title: HybridPoplar_H11-11_OralSecretion6hLocal_vs_OralSecretion6hSource_Hyb1

description: Gene expression.

value: sink leaf

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: SLN:1183 - A - mAdbID:37981

status: Public on Jun 03 2009

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 37981

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133A/B GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

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

label: biotin

molecule: polyA RNA

organism: Homo sapiens

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
FastTrack 2.0 mRNA Isolation Kit
Extraction method: oligo dt cellulose
Other: mRNA was extracted using the FastTrack 2.0 mRNA Isolation Kit according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: tissue

value: Lymph node

tag: disease state

value: Follicular Lymphoma

tag: individual

tag: clinical info

value: Follow up status:dead

value: Follow up years:11.56

value: Stage >2:yes

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.31

value: Immune response 2:8.53

value: With translocation:yes


title: UPF1_knockdown_biological_replicate_1

city: Berkeley

first: Kasper

middle: Daniel

last: Hansen

state: CA

address: 461 Koshland Hall

department: PMB

institute: UC Berkeley

hyb_protocol: A custom protocol, see Blanchette et al. (2005) Genes Dev, PMID: 15937219 as well as Castle et al. (2003) Genome Biology, PMID: 14519201

scan_protocol: Feature Extractor version 7.5.1. Scanner settings can be found in the raw data file.

data_processing: Arrays were background corrected using the normexp methods with an offset of 10, from the limma package from Bioconductor version 2.2. After background correction, the two channels were normalized using loess. The normalized data are on the log2 scale.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Schneider SL2

label_protocol: A custom labeling protocol described in Blanchette et al. (2005) Genes Dev., PMID: 15937219

extract_protocol: Total RNA was isolated using TRIzol Reagent (Life Technologies). For more detail see  Rehwinkel et al. (2005) RNA, PMID: 16199763

tag: RNAi knockdown of Upf1, extracted at day 8 after a re-knockdown at day 4, as described in Rehwinkel et al. (2005) RNA, PMID

source_name: S2 cell line

tag: SL2 Cell line, for more detail see Rehwinkel et al. (2005) RNA, PMID


title: fenamiphos_high_dose-rep3

city: Ft. Detrick

first: John

middle: A.

last: Lewis

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

description: nominal concentration 200 mg/L

hyb_protocol: cRNA samples fragmented according Affymetrix recommendations were hybridized to C. elegans whole genome GeneChips (Affymetrix, Santa Clara, CA) at the Walter Reed Army Institute of Research Vaccine Genomics Laboratory, Rockville, MD using Affymetrix instrumentation and with hybridization and washing parameters provided by the manufacturer.

scan_protocol: The C. elegans whole genome GeneChips (Affymetrix, Santa Clara, CA) were scanned at the Walter Reed Army Institute of Research Vaccine Genomics Laboratory, Rockville, MD using Affymetrix instrumentation with scanning parameters provided by the manufacturer.

data_processing: Microarray data was processed using the robust multi-array averaging method (RMA) as implemented in Partek Pro Genomics Suite v. 6.3. To verify inter-replicate reproducibility, replicate samples were subjected to pairwise correlation analysis of all probe sets. For the vast majority of replicate pairs, the R2 value was greater than or equal to 0.95, and no replicates were included with R2 < 0.92. A Present, Absent, or Marginal call for each probe set was determined using the R statistical package and the Bioconductor implementation of the Affymetrix MAS 5.0 algorithm (affy package 1.12.2).

organism: Caenorhabditis elegans

source_name: whole organism, fenamiphos, 200 mg/L

label_protocol: Biotin labeled cRNA was synthesized from the T7 promoter incorporated in the cDNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) per the manufacturer’s recommendations; approximately 1 µg of cDNA was used for synthesis. cRNA was purified from unincorporated nucleotides and other reaction components using the RNEasy Mini kit (Qiagen).

growth_protocol: C. elegans were maintained in synchronized cultures grown in CeHR medium. All cultures were grown at 22.5° C with shaking at 70 rpm. Typically, 5 x 105 L1 larvae were used to inoculate 40 mL of medium in a T-75 flask. Cultures were harvested every generation to maintain synchronization. CeHR medium is a sterile, defined medium, supplemented with 20% (v/v) ultrapasteurized organic, fat-free milk for the axenic propagation of C. elegans. A detailed description of the preparation of the medium is available from the USACEHR on request.

extract_protocol: Frozen worm droplets were pulverized in liquid N2 using a pre-chilled mortar and pestle. The pulverized worms were transferred to 6 mL Trizol (Invitrogen, Carlsbad, CA) and homogenized in a dounce homogenizer. RNA was purified according to the manufacturer’s protocol and precipitated with isopropyl alcohol. After centrifugation, the RNA pellet was dried, dissolved in water, and subjected to an additional round of purification using the RNEasy Maxi Kit (Qiagen, Valencia, CA) according to the manufacturer’s directions. The quality and yield of the preparation was assessed throughout processing and labeling using a 2100 Bioanalyzer (Agilent, Santa Clara, CA), and when necessary, the mass yield was confirmed using an ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).  Poly(A)+ RNA was isolated from the total RNA using OligoTex (Qiagen) essentially as described by the manufacturer. Two micrograms of poly(A)+ RNA (adjusted for rRNA contamination) was used as the template for cDNA synthesis using the SuperScript Choice kit (Invitrogen) per the manufacturer’s recommendations except that (1) a high pressure liquid chromatography (HPLC)-purified T24T7 promoter primer (Integrated DNA Technologies, Coralville, IA) was used to initiate first strand synthesis; (2) the second strand synthesis was not terminated using EDTA since we found that EDTA carryover interfered with subsequent enzymatic manipulations; and (3) PelletPaint (Novagen, Madison, WI) was used in place of glycogen for precipitation.

treatment_protocol: L1 larvae (2.5 x 105) were suspended in T-75 flasks containing 30 mL CeHR medium and grown until 90% of the population had developed to the mid-vulval L4 larval stage. The worms were dosed with mefloquine (Ash Stevens, Inc., Detroit, MI), dichlorvos, or fenamiphos (Chem Service, Inc., West Chester, PA) for 8 h or allowed to develop as a control. Each exposure was repeated three times.  Worms were harvested by centrifugation (800 x g for 3 min at 4° C), and the supernatant was aspirated. The pellets for were suspended in the residual liquid, flash frozen by drop-wise addition to liquid nitrogen, and stored at -80° C.

tag: N2 wild type, DR subclone of CB original (Tcl pattern I) L4 larvae


title: BC-9ppm replicate 1

city: Ås

first: Birgitte

last: Moen

address: Osloveien 1

country: Norway

institute: Nofima Mat

description: The E. coli microarrays consisted of E. coli oligos (Operon) printed on Corning Ultra GAPS slides as described previously

hyb_protocol: Microarray slides were treated with a pre-soak solution (Promega/Corning) before incubation in a pre-hybridization solution (5´SSC [1´SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% dodecyl sulfate [SDS], 1 mg/ml bovine serum albumin) at 42°C for 30-60 minutes. After pre-hybridization, the slides were washed briefly in distilled water, followed by a brief wash in isopropanol. The dried Cy3- and Cy5-labeled cDNA was resuspended in 55 ml hybridization solution (30% formamide, 5´SSC, 0.1%SDS and 0.1 mg/ml Salmon Sperm DNA), denatured and applied to the prehybridized microarray underneath a 25- by 60-mm mSeries LifterSlip coverslip (Erie Scientific Company). The slides were hybridized at 42°C overnight (~16 h). After hybridization the slides were washed twice in 2´SSC buffer with 0.1% SDS at 42°C for 5 minutes, followed by two washes in 0.1´SSC buffer with 0.1% SDS for 10 min at room temperature and four washes in 0.1´ SSC buffer for 1 minute at room temperature. The slides were dried by centrifugation (90´g for 12 min). The reference used in the microarray experiments was pooled RNA from all the growth conditions including the control.

scan_protocol: Slides were scanned with the ScanArray Express 1.0 scanner (Packard BioScience) following the manufacturers guidelines.

data_processing: The fluorescent spot intensities were quantified using ImaGeneÔ 5.6.1 (BioDiscovery Inc.) software. Background subtraction and normalization (LOWESS) was performed in GeneSpringä 7 (Silicon Genetics). (A lowess curve was fit to the log-intensity versus log-ratio plot. 20% of the data was used to calculate the lowess fit at each point. The curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then the value was set to 10). Only data from spots representing E. coli K-12 MG1655 genes were analyzed in our studies. All analyses were based on 3 biological replicates with the exception of the second biological replicate from conditions HCl and NaOH. These two observations were removed due to bad hybridization giving a total of 34 array hybridizations (observations). Genes not present in any of the 34 observations were filtered out, resulting in the analysis of 4279 out of 4289 MG1655 genes on the array. Missing values (data points) were replaced by using the KNNimpute procedure (k=10) on log2 transformed data.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: pooled RNA from all conditions including the control, reference

label_protocol: Total RNA (5 mg) and 0.5 ml test/reference Lucidea spike controls RNA (Amersham Biosciences) were reverse transcribed by using random hexamers in the presence of aminoallyl-dUTP (2 aa-dUTP  (Ambion): 3 dTTP (Invitrogen)) as described in standard operating procedure no. M007 (The Institute for Genomic Research [TIGR] protocol). The removal of unincorporated aa-dUTP and free amines was performed according to the TIGR protocol using the Qiagen QIAquick PCR purification kit. After drying in a Speed vac, the samples were stored at -20°C. Coupling aminoallyl-labeled cDNA to Cy3/Cy5 mono reactive dyes (Amersham Biosciences) was done according to the TIGR protocol. The reference (labeled Cy3) used in the microarray experiments was pooled RNA from all the growth conditions including the control.

growth_protocol: The cultures were prepared by inoculating one colony from tryptone soya agar (TSA) (Oxoid) (overnight growth at 37°C) to 5 ml TSB and incubating overnight at 37°C, with shaking (200 rpm). This culture was initially diluted 1:10 in medium and used to inoculate room-temperature TSB for each of the different stress factors (40 ml total volume) to a final concentration of approx. 1´107 CFU/ml (1:100 dilution of overnight culture). For cold stress experiment the medium was chilled to 15°C prior to inoculation. The cultures were incubated at 37°C (except fpr 15°C and 46°C conditions), shaking at 200 rpm and samples were collected during exponential growth at a cell density of approx. 1´108 CFU/ml. All the stress conditions, including the control, were inoculated with the same overnight culture and started at the same time point. The experiment was performed 3 times at different days and with freshly prepared solutions, resulting in 3 biological replicates.

extract_protocol: Total RNA was extracted from 1 ml cells using the RNeasy Protect Bacteria Mini Prep kit (Qiagen) as recommended by the manufacturer including the “on-column” DNase treatment.

source_name: BC-9ppm replicate 1

tag: BC-9ppm replicate 1


title: EtOH replicate 1

tag: pooled RNA from all conditions including the control, reference

source_name: EtOH replicate 1

tag: EtOH replicate 1


title: SLN:1107 - A - mAdbID:37980

description: mAdb experiment ID: 37980

value: Follow up years:5.01

value: Immune response 1:9.41

value: Immune response 2:9.32

value: With translocation:NA


title: SLN:1106 - A - mAdbID:37979

description: mAdb experiment ID: 37979

value: Follow up status:alive

value: Follow up years:7.94

value: Number of extranodal sites >1:yes

value: IPI score:2

value: Immune response 1:9.13

value: Immune response 2:9.19


title: HybridPoplar_H11-11_UntreatedControl6hSource_vs_OralSecretion6hSource_Hyb1

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: Gene expression.

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 µL hybridization solution consisting of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, 1 mM EDTA, 4.0 µL LNA d(T) blocker, 2 µg sheared salmon testes DNA (Invitrogen) and 0.75 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 3´ 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 95°C in MilliQ-H2O, and dried by centrifugation (3 minutes 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 80°C for 10 min, then maintained at 65°C prior to adding to a microarray slide heated to 55°C, covered with a 22 ´ 60 ´ 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 48°C. Arrays were washed in 2´ SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65°C in the same solution, then three washes of 5 min in 2´ SSC at room temperature, and three washes of 5 min in 0.2´ 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 25% formamide, 4x SSC, 0.5% SDS, 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 48°C, 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 for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). For the oral secretion treatment using pooled biological replicates, total RNA from treated and untreated control leaves of the same source/sink group was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations. To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 54 microarray slides. The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point. Expression variance was obtained from technical variance among slides. Next, the ratio of the treatment minus untreated control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003). All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).

organism: Populus trichocarpa x Populus deltoides

source_name: Hybrid poplar, untreated control for 6 hours, systemic source leaves

label_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere) following manufacturer’s instructions. Forty µg 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 65°C for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Trees were grown under standard greenhouse conditions. See Ralph et al. (2006) Molecular Ecology 15: 1275-1297.

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. Poly(A)+ RNA was isolated by oligo d(T) cellulose using the Poly(A) Pure kit (Ambion, Austin, USA), following manufacturer's instructions. 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).

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic source leaves were harvested 6 hours after the initiation of the experiment.

value: sink leaf

tag: genotype

tag: experimental protocol

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 6 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic source leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_UntreatedControl24hLocal_vs_OralSecretion24hLocal_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 24 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated source leaves were harvested 24 hours after the initiation of the experiment.

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Local/treated source leaves were harvested 24 hours after the initiation of treatment.


title: fenamiphos_control-rep3

description: no chemical

source_name: whole organism, fenamiphos, control


title: fenamiphos_mid_dose-rep3

description: nominal concentration 60 mg/L

source_name: whole organism, fenamiphos, 60 mg/L


title: SLN:1102 - A - mAdbID:37878

description: mAdb experiment ID: 37878

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:13.2

value: Stage >2:yes

value: LDH ratio >1:no

value: Age >60:no

value: Immune response 1:9.45

value: Immune response 2:8.89


title: BC-7ppm replicate 1

source_name: BC-7ppm replicate 1

tag: BC-7ppm replicate 1


title: SLN:1099 - A - mAdbID:37876

description: mAdb experiment ID: 37876

value: Follow up status:alive

value: Follow up years:7.65

value: Stage >2:no

value: LDH ratio >1:NA

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.73

value: Immune response 2:9.04

value: With translocation:yes


title: fenamiphos_low_dose-rep3

description: nominal concentration 10 mg/L

source_name: whole organism, fenamiphos, 10 mg/L


title: fenamiphos_mid_dose-rep2

description: nominal concentration 60 mg/L


title: HybridPoplar_H11-11_OralSecretion24hSource_vs_OralSecretion24hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic sink leaves were harvested 24 hours after the initiation of treatment.

value: sink leaf

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic source leaves were harvested 24 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: HCl replicate 1

source_name: HCl replicate 1

tag: HCl replicate 1


title: SLN:1104 - A - mAdbID:37879

description: mAdb experiment ID: 37879

value: Lymph node

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:8.42

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.3

value: Immune response 2:8.27


title: fenamiphos_high_dose-rep2

description: nominal concentration 200 mg/L


title: BC-7ppm replicate 2

source_name: BC-7ppm replicate 2

tag: BC-7ppm replicate 2


title: fenamiphos_low_dose-rep2

description: nominal concentration 10 mg/L


title: HybridPoplar_H11-11_OralSecretion24hLocal_vs_OralSecretion24hSource_Hyb1

description: Gene expression.

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: HybridPoplar_H11-11_UntreatedControl2hLocal_vs_UntreatedControl2hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 2 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated source leaves were harvested 2 hours after the initiation of the experiment.

source_name: Hybrid poplar, untreated control for 2 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic sink leaves were harvested 2 hours after the initiation of the experiment.


title: SLN:1090 - A - mAdbID:37871

description: mAdb experiment ID: 37871

value: Follow up status:alive

value: Follow up years:10.2

value: Stage >2:yes

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Immune response 1:9.27

value: Immune response 2:8.37


title: fenamiphos_control-rep2

description: no chemical


title: Control replicate 1

source_name: pooled RNA from all conditions including the control, reference

source_name: Control replicate 1

tag: Control replicate 1


title: 46degrees replicate 3

source_name: 46degrees replicate 3

tag: 46degrees replicate 3


title: SLN:1089 - A - mAdbID:37868

description: mAdb experiment ID: 37868

tag: tissue

value: Lymph node

value: Follow up years:10.72

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.42

value: Immune response 2:8.35

value: With translocation:yes


title: SLN:1098 - A - mAdbID:37873

description: mAdb experiment ID: 37873

tag: disease state

value: Follicular Lymphoma

value: Follow up status:dead

value: Follow up years:5.34

value: IPI score:2

value: Immune response 1:9.33

value: Immune response 2:8.81


title: fenamiphos_high_dose-rep1

description: nominal concentration 200 mg/L

source_name: whole organism, fenamiphos, 200 mg/L


title: HybridPoplar_H11-11_UntreatedControl6hLocal_vs_UntreatedControl24hLocal_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 6 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated source leaves were harvested 6 hours after the initiation of the experiment.

value: sink leaf

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: SLN:1097 - A - mAdbID:37875

description: mAdb experiment ID: 37875

tag: individual

value: Follow up years:8.79

value: Stage >2:no

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:yes

value: Immune response 1:9.87

value: Immune response 2:8.92


title: fenamiphos_low_dose-rep1

description: nominal concentration 10 mg/L


title: SLN:1088 - A - mAdbID:37865

description: mAdb experiment ID: 37865

value: Lymph node

tag: clinical info

value: Follow up status:alive

value: Follow up years:5.3

value: Stage >2:yes

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.22

value: Immune response 2:8.47


title: NaOH replicate 1

source_name: NaOH replicate 1

tag: NaOH replicate 1


title: HybridPoplar_H11-11_OralSecretion2hLocal_vs_OralSecretion6hLocal_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 2 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Local/treated source leaves were harvested 2 hours after the initiation of treatment.

value: sink leaf

source_name: Hybrid poplar, oral secretion treatment for 6 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Local/treated source leaves were harvested 6 hours after the initiation of treatment.


title: BC-9ppm replicate 2

source_name: BC-9ppm replicate 2

tag: BC-9ppm replicate 2


title: EtBr replicate 2

source_name: EtBr replicate 2

tag: EtBr replicate 2


title: EtBr replicate 1

source_name: EtBr replicate 1

tag: EtBr replicate 1


title: fenamiphos_mid_dose-rep1

description: nominal concentration 60 mg/L

source_name: whole organism, fenamiphos, 60 mg/L

tag: N2 wild type, DR subclone of CB original (Tcl pattern I) L4 larvae


title: fenamiphos_control-rep1

description: no chemical

source_name: whole organism, fenamiphos, control


title: HybridPoplar_H11-11_UntreatedControl24hSource_vs_OralSecretion24hSource_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 24 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic source leaves were harvested 24 hours after the initiation of the experiment.

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, systemic source leaves


title: HybridPoplar_H11-11_UntreatedControl24hLocal_vs_UntreatedControl24hSource_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 24 hours, local source leaves

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: HybridPoplar_H11-11_OralSecretion6hLocal_vs_OralSecretion24hLocal_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, local source leaves


title: dichlorvos_high_dose-rep3

description: nominal concentration 50 mg/L

source_name: whole organism, dichlorvos, 50 mg/L


title: SLN:1087 - A - mAdbID:37864

description: mAdb experiment ID: 37864

value: Follicular Lymphoma

value: Follow up years:8.19

value: Stage >2:no

value: Immune response 1:9.98

value: Immune response 2:9.27

value: With translocation:yes


title: SLN:1086 - A - mAdbID:37863

description: mAdb experiment ID: 37863

value: Lymph node

value: Follow up status:dead

value: Follow up years:1.98

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Immune response 1:9.49

value: Immune response 2:9.09


title: HybridPoplar_H11-11_UntreatedControl2hLocal_vs_OralSecretion2hLocal_Hyb2

description: Gene expression.

source_name: Hybrid poplar, untreated control for 2 hours, local source leaves


title: HybridPoplar_H11-11_OralSecretion2hSink_vs_OralSecretion6hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 2 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic sink leaves were harvested 2 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 6 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic sink leaves were harvested 6 hours after the initiation of treatment.


title: Control replicate 2

source_name: pooled RNA from all conditions including the control, reference

source_name: Control replicate 2

tag: Control replicate 2


title: HybridPoplar_H11-11_UntreatedControl2hLocal_vs_OralSecretion2hLocal_Hyb1

description: Gene expression.

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated leaves were harvested 2 hours after the initiation of treatment.

value: sink leaf

tag: genotype

source_name: Hybrid poplar, oral secretion treatment for 2 hours, local source leaves


title: dichlorvos_mid_dose-rep3

description: nominal concentration 15 mg/L

source_name: whole organism, dichlorvos, 15 mg/L


title: BC-9ppm replicate 3

tag: pooled RNA from all conditions including the control, reference

source_name: BC-9ppm replicate 3

tag: BC-9ppm replicate 3


title: EtBr replicate 3

source_name: EtBr replicate 3

tag: EtBr replicate 3


title: SLN:1083 - A - mAdbID:37859

description: mAdb experiment ID: 37859

value: Follow up status:alive

value: Follow up years:10.01

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.82

value: Immune response 2:8.72


title: SLN:1085 - A - mAdbID:37862

description: mAdb experiment ID: 37862

value: Follicular Lymphoma

value: Follow up years:8.84

value: Stage >2:yes

value: LDH ratio >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.31

value: Immune response 2:8.58


title: SLN:1080 - A - mAdbID:37857

description: mAdb experiment ID: 37857

value: Lymph node

value: Follow up years:6.05

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Immune response 1:9.45

value: Immune response 2:8.94

value: With translocation:yes


title: HybridPoplar_H11-11_UntreatedControl24hSource_vs_UntreatedControl24hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 24 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic sink leaves were harvested 24 hours after the initiation of treatment.

value: sink leaf

tag: experimental protocol

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic source leaves were harvested 24 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: SLN:1077 - A - mAdbID:37847

description: mAdb experiment ID: 37847

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:7.06

value: Age >60:no

value: IPI score:1

value: Immune response 1:9.8

value: Immune response 2:8.46


title: dichlorvos_low_dose-rep3

description: nominal concentration 3 mg/L

source_name: whole organism, dichlorvos, 3 mg/L

treatment_protocol: L1 larvae (2.5 x 105) were suspended in T-75 flasks containing 30 mL CeHR medium and grown until 90% of the population had developed to the mid-vulval L4 larval stage. The worms were dosed with mefloquine (Ash Stevens, Inc., Detroit, MI), dichlorvos, or fenamiphos (Chem Service, Inc., West Chester, PA) for 8 h or allowed to develop as a control. Each exposure was repeated three times.  Worms were harvested by centrifugation (800 x g for 3 min at 4° C), and the supernatant was aspirated. The pellets for were suspended in the residual liquid, flash frozen by drop-wise addition to liquid nitrogen, and stored at -80° C.


title: SLN:1078 - A - mAdbID:37850

description: mAdb experiment ID: 37850

value: Lymph node

value: Follow up years:4.95

value: Stage >2:no

value: Immune response 1:9.32

value: Immune response 2:8.23


title: SLN:1076 - A - mAdbID:37844

description: mAdb experiment ID: 37844

value: Follow up status:dead

value: Follow up years:3.22

value: Stage >2:yes

value: LDH ratio >1:no

value: Number of extranodal sites >1:no

value: Age >60:yes

value: IPI score:2

value: Immune response 1:9.2

value: Immune response 2:8.55

value: With translocation:no


title: HybridPoplar_H11-11_UntreatedControl6hSink_vs_UntreatedControl24hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 6 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic sink leaves were harvested 6 hours after the initiation of treatment.

value: sink leaf

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: 15degrees replicate 3

source_name: 15degrees replicate 3

tag: 15degrees replicate 3


title: NaCl replicate 3

source_name: NaCl replicate 3

tag: NaCl replicate 3


title: dichlorvos_control-rep3

description: no chemical

source_name: whole organism, dichlorvos, control


title: HybridPoplar_H11-11_UntreatedControl6hSink_vs_OralSecretion6hSink_Hyb2

description: Gene expression.

tag: tissue


title: dichlorvos_mid_dose-rep2

description: nominal concentration 15 mg/L


title: Control replicate 3

source_name: Control replicate 3

tag: Control replicate 3


title: BC-7ppm replicate 3

source_name: BC-7ppm replicate 3

tag: BC-7ppm replicate 3


title: dichlorvos_low_dose-rep2

description: nominal concentration 3 mg/L


title: dichlorvos_control-rep2

description: no chemical


title: HybridPoplar_H11-11_UntreatedControl2hLocal_vs_UntreatedControl2hSource_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 2 hours, systemic source leaves

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, untreated control for 2 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated source leaves were harvested 2 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Leaves act as carbon sources in relation to systemic source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: dichlorvos_high_dose-rep2

description: nominal concentration 50 mg/L

source_name: whole organism, dichlorvos, 50 mg/L


title: SLN:1074 - A - mAdbID:37837

description: mAdb experiment ID: 37837

value: Lymph node

tag: disease state

value: Follicular Lymphoma

tag: individual

tag: clinical info

value: Follow up years:4.52

value: Immune response 1:9.1

value: Immune response 2:8.57

value: With translocation:yes


title: EtOH replicate 3

source_name: pooled RNA from all conditions including the control, reference

source_name: EtOH replicate 3

tag: EtOH replicate 3


title: HybridPoplar_H11-11_UntreatedControl6hLocal_vs_OralSecretion6hLocal_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 6 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/treated source leaves were harvested 6 hours after the initiation of treatment.

source_name: Hybrid poplar, oral secretion treatment for 6 hours, local source leaves


title: Glycerol replicate 3

source_name: Glycerol replicate 3

tag: Glycerol replicate 3


title: HybridPoplar_H11-11_OralSecretion2hLocal_vs_OralSecretion2hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 2 hours, local source leaves

source_name: Hybrid poplar, oral secretion treatment for 2 hours, systemic sink leaves


title: HybridPoplar_H11-11_UntreatedControl24hLocal_vs_OralSecretion24hLocal_Hyb2

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Local/treated source leaves were harvested 24 hours after the initiation of treatment.

source_name: Hybrid poplar, untreated control for 24 hours, local source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Local/bagged source leaves were harvested 24 hours after the initiation of the experiment.


title: 15degrees replicate 2

source_name: 15degrees replicate 2

tag: 15degrees replicate 2


title: Glycerol replicate 1

source_name: Glycerol replicate 1

tag: Glycerol replicate 1


title: HybridPoplar_H11-11_UntreatedControl6hSink_vs_OralSecretion6hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, untreated control for 6 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic sink leaves were harvested 6 hours after the initiation of the experiment.

tag: genotype

source_name: Hybrid poplar, oral secretion treatment for 6 hours, systemic sink leaves


title: dichlorvos_low_dose-rep1

description: nominal concentration 3 mg/L

source_name: whole organism, dichlorvos, 3 mg/L

tag: N2 wild type, DR subclone of CB original (Tcl pattern I) L4 larvae


title: dichlorvos_control-rep1

description: no chemical

source_name: whole organism, dichlorvos, control


title: dichlorvos_mid_dose-rep1

description: nominal concentration 15 mg/L

source_name: whole organism, dichlorvos, 15 mg/L


title: HybridPoplar_H11-11_UntreatedControl6hSource_vs_OralSecretion6hSource_Hyb2

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 6 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic source leaves were harvested 6 hours after the initiation of treatment.

source_name: Hybrid poplar, untreated control for 6 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic source leaves were harvested 6 hours after the initiation of the experiment.


title: SLN:1073 - A - mAdbID:37836

description: mAdb experiment ID: 37836

value: Follow up status:dead

value: Follow up years:7.68

value: Stage >2:yes

value: LDH ratio >1:no

value: Immune response 2:8.67


title: 46degrees replicate 1

source_name: pooled RNA from all conditions including the control, reference

source_name: 46degrees replicate 1

tag: 46degrees replicate 1


title: SLN:888 - A - mAdbID:37833

description: mAdb experiment ID: 37833

value: Follow up years:1.32

value: Number of extranodal sites >1:yes

value: Age >60:yes

value: IPI score:2

value: Immune response 1:8.76

value: Immune response 2:8.49


title: SLN:1075 - A - mAdbID:37839

description: mAdb experiment ID: 37839

value: Lymph node

value: Age >60:no

value: Immune response 1:8.97

value: Immune response 2:8.69


title: mefloquine_high_dose-rep3

description: nominal concentration 500 mg/L

source_name: whole organism, mefloquine, 500 mg/L


title: dichlorvos_high_dose-rep1

description: nominal concentration 50 mg/L

source_name: whole organism, dichlorvos, 50 mg/L


title: SLN:886 - A - mAdbID:37830

description: mAdb experiment ID: 37830

value: Follicular Lymphoma

value: Follow up status:alive

value: Follow up years:3.29

value: Number of extranodal sites >1:no

value: IPI score:1

value: Immune response 1:9.43

value: Immune response 2:8.72


title: SLN:879 - A - mAdbID:37828

description: mAdb experiment ID: 37828

value: Follow up status:dead

value: Follow up years:4.34

value: Stage >2:yes

value: LDH ratio >1:no

value: Immune response 1:8.95

value: Immune response 2:8.74

value: With translocation:yes


title: CH3COOH replicate 1

tag: pooled RNA from all conditions including the control, reference

source_name: CH3COOH replicate 1

tag: CH3COOH replicate 1


title: HybridPoplar_H11-11_OralSecretion2hSink_vs_OralSecretion24hSink_Hyb1

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic sink leaves were harvested 24 hours after the initiation of treatment.

value: sink leaf

tag: experimental protocol

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 2 hours, systemic sink leaves


title: HybridPoplar_H11-11_UntreatedControl2hSource_vs_OralSecretion2hSource_Hyb2

description: Gene expression.

source_name: Hybrid poplar, oral secretion treatment for 2 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic source leaves were harvested 2 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic sink leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, untreated control for 2 hours, systemic source leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic source leaves were harvested 2 hours after the initiation of treatment.


title: HybridPoplar_H11-11_OralSecretion2hSource_vs_OralSecretion2hSink_Hyb1

description: Gene expression.

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags. For oral secretion treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel, and 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Systemic sink leaves were harvested 2 hours after the initiation of treatment.

value: Six month old clonal trees grown under greenhouse conditions. Five leaves acropetally adjacent to treatment leaves were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sources in relation to treated source and systemic leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.


title: NaCl replicate 1

source_name: NaCl replicate 1

tag: NaCl replicate 1


title: mefloquine_mid_dose-rep3

description: nominal concentration 250 mg/L

source_name: whole organism, mefloquine, 250 mg/L


title: 15degrees replicate 1

source_name: 15degrees replicate 1

tag: 15degrees replicate 1


title: SLN:878 - A - mAdbID:37827

description: mAdb experiment ID: 37827

tag: tissue

value: Lymph node

value: Follicular Lymphoma

value: Follow up years:3.87

value: Number of extranodal sites >1:yes

value: Age >60:yes

value: IPI score:3

value: Immune response 1:8.85

value: Immune response 2:8.54


title: mefloquine_low_dose-rep3

description: nominal concentration 10 mg/L

source_name: whole organism, mefloquine, 10 mg/L


title: HybridPoplar_H11-11_UntreatedControl24hSink_vs_OralSecretion24hSink_Hyb2

description: Gene expression.

source_name: Hybrid poplar, untreated control for 24 hours, systemic sink leaves

treatment_protocol: Five lowest, fully-expanded, healthy source leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Systemic sink leaves were harvested 24 hours after the initiation of the experiment.


title: SLN:739 - A - mAdbID:37826

description: mAdb experiment ID: 37826

value: Follow up status:dead

value: Follow up years:10.8

value: Stage >2:yes

value: Number of extranodal sites >1:no

value: Age >60:no

value: IPI score:2

value: Immune response 1:9.29

value: Immune response 2:8.77


title: SLN:738 - A - mAdbID:37825

description: mAdb experiment ID: 37825

value: Follow up years:10.15

value: LDH ratio >1:no

value: IPI score:1

value: Immune response 1:9.19

value: Immune response 2:8.79

value: With translocation:yes


title: NaOH replicate 3

source_name: NaOH replicate 3

tag: NaOH replicate 3


title: EtOH replicate 2

source_name: EtOH replicate 2

tag: EtOH replicate 2


title: CH3COOH replicate 3

source_name: CH3COOH replicate 3

tag: CH3COOH replicate 3


title: CH3COOH replicate 2

source_name: pooled RNA from all conditions including the control, reference

source_name: CH3COOH replicate 2

tag: CH3COOH replicate 2


title: mefloquine_mid_dose-rep2

description: nominal concentration 250 mg/L


title: HCl replicate 3

source_name: HCl replicate 3

tag: HCl replicate 3


title: PCA_biofilm_potentiostat_BR3A

city: Amherst

first: Derek

last: Lovley

state: MA

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

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was directly labeled with the Micromax ASAP labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap.

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

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

organism: Geobacter sulfurreducens

source_name: wildtype Geobacter grown on a 10 mA potentiostat; experimental condition

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: TE-sucrose hot-phenol extraction method, subsequent DNAse treatment with Ambion DNA-free protocol.

tag: Geobacter sulfurreducens was grown in a Geobattery in flow-through potentiostat mode

source_name: wildtype Geobacter grown in a fumarate biofilm (in a potentiostat); control condition

tag: Geobacter sulfurreducens was grown in an open circuit Geobattery in flow-through mode


title: mefloquine_control-rep3

description: no chemical

source_name: whole organism, mefloquine, control


title: Glycerol replicate 2

source_name: Glycerol replicate 2

tag: Glycerol replicate 2


title: mefloquine_low_dose-rep2

description: nominal concentration 10 mg/L


title: NaCl replicate 2

source_name: NaCl replicate 2

tag: NaCl replicate 2


title: SLN:735 - A - mAdbID:36961

description: mAdb experiment ID: 36961

value: Lymph node

tag: disease state

value: Follicular Lymphoma

tag: individual

tag: clinical info

value: Follow up years:11.05

value: LDH ratio >1:yes

value: Immune response 1:8.81

value: Immune response 2:8.23


title: mefloquine_high_dose-rep1

description: nominal concentration 500 mg/L

source_name: whole organism, mefloquine, 500 mg/L

tag: N2 wild type, DR subclone of CB original (Tcl pattern I) L4 larvae


title: mefloquine_control-rep2

description: no chemical


title: 46degrees replicate 2

tag: pooled RNA from all conditions including the control, reference

source_name: 46degrees replicate 2

tag: 46degrees replicate 2


status: Public on Jun 02 2009

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: For array hybridization, 2ug of the labeled DNA material was hybridized per chip for 18 h at 45C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100?g/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Scanned at 0.7 microns/pixel.

data_processing: Three biological replicates were hybridized for this experiment. The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity given (e.g. 361). Processed data are obtained using following parameters: median value is 361   The sliding window approach (bandwidth 50) has been used to estimate RNA abundance (signal which is listed in column #2). It was found by calculating the median of all pairwise average PM-MM values, where PM is a perfect match and MM is a mismatch. Processed data are obtained using following parameters: bandwidth is 50   genome version is r5

label: Biotin

source_name: WPP + 24 hr (Celniker/RNA:342) extraction2_array1 channel_1

label_protocol: Double-stranded cDNA was treated with RNase H (Epicentre Technologies) and RNases A/T1 (Ambion), extracted by using a QIAquick PCR purification kit (Qiagen), and subjected to further fragmentation to 50-100 bp by DNase I (1 unit/ul; Epicentre Technologies; size distribution of fragmented DNA was verified on a 2% agarose gel).The fragmented cDNA was then end-labeled with 2.5mM biotinylated DNA labeling reagent (Affymetrix) by using 100 units of terminal deoxynucleotidyltransferase (TdT; Roche Diagnostics) in 1x TdT buffer (Roche Diagnostics) and 5 mM CoCl2 (Roche Diagnostics) for 2 h at 37C.

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
Fly populations consisted of the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. These flies were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. These animals were grown in 250ml (pint) bottle that contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). Approximately seven days after being introduced into the bottles, white prepupa were collected by individually transferring staged animals to a tube on crushed dry ice. In order to collect synchronized pupal stages, white prepupa were marked on the overlaying glass with a Sharpie®. These marked bottles containing synchronized white prepupa were aged the indicated amount of time at 24C, and transferred to a tube on crushed dry ice. All frozen biological samples were stored at -80C until the RNA could be isolated. A yield of approximately 4 micrograms total RNA per milligram tissue was typical from these stages. Animals were staged according to Ashburner, et. al. (2005)[2].

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.Materials	TRIzol® reagent: Invitrogen, cat. no. 15596-026 (100 ml) or 15596-018 (200 ml).	DNase/RNase-free water: Invitrogen cat. no. 10977.	75% ethanol, prepared with DNase/RNase-free water.	RNase-free DNase: Qiagen cat. no. 79254.	RNeasy® spin columns: RNeasy midi kit, Qiagen cat. no. 75144.	TenBroeck homogenizer: Bellco biotechnology cat no. 1982-10002.Procedure1.	Homogenize insect samples in TRIzol reagent using a TenBroeck tissue homogenizer. The sample volume should not exceed 10% of the volume of TRIzol reagent used for homogenization.2.	Incubate at room temperature for 5 minutes.  3.	Aliquot samples into 1.5 ml microcentifuge tubes.4.	Add 0.267 ml chloroform per ml of TRIzol used.5.	Shake tubes vigorously for 15 seconds.6.	Incubate at room temperature for 2 minutes.7.	Centrifuge for 15 minutes at 4degC at 12,000 x g.8.	Transfer the top (aqueous) phases to clean tubes.9.	Precipitate the RNA from the aqueous phase by adding 0.67 ml of isopropanol per ml of TRIzol used in step 5.10.	Invert tubes once to mix gently.11.	Incubate samples at room temperature for 10 minutes.12.	Centrifuge for 10 minutes at 4degC at 12,000 x g.13.	Remove the supernatant.14.	Wash RNA pellet once with 75% ethanol, using 0.7 ml per microcentrifuge tube.15.	Vortex briefly.16.	Centrifuge at 7,500 x g for 5 minutes at 4degC.17.	Let the pellet air dry for 10 minutes. Note: DO NOT let the pellet dry completely.18.	Dissolve in RNase-free water. 19.	Incubate at 37degC overnight to dissolve the RNA. Determine concentration using a Nanodrop® ND-1000 Spectrophotometer. RNA may be stored at -80degC at this point if desired.20.	Purify up to 1 mg of RNA on an RNeasy spin column, with DNase treatment, precisely as described in Qiagen's RNeasy Midi/Maxi Handbook, supplied with the RNeasy kit. Do the optional second wash on the column. Elute twice using DNase/RNase-free water.21.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. If necessary, the RNA can be concentrated on a SpeedVac. Store at -80degC.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

tag: strain

value: Y cn bw sp

tag: developmental stage

value: WPP + 24 hr

tag: genotype


title: PCA_biofilm_potentiostat_BR2B


title: mefloquine_high_dose-rep2

description: nominal concentration 500 mg/L


source_name: pupae,WPP + 4 days (Celniker/RNA:358) extraction3_array1 channel_1

value: Pupae, WPP + 4 days


source_name: WPP + 24 hr (Celniker/RNA:340) extraction3_array1 channel_1


title: PCA_biofilm_potentiostat_BR1B


title: PCA_biofilm_potentiostat_BR2A


title: Normoxia-HIF1-7

type: genomic

city: Boston

first: Xiaobo

last: Xia

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 7

hyb_protocol: Approximately 2ug of DNA was hybridzed per array.

scan_protocol: Both hybridization and scan were performed by Microarray Core at Dana-Farber Cancer Institute.

data_processing: The model-based analysis of tiling-array (MAT) algorithm was used to identify regions enriched by ChIP-chip (‘‘hits’’) on Affymetrix whole-genome or promoter tiling arrays. MAT was used to identify probe intensity peaks comparing triplicate hypoxic ChIP vs. hypoxic input (‘‘Hypoxic’’) and normoxic ChIP vs. normoxic input (‘‘Normoxic’’). MAT was run with the same parameters for each: bandwidth = 200, maximum gap = 400, minimum probes  = 10, and P value cutoff  = 1e - 5. Hits appearing solely in the hypoxic samples were retained as hypoxia-unique. In cases where hypoxic and normoxic hits overlapped, hits for which the MAT score of hypoxic subtracted by that of normoxic samples were above the cutoff were also retained. The MAT library and mapping files were based on the March 2006 Human Genome Assembly (HG18). Hits flagged by MAT as mapping to repeat  regions were excluded from consideration.

molecule: genomic DNA

source_name: IP: HepG2 cells under normoxic condition

label_protocol: Amplified ChIP and Input samples were fragmented with DNase to 50~100bp size and labeled using the Terminal transferase (TdT, Promega) to add biotinylated-ddATP to the ends of the fragments.

extract_protocol: HepG2 cells were cultured under normoxic (ambient) or hypoxic (0.5% O2, 4 h) conditions. Cells were cross-linked with 1% formaldehyde for 10 minutes at 37ºC, washed with cold PBS, and lysed with 0.5% SDS Buffer. Chromatins were then sonicated in 0.5% SDS Buffer using 3 x 10 second pulses on setting 5 with a Fisher Scientific Sonic Dismembrator (model 100) into 500bp~1kb fragments. Lysates were then diluted with dilution buffer into final SDS concentration being 0.1%. Three ChIP biological replicates were performed for both normoxic and hypoxic samples with HIF-1a pAb (Novus, NB 100-134). A small aliquot for each biological sample are reserved for an input control. Both Chiped DNA and Input samples were amplified by LM-PCR.

tag: cell line

tag: cell type

value: hepatocellular carcinoma

tag: cell tissue

value: liver

tag: antibody

value: HIF-1 polyclonal

source_name: Input: HepG2 cells under normoxic condition


source_name: pupae,WPP + 4 days (Celniker/RNA:360) extraction1_array1 channel_1


source_name: WPP + 24 hr (Celniker/RNA:338) extraction1_array1 channel_1


title: Hypoxia-HIF1-5

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 5

source_name: IP: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)

source_name: Input: HepG2 cells under hypoxic condition (0.5%O2, 4 hours)


source_name: pupae,WPP + 3 days (Celniker/RNA:354) extraction2_array1 channel_1

value: Pupae, WPP + 3 days


source_name: embryos,OR,14-16 hrs after egg laying (Celniker/RNA:130) extraction3_array1 channel_1

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
''This protocol was used for staging and collection of Drosophila melanogaster embryos by Dave Miller''''(Kaufman Lab, IU Bloomington) for transcriptome analysis by the Celniker group.''All Drosophila tissue collections were made from the sequenced ''D. melanogaster'' isogenic strain containing the mutations; ''yellow'' (y1), ''cinnabar'' (cn1), ''brown'' (bw1), and ''speck'' (sp1) [1].  Synchronized embryos were collected from population cages that were less than one week old and maintained at 24 C.  At least one ? two hour pre-lay was made prior to the start of timed collections each day. Embryos were collected for two hours on three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies.Staged embryos were passed through an 850 micron screen and collected on a 75 micron screen to remove adults and yeast paste.  Embryos were then dechorionated by treatment with 50% bleach (3% sodium hypochlorite), 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes.  Embryos were washed twice with 0.2% NaCl, 0.02% Triton buffer and split into two samples.  Most of the sample (approximately 95%) was rinsed with de-ionized water in a buchner funnel under mild vacuum, dried briefly, immediately frozen on dry ice and stored at -80 C for RNA preparations.  The small aliquot was transferred to a clean tube and fixed for staging.  Fixation was accomplished in 0.1 M Pipes (pH 6.9), 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde, 0.1% glutaraldehyde (percentages are relative to aqueous volumes), and 50% heptane, as describe previously [2].  Samples were shaken for five minutes in the fixative, centrifuged briefly and the aqueous fraction was removed.  An equal volume of methanol containing 2 mM EGTA was added and the sample was shaken for five additional minutes.  Tissue was washed twice in methanol with 2 mM EGTA and saved at -80 C for the characterization of developmental stages. Fixed embryos were used to determine the embryonic stages present in each biological sample X (BS#X). Each biological sample was washed in 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes and placed in a P0042G Sedgewick Rafter Grid slide. The developmental stages present in each sample were counted under a dissecting scope. The criteria used for stage identifications are describe in detail at FlyBase [3] and Campos Ortega, J. A. and Hartenstein, V (1997)[4]. Embryonic stages were not assessed by morphology associated with head involution due to the observed defects in this process associated with the isogenic strain. Data were entered into a Microsoft Exel worksheet for graphing. Biological samples that required pooled collections for adequate RNA yields were staged independently and normalized according to the fraction of the final mass of tissue in the pooled biological sample

extract_protocol:
RNA extraction: TRIzol procedure for Insects followed by DNase and RNeasyNote: This protocol is used to prepare RNA that will be used for microarray hybridization or RT-PCR.Materials	TRIzol® reagent: Invitrogen, cat. no. 15596-026 (100 ml) or 15596-018 (200 ml).	DNase/RNase-free water: Invitrogen cat. no. 10977.	75% ethanol, prepared with DNase/RNase-free water.	RNase-free DNase: Qiagen cat. no. 79254.	RNeasy® spin columns: RNeasy midi kit, Qiagen cat. no. 75144.	TenBroeck homogenizer: Bellco biotechnology cat no. 1982-10002.Procedure1.	Homogenize insect samples in TRIzol reagent using a TenBroeck tissue homogenizer. The sample volume should not exceed 10% of the volume of TRIzol reagent used for homogenization.2.	Incubate at room temperature for 5 minutes.  3.	Aliquot samples into 1.5 ml microcentifuge tubes.4.	Add 0.267 ml chloroform per ml of TRIzol used.5.	Shake tubes vigorously for 15 seconds.6.	Incubate at room temperature for 2 minutes.7.	Centrifuge for 15 minutes at 4degC at 12,000 x g.8.	Transfer the top (aqueous) phases to clean tubes.9.	Precipitate the RNA from the aqueous phase by adding 0.67 ml of isopropanol per ml of TRIzol used in step 5.10.	Invert tubes once to mix gently.11.	Incubate samples at room temperature for 10 minutes.12.	Centrifuge for 10 minutes at 4degC at 12,000 x g.13.	Remove the supernatant.14.	Wash RNA pellet once with 75% ethanol, using 0.7 ml per microcentrifuge tube.15.	Vortex briefly.16.	Centrifuge at 7,500 x g for 5 minutes at 4degC.17.	Let the pellet air dry for 10 minutes. Note: DO NOT let the pellet dry completely.18.	Dissolve in RNase-free water. 19.	Incubate at 37degC overnight to dissolve the RNA. Determine concentration using a Nanodrop® ND-1000 Spectrophotometer. RNA may be stored at -80degC at this point if desired.20.	Purify up to 1 mg of RNA on an RNeasy spin column, with DNase treatment, precisely as described in Qiagen's RNeasy Midi/Maxi Handbook, supplied with the RNeasy kit. Do the optional second wash on the column. Elute twice using DNase/RNase-free water.21.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. If necessary, the RNA can be concentrated on a SpeedVac. Store at -80degC.
Poly (A)+ RNA isolation: Qiagen Oligotex mRNA Spin-Column procedureThis protocol is used to prepare poly (A)+ RNA from total RNA.  It utilizes the Oligotex mRNA Midi kit (Qiagen Cat# 70042), and the procedure is unmodified from Qiagen Oligotex Handbook Second Edition, May 2002.Materials?	Oligotex mRNA Midi kit (Qiagen Cat# 70042)?	Oligotex Suspension: 10% (w/v) suspension Oligotex particles in: 10 mM Tris?Cl, pH 7.5; 500 mM NaCl; 1 mM EDTA; 0.1% SDS; 0.1% NaN3 (sodium azide)?	Wash Buffer OW2: 10 mM Tris?Cl, pH 7.5; 150 mM NaCl; 1 mM EDTA?	Elution Buffer OEB: 5 mM Tris?Cl, pH 7.5?	Buffer OBB: 20 mM Tris?Cl, pH 7.5; 1 M NaCl; 2 mM EDTA; 0.2% SDSProcedure1.	Determine the concentration of the starting total RNA solution.  Add 250 ? 500 microgram total RNA (maximum volume 500 microliters) to a 1.5 ml microcentifuge tube and adjust the volume to 500 microliters with RNase-free water.2.	Add 500  microliters buffer OBB and mix.3.	Add 30 microliters Oligotex suspension (ensure that the resin is in suspension), and mix.4.	Incubate the sample for 3 minutes at 70degC in a heating block.5.	Remove the sample from heating block and place at 20 to 30degC for 10 minutes.6.	Centrifuge for 2 minutes at 15,000 g to pellet the Oligotex:mRNA, and carefully remove the supernatant.7.	Resuspend the Oligotex:mRNA pellet in 400 microliters of Buffer OW2 by pipetting up and down.  Transfer the suspension onto a small spin column placed in a 1.5 ml microcentrifuge tube.8.	Centrifuge for 1 minute at 15,000 g.9.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube, and apply 400 microliters of Buffer OW2 to the column.10.	Centrifuge for 1 minute at 15,000 g.  11.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube. Add 50-80 microliters pre-heated (70degC) Buffer OEB to the column and resuspend the resin by pipetting up and down 3 or 4 times.12.	Centrifuge for 1 minute at 15,000 g.13.	Add another 40-50 microliters pre-heated (70degC) Buffer OEB onto the column resuspend the resin by pipetting up and down 3 or 4 times.14.	Centrifuge for 1 min at 15,000 g. 15.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. Store at -80degC.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: Oregon-R

value: Embryo 14-16h

value: TBA

tag: sex

value: Unknown


source_name: pupae,WPP + 3 days (Celniker/RNA:352) extraction1_array1 channel_1


title: Hypoxia-HIF1-7

description: HIF-1 ChIP Hypoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 7


title: Normoxia-HIF1-5

description: HIF-1 ChIP Normoxia Biological Rep 1-3, Affymetrix Human Tiling 2.0R Set, Array 5


title: mefloquine_low_dose-rep1

description: nominal concentration 10 mg/L

source_name: whole organism, mefloquine, 10 mg/L


title: PCA_biofilm_potentiostat_BR3B

source_name: wildtype Geobacter grown on a 10 mA potentiostat; experimental condition

tag: Geobacter sulfurreducens was grown in a Geobattery in flow-through potentiostat mode

source_name: wildtype Geobacter grown in a fumarate biofilm (in a potentiostat); control condition

tag: Geobacter sulfurreducens was grown in an open circuit Geobattery in flow-through mode


source_name: embryos,OR,14-16 hrs after egg laying (Celniker/RNA:131) extraction2_array1 channel_1


title: HybridPoplar_H11-11_UntreatedControl24hSink_vs_OralSecretion24hSink_Hyb1

description: Gene expression

source_name: Hybrid poplar, untreated control for 24 hours, systemic sink leaves

tag: tissue

value: sink leaf

tag: experimental protocol

value: Six month old clonal trees grown under greenhouse conditions. Leaves at the crown with a midvein length < 6cm were harvested with petioles removed from five trees subjected to the same treatment. Leaves act as carbon sinks in relation to systemic source and treated source leaves. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar, oral secretion treatment for 24 hours, systemic sink leaves


title: mefloquine_mid_dose-rep1

description: nominal concentration 250 mg/L

source_name: whole organism, mefloquine, 250 mg/L


source_name: embryos,OR,2-4 hrs after egg laying (Celniker/RNA:129) extraction1_array1 channel_1

value: Embryo 2-4h, OregonR


source_name: embryos,OR,2-4 hrs after egg laying (Celniker/RNA:127) extraction2_array1 channel_1


source_name: embryos,OR,2-4 hrs after egg laying (Celniker/RNA:128) extraction3_array1 channel_1


title: mefloquine_control-rep1

description: no chemical

source_name: whole organism, mefloquine, control


title: PCA_biofilm_potentiostat_BR1A


source_name: embryos,OR,14-16 hrs after egg laying (Celniker/RNA:132) extraction1_array1 channel_1


source_name: ML-DmBG2-c2 (Celniker/RNA:474) extraction3_array1 channel_1

extract_protocol:
This protocol is used by the IU Bloomington labs to prepare RNA from cell lines that will be used for for microarray hybridization or RT-PCR.This is a standard TRIzol purification procedure, followed by DNase and RNeasy (Qiagen).  Concentration was determined by Nanodrop absorbance.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: CNS-derived cell-line

value: y v f mal


source_name: ML-DmBG2-c2 (Celniker/RNA:472) extraction2_array1 channel_1


source_name: Kc167 (Celniker/RNA:146) extraction1_array1 channel_1

extract_protocol:
This protocol is used by the IU Bloomington labs to prepare RNA from cell lines that will be used for for microarray hybridization or RT-PCR.This is a standard TRIzol purification procedure, followed by DNase and RNeasy (Qiagen).  Concentration was determined by Nanodrop absorbance.
Poly (A)+ RNA isolation: Qiagen Oligotex mRNA Spin-Column procedureThis protocol is used to prepare poly (A)+ RNA from total RNA.  It utilizes the Oligotex mRNA Midi kit (Qiagen Cat# 70042), and the procedure is unmodified from Qiagen Oligotex Handbook Second Edition, May 2002.Materials?	Oligotex mRNA Midi kit (Qiagen Cat# 70042)?	Oligotex Suspension: 10% (w/v) suspension Oligotex particles in: 10 mM Tris?Cl, pH 7.5; 500 mM NaCl; 1 mM EDTA; 0.1% SDS; 0.1% NaN3 (sodium azide)?	Wash Buffer OW2: 10 mM Tris?Cl, pH 7.5; 150 mM NaCl; 1 mM EDTA?	Elution Buffer OEB: 5 mM Tris?Cl, pH 7.5?	Buffer OBB: 20 mM Tris?Cl, pH 7.5; 1 M NaCl; 2 mM EDTA; 0.2% SDSProcedure1.	Determine the concentration of the starting total RNA solution.  Add 250 ? 500 microgram total RNA (maximum volume 500 microliters) to a 1.5 ml microcentifuge tube and adjust the volume to 500 microliters with RNase-free water.2.	Add 500  microliters buffer OBB and mix.3.	Add 30 microliters Oligotex suspension (ensure that the resin is in suspension), and mix.4.	Incubate the sample for 3 minutes at 70degC in a heating block.5.	Remove the sample from heating block and place at 20 to 30degC for 10 minutes.6.	Centrifuge for 2 minutes at 15,000 g to pellet the Oligotex:mRNA, and carefully remove the supernatant.7.	Resuspend the Oligotex:mRNA pellet in 400 microliters of Buffer OW2 by pipetting up and down.  Transfer the suspension onto a small spin column placed in a 1.5 ml microcentrifuge tube.8.	Centrifuge for 1 minute at 15,000 g.9.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube, and apply 400 microliters of Buffer OW2 to the column.10.	Centrifuge for 1 minute at 15,000 g.  11.	Transfer the spin column to a new RNase-free 1.5 ml microcentrifuge tube. Add 50-80 microliters pre-heated (70degC) Buffer OEB to the column and resuspend the resin by pipetting up and down 3 or 4 times.12.	Centrifuge for 1 minute at 15,000 g.13.	Add another 40-50 microliters pre-heated (70degC) Buffer OEB onto the column resuspend the resin by pipetting up and down 3 or 4 times.14.	Centrifuge for 1 min at 15,000 g. 15.	Determine concentration by absorbance, using a Nanodrop® ND-1000 Spectrophotometer. Store at -80degC.
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.

value: embryo-derived cell-line

value: se/e

value: Female


source_name: Kc167 (Celniker/RNA:147) extraction2_array1 channel_1


source_name: Kc167 (Celniker/RNA:477) extraction3_array1 channel_1

extract_protocol:
For isolation of nuclear RNA from cell cultures.  Nuclei are isolated by differential centrifugation and RNA is collected using the TRIzol protocol for cell lines. This protocol is modified from Zimmerman et al 1982 (PNAS 79:3148) and used to prepare nuclear RNA from cell lines
First-strand cDNA synthesis was performed by using SuperScript II reverse transcriptase in the reaction volume of 105 ul for 15 ug of starting RNA material. The RNA was mixed with random hexamers (83.3 ng/g mRNA), heated to 70C for 10 min, and cooled to 15C after which 5x SuperScript II First Strand buffer, DTT (10 mM), and dNTPs (0.5 mM) were added. SuperScript II was added after a 20-min incubation (200 units/ug RNA) followed by a 20-min ramp to 42C and 60-min incubation at 420C. SuperScript II was inactivated at 75C for 15 min.The second-strand cDNA was synthesized by addition of 50 units of Escherichia coli DNA ligase, 200 units of E. coli DNA polymerase I, 10 units of E. coli RNase H, and 0.2 mM dNTPs to the first-strand synthesis reaction at 16C for 2 h.


source_name: ML-DmBG2-c2 (Celniker/RNA:470) extraction1_array1 channel_1


source_name: Kc167 (Celniker/RNA:145) extraction3_array1 channel_1


source_name: Kc167 (Celniker/RNA:476) extraction2_array1 channel_1


source_name: Kc167 (Celniker/RNA:475) extraction1_array1 channel_1


source_name: CME-W2 (Celniker/RNA:464) extraction3_array1 channel_1

value: CME W2

value: dorsal mesothoracic disc


source_name: mbn2 (Celniker/RNA:46) extraction2_array1 channel_1

value: embryonic/larval hemocyte

value: l(2)malignant blood neoplasm


source_name: embryos,6-8 hr after egg laying (Celniker/RNA:412) extraction3_array1 channel_1

value: Y cn bw sp

value: Embryo 6-8h


source_name: mbn2 (Celniker/RNA:44) extraction1_array1 channel_1


source_name: embryos,6-8 hr after egg laying (Celniker/RNA:414) extraction1_array1 channel_1


source_name: CME-W2 (Celniker/RNA:460) extraction1_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:224) extraction2_array1 channel_1

growth_protocol:
Fly population cages contained the sequenced D. melanogaster isogenic strain with the mutations; yellow (y1), cinnabar (cn1), brown (bw1), and speck (sp1) [1]. Two homemade Plexiglas cages approximately 25cm x 25cm x 25cm, were used for staged embryo collections. These population cages were constructed from ¼ inch solid Plexiglas except for the open front panel. The fronts of the cages were covered with sleeves constructed of muslin cloth that were attached to the Plexiglas sides using Velcro strips. Each muslin sleeve was then twisted and held closed with a hose clamp. Flies were fed with three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies. The two population cages were maintained at 24? C in a controlled environment on a 24-hour light cycle (14 hours light / 10 hours dark) using three 60W bulbs on a timer. Flies were introduced to the cages at least four days prior to collections and fertility counts. These animals were initially grown in bottles at the same controlled environment described above. Each population cage was established from four trays with 35 bottles per tray containing newly eclosed adult flies. Each 250ml (pint) bottle contained approximately 40ml standard Drosophila medium in use at Bloomington (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/media-recipes.htm). The isogenic Drosophila mutant strain was propagated in bottles (A) starting with approximately 40-50 adults per bottle on day zero. New bottles (B) were generated from these bottles (A) on day 14. Cages were established by clearing the ?A? bottles into an empty bottle (without food) and transferring the newly eclosed adult flies in the ?A? bottles into the two population cages on day 18. The next round of cages and bottles (C) were established from the ?B? bottles in the same manner. Two-hour embryo collections were made during the light cycles following at least one two-hour pre-lay.
''This protocol was used for staging and collection of Drosophila melanogaster embryos by Dave Miller''''(Kaufman Lab, IU Bloomington) for transcriptome analysis by the Celniker group.''All Drosophila tissue collections were made from the sequenced ''D. melanogaster'' isogenic strain containing the mutations; ''yellow'' (y1), ''cinnabar'' (cn1), ''brown'' (bw1), and ''speck'' (sp1) [1].  Synchronized embryos were collected from population cages that were less than one week old and maintained at 24 C.  At least one ? two hour pre-lay was made prior to the start of timed collections each day. Embryos were collected for two hours on three hard egg lay collection plates made in 150 X 15 mm Petri dishes containing a substrate of 3.3% agar, 13% unsulfured molasses, and 0.15% Tegasept. The hard egg lay plates were completely covered with a thin layer of moist yeast paste (Fleischmann?s Baker?s Dry Yeast) and placed horizontally on a short 1cm raised Plexiglas bar in the bottom of each cage to avoid crushing flies.Staged embryos were passed through an 850 micron screen and collected on a 75 micron screen to remove adults and yeast paste.  Embryos were then dechorionated by treatment with 50% bleach (3% sodium hypochlorite), 0.2% sodium chloride, and 0.02% Triton-X-100 for five minutes.  Embryos were washed twice with 0.2% NaCl, 0.02% Triton buffer and split into two samples.  Most of the sample (approximately 95%) was rinsed with de-ionized water in a buchner funnel under mild vacuum, dried briefly, immediately frozen on dry ice and stored at -80? C for RNA preparations.  The small aliquot was transferred to a clean tube and fixed for staging.  Fixation was accomplished in 0.1 M Pipes (pH 6.9), 2 mM EGTA, 1 mM MgSO4, 4% paraformaldehyde, 0.1% glutaraldehyde (percentages are relative to aqueous volumes), and 50% heptane, as describe previously [2].  Samples were shaken for five minutes in the fixative, centrifuged briefly and the aqueous fraction was removed.  An equal volume of methanol containing 2 mM EGTA was added and the sample was shaken for five additional minutes.  Tissue was washed twice in methanol with 2 mM EGTA and saved at -80? C for the characterization of developmental stages.

value: Embryo 4-6h


source_name: embryos,6-8 hr after egg laying (Celniker/RNA:413) extraction2_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:228) extraction3_array1 channel_1


source_name: mbn2 (Celniker/RNA:48) extraction3_array1 channel_1


source_name: embryos,4-6 hr after egg laying (Celniker/RNA:226) extraction1_array1 channel_1


source_name: CME-W2 (Celniker/RNA:462) extraction2_array1 channel_1


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:218) extraction1_array1 channel_1

value: Embryo 2-4h


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:220) extraction3_array1 channel_1

value: Unknown


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:406) extraction2_array1 channel_1


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:408) extraction3_array1 channel_1


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:407) extraction1_array1 channel_1


source_name: embryos,22-24 hr after egg laying (Celniker/RNA:280) extraction1_array1 channel_1

value: Embryo 22-24hSC


source_name: embryos,2-4 hr after egg laying (Celniker/RNA:222) extraction2_array1 channel_1


source_name: embryos,22-24 hr after egg laying (Celniker/RNA:278) extraction2_array1 channel_1


source_name: embryos,20-22 hr after egg laying (Celniker/RNA:435) extraction2_array1 channel_1

value: Embryo 20-22h


source_name: embryos,20-22 hr after egg laying (Celniker/RNA:276) extraction1_array1 channel_1


source_name: embryos,20-22 hr after egg laying (Celniker/RNA:274) extraction2_array1 channel_1


source_name: embryos,22-24 hr after egg laying (Celniker/RNA:282) extraction3_array1 channel_1


source_name: embryos,18-20 hr after egg laying (Celniker/RNA:270) extraction3_array1 channel_1

value: Embryo 18-20h


source_name: embryos,20-22 hr after egg laying (Celniker/RNA:433) extraction3_array1 channel_1


source_name: embryos,16-18 hr after egg laying (Celniker/RNA:429) extraction2_array1 channel_1

value: Embryo 16-18h


source_name: embryos,20-22 hr after egg laying (Celniker/RNA:434) extraction1_array1 channel_1


source_name: embryos,18-20 hr after egg laying (Celniker/RNA:268) extraction1_array1 channel_1


source_name: embryos,18-20 hr after egg laying (Celniker/RNA:431) extraction2_array1 channel_1