981
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley dorsal striatum
file:R3MH01022302


title: thymus sprague2

description:
thymus sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley thymus
file:R3JW02103018


title: ventral tegmental area sprague1

description:
ventral tegmental area sprague1
obtained with a 16 gauge punch from coronal brain slices from 5.0-6.3 mm posterior to bregma, pool of 5 animals, 16 weeks old, male
Sprague Dawley ventral tegmental area
file:R3KJF02012263


title: dorsal raphe sprague2

description:
dorsal raphe sprague2
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley dorsal raphe nucleus
file:R3MH02060702


title: dorsal raphe sprague1

description:
dorsal raphe sprague1
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley dorsal raphe nucleus
file:R3MH02060701


title: locus coeruleus sprague1

description:
locus coeruleus sprague1
whole tissue, pool of 5 animals, 16 weeks old, male
Sprague Dawley locus coeruleus
file:R3MH02051601


title: spleen sprague2

description:
spleen sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley spleen
file:R3JW02103016


title: ventral tegmental area sprague2

description:
ventral tegmental area sprague2
obtained with a 16 gauge punch from coronal brain slices from 5.0-6.3 mm posterior to bregma, pool of 5 animals, 16 weeks old, male
Sprague Dawley ventral tegmental area
file:R3KJF02012264


title: thymus sprague1

description:
thymus sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley thymus
file:R3JW02103017


title: spleen sprague1

description:
spleen sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley spleen
file:R3JW02103015


title: large intestine sprague1

description:
large intestine sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley large intestine
file:R3JW02103013


title: large intestine sprague2

description:
large intestine sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley large intestine
file:R3JW02103014


title: kidney sprague2

description:
kidney sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley kidney
file:R3JW02103008


title: heart sprague2

description:
heart sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley heart
file:R3JW02103012


title: bone marrow sprague2

description:
bone marrow sprague2
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley bone marrow
file:R3JW02103006


title: kidney sprague1

description:
kidney sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley kidney
file:R3JW02103007


title: bone marrow sprague1

description:
bone marrow sprague1
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley bone marrow
file:R3JW02103005


title: heart sprague1

description:
heart sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley heart
file:R3JW02103011


title: skeletal muscle sprague2

description:
skeletal muscle sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley skeletal muscle
file:R3JW02103004


title: nucleus accumbens_core sprague2

description:
nucleus accumbens_core sprague2
Obtained with a 14 gauge punch from chilled coronal brain slices (0.7-2.2 mm anterior to bregma; Paxinos and Watson, 1998; pool of 5 animals, 20 weeks old, male
Sprague Dawley nucleus accumbens core
file:R3JV01080108


title: pituitary sprague2

description:
pituitary sprague2
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley pituitary
file:R3JBH02100404


title: small intestine sprague1

description:
small intestine sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley small intestine
file:R3JW02103001


title: skeletal muscle sprague1

description:
skeletal muscle sprague1
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley skeletal muscle
file:R3JW02103003


title: small intestine sprague2

description:
small intestine sprague2
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley small intestine
file:R3JW02103002


title: nucleus accumbens_core sprague1

description:
nucleus accumbens_core sprague1
Obtained with a 14 gauge punch from chilled coronal brain slices (0.7-2.2 mm anterior to bregma; Paxinos and Watson, 1998; pool of 5 animals, 20 weeks old, male
Sprague Dawley nucleus accumbens core
file:R3JV01080107


title: nucleus accumbens, whole wistar2

description:
nucleus accumbens, whole wistar2
Obtained with a 1.5 mm diameter punch, using a 2mm thick slice, and anterior commisure was in dorsolateral portion of punch.
Wistar whole nucleus accumbens
file:R3JV01080106


title: pineal sprague1

description:
pineal sprague1
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley pineal
file:R3JBH02100401


title: pineal sprague2

description:
pineal sprague2
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley pineal
file:R3JBH02100402


title: dorsal striatum wistar ky 3972

description:
dorsal striatum wistar ky 3972
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto dorsal striatum
file:p3978w


title: dorsal striatum wistar 3966

description:
dorsal striatum wistar 3966
whole tissue, individual animal, 10 weeks old, male
Wistar dorsal striatum
file:p3981w


title: dorsal root ganglion fisher1

description:
dorsal root ganglion fisher1
whole tissue, pool of 5 animals, 16 weeks old, male
Fisher dorsal root ganglion
file:p3970w


title: pituitary sprague1

description:
pituitary sprague1
whole tissue, pool of 5 animals, 10 weeks old, male
Sprague Dawley pituitary
file:R3JBH02100403


title: dorsal root ganglion fisher2

description:
dorsal root ganglion fisher2
whole tissue, pool of 5 animals, 16 weeks old, male
Fisher dorsal root ganglion
file:p3972w


title: ventral striatum wistar ky 3960

description:
ventral striatum wistar ky 3960
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Wistar Kyoto ventral striatum
file:p3960w


title: ventral striatum sprague 3963

description:
ventral striatum sprague 3963
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Sprague Dawley ventral striatum
file:p3963w


title: ventral striatum sprague 3961

description:
ventral striatum sprague 3961
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Sprague Dawley ventral striatum
file:p3961w


title: ventral striatum wistar 4028

description:
ventral striatum wistar 4028
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Wistar ventral striatum
file:p4028w


title: ventral striatum wistar 4026

description:
ventral striatum wistar 4026
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Wistar ventral striatum
file:p4026w


title: nucleus accumbens, whole wistar1

description:
nucleus accumbens, whole wistar1
Obtained with a 1.5 mm diameter punch, using a 2mm thick slice, and anterior commisure was in dorsolateral portion of punch, pool of 5 animals, 16 weeks old, male
Wistar whole nucleus accumbens
file:R3JV01080105


title: hippocampus wistar ky 3956

description:
hippocampus wistar ky 3956
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto hippocampus
file:p3956w


title: ventral striatum wistar ky 3959

description:
ventral striatum wistar ky 3959
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Wistar Kyoto ventral striatum
file:p3959w


title: frontal cortex sprague 3936

description:
frontal cortex sprague 3936
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3936w


title: hippocampus sprague 3957

description:
hippocampus sprague 3957
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley hippocampus
file:p3957w


title: frontal cortex sprague 3935

description:
frontal cortex sprague 3935
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3935w


title: dorsal striatum wistar ky 3970

description:
dorsal striatum wistar ky 3970
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto dorsal striatum
file:p3966w


title: frontal cortex sprague 3934

description:
frontal cortex sprague 3934
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3934w


title: frontal cortex sprague 3937

description:
frontal cortex sprague 3937
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3937w


title: ventral striatum sprague 3962

description:
ventral striatum sprague 3962
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Sprague Dawley ventral striatum
file:p3962w


title: amygdala wistar 3721

description:
amygdala wistar 3721
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3946w


title: ventral striatum wistar 3958

description:
ventral striatum wistar 3958
freehand block dissections, removed only cortex, individual animal, 10 weeks old, male
Wistar ventral striatum
file:p3958w


title: amygdala wistar 3720

description:
amygdala wistar 3720
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3950w


title: HeLa, mock, 20 hr vs. HeLa, 193-MAPK14, AS_pos1+2_modified, 20 hr

description: For details please see: Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Kvorova A, and Linsley PS. RNA (2006) 12(7):1197-1205

value: mock, 20 hr

value: 193-MAPK14, AS_pos1+2_modified, 20 hr


title: HeLa, mock, 20hr vs. HeLa, MAPK14-193, unmodified, 20hr

value: mock, 20hr

value: MAPK14-193, unmodified, 20hr


title: frontal cortex sprague 3933

description:
frontal cortex sprague 3933
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3933w


title: frontal cortex wistar ky 3930

description:
frontal cortex wistar ky 3930
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3930w


title: frontal cortex wistar ky 3928

description:
frontal cortex wistar ky 3928
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3928w


title: frontal cortex sprague 3932

description:
frontal cortex sprague 3932
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley frontal cortex
file:p3932w


title: frontal cortex wistar ky 3929

description:
frontal cortex wistar ky 3929
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3929w


title: frontal cortex wistar ky 3931

description:
frontal cortex wistar ky 3931
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3931w


title: frontal cortex wistar ky 3927

description:
frontal cortex wistar ky 3927
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3927w


title: frontal cortex wistar 3922

description:
frontal cortex wistar 3922
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3922w


title: frontal cortex wistar ky 3926

description:
frontal cortex wistar ky 3926
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto frontal cortex
file:p3926w


title: frontal cortex wistar 3923

description:
frontal cortex wistar 3923
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3923w


title: frontal cortex wistar 3925

description:
frontal cortex wistar 3925
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3925w


title: frontal cortex wistar 3921

description:
frontal cortex wistar 3921
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3921w


title: cerebral cortex sprague 3916

description:
cerebral cortex sprague 3916
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3916w


title: cerebral cortex sprague 3919

description:
cerebral cortex sprague 3919
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3919w


title: frontal cortex wistar 3920

description:
frontal cortex wistar 3920
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3920w


title: cerebral cortex wistar 3902

description:
cerebral cortex wistar 3902
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar cerebral cortex
file:p3902w


title: cerebral cortex wistar ky 3913

description:
cerebral cortex wistar ky 3913
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar Kyoto cerebral cortex
file:p3913w


title: cerebral cortex sprague 3918

description:
cerebral cortex sprague 3918
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3918w


title: cerebral cortex sprague 3917

description:
cerebral cortex sprague 3917
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3917w


title: cerebral cortex wistar 3903

description:
cerebral cortex wistar 3903
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar cerebral cortex
file:p3903w


title: cerebral cortex sprague 3915

description:
cerebral cortex sprague 3915
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3915w


title: cerebral cortex wistar ky 3911

description:
cerebral cortex wistar ky 3911
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar Kyoto cerebral cortex
file:p3911w


title: cerebral cortex wistar ky 3912

description:
cerebral cortex wistar ky 3912
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar Kyoto cerebral cortex
file:p3912w


title: cerebellum sprague 3901

description:
cerebellum sprague 3901
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3901w


title: frontal cortex wistar 3924

description:
frontal cortex wistar 3924
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3924w


title: cerebral cortex sprague 3914

description:
cerebral cortex sprague 3914
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Sprague Dawley cerebral cortex
file:p3914w


title: cerebellum sprague 3899

description:
cerebellum sprague 3899
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3899w


title: cerebral cortex wistar 3904

description:
cerebral cortex wistar 3904
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar cerebral cortex
file:p3904w


title: cerebellum sprague 3896

description:
cerebellum sprague 3896
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3896w


title: cerebellum sprague 3900

description:
cerebellum sprague 3900
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3900w


title: cerebellum wistar ky 3894

description:
cerebellum wistar ky 3894
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto cerebellum
file:p3894w


title: cerebellum sprague 3898

description:
cerebellum sprague 3898
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3898w


title: cerebral cortex wistar ky 3910

description:
cerebral cortex wistar ky 3910
all cortical minus the frontal cortex, individual animal, 10 weeks old, male
Wistar Kyoto cerebral cortex
file:p3910w


title: cerebellum wistar 3889

description:
cerebellum wistar 3889
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3889w


title: cerebellum wistar ky 3893

description:
cerebellum wistar ky 3893
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto cerebellum
file:p3893w


title: cerebellum wistar ky 3891

description:
cerebellum wistar ky 3891
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto cerebellum
file:p3891w


title: cerebellum wistar 3888

description:
cerebellum wistar 3888
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3888w


title: cerebellum wistar ky 3890

description:
cerebellum wistar ky 3890
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto cerebellum
file:p3890w


title: cerebellum wistar ky 3892

description:
cerebellum wistar ky 3892
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto cerebellum
file:p3892w


title: amygdala wistar 3723

description:
amygdala wistar 3723
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3721w


title: sal-PVH3_2

status: Public on Apr 17 2003

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, saline, 3 hour


title: cerebellum wistar 3887

description:
cerebellum wistar 3887
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3887w


title: frontal cortex wistar 3659

description:
frontal cortex wistar 3659
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3659w


title: amygdala wistar 3942

description:
amygdala wistar 3942
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3723w


title: frontal cortex wistar 3660

description:
frontal cortex wistar 3660
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3660w


title: cerebellum wistar 3886

description:
cerebellum wistar 3886
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3886w


title: frontal cortex wistar 3658

description:
frontal cortex wistar 3658
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3658w


title: hippocampus wistar 3772

description:
hippocampus wistar 3772
whole tissue, individual animal, 10 weeks old, male
Wistar hippocampus
file:p3772w


title: RST-PVH_2

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, restraint stress, 1 hours


title: cerebellum wistar 3884

description:
cerebellum wistar 3884
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3884w


title: cerebellum wistar 3885

description:
cerebellum wistar 3885
whole tissue, individual animal, 10 weeks old, male
Wistar cerebellum
file:p3885w


title: frontal cortex wistar 3662

description:
frontal cortex wistar 3662
whole tissue, individual animal, 10 weeks old, male
Wistar frontal cortex
file:p3662w


title: sal-PVH3_1

description: male C57BL6, double amplification


title: sal-PVH_2

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, saline, 1 hour


title: RST-PVH_1

description: male C57BL6, double amplification


title: amygdala wistar 3724

description:
amygdala wistar 3724
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3722w


title: LPS-PVH_1

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, LPS, 10 micrograms, 1 hours


title: sal-PVH_1

description: male C57BL6, double amplification


title: RST-PVH3_1

description: male C57/BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, restraint stress, 3 hours


title: LPS-PVH3_2

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, LPS, 10 micrograms, 3 hours


title: LPS-PVH3_1

description: male C57BL6, double amplification


title: RST-PVH3_2

description: male C57BL6, double amplification


title: LPS-PVH_2

status: Public on Apr 15 2003

description: male C57BL6, double amplification

source_name: paraventricular nucleus of the hypothalamus, LPS, 1 hour


title: cerebellum sprague 3897

description:
cerebellum sprague 3897
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley cerebellum
file:p3897w


title: PCA_wildtype_rpoN_BR2B

status: Public on Jul 13 2009

city: Amherst

first: Derek

last: Lovley

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: Total RNA (10 ug) was directly labeled with cy5 (pCDrpoN) or cy3 (pCD341)

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner.

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: rpoN overexpressor

label_protocol: Micromax ASAP direct RNA labeling kit

extract_protocol: Qiagen RNEasy Midi protocol

tag: DL1/pCDrpoN was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: rpoN overexpression from plasmid pCDrpoN.

source_name: wildtype (pCD341)

label_protocol: Micromax direct RNA labeling kit

tag: DL1/pCD341 was grown in medium containing acetate as the electron donor and fumarate as the electron acceptor.  1mM IPTG was added to induce

tag: control plasmid pCD341.


title: Mouse undifferentiated ESCs, biological rep2

status: Public on Jul 10 2009

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Exon-junction, exon, constitutive region hybridizing probesets from undifferentiated wild-type E14 embryonic stem cells

hyb_protocol: According to manufacturer's (Affymetrix) recommendations

data_processing: Probeset intensity values for Affymetrix AltMouseA Array(perfect match only custom array) CEL files were obtained using the RMA package from Bioconductor, using the appropriate CDF file

source_name: Mouse embryonic stem cell

label_protocol: RNA was converted to cDNA primed with random hexamers using the SuperScript II enzyme (Invitrogen), fragmented with DNAse1 (0.6U/ul) (Amersham Pharmacia Biotech) at 37 C to yield 50-200nt fragements (Agilent Bioanalyzer),  purifie

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

treatment_protocol: Mouse E14 ESCs were grown in a monolayer on gelatin-coated culture plates, maintained in medium supplemented with 10% FBS, sodium pyruvate, non-essential amino-acids, beta-mercaptoethanol, LIF, and passaged with trypsin.

tag: cell type


title: FMO Root 7 month/TYA Rhizome 7 month

status: Public on Jul 09 2009

city: Tucson

first: David

last: Gang

state: AZ

address: 1657 E Helen Street

department: Plant Sciences

institute: The University of Arizona

description: After samples were collected from the greenhouse, they were stored in a -80 freezer until processing.

hyb_protocol: We followed Agilent's protocols using Agilent reagents and hybridization chamber for blocking, hybridization and washing.

scan_protocol: Hardware: GenePix 4000B Software: GenePix Pro 6.0

data_processing: Agilent Feature Extract program processed the TIF image and generated the processed data in log with 10 as base.

organism: Curcuma longa

source_name: FMO Root 7 month

label_protocol: We used aaUTP to make aRNA using Amino Allyl MessageAmp™ II aRNA Amplification, then dye coupled for 2 h.

extract_protocol: Qiagen RNeasy Plant kit

tag: variety

value: Curcuma Longa FMO (Fat Mild Orange)

tag: developmental stage

value: 7 months old

tag: tissue

value: root sample

source_name: TYA Rhizome 7 month

value: Curcuma Longa TYA (Thin Yellow Aromatic)

value: rhizome sample


title: amygdala wistar 3722

description:
amygdala wistar 3722
whole tissue, individual animal, 10 weeks old, male
Wistar amygdala
file:p3720w