title: partial response P23

source_name: partial response

value: plasma sample from patient with partial response to doublet therapy

value: partial response


title: Year2 day16 Control rep1

status: Public on Dec 01 2012

type: RNA

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

country: Canada

institute: Simon Fraser University

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

scan_protocol: Slides were scanned at 10 um resolution on a PerkinElmer ScanArray Express or PerkinElmer ProScanArray.

data_processing: Image TIFF files from the scanned microarrays were imported into ImaGene software version 6.1 (BioDiscovery Inc.).  ImaGene output files were imported into GeneSpring software version 7.3.1 (Agilent Technologies Inc.) for statistical analysis.  Each timepoint for each experiment was treated as a unique block and analyzed independently of other timepoints.  The data were normalized to the 50th percentile of the median values for all genes across the microarrays within each timepoint.  Statistical analysis of this normalized data was performed using one-way ANOVA, and then Welch t-tests (variances not assumed equal) were performed to compare the gene expressions in a sewage treatment versus the control with significant differences noted when p < 0.05.  NOTE: Extracted GeneSpring v7 files into GeneSpring v11 in 2012 to obtain data for each slide (in contrast, for thesis and manuscript data analysis, data was exported from GS by treatment).

molecule: total RNA

organism: Oncorhynchus tshawytscha

source_name: liver, neg control, Yr2d16

label_protocol: 25 ug of liver total RNA was labelled with Cy5-dUTP using Superscript Direct cDNA Labeling System kits (Invitrogen), as per the manufacturer's instructions.  Cy3-labelled UDR cDNA sample was made from 600 ng of UDR stock material using 1 nmol of Cy3-dCTP dye (Amersham) and Ready-To-Go beads (Amersham) as per the manufacturer’s protocol, except a 2 h incubation at 37 degree Celcius was used to maximize yield.

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

treatment_protocol: Two experiments were conducted in the month of June but exactly one year apart (called Yr 1 and Yr 2), using untreated sewage from the Capital Regional District in Victoria, British Columbia, Canada.  Juvenile chinook salmon were exposed to seawater negative control, or sewage concentrations made in seawater of 0.05%, 0.1%, 0.7%, 2% and 5/10% for 8 days (with sampling events at days 1, 4 and 8), and then a portion of fish were transferred to clean seawater to recover for 8 days and sampled at the day 16 timepoint.

tag: treatment

value: neg control

tag: time

value: year 2 day 16

tag: tissue

value: liver

tag: developmental stage

value: juvenile

organism: Oncorhynchus mykiss

source_name: liver, mixture of Universal DNA Reference (UDR) material

tag: sample type


title: stable disease P22

city: Phoenix

first: Irene

last: Cherni

state: AZ

address: 445 N. fifth Street

department: Cancer and Cell Biology

country: USA

institute: Translational Genomics Research Institute

description: plasma sample obtained prior to treatment with 2 cycles of carboplatin + gemcitabine

hyb_protocol: All hybridizations were performed in automated hybridization stations with slow mixing mechanism. GenoExplorer microRNA arrays - human (GenoSensor Corporation, Tempe, AZ; containing probes in triplicate for 900 validated human mature miRNAs with an additional 450 validated human pre-miRNAs along with positive and negative control probes) were used for hybridization. One miRNA microarray chip hybridization was performed per patient sample. The reaction was incubated at 42oC for 16 hours. The array was then stained by straptavidin-Cy5 dye. After washes, the arrays were dried and scanned. each miRNA was represented by 3 probes.

scan_protocol: Array was scanned using Axon 4000B. Raw data with signal intensity was analyzed by GenePix software.

data_processing: Raw intensity values for each of the three probes for every miRNA were averaged and standard deviation was also calculated. To calculate the fold change, the averaged miRNA intensities were divided by the signal threshold [Threshould was determined by array background + 2x background SD (standard deviation)] for the respective arrays. PC-UB6, U6-337, 5s-rRNA and PC-HU5s were used for normalization.

organism: Homo sapiens

source_name: stable disease

label_protocol: Total RNA (a minimum of 1µg) was labeled using GenoExplorer microRNA labeling kit (GenoSensor, Tempe, AZ). Briefly, a biotinylated adaptor is labeled at the 5'end of miRNA and other non-capped small non-coding RNA. The reaction was incubated at 20oC for 2 hours. The labeled samples were then used for hybridization.

extract_protocol: Serum and plasma samples were stored at -80°C until processing. Total RNA was isolated from a volume of 40-200 µl of serum or plasma using phenol and guanidine thiocyanate. Final RNA concentrations were measured with NanoDrop instrument (Thermo) using the absorbance value at 260ª. Total RNA extracts were stored at -80°C until further use

value: plasma sample from patient with stable disease after doublet therapy

tag: response

value: stable disease

tag: disease state

value: non-small cell lung cancer


title: stable disease P20


title: partial response P16


title: Year2 day8 5% sewage rep3

source_name: liver, 5% sewage, Yr2d8

value: 5% sewage

value: year 2 day 8

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day8 5% sewage rep4


title: stable disease P15


title: 15269_normal_olfactory bulb

city: Philadelphia

first: Michael

middle: K.

last: Parente

state: PA

address: 3615 Civic Center Blvd.

department: Neurology

institute: Children's Hospital of Philadelphia

description: File descriptor - Animal number-sex-genotype-part of brain.cel

hyb_protocol: Hybridization, staining and washing were performed on an Affymetrix Fluidics Station 400 according to Affymetrix protocols.

scan_protocol: Affymetrix Gene Chip Scanner 3000 controlled by a GeneChip Operating software 1.4

data_processing: Raw microarray image files were processed using  Affymetrix GCOS 1.4 software to calculate individual probe cell intensity data and generate CEL data files and the CEL files were imported into Partek Genomics Suite (v6.5, Partek Inc. St. Louis, MO) where GCRMA was applied.

label: biotin-aRNA

organism: Mus musculus

source_name: normal_olfactory bulb

label_protocol: 1 µg RNA from each brain region was used to prepare biotinylated aRNA using MessageAMP II-biotin Enhanced Signal Round aRNA Amplification Kit

growth_protocol: Animals maintained in breeding colony through carrier-carrier brother-sister mating.  Normals and mutants housed together

extract_protocol: Total RNA was isolated separately from each of the six regions of the right hemisphere which were placed into TRIzol (Invitrogen)  purified using the RNeasy Lipid Tissue mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Diseased and normal mice were housed together until brain harvest at 5 months of age

tag: strain

tag: genotype

value: normal

value: Brain

tag: region

value: olfactory bulb


title: Year2 day8 5% sewage rep1


title: 15269_normal_hippocampus

value: hippocampus


title: 15269_normal_brainstriatum/thalmus/restem

value: brainstriatum/thalmus/restem


title: Year2 day8 2% sewage rep4

source_name: liver, 2% sewage, Yr2d8

value: 2% sewage


title: progressed disease P14

source_name: progressed disease

value: plasma sample from patient with progressed disease after doublet therapy

value: progressed disease


title: stable disease P13


title: 15268_normal_striatum/thalmus/rest

value: striatum/thalmus/rest


city: Vancouver

first: Joerg

last: Bohlmann

department: Michael Smith Laboratories

institute: University of British Columbia

description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb26

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 μL hybridization solution consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.75 μL LNA d(T) blocker, 2 μg sheared salmon testes DNA (Invitrogen) and 0.3 μL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech). Immediately prior to use, arrays were pre-washed 2x in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80ºC for 10 min, then maintained at 65ºC prior to adding to a microarray slide heated to 55ºC, covered with a 22 x 60 x 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 60ºC. Arrays were washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, then three washes of 5 min in 2x SSC at room temperature, and three washes of 5 min in 0.2x SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 μL volume consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.5 μL Cy3 capture reagent and 2.5 μL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 60ºC, then washed and dried as before.

scan_protocol: Fluorescent images of hybridized arrays were acquired by using ScanArray Express (PerkinElmer, Foster City, USA). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively. All scans were performed at the same laser power (90%), but with the photomultiplier tube settings for the two channels adjusted such that the ratio of the mean signal intensities was ~1, and the percentage of saturated array elements was < 0.5% but > 0%, while minimizing background fluorescence. Fluorescent intensity data were extracted by using the ImaGene 5.5 software (Biodiscovery, El Segundo, USA).

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct background intensity. After quantification of the signal intensities, data were normalized using the variance stabilizing normalization (VSN) method of Huber et al. (2002) Bioinformatics 18:S96-S104. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points. The experiment was designed to be Cy3 Cy5 dye balanced. To calculate changes in gene expression, a linear mixed-effect model was used for 36 hybridizations (slides) for the experiment. P values were calculated for each EST-by-treatment effect (including wounding vs. control, fungus vs. control and fungus vs. wounding comparisons for each time point) and q values were calculated to correct for false discovery rate for each p value (Storey and Tibshirani, 2003). All statistical analyses were done using the R statistical package (www.r-project.org/).

organism: Picea engelmannii x Picea glauca

source_name: Interior Spruce bark, tree 2, wounding at 2 weeks

label_protocol: Hybridizations were performed using the Genisphere Array900 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. Ten micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments. Standard greenhouse conditions are described in Ralph et al (2006) Plant Cell & Environment 29: 1545-1570.

extract_protocol: Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824. Total RNA was quantified by spectrophotometer and the quality was evaluated by 2100 Bioanalyzer (Agilent Technologies). RNA was also evaluated for the presence of contaminants using reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, USA) with an oligo d(T18) primer. The resulting cDNA smear was evaluated using gel electrophoresis.

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 weeks after treatment.

tag: tree type

value: Interior Spruce

value: bark

tag: tree number

tag: stress

value: wounding

value: 2 weeks

source_name: Interior Spruce bark, tree 2, control at 2 weeks

treatment_protocol: Untreated control collected at 2 weeks of the experiment time course.

value: control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb24

source_name: Interior Spruce bark, tree 2, wounding at 2 days

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 days after treatment.

value: 2 days

source_name: Interior Spruce bark, tree 2, control at 2 days

treatment_protocol: Untreated control collected at 2 days of the experiment time course.


title: 15269_normal_cerebellum

value: cerebellum


title: Year2 day8 2% sewage rep3

value: year 2 day 8

value: liver

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: stable disease P12

value: plasma sample from patient with stable disease after doublet therapy

value: stable disease

value: non-small cell lung cancer


title: Year2 day8 2% sewage rep2

value: 2% sewage


title: 15269_normal_cortex

value: normal

value: Brain

value: cortex


title: stable disease P10


title: Year2 day8 5% sewage rep2

value: 5% sewage


title: 15268_normal_cortex


title: 15268_normal_olfactory bulb

value: olfactory bulb


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb23

source_name: Interior Spruce bark, tree 2, Leptographium abietinum 6 hours after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 6 hours after treatment.

value: Interior Spruce

value: bark

value: Leptographium abietinum

value: 6 hours

source_name: Interior Spruce bark, tree 2, wounding at 6 hours

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 6 hours after treatment.

value: wounding


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb22

source_name: Interior Spruce bark, tree 1, wounding at 2 weeks

value: 2 weeks

source_name: Interior Spruce bark, tree 1, control at 2 weeks

value: control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb25

source_name: Interior Spruce bark, tree 1, wounding at 6 hours


title: 15268_normal_hippocampus

value: hippocampus


title: Year2 day8 2% sewage rep1

value: year 2 day 8

value: liver

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: stable disease P9

value: plasma sample from patient with stable disease after doublet therapy

value: stable disease

value: non-small cell lung cancer


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb20

source_name: Interior Spruce bark, tree 1, control at 6 hours

treatment_protocol: Untreated control collected at 6 hours of the experiment time course.


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb21

source_name: Interior Spruce bark, tree 2, Leptographium abietinum 2 days after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 2 days after treatment.

value: 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb19

source_name: Interior Spruce bark, tree 1, wounding at 2 days

source_name: Interior Spruce bark, tree 1, control at 2 days


title: 15268_normal_brainstriatum/thalmus/restem

value: normal

value: Brain

value: brainstriatum/thalmus/restem


title: 15268_normal_cerebellum

value: cerebellum


title: Year2 day8 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr2d8

value: 0.7% sewage

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: partial response P8

source_name: partial response

value: plasma sample from patient with partial response to doublet therapy

value: partial response


title: Year2 day8 0.7% sewage rep3


title: stable disease P6

source_name: stable disease


title: progressed disease P7

source_name: progressed disease

value: plasma sample from patient with progressed disease after doublet therapy

value: progressed disease


title: Year2 day8 0.7% sewage rep1

value: year 2 day 8


title: Year2 day8 0.7% sewage rep2

value: liver


title: stable disease P5


title: 15267_normal_striatum/thalmus/rest

value: striatum/thalmus/rest


title: Year2 day8 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr2d8

value: 0.1% sewage

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: partial response P4

value: non-small cell lung cancer


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb18

value: Interior Spruce

value: bark

value: control

value: 6 hours

value: 2 days


title: 15267_normal_cortex

value: normal

value: Brain

value: cortex


title: 15267_normal_hippocampus

value: hippocampus


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb14

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 weeks after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 2 weeks after treatment.

value: Leptographium abietinum

value: 2 weeks

value: wounding


title: 15267_normal_olfactory bulb

source_name: normal_olfactory bulb

value: olfactory bulb


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb15

source_name: Interior Spruce bark, tree 2, control at 2 days


title: Year2 day8 0.1% sewage rep3

value: 0.1% sewage

value: year 2 day 8

value: liver


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb13

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 6 hours after inoculation

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 days after inoculation


title: 15267_normal_brainstriatum/thalmus/restem

value: brainstriatum/thalmus/restem


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb12

value: Interior Spruce


title: 15267_normal_cerebellum

value: cerebellum


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb16

source_name: Interior Spruce bark, tree 3, Leptographium abietinum 2 weeks after inoculation

value: bark

source_name: Interior Spruce bark, tree 3, control at 2 weeks

value: control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb17

source_name: Interior Spruce bark, tree 3, control at 6 hours

value: 6 hours

source_name: Interior Spruce bark, tree 3, wounding at 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb11

source_name: Interior Spruce bark, tree 1, wounding at 6 hours


title: progressed disease P2

description: plasma sample obtained prior to treatment with 2 cycles of carboplatin + gemcitabine

value: plasma sample from patient with progressed disease after doublet therapy

value: progressed disease

value: non-small cell lung cancer


title: partial response P1

value: plasma sample from patient with partial response to doublet therapy

value: partial response


title: progressed disease P3


title: Year2 day8 0.1% sewage rep2

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day8 0.1% sewage rep1


title: Year2 day8 0.05% sewage rep4

source_name: liver, 0.05% sewage, Yr2d8

value: 0.05% sewage


title: Year2 day8 0.05% sewage rep3


title: 15261_normal_olfactory bulb

description: File descriptor - Animal number-sex-genotype-part of brain.cel

value: normal

value: Brain

value: olfactory bulb


title: 15261_normal_striatum/thalmus/rest

value: striatum/thalmus/rest


title: Year2 day8 0.05% sewage rep1

value: year 2 day 8

value: liver


title: Year2 day8 0.05% sewage rep2


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb10

source_name: Interior Spruce bark, tree 1, wounding at 2 days

value: Interior Spruce

value: bark

value: wounding

value: 2 days

source_name: Interior Spruce bark, tree 1, wounding at 2 weeks

value: 2 weeks


title: 15261_normal_cortex

value: cortex


title: 15261_normal_hippocampus

value: hippocampus


title: Year2 day8 Control rep4

source_name: liver, neg control, Yr2d8

value: neg control

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day8 Control rep3

value: juvenile


title: 15261_normal_cerebellum

value: cerebellum


title: Year2 day8 Control rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: PBMC_rhGH IGF-1

city: Worcester

first: Mahesh

last: Appari

state: MA

address: 381 Plantation St

department: Medicine, Diabetes division

institute: University of Massachusetts Medical School - Worcester

hyb_protocol: 2 µg of RNA from day 1, and 3 µg of RNA from day 5 were hybridized to each spotted cDNA microarray.  Arrays were incubated for 14-18 hrs in a water bath at 65°C.

scan_protocol: Arrays were scanned by using Genepix 4000B microarray scanner.

data_processing: Image analysis (gridding) was performed by using GenePix Pro 4.0 software. Gene pix analyzed images were calculated and uploaded into the Stanford microarray database (SMD). Data were retrived from SMD, and analyzed by using Panter software, Cluster, and Gene Tree.

source_name: PBMC

label_protocol: Labeling was performed according to the protocols from Dr. Patrick Brown website 'Stanford university'. RNA from day 1 (before hormone therapy) was labeled with Cy3, and RNA from day 5 (after GH therapy) was labeled with Cy5.

extract_protocol: Total RNA was isolated by using Trizol method, followed by RNeasy mini kit according to the manufacturers's instructions. Possible Genomic DNA contamination was eliminated by using DNA-free™ kit.

tag: therapy

value: (day 1) before hormone therapy

value: (day 5) after hormone therapy


title: PBMC_rhGH_IGF-1 rep


title: PBMC_rhGH ND6


title: 15260_mutant_hippocampus

value: mutant

value: Brain


title: 15260_mutant_striatum/thalmus/rest

value: striatum/thalmus/rest


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb9

source_name: Interior Spruce bark, tree 1, control at 2 days

value: control

source_name: Interior Spruce bark, tree 1, control at 2 weeks


title: PBMC_rhGH ND5


title: PBMC_rhGH TS4


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb6

source_name: Interior Spruce bark, tree 3, wounding at 2 weeks

value: Interior Spruce

value: Leptographium abietinum


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb5

source_name: Interior Spruce bark, tree 2, wounding at 6 hours

value: bark

value: wounding

value: 6 hours

source_name: Interior Spruce bark, tree 2, control at 6 hours


title: 15261_normal_brainstriatum/thalmus/restem

value: normal

value: brainstriatum/thalmus/restem


title: Year2 day8 Control rep1

value: neg control

value: year 2 day 8

value: liver


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb7

value: 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb8

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 days after inoculation


title: 15260_mutant_olfactory bulb

source_name: mutant_olfactory bulb

value: olfactory bulb


title: PBMC_rhGH ND3

value: (day 1) before hormone therapy

value: (day 5) after hormone therapy


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb2

source_name: Interior Spruce bark, tree 2, Leptographium abietinum 6 hours after inoculation


title: Year2 day4 5% sewage rep4

source_name: liver, 5% sewage, Yr2d4

value: 5% sewage

value: year 2 day 4

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb3

value: Interior Spruce

value: control

value: 2 weeks

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 weeks after inoculation

value: Leptographium abietinum


title: 15260_mutant_cerebellum

value: mutant

value: Brain

value: cerebellum


title: 15260_mutant_cortex

value: cortex


title: Year2 day4 5% sewage rep3

value: liver


title: Year2 day4 5% sewage rep2


title: PBMC_rhGH_ND rep3


title: Year2 day4 5% sewage rep1


title: Year2 day4 2% sewage rep4

source_name: liver, 2% sewage, Yr2d4

value: 2% sewage


title: Year2 day4 2% sewage rep3


title: PBMC_rhGH KS2


title: 15260_mutant_brainstriatum/thalmus/restem

value: brainstriatum/thalmus/restem


title: PBMC_rhGH GHD1

value: (day 1) before hormone therapy


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb36

organism: Pinus contorta

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 2 days after inoculation

extract_protocol: Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824. Total RNA was quantified and quality checked by spectrophotometer and agarose gel. RNA was also evaluated for integrity and the presence of contaminants using reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, USA) with an oligo d(T18) primer and _P32 dGTP incorporation. After removal of unincorporated nucleotides using gel filtration columns (Microspin S-300 HR columns, Amersham Pharmacia Biotech, Buckinghamshire, UK) the resulting cDNA smear was resolved using a vertical 1% agarose alkaline gel and visualized using a Storm 860 phosphorimager (Amersham Pharmacia Biotech).

value: Lodgepole pine bark

value: Grosmannia clavigera

tag: time point

value: 2 days after inoculation

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 2 weeks after inoculation

value: 2 weeks after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb35

source_name: Lodgepole pine bark, tree 3, wounding at 6 hours

value: wounding

value: 6 hours

source_name: Lodgepole pine bark, tree 3, Grosmannia clavigera 6 hours after inoculation

value: 6 hours after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb4

source_name: Interior Spruce bark, tree 2, control at 2 weeks

value: Interior Spruce

value: bark

value: control

value: 2 weeks

source_name: Interior Spruce bark, tree 2, Leptographium abietinum 2 weeks after inoculation


title: 15259_mutant_hippocampus

value: mutant

value: Brain

value: hippocampus


title: 15259_mutant_striatum/thalmus/rest

value: striatum/thalmus/rest


title: 15259_mutant_cortex

value: cortex


title: 15259_mutant_cerebellum

value: cerebellum


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb1

source_name: Interior Spruce bark, tree 1, control at 6 hours

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 6 hours after inoculation

value: Leptographium abietinum


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb34

value: Lodgepole pine bark

value: Grosmannia clavigera

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 6 hours after inoculation


title: 15259_mutant_olfactory bulb

value: olfactory bulb


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb33

source_name: Lodgepole pine bark, tree 1, control at 2 weeks

source_name: Lodgepole pine bark, tree 1, control at 6 hours


title: Year2 day4 2% sewage rep2

value: 2% sewage

value: year 2 day 4

value: liver

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day4 2% sewage rep1

value: liver, mixture of Universal DNA Reference (UDR) material


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb31

source_name: Lodgepole pine bark, tree 3, control at 2 weeks

value: control

source_name: Lodgepole pine bark, tree 3, wounding at 2 weeks

value: wounding


title: Year2 day4 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr2d4

value: 0.7% sewage


title: 15259_mutant_brainstriatum/thalmus/restem

value: mutant

value: Brain

value: brainstriatum/thalmus/restem


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb28

value: 6 hours after inoculation

source_name: Lodgepole pine bark, tree 3, control at 6 hours

value: 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb32

source_name: Lodgepole pine bark, tree 3, Grosmannia clavigera 2 days after inoculation

value: 2 days after inoculation

source_name: Lodgepole pine bark, tree 3, control at 2 days

value: 2 days


title: Year2 day4 0.7% sewage rep3


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb29

source_name: Lodgepole pine bark, tree 2, Grosmannia clavigera 2 weeks after inoculation

value: Lodgepole pine bark

value: Grosmannia clavigera

value: 2 weeks after inoculation

source_name: Lodgepole pine bark, tree 2, wounding at 2 weeks

value: 2 weeks


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb27

source_name: Lodgepole pine bark, tree 3, wounding at 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb30


title: Year2 day4 0.7% sewage rep1

value: year 2 day 4

value: liver


title: 15258_mutant_hippocampus

description: File descriptor - Animal number-sex-genotype-part of brain.cel

value: hippocampus


title: 15258_mutant_striatum/thalmus/rest

value: striatum/thalmus/rest


title: Year2 day4 0.7% sewage rep2

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb25

source_name: Lodgepole pine bark, tree 1, wounding at 2 weeks

extract_protocol:
Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824.
Total RNA was quantified and quality checked by spectrophotometer and agarose gel. RNA was also evaluated for integrity and the presence of contaminants using reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, USA) with an oligo d(T18) primer and _P32 dGTP incorporation. After removal of unincorporated nucleotides using gel filtration columns (Microspin S-300 HR columns, Amersham Pharmacia Biotech, Buckinghamshire, UK) the resulting cDNA smear was resolved using a vertical 1% agarose alkaline gel and visualized using a Storm 860 phosphorimager (Amersham Pharmacia Biotech).

value: wounding

source_name: Lodgepole pine bark, tree 1, wounding at 6 hours


title: 15258_mutant_olfactory bulb

source_name: mutant_olfactory bulb

value: mutant

value: Brain

value: olfactory bulb


title: 15258_mutant_cerebellum

value: cerebellum


title: 15258_mutant_cortex

value: cortex


title: 15258_mutant_brainstriatum/thalmus/restem

value: brainstriatum/thalmus/restem


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb24

source_name: Lodgepole pine bark, tree 2, wounding at 2 days

value: Lodgepole pine bark

value: 2 days

source_name: Lodgepole pine bark, tree 2, control at 2 days

value: control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb26

value: 2 weeks

value: 6 hours


title: Year2 day4 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr2d4

value: 0.1% sewage

value: year 2 day 4

value: liver


title: Year2 day4 0.1% sewage rep2

value: juvenile


title: Year2 day4 0.05% sewage rep4

source_name: liver, 0.05% sewage, Yr2d4

value: 0.05% sewage

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day4 0.1% sewage rep1

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day4 0.1% sewage rep3


title: RTYV infected rice rep2

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 2 of 3, RTYV infected rice

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Japonica Group

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Grwoth media :commercial soil (Bonsol: Sumitomo Chemical, Osaka,Japan)
No of seedling per pot : 14
Light condition: Natural conditions
Tempareture: 25±3℃
Growth environment: greenhouse study
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 24 days past inoculation

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen Rneasy maxi kit
manual: Qiagen

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: Rice transitory yellow virus
virus inoculation: five viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible

tag: cultivar

value: Nipponbare

value: shoot

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: mock inoculation
virus inoculation: five virus free green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours


title: RTYV infected rice rep3

description: Biological replication 3 of 3, RTYV infected rice


title: Year2 day4 0.05% sewage rep3


title: Year2 day4 0.05% sewage rep2


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb19

source_name: Lodgepole pine bark, tree 1, wounding at 2 days

value: wounding

source_name: Lodgepole pine bark, tree 1, control at 2 days

treatment_protocol: Untreated control collected at 2 days of the experiment time course


title: RRSV infected rice rep3

description: Biological replication 3 of 3, RRSV infected rice

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Grwoth media :commercial soil (Bonsol: Sumitomo Chemical, Osaka,Japan)
No of seedling per pot : 14
Light condition: Natural conditions
Tempareture: 25±3℃
Growth environment: greenhouse study
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 28 days past inoculation

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: Rice ragged stunt virus
virus inoculation: five viruliferous brown planthopper (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: mock inoculation
virus inoculation: five virus free brown planthopper (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours

value: Shoot


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb21

source_name: Lodgepole pine bark, tree 2, Grosmannia clavigera 2 days after inoculation

value: Grosmannia clavigera

value: 2 days after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb22

value: Lodgepole pine bark

source_name: Lodgepole pine bark, tree 1, control at 2 weeks


title: Year2 day4 Control rep4

source_name: liver, neg control, Yr2d4

value: neg control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb23

source_name: Lodgepole pine bark, tree 2, Grosmannia clavigera 6 hours after inoculation

value: 6 hours after inoculation

source_name: Lodgepole pine bark, tree 2, wounding at 6 hours


title: Year2 day4 0.05% sewage rep1


title: RTYV infected rice rep1

description: Biological replication 1 of 3, RTYV infected rice


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb20

source_name: Lodgepole pine bark, tree 1, control at 6 hours

treatment_protocol: Untreated control collected at 6 hours of the experiment time course

value: control


title: RRSV infected rice rep2

description: Biological replication 2 of 3, RRSV infected rice


title: RRSV infected rice rep1

description: Biological replication 1 of 3, RRSV infected rice


title: RGDV infected rice rep2

description: Biological replication 2 of 3, RGDV infected rice

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: Rice gall dwarf virus
virus inoculation: five viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible


title: Year2 day4 Control rep2

treatment_protocol: Two experiments were conducted in the month of June but exactly one year apart (called Yr 1 and Yr 2), using untreated sewage from the Capital Regional District in Victoria, British Columbia, Canada.  Juvenile chinook salmon were exposed to seawater negative control, or sewage concentrations made in seawater of 0.05%, 0.1%, 0.7%, 2% and 5/10% for 8 days (with sampling events at days 1, 4 and 8), and then a portion of fish were transferred to clean seawater to recover for 8 days and sampled at the day 16 timepoint.


title: Year2 day4 Control rep1


title: Year2 day4 Control rep3


title: Year2 day1 5% sewage rep4

source_name: liver, 5% sewage, Yr2d1

value: 5% sewage

value: year 2 day 1


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb16

source_name: Lodgepole pine bark, tree 3, Grosmannia clavigera 2 weeks after inoculation

value: 2 weeks after inoculation

source_name: Lodgepole pine bark, tree 3, control at 2 weeks

treatment_protocol: Untreated control collected at 2 weeks of the experiment time course

value: 2 weeks


title: RGDV infected rice rep3

description: Biological replication 3 of 3, RGDV infected rice


title: Year2 day1 5% sewage rep3

value: liver

value: juvenile


title: Year2 day1 5% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: RGDV infected rice rep1

description: Biological replication 1 of 3, RGDV infected rice

value: Nipponbare


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb15

value: 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb14

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 2 weeks after inoculation

source_name: Lodgepole pine bark, tree 1, wounding at 2 weeks

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 weeks after treatment.

value: wounding


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb17

source_name: Lodgepole pine bark, tree 3, control at 6 hours

value: 6 hours

source_name: Lodgepole pine bark, tree 3, wounding at 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb13

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 6 hours after inoculation

value: Grosmannia clavigera

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 2 days after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb11

source_name: Lodgepole pine bark, tree 1, wounding at 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb12

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct background intensity. After quantification of the signal intensities, data were normalized using the variance stabilizing normalization (VSN) method of Huber et al. (2002) Bioinformatics 18:S96-S104. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6hours, 2days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points. The experiment was designed to be Cy3 Cy5 dye balanced. To calculate changes in gene expression, a linear mixed-effect model was used for 36 hybridizations (slides) for the experiment. P values were calculated for each EST-by-treatment effect (including wounding vs. control, fungus vs. control and fungus vs. wounding comparisons for each time point) and q values were calculated to correct for false discovery rate for each p value (Storey and Tibshirani, 2003). All statistical analyses were done using the R statistical package (www.r-project.org/).

value: 2 days after inoculation

source_name: Lodgepole pine bark, tree 1, wounding at 2 days

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 days after treatment.


title: AGR2 null

city: Stanford

first: Anson

middle: W

last: Lowe

state: CA

address: 300 Pasteur Drive

department: Medicine

institute: Stanford University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Total intensity normalization was applied to both microarrays.

label: Biotin

source_name: stomach

label_protocol: Standard Illumina label protocol (Biotinylated Cy3)

extract_protocol: The stomachs were removed, the contents emptied, and rinsed with cold phosphate-buffered saline.  Total RNA was then extracted from the glandular stomach using TRIzol reagent (Invitrogen, Carlsbad, CA).

tag: gender

value: female

tag: genotype/variation

value: AGR2 null


title: AGR2 wild-type

value: AGR2 wild-type


title: RBSDV infected rice rep1

description: Biological replication 1 of 3, RBSDV infected rice

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: Rice black streak virus
virus inoculation: five viruliferous small brown planthoppers (Laodelphax striatellus) per 1 seedling
virus inoculation: 24 hours
growth stage: two leaves visible

value: shoot

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: mock inoculation
virus inoculation: five virus free small brawn planthoppers (Laodelphax striatellus) per 1 seedling
virus inoculation: 24 hours


title: Year2 day1 2% sewage rep4

source_name: liver, 2% sewage, Yr2d1

tag: treatment

value: 2% sewage

tag: time

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day1 2% sewage rep3

value: year 2 day 1

tag: tissue

tag: developmental stage


title: Year2 day1 5% sewage rep1

value: 5% sewage

tag: sample type


title: RBSDV infected rice rep2

description: Biological replication 2 of 3, RBSDV infected rice


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb10

value: Lodgepole pine bark

value: 2 weeks


title: RBSDV infected rice rep3

description: Biological replication 3 of 3, RBSDV infected rice


title: Year2 day1 2% sewage rep2

value: liver

value: juvenile


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb18

value: control

source_name: Lodgepole pine bark, tree 1, control at 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb9

value: 2 days

source_name: Lodgepole pine bark, tree 1, control at 2 weeks


title: Year2 day1 2% sewage rep1

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day1 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr2d1

value: 0.7% sewage


title: Year2 day1 0.7% sewage rep3


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb8

value: Grosmannia clavigera


title: Year2 day1 0.7% sewage rep2


title: Year2 day1 0.7% sewage rep1


title: Year2 day1 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr2d1

value: 0.1% sewage


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb5

source_name: Lodgepole pine bark, tree 2, wounding at 6 hours

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 6 hours after treatment.

value: wounding

value: 6 hours

source_name: Lodgepole pine bark, tree 2, control at 6 hours


title: Year2 day1 0.1% sewage rep3


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb4

source_name: Lodgepole pine bark, tree 2, control at 2 weeks

source_name: Lodgepole pine bark, tree 2, Grosmannia clavigera 2 weeks after inoculation

value: 2 weeks after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb6

source_name: Lodgepole pine bark, tree 3, wounding at 2 weeks

source_name: Lodgepole pine bark, tree 3, Grosmannia clavigera 2 weeks after inoculation


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb3

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 2 weeks after inoculation


title: U251 FGFR3-TACC3

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

hyb_protocol: According to Agilent's protocol.

scan_protocol: Arrays were scanned with Agilent's dual-laser-based scanner. Image processing was performed using Agilent Feature Extraction Software version 9.1.3.1.

source_name: U251 cells transfected with FGFR3-TACC3 fusion

label_protocol: According to Agilent's protocol.

growth_protocol: All tissue cultures were maintained in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS) in a 37°C humidified incubator containing 5% CO2.

extract_protocol: According to Agilent's protocol.

treatment_protocol: SNB-19 and U251 cells (600,000) were transfected with 10mg FGFR3-TACC3, FGFR3 WT, or TACC3 WT cDNA with Lipofectamine (Invitrogen) per the manufacturer’s instructions. Stably transfected cells were selected for with 0.4mgml-1 G418 (Invitrogen) for 2 weeks, after which SNB19 clones were selected and amplified.

tag: cell line

value: FGFR3-TACC3 fusion

source_name: U251 cells transfected with empty vector

value: empty vector


title: Year2 day1 0.1% sewage rep2

value: year 2 day 1


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb7

source_name: Lodgepole pine bark, tree 1, wounding at 6 hours

source_name: Lodgepole pine bark, tree 1, wounding at 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb2

treatment_protocol: Untreated control collected at 6 hours of the experiment's time course

source_name: Lodgepole pine bark, tree 2, Grosmannia clavigera 6 hours after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 6 hours after treatment.

value: 6 hours after inoculation


title: siACL 2.0 mM But replicate 3

city: Chapel Hill

first: Dallas

middle: Ross

last: Donohoe

state: NC

address: 120 Mason Farm Rd.

department: Genetics

institute: University of North Carolina at Chapel Hill

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol, hybridizations to the Human WG-6 v2.0 BeadChip arrays (Illumina, San Diego, CA)

scan_protocol: Standard Illumina scanning protocol, scanning was performed at the University of Tennessee at Memphis Core Facility.

data_processing: Probe level data was collapsed to generate gene level expression data, the genes with detection p-value larger than 0.05 in all samples were removed, and then the expression of each sample was normalized by quantile normaization.

label: biotin

source_name: HCT116 cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: siMock and siACL transfected HCT116 cells were grown in DMEM with glucose and treated with butyrate for three days.

extract_protocol: Total RNA was prepared using Trizol reagent (Invitrogen, Carlsbad, CA), and integrity was assessed using the RNA 6000 Nano-LabChip kit followed by analysis using a Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Cells were prepared from each experimental group (3 biological replicates per experimental group) and flash-frozen.

value: 2.0 mM butyrate over three days

tag: transfected

value: siACL


title: U251 TACC3

data_processing: Agilent Feature Extraction Software version 9.1.3.1.

source_name: U251 cells transfected with TACC3 wt

value: TACC3 wt


title: siACL 5.0 mM But replicate 1

description: replicate 1

value: 5.0 mM butyrate over three days


title: siACL 2.0 mM But replicate 2

description: replicate 2


title: SNB19 FGFR3

source_name: SNB19 cells transfected with FGFR3 wt

value: FGFR3 wt

source_name: SNB19 cells transfected with empty vector


title: U251 FGFR3

source_name: U251 cells transfected with FGFR3 wt


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Lodgepole pine_Bark_Grosmannia clavigera_inoculation_hyb1

source_name: Lodgepole pine bark, tree 1, control at 6 hours

value: Lodgepole pine bark

value: control

source_name: Lodgepole pine bark, tree 1, Grosmannia clavigera 6 hours after inoculation


title: siACL 5.0 mM But replicate 3

description: replicate 3


title: SNB19 TACC3

source_name: SNB19 cells transfected with TACC3 wt


title: siACL 5.0 mM But replicate 2

description: replicate 2


title: Year2 day1 0.05% sewage rep4

source_name: liver, 0.05% sewage, Yr2d1

value: 0.05% sewage

value: liver

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: siACL 2.0 mM But replicate 1

description: replicate 1


title: SNB19 FGFR3-TACC3 clone #5

source_name: SNB19 cells transfected with FGFR3-TACC3 clone #5

value: FGFR3-TACC3 clone #5


title: Year2 day1 0.05% sewage rep3

value: liver, mixture of Universal DNA Reference (UDR) material


title: siACL 0.5 mM But replicate 2

description: replicate 2

value: 0.5 mM butyrate over three days


title: Year2 day1 0.1% sewage rep1

source_name: liver, 0.1% sewage, Yr2d1

value: 0.1% sewage


title: siACL untreated replicate 3

description: replicate 3

value: untreated


title: Year2 day1 0.05% sewage rep2

value: year 2 day 1


title: Year2 day1 0.05% sewage rep1


title: siACL 0.5 mM But replicate 1

description: replicate 1


city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

description:
Sample name: R5020_6h_3
R5020 6h replicate 3 hybridized against UHRR

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above the 95% rank in the B empirical Bayes statistic and a set fold change. All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: T47D-MTVL cells were plated in RPMI medium without phenol red supplemented with 10% dextran coated charcoal treated FBS and 48h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10nM R5020 for 0, 1 and 6 hr at 37ºC.

extract_protocol: RNA was extracted using standard total RNA extraction protocol (QIAGEN - RNeasy  Kit)

value: T47D-MTVL breast cancer cell line

tag: agent

value: progestin R5020

source_name: Universal Human Reference RNA

tag: reference

value: Universal Human Reference RNA (Stratagene ref. 740000)


title: SNB19 FGFR3-TACC3 fusion mixture

source_name: SNB19 cells transfected with FGFR3-TACC3 mixture

value: FGFR3-TACC3 clones #2,5,and 8 mixture

value: empty vector


title: siACL untreated replicate 1

description: replicate 1

value: siACL


title: SNB19 FGFR3-TACC3 clone #8

source_name: SNB19 cells transfected with FGFR3-TACC3 clone #8

value: FGFR3-TACC3 clone #8


title: siACL untreated replicate 2

description: replicate 2


title: Year2 day1 Control rep4

source_name: liver, neg control, Yr2d1

value: neg control


title: Year2 day1 Control rep3


title: SNB19 FGFR3-TACC3 clone #2

source_name: SNB19 cells transfected with FGFR3-TACC3 clone #2

value: FGFR3-TACC3 clone #2


title: Year2 day1 Control rep2

value: liver


title: siACL 0.5 mM But replicate 3

description: replicate 3

source_name: HCT116 cells


description:
Sample name: R5020_6h_1
R5020 6h replicate 1 hybridized against UHRR


title: Year2 day1 Control rep1

value: juvenile


title: siMock 5.0 mM But replicate 3

description: replicate 3

value: 5.0 mM butyrate over three days

value: siMock


description:
Sample name: R5020_6h_2
R5020 6h replicate 2 hybridized against UHRR


title: siMock 5.0 mM But replicate 2

description: replicate 2


description:
Sample name: R5020_1h_4
R5020 1h replicate 4 hybridized against UHRR


title: Year1 day16 10% sewage rep4

source_name: liver, 10% sewage, Yr1d16

value: 10% sewage

value: year 1 day 16

value: liver, mixture of Universal DNA Reference (UDR) material


title: UT-SCC-46

type: genomic

city: Linkoping

first: Fredrik

last: Jerhammar

country: Sweden

institute: Linkoping University

hyb_protocol: Hybridized in GeneChip Hybrydization oven 16-18h, stained with R-phycoerythrin streptavidin and biotinylated goat-anti-streptavidin antibodies

scan_protocol: GeneChip scanner 3000 7G

data_processing: Genotyping console, CN5 algorithm

molecule: genomic DNA

source_name: HNSCC

label_protocol: DNA fragments were biotin labelled using terminal deoxynucleotidyl transferase

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 2 mM glutamine, 1% NE amino acids, and penicillin and streptomycin

extract_protocol: DNA was extracted with Maxwell 16 Cell purification kit

treatment_protocol: Cells were seeded and allowed to attach for 24h, then treated with 30 nM cetuximab for 48h, supplemented with fresh medium and grown for another 7 days

value: HNSCC

tag: cetuximab response

value: cetuximab sensitive


title: Year1 day16 10% sewage rep3


title: siMock 5.0 mM But replicate 1

description: replicate 1


description:
Sample name: R5020_1h_2
R5020 1h replicate 2 hybridized against UHRR

value: T47D-MTVL breast cancer cell line

value: progestin R5020


title: siMock 2.0 mM But replicate 3

description: replicate 3

value: 2.0 mM butyrate over three days


title: UT-SCC-23


description:
Sample name: R5020_1h_1
R5020 1h replicate 1 hybridized against UHRR

value: Universal Human Reference RNA (Stratagene ref. 740000)


title: UT-SCC-47


title: UT-SCC-17


description:
Sample name: R5020_T0_3
R5020 T0 replicate 3 hybridized against UHRR

value: control


title: Year1 day16 10% sewage rep1


description:
Sample name: R5020_1h_3
R5020 1h replicate 3 hybridized against UHRR


title: UT-SCC-25

value: cetuximab resistant


title: Year1 day16 10% sewage rep2


title: 46,XY 5hmC immunopreciptated DNA Sample 8hM IF

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

institute: Lund University

description: Hydroxymethylation array

hyb_protocol: by the NimbleGen Service Group (Reykjavik, Iceland), which performed the quality control, labeling, hybridization, and scanning.

scan_protocol: standard NimbleGen protocol

data_processing: Signal intensity data were extracted from the scanned images, with each feature on the array having a corresponding log2 ratio, i.e, the ratio of the input signals for the precipitated and the input fraction DNAs. PCA and HCA were performed as above. In addition, the log2 ratio was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. A modified ACME algorithm,{Scacheri, 2006 #280} where a fixed-length window (750 bp) is placed around each consecutive probe, and the one-sided Kolmogorov-Smirnov test were then applied on the scaled log2 ratio data to determine whether the probes were drawn from a significantly more positive distribution (peak) of intensity log2 ratios than the other probes in the array. The resulting score for each probe is the -log10 p value from the windowed Kolmogorov-Smirnov test around that probe.

source_name: 5hmC immunopreciptated DNA

label_protocol: Of the methylated and input fraction DNAs, 1.5 µg was differentially labeled with Cy3 and Cy5, respectively

growth_protocol: cells were maintained and passaged in RPMI 1640 medium (Invitrogen) containing 10% FBS (Sigma-Aldrich) in 250 ml cell culture flasks (BD Falcon) for 8 weeks.

extract_protocol: From each sample (fibroblasts from the CT8M patient and the references), 12 µg of DNA was diluted in standard TE buffer to a concentration of 75 ng/μl. The DNA was sonicated for 90 s with a Covaris S220 (Covaris, Woburn, MA) set to a 5% duty cycle, intensity value 3, and 200 cycles per burst to generate fragments ranging from 200-1,000 bp, as verified by gel electrophoresis. The fragmented DNA was then diluted to a concentration of 13.4 ng/μl and denatured for 10 min at 95°C, after which two input fractions (approximately 250 ng each), serving as references in subsequent microarray hybridizations (see below), were collected and stored at -80°C. The remaining DNA aliquots were immunoprecipitated overnight with monoclonal antibodies against either 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) using magnetic bead-based MeDIP and hMeDIP kits (Diagenode, Liège, Belgium) to purify and isolate the precipitated DNA. Both the input fraction and the immunoprecipitated DNAs were then amplified using the WGA2 kit (Sigma-Aldrich), generating sufficient amounts (approximately 6 µg) for the various microarray hybridizations

treatment_protocol: Reference fibroblasts

tag: genotype

tag: cell type

value: fibroblast

tag: antibody

tag: antibody manufacturer

value: Diagenode

source_name: Input untreated DNA


title: siMock 2.0 mM But replicate 1

description: replicate 1


title: UT-SCC-2


title: Year1 day16 2% sewage rep4

source_name: liver, 2% sewage, Yr1d16

value: 2% sewage

value: liver


title: UT-SCC-29


title: siMock 0.5 mM But replicate 3

description: replicate 3

value: 0.5 mM butyrate over three days


title: UT-SCC-16


title: 46,XX 5hmC immunopreciptated DNA Sample 7hM IF

description: Hydroxymethylation array


title: siMock 0.5 mM But replicate 2

description: replicate 2

value: siMock


title: Year1 day16 2% sewage rep3

value: juvenile


title: Year1 day16 2% sewage rep2

value: year 1 day 16


title: UT-SCC-1A


title: Year1 day16 2% sewage rep1

value: liver, mixture of Universal DNA Reference (UDR) material


title: 46,XY 5hmC immunopreciptated DNA Sample 5hM IF

description: Hydroxymethylation array

treatment_protocol: Single-cell cloned fibroblasts


title: SchuS4_RWV_22h_6

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours

scan_protocol: scanned using the Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and data was extracted using GenePix® pro 6.1

data_processing: 75th percentile normalisation using GeneSpring GX v 11.5.1

source_name: SchuS4 Infected, RWV A549s, 22 hour post infection

label_protocol: RNA was labelled with Cy3 using the Quick Amp Labelling kit (Agilent) as per the manufacturer’s instructions.

growth_protocol: Grown in RWVs in Dulbeccos modified eagle's media with 10% foetal calf serum and 4mM l-glutamine

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: Cells infected with F. tularensis SchuS4 for 3 hours MOI 100. RNA extracted from RWVs or Monolayers at 2, 6 and 22 hours postin infection and placed into Qiagen RLT (lysis buffer) containing B-mercaptoethanol

value: Male

value: A549 epithelial cells

tag: culture condition

value: RWV

tag: infection

value: SchuS4 Infected

value: 22 hour


title: Year1 day16 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr1d16

value: 0.7% sewage


title: SchuS4_RWV_22h_4

tag: gender


title: siMock untreated replicate 3

description: replicate 3

tag: treatment

value: untreated


title: SchuS4_RWV_22h_5

tag: time


title: siMock untreated replicate 2

description: replicate 2


title: UT-SCC-15

value: HNSCC

value: cetuximab sensitive


title: 46,XY 5hmC immunopreciptated DNA Sample 6hM IF

description: Hydroxymethylation array

value: fibroblast

value: Diagenode


title: Year1 day16 0.7% sewage rep3

tag: tissue

value: liver


title: Year1 day16 0.7% sewage rep2

tag: developmental stage


title: 47,XY,+8 5hmC immunopreciptated DNA Sample 4hM IF

description: Hydroxymethylation array


title: siMock untreated replicate 1

description: replicate 1


title: siMock 2.0 mM But replicate 2

description: replicate 2

value: 2.0 mM butyrate over three days


title: siMock 0.5 mM But replicate 1

description: replicate 1

value: 0.5 mM butyrate over three days

value: siMock


title: Kidney_Wilms' Tumor/Xenografts_rep3

city: Pittburgh

first: Marcus

middle: James

last: Magister

address: 3500 Terrace St.

department: Medicine - PACCM

institute: University of Pittsburgh Medical Center - UPMC

description: 12-W014 Xn

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55 C on Agilent-019118 Human miRNA microarray 2.0 G4470B. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting

data_processing: Agilent Feature Extraction v10.7.3.1 default parameters was used to gather raw data. GeneSpring GX 11.0 was used to Quantile normalize the data, baseline transform the data to the median of the controls, and preform a One-Way ANOVA test with Benjamini-Hochberg correction. miRNAs which were unexpressed across all samples were excluded prior to statistical analysis.

source_name: Kidney Tissue

label_protocol: pCp-Cy3  labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA from tissues was isolated using a miRNeasy mini kit (Qiagen, Valencia, CA) using the manufacturer’s protocol

value: Un-sorted propagatable Wilms' Tumor xenografts

tag: host organism (for xenografts only)

value: NOD/ SCID mus musculus


title: biceps 13wk FRG1 rep2

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
probe group file: GPL13185_mjay.pgf
meta-probeset file: GPL13185_mjay.clf

source_name: biceps brachii

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

growth_protocol: Vastus lateralis and biceps brachii dissected from 4wk and 13wk wild type and FRG1 mice into RNAlater (Ambion).

extract_protocol: RNA was isolated using Rneasy Fibrous Tissue Mini kit (Qiagen), and treated with Dnase I.

tag: muscle

value: biceps brachii

tag: time point

tag: genotype/variation

value: FRG1 over-expressing

tag: background mouse strain


title: SchuS4_RWV_22h_1

value: Male

tag: cell line

value: A549 epithelial cells

value: RWV


description:
Sample name: R5020_T0_1
R5020 T0 replicate 1 hybridized against UHRR

value: T47D-MTVL breast cancer cell line

tag: agent

value: control

tag: reference

value: Universal Human Reference RNA (Stratagene ref. 740000)


title: biceps 13wk FRG1 rep1


title: SchuS4_RWV_22h_2

value: SchuS4 Infected

value: 22 hour


title: 46,XY 5hmC immunopreciptated DNA Sample 1hM IF

description: Hydroxymethylation array

tag: genotype

tag: cell type

value: fibroblast

tag: antibody

value: Diagenode


title: biceps 13wk FRG1 rep3


title: biceps 4wk FRG1 rep2


title: SchuS4_RWV_6h_6

source_name: SchuS4 Infected, RWV A549s, 6 hour post infection

tag: culture condition

tag: infection

value: 6 hour


title: Kidney_Wilms' Tumor/Xenografts_rep2

description: 11-W013 Xn


title: Year1 day16 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr1d16

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

tag: treatment

value: 0.1% sewage

value: year 1 day 16

value: liver

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material

tag: sample type


description:
Sample name: R5020_T0_2
R5020 T0 replicate 2 hybridized against UHRR

tag: time

source_name: Universal Human Reference RNA


title: biceps 4wk FRG1 rep3

value: biceps brachii


title: 47,XY,+8 5mC immunoprecipitated DNA Sample 6 IF

description: Methylation array

source_name: 5mC immunoprecipitated DNA

tag: antibody manufacturer


title: Year1 day16 0.7% sewage rep1

value: 0.7% sewage

tag: tissue

tag: developmental stage

value: liver, mixture of Universal DNA Reference (UDR) material


title: 46,XY 5mC immunoprecipitated DNA Sample 8 IF

description: Methylation array


title: Year1 day16 0.1% sewage rep3


title: Kidney_Wilms' Tumor/Xenografts_rep1

description: 10-W011 Xn

value: Un-sorted propagatable Wilms' Tumor xenografts

tag: host organism (for xenografts only)

value: NOD/ SCID mus musculus


title: Kidney_NCAM+ALDH_rep4

description: 26-WO14 Xn NCAM ALDH

value: p-WT NCAM+ALDH1+-derived Xn


title: 47,XY,+8 5hmC immunopreciptated DNA Sample 2hM IF

description: Hydroxymethylation array


title: Year1 day16 0.1% sewage rep2


title: SchuS4_RWV_6h_4

tag: gender

value: Male

value: A549 epithelial cells

value: RWV


title: SchuS4_RWV_6h_5

value: SchuS4 Infected


title: biceps 4wk FRG1 rep1

tag: muscle

tag: time point

tag: genotype/variation

value: FRG1 over-expressing

tag: background mouse strain


title: Kidney_Wilms' Tumor/Xenografts_rep4

description: 13-W016 XnP1


title: 47,XY,+8 5mC immunoprecipitated DNA Sample 4 IF

description: Methylation array

tag: genotype

value: fibroblast

value: Diagenode


title: SchuS4_RWV_22h_3

tag: cell line

value: 22 hour


title: 46,XX 5mC immunoprecipitated DNA Sample 7 IF

description: Methylation array

tag: cell type

tag: antibody


title: biceps 13wk WT rep3

value: wild type


title: Kidney_NCAM+ALDH_rep2

description: 24-W013 Xn NCAM ALDH


title: Year1 day16 0.05% sewage rep4

source_name: liver, 0.05% sewage, Yr1d16

value: 0.05% sewage

value: year 1 day 16

value: liver


title: SchuS4_RWV_6h_2

tag: culture condition

tag: infection

value: 6 hour


title: Year1 day16 0.05% sewage rep3

tag: treatment

value: juvenile

tag: sample type

value: liver, mixture of Universal DNA Reference (UDR) material


title: SchuS4_RWV_6h_1

tag: time


title: Year1 day16 0.05% sewage rep2

tag: tissue


title: 46,XY 5mC immunoprecipitated DNA Sample 3 IF

description: Methylation array

tag: antibody manufacturer


title: Kidney_NCAM+ALDH_rep1

description: 17-W014 NCAM ALDH1 ns

tag: host organism (for xenografts only)

value: NOD/ SCID mus musculus


title: Kidney_Fetal (control)_rep3

description: 3-FK III

value: Human Fetal Kidney


title: Year1 day16 0.05% sewage rep1

tag: developmental stage


title: biceps 13wk WT rep2

tag: muscle

value: biceps brachii


title: biceps 13wk WT rep1

tag: time point


title: SchuS4_RWV_2h_6

source_name: SchuS4 Infected, RWV A549s, 2 hour post infection

tag: gender

value: Male

value: A549 epithelial cells

value: 2 hour


title: SchuS4_RWV_2h_5

value: RWV

value: SchuS4 Infected


title: biceps 4wk WT rep3

tag: genotype/variation

tag: background mouse strain


title: Kidney_NCAM+ALDH_rep3

description: 25-WO13 NCAM ALDH

value: p-WT NCAM+ALDH1+-derived Xn


title: SchuS4_RWV_6h_3

tag: cell line


title: SchuS4_RWV_2h_4


title: Kidney_Fetal (control)_rep2

description: 2-FK II


title: 47,XY,+8 5hmC immunopreciptated DNA Sample 3hM IF

description: Hydroxymethylation array

tag: genotype

tag: cell type

value: fibroblast

value: Diagenode


title: SchuS4_RWV_2h_3

tag: culture condition


title: Year1 day16 Control rep4

source_name: liver, neg control, Yr1d16

value: neg control


title: biceps 4wk WT rep2

value: wild type


title: Year1 day16 Control rep2

value: year 1 day 16

value: liver


title: Year1 day16 Control rep3

value: juvenile


title: biceps 4wk WT rep1


title: SchuS4_RWV_2h_2

tag: infection


title: Kidney_Fetal (control)_rep1

description: 1-FK I


title: vastus 13wk FRG1 rep3

source_name: vastus lateralis

value: vastus lateralis

value: FRG1 over-expressing


title: Kidney_Fetal (control)_rep4

description: 5-FK IV

value: Human Fetal Kidney


title: 46,XY 5mC immunoprecipitated DNA Sample 2 IF

description: Methylation array

tag: antibody


title: 14162908 - col T10 BR2 vs col T0 BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Short term nitrate induction kinetics in wildtype, nlp7-1, nlp7-3 and nlp6nlp7

hyb_protocol: col T0 BR2 Cy5 / col T10 BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: col T0 BR2

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

growth_protocol: whole plant - Media: modified Hoagland  hygrometry: 80  Temperature: 22  Light: 100

extract_protocol: col T0 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 00min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 0min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.

tag: ecotype

value: Columbia

tag: age

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col

source_name: col T10 BR2

extract_protocol: col T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 10min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 10min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.