title: Lead_EC50_rep3

description: Gene expression after 2 d exposure to lead (EC50;1158.6 mg/kg)

source_name: Lead, 2d, EC50 (1158.6 mg/kg), replicate 3


title: Lead_EC50_rep5

status: Public on Feb 05 2010

type: RNA

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

hyb_protocol: 300 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Custom Gene Expression Microarrays with 8 × 15 k format (GPL7150) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm)  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), washed in acetonitril for 10 seconds, then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red&Green and PMT is set to 100%, XDR Hi 100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2-v5_95 and Grid: 016342_D_F_20070323) to obtain mean Red or Green intensities and median Red or Green background intesities. In limma, edwards method for background correction was used (offset = 30), and quantile normalizion was done between all arrays.

molecule: total RNA

organism: Folsomia candida

source_name: Lead, 2d, EC50 (1158.6 mg/kg), replicate 5

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer’s guidelines with a slight modification where the transcription (labeling) reactions were done in half the volume, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures were first age synchronized before exposure to soil as follows, 10-20 adult animals were incubated per plastic rings; containing plaster of Paris mixed with charcoal, to lay eggs and were removed after 2 days. The incubation conditions were 20°C with a 12 hour light/dark regime. It took approximately 10 days before the eggs hatched.

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 30 animals, 23 d old, were exposed for two days in glass jars containing ~30 g of: soil spiked with (EC10 or EC50 of) a metal (Ba, Cd, Co, Cr, Pb, or Zn), non-spiked soil, or field soil samples. Exposure was done at 20°C, a 12 h light/dark regime, and 75% humidity. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: sample type

value: pool of ~30 animals

tag: series

tag: classification set

value: training set


title: Lead_EC10_rep5

description: Gene expression after 2 d exposure to lead (EC10;540.1 mg/kg)

source_name: Lead, 2d, EC10 (540.1 mg/kg), replicate 5


title: Lead_EC50_rep4

source_name: Lead, 2d, EC50 (1158.6 mg/kg), replicate 4


title: Lead_EC50_rep1

source_name: Lead, 2d, EC50 (1158.6 mg/kg), replicate 1


title: 26 days pf vs control reference rep 6

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

country: USA

institute: Stanford University

hyb_protocol: cDNA was labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

scan_protocol: Microarray chips were scanned using a Genepix 4000B scanner (Axon Instruments, Union City, CA, USA) at 10 µm pixel resolution. ImaGene (BioDiscovery Inc., El Segundo, CA, USA) was used to process raw scanner images and create spot intensity reports, while CloneTracker (Biodiscovery Inc.) generated gene ID mapping files and assigned gene identification. Final intensity reports were retrieved as raw spot intensities in tab-delimited files.

data_processing: Data was pre-processed and normalized in the following sequence, applying background correction, omitting multiple flagged spots, applying floor correction, omitting low expression spots, calculating ratio values, log-transformation of intensity ratios (base 2), and global LOESS normalization. GeneSight 3.0 was used.

organism: Pinctada maxima

source_name: larvae 26 days

label_protocol: 2 ug of total RNA from pooled temporal larval samples and reference samples (unfertilized eggs) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

extract_protocol:
Pearl oyster Pinctada maxima animals were collected during a commercial spawning run, courtesy of the Paspaley Pearling Company (Broome, Australia). Samples were taken at a series of time points post fertilization (pf) to accurately represent transitions between larval stages and metamorphosis to juveniles ranging from 24 hrs to 40 days pf. Unfertilized eggs were also collected to serve as an experimental control.
Total RNA was isolated from pools of P. maxima larvae at each stage using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.

tag: whole larvae pooled

tag: Age

value: 26 Days

source_name: control reference

tag: unfertilized eggs pooled


title: 30 days pf vs control reference rep 3

source_name: larvae 30 days

value: 30 Days


title: Lead_EC10_rep2

source_name: Lead, 2d, EC10 (540.1 mg/kg), replicate 2


title: Lead_EC10_rep4

source_name: Lead, 2d, EC10 (540.1 mg/kg), replicate 4


title: 35 days pf vs control reference rep 2

source_name: larvae 35 days

value: 35 Days


title: 26 days pf vs control reference rep 5


title: 30 days pf vs control reference rep 4


title: 26 days pf vs control reference rep 4


title: Non-spiked_LUFA_Soil_Series_1_rep4

description: Gene expression after 2 d exposure to LUFA non-spiked soil (series1)

source_name: LUFA, 2d, non-spiked soil (series1), replicate 4


title: 26 days pf vs control reference rep 1


title: Non-spiked_LUFA_Soil_Series_1_rep2

source_name: LUFA, 2d, non-spiked soil (series1), replicate 2


title: 26 days pf vs control reference rep 3


title: Non-spiked_LUFA_Soil_Series_1_rep3

source_name: LUFA, 2d, non-spiked soil (series1), replicate 3


title: 23 days pf vs control reference rep 7

source_name: larvae 23 days

value: 23 Days


title: 23 days pf vs control reference rep 6


title: Noy_Field_Soil_rep5

description: Gene expression after 2 d exposure to Noy field soil

source_name: Noy, 2d, field soil, replicate 5

value: field soil set


title: Lead_EC10_rep1

source_name: Lead, 2d, EC10 (540.1 mg/kg), replicate 1

value: validation set


title: 23 days pf vs control reference rep 2


title: 23 days pf vs control reference rep 5


title: Noy_Field_Soil_rep2

source_name: Noy, 2d, field soil, replicate 2


title: 23 days pf vs control reference rep 3


title: Noy_Field_Soil_rep3

source_name: Noy, 2d, field soil, replicate 3


title: 20 days pf vs control reference rep 4

source_name: larvae 20 days

value: 20 Days


title: 20 days pf vs control reference rep 3


title: Non-spiked_LUFA_Soil_Series_1_rep1

source_name: LUFA, 2d, non-spiked soil (series1), replicate 1


title: 26 days pf vs control reference rep 2


title: Non-spiked_LUFA_Soil_Series_2_rep3

description: Gene expression after 2 d exposure to LUFA non-spiked soil (series2)

source_name: LUFA, 2d, non-spiked soil (series2), replicate 3


title: Non-spiked_LUFA_Soil_Series_2_rep5

source_name: LUFA, 2d, non-spiked soil (series2), replicate 5


title: Non-spiked_LUFA_Soil_Series_2_rep2

source_name: LUFA, 2d, non-spiked soil (series2), replicate 2


title: 23 days pf vs control reference rep 1

source_name: control reference


title: 23 days pf vs control reference rep 4


title: Chromium_EC50_rep5

description: Gene expression after 2 d exposure to chromium (EC50;43.5 mg/kg)

source_name: Chromium, 2d, EC50 (43.5 mg/kg), replicate 5


title: Chromium_EC50_rep4

source_name: Chromium, 2d, EC50 (43.5 mg/kg), replicate 4


title: Chromium_EC50_rep3

source_name: Chromium, 2d, EC50 (43.5 mg/kg), replicate 3


title: 20 days pf vs control reference rep 1


title: 17 days pf vs control reference rep 6

source_name: larvae 17 days

value: 17 Days


title: 20 days pf vs control reference rep 2


title: Non-spiked_LUFA_Soil_Series_2_rep1

source_name: LUFA, 2d, non-spiked soil (series2), replicate 1


title: Chromium_EC50_rep2

source_name: Chromium, 2d, EC50 (43.5 mg/kg), replicate 2


title: 17 days pf vs control reference rep 5


title: 17 days pf vs control reference rep 4


title: Chromium_EC10_rep4

description: Gene expression after 2 d exposure to chromium (EC10;29.3 mg/kg)

source_name: Chromium, 2d, EC10 (29.3 mg/kg), replicate 4


title: Chromium_EC10_rep3

source_name: Chromium, 2d, EC10 (29.3 mg/kg), replicate 3


title: 17 days pf vs control reference rep 1


title: WT-smoke-med-2 month-R3

status: Public on Feb 06 2010

city: Koeln

first: Stephan

last: Gebel

address: Fuggerstr. 3

country: Germany

institute: Philip Morris Research Laboratories

description:
RNA isolated from lung tissue of CD-1 wildtype mouse, smoke treated
gene expression data

hyb_protocol: Ten µg of biotinylated fragmented cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 for 16 hours at 60 rpm in a 45°C GeneChip® Hybridization Oven 640 (Affymetrix)

scan_protocol: Affymetrix.com:Protocol:Scan-M10, Agilent GeneArray® Scanner 3000 7G

data_processing: .CEL files were processed using R/Biocondcutor packages affy and gcrma.

label: biotin

organism: Mus musculus

source_name: Lung tissue of CD-1 wildtype mouse, smoke treated

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

extract_protocol: RNA was extracted from left lung lobes, which were deep-frozen in liquid N2 immediately after dissection and stored at -70°C, by using RNeasy Midi Kit (Qiagen, Hilden, Germany). RNA integrity was determined using Agilent 2100 Bioanalyzer

treatment_protocol: Mice were exposed in whole body exposure chambers to diluted mainstream cigarette smoke (CS) at a target concentration of 750 µg TPM/l for 2, 3, or 4 h/day or to conditioned fresh air (control) for 4 h/day. The CS exposure started with a dose adaptation period, i.e. 125 µg TPM/l on day 1 and gradually reached the target concentration on day 17.

tag: tissue

value: lung tissue

tag: genotype

tag: age

value: 13 weeks + 2 month

tag: treatment

value: 2R4F whole mainstream smoke 750 µg/ml, treatment over 2 month, 3x1h exposure per day


title: Chromium_EC10_rep1

source_name: Chromium, 2d, EC10 (29.3 mg/kg), replicate 1


title: Chromium_EC10_rep2

source_name: Chromium, 2d, EC10 (29.3 mg/kg), replicate 2


title: Cobalt_EC50_rep5

description: Gene expression after 2 d exposure to cobalt (EC50;368.7 mg/kg)

source_name: Cobalt, 2d, EC50 (368.7 mg/kg), replicate 5


title: 17 days pf vs control reference rep 3


title: 3 days pf vs control reference rep 2

source_name: larvae 3 days

value: 3 Days


title: Cobalt_EC50_rep1

source_name: Cobalt, 2d, EC50 (368.7 mg/kg), replicate 1


title: Cobalt_EC50_rep4

source_name: Cobalt, 2d, EC50 (368.7 mg/kg), replicate 4


title: 3 days pf vs control reference rep 3


title: 3 days pf vs control reference rep 4


title: 3 days pf vs control reference rep 6


title: 17 days pf vs control reference rep 2


title: 3 days pf vs control reference rep 1


title: 3 days pf vs control reference rep 5


title: 24hrs pf vs control reference rep 6

source_name: larvae 24 hrs

value: 24 hrs


title: Cobalt_EC50_rep3

source_name: Cobalt, 2d, EC50 (368.7 mg/kg), replicate 3


title: Cobalt_EC10_rep5

description: Gene expression after 2 d exposure to cobalt (EC10;272.4 mg/kg)

source_name: Cobalt, 2d, EC10 (272.4 mg/kg), replicate 5


title: Cobalt_EC10_rep4

source_name: Cobalt, 2d, EC10 (272.4 mg/kg), replicate 4


title: Cobalt_EC10_rep2

source_name: Cobalt, 2d, EC10 (272.4 mg/kg), replicate 2


title: 24hrs pf vs control reference rep 4

source_name: control reference


title: 24hrs pf vs control reference rep 5


title: Cobalt_EC10_rep1

source_name: Cobalt, 2d, EC10 (272.4 mg/kg), replicate 1


title: 24hrs pf vs control reference rep 2


title: 24hrs pf vs control reference rep 3


title: Inner fold v control 4

source_name: Inner fold

label_protocol: 2 ug of total RNA from pooled tissue samples and reference samples (combined tissues) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

extract_protocol:
P. maxima animals were collected from several locations on the West Australian and Northern Territory coasts, Australia, courtesy of Paspaley Pearling Company. Animals were immediately anesthetized in 1% propylene phenoxyetol seawater solution until valves were open and non-responsive. Specimens were then sacrificed and mantle tissue dissected into into 5 separate sections: outer fold (OF), middle fold (MF), inner fold (IF), ventral mantle tissue (VM) and dorsal mantle tissue (DM).
Total RNA was isolated from each tissue using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.

tag: Tissue

value: Inner fold

tag: equally combined treatment tissues


title: Inner fold v control 5


title: Inner fold v control 6


title: 24hrs pf vs control reference rep 1


title: Cadmium_EC50_rep5

description: Gene expression after 2 d exposure to cadmium (EC50;41.2 mg/kg)

source_name: Cadmium, 2d, EC50 (41.2 mg/kg), replicate 5


title: Middle fold v control 6

source_name: Middle fold

value: Middle fold


title: Middle fold v control 4


title: Middle fold v control 3


title: Cadmium_EC50_rep4

source_name: Cadmium, 2d, EC50 (41.2 mg/kg), replicate 4

value: pool of ~30 animals


title: Inner fold v control 1


title: Cadmium_EC50_rep3

source_name: Cadmium, 2d, EC50 (41.2 mg/kg), replicate 3

value: training set


title: Inner fold v control 3


title: Outer fold v control 5

source_name: Outer fold

value: Outer fold


title: Inner fold v control 2


title: Middle fold v control 5


title: Middle fold v control 2


title: Cadmium_EC50_rep1

source_name: Cadmium, 2d, EC50 (41.2 mg/kg), replicate 1


title: Middle fold v control 1


title: Cadmium_EC10_rep2

description: Gene expression after 2 d exposure to cadmium (EC10;27.7 mg/kg)

source_name: Cadmium, 2d, EC10 (27.7 mg/kg), replicate 2


title: Cadmium_EC10_rep3

source_name: Cadmium, 2d, EC10 (27.7 mg/kg), replicate 3


title: Cadmium_EC10_rep4

source_name: Cadmium, 2d, EC10 (27.7 mg/kg), replicate 4


title: Outer fold v control 3


title: Outer fold v control 4


title: Barium_EC50_rep5

description: Gene expression after 2 d exposure to barium (EC50;1159.3 mg/kg)

source_name: Barium, 2d, EC50 (1159.3 mg/kg), replicate 5


title: Ventral mantle v control 6

source_name: Ventral mantle

value: Ventral mantle


title: Outer fold v control 2


title: Outer fold v control 1


title: Outer fold v control 6


title: Ventral mantle v control 5


title: Cadmium_EC10_rep1

source_name: Cadmium, 2d, EC10 (27.7 mg/kg), replicate 1


title: Barium_EC50_rep3

source_name: Barium, 2d, EC50 (1159.3 mg/kg), replicate 3


title: Ventral mantle v control 2


title: Ventral mantle v control 4


title: Ventral mantle v control 3


title: Dorsal mantle v control 6

source_name: Dorsal mantle

value: Dorsal mantle


title: Barium_EC50_rep2

source_name: Barium, 2d, EC50 (1159.3 mg/kg), replicate 2


title: Dorsal mantle v control 5

source_name: control reference


title: Barium_EC10_rep5

description: Gene expression after 2 d exposure to barium (EC10;583.3 mg/kg)

source_name: Barium, 2d, EC10 (583.3 mg/kg), replicate 5


title: Ventral mantle v control 1


title: Dorsal mantle v control 4


title: Barium_EC50_rep1

source_name: Barium, 2d, EC50 (1159.3 mg/kg), replicate 1


title: Dorsal mantle v control 1


title: Dorsal mantle v control 3


title: TBT treatment v control rep 6

data_processing: Data was pre-processed and normalized in the following sequence, applying background correction, omitting multiple flagged spots, applying floor correction, omitting low expression spots, calculating ratio values, log-transformation of intensity ratios (base 2), and global LOESS normalization. GeneSight 3.0 software was used.

source_name: TBT exposed mantle

label_protocol: 2 ug of total RNA from treatment and controls animals was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.

growth_protocol: Pearl oysters were housed in static culture systems, whereby 100% seawater exchanges were performed every 24hrs. Animals were fed a mixture of live microalgae via a drip feeding apparatus over the 24hr period.

extract_protocol: Total RNA was isolated from each sample using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.

treatment_protocol: TBT 50 ng1-1 (bis tri-n-butyltin oxide, 96%, Sigma-Aldrich, Sydney, Australia) in absolute ethanol was added to treatment tanks (250 µl) every 24hrs following seawater renewal of contaminate would yield the desired exposure concentration in each tank. Ethanol (250 µl) was likewise added to the control tanks. These experimental conditions were maintained for 21 days.

value: mantle

source_name: Untreated mante control


title: Barium_EC10_rep1

source_name: Barium, 2d, EC10 (583.3 mg/kg), replicate 1


title: Barium_EC10_rep2

source_name: Barium, 2d, EC10 (583.3 mg/kg), replicate 2


title: TBT treatment v control rep 3


title: TBT treatment v control rep 5


title: TBT treatment v control rep 2


title: Dicer knockout MII-stage oocytes, biological replicate 3

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

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

data_processing: Data were normalized using the GCRMA algorithm

source_name: Dicer knockout mouse oocytes collected 16 h post-hCG (human chorionic gonadotropin) injection

growth_protocol: MII oocytes were collected and washed thoroughly in M2 medium (Sigma) to ensure that no cumulus cells were present.

extract_protocol: Total RNA was prepared using the Picopure RNA isolation Kit (Arcturus, Mountain View, CA).

treatment_protocol: Ovarian follicular development was stimulated by intraperitoneal injection of 7.5 IU of PMSG (Calbiochem).  Mice were then injected with hCG (7.5IU/mouse), and the oviducts were removed 14-16 h post hCG injection.  Ovulated OCCs (oocyte cumulus complexes) were released by gently teasing apart the ampulla of oviducts.  Denuded oocytes were obtained by incubating the mass of OCCs in M2 medium containing 0.3 mg/ml of hyaluronidase for about 3-5 min.  Oocytes were then collected and washed thoroughly in M2 medium to ensure that no cumulus cells were present.

tag: cell type

value: mouse oocyte

tag: strain

tag: developmental stage

value: Metaphase II (MII)

value: Dicer knockout


title: Barium_EC10_rep4

source_name: Barium, 2d, EC10 (583.3 mg/kg), replicate 4


title: TBT treatment v control rep 4


title: TBT treatment v control rep 1


title: wild-type MII-stage oocytes, biological replicate 3

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

source_name: wild-type mouse oocytes collected 16 h post-hCG (human chorionic gonadotropin) injection

value: wild-type


title: Dicer knockout MII-stage oocytes, biological replicate 2

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


title: Dorsal mantle v control 2


title: Dicer knockout MII-stage oocytes, biological replicate 1


title: C. elegans N2_E. coli OP50_24h_Sample C

city: Durham

first: Devin

last: Bolz

state: NC

address: 270 Jones Building, Research Drive, Box 3580

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

data_processing: Affymetrix GeneChip Operating System (GCOS)

organism: Caenorhabditis elegans

source_name: C. elegans N2_E. coli OP50_24h

label_protocol: Standard Affymetrix Procedures

growth_protocol: Gravid adult N2 nematodes were lysed using a solution of sodium hydroxide and bleach, washed, and eggs synchronized overnight in S basal liquid medium at room temperature. Synchronized L1 larval animals were seeded onto modified NGM plates with 0.35% peptone containing E. coli OP50 and incubated at 25oC until the nematodes had reached the L4 larval stage. Animals were collected and washed with M9 buffer before transferring to modified NGM plates containing Y. pestis KIM5 or E. coli OP50 for 24h.

extract_protocol: After 24h on modified NGM plates, animals were collected, washed with M9 buffer, and RNA extracted using Trizol reagent (Invitrogen). Residual genomic DNA was removed by DNAse treatment (Ambion).

tag: developmental stage at time of exposure

tag: exposure

value: E. coli OP50 (24h)

value: Whole animal


title: Gonad_SWIMvsREST_20days

city: Barcelona

first: Arjan

last: Palstra

address: Av. Diagonal 645

country: Spain

institute: Universitat de Barcelona

hyb_protocol: The slides were pretreated with 1% BSA(fraction V), 20 × SSC, 10% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight in cocktail containing 50 × Denhardt's, 20 × SSC, 10% SDS, 10μg/μl polyadenylate and 10 μg/μl yeast tRNA. All chemicals were from Sigma-Aldrich.

scan_protocol: Scanning was performed with ScanArray 5000 and images were processed with QuantArray (GSI Luminomics).

data_processing: The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalization was performed. To assess differential expression of genes, the normalized log intensity ratios (expression ratio) were analyzed with Student's t-test (P <0.05).

organism: Oncorhynchus mykiss

label_protocol: Total RNA corresponding to pooled samples from the swim or rest groups was labeled with Cye3 and Cye5-dCTP (GE Healthcare, Barcelona, Spain) using SuperScript III reverse transcriptase (Invitrogen, Baro, Spain) and oligo(dT) primer. In our experience, reverse labeling combined with multiple replication of spots provide robust normalization and high statistical power of analyses. cDNA was purified with MicroconYM30 (Millipore).

extract_protocol: RNA was isolated from pituitary and ovary samples according to the TRIZOL reagent protocol by Invitrogen (Baro, Spain). Isolated RNA was DNAse treated using RQ1 DNAse Promega (Madison, USA) and reverse transcribed using Superscript IIITM (Baro, Spain) according to the manufacturer’s protocol.

treatment_protocol:
Pubertal autumn spawning rainbow trout (n=26; ~50 cm, ~1.5 kg) were purchased from a Danish exporter (Frederiksvaerk Aleexport) where they had been raised for 2 years in freshwater followed by 4 months in sea water cages at 10 ‰. They were transferred by truck within 16 h to Spakenburg (Spakenburg Paling, The Netherlands) and subsequently in the same water in a similar holding tank to the swim-flume at Leiden University (The Netherlands). The next day, 5 randomly chosen fish were sampled as ‘start’-group while others were randomly divided into a ‘rest’-group (n=10) and a ‘swim’-group (n=11). During the following 4 days, the brackish 10 ‰ water was stepwise replaced by freshwater at 16 °C and photoperiod was changed from 16L:8D to 8L:16D. Fish were then acclimatized for two days to their new conditions. Subsequently, swimmers were first swum at a speed of 0.33 body-lengths per second (BL/s) which was increased the next day to the final, near optimal speed of 0.75 BL/s (0.34 m/s or 29.4 km/day). Fish were sampled after 20 days (5 resters and 6 swimmers).
At sampling, fish were anesthetized using oil of cloves that was commercially purchased from a drugstore (diluted 1:10 in ethanol and used at a dosage of 1.5 ml/l). Tissues were weighted and samples were flash frozen in liquid nitrogen and stored at -80 °C for microarray analyses (ovary).

tag: protocol

value: swam 20 days

value: rested 20 days


title: Dgcr8 knockout MII-stage oocytes, biological replicate 3

source_name: Dgcr8 knockout mouse oocytes collected 16 h post-hCG (human chorionic gonadotropin) injection

value: Dgcr8 knockout


title: Dgcr8 knockout MII-stage oocytes, biological replicate 1


title: Gonad_RESTvsSWIM_20days


title: C. elegans N2_Y. pestis KIM5_24h_Sample B

source_name: C. elegans N2_Y. pestis KIM5_24h

value: Yersinia pestis (24h)


title: Dgcr8 knockout MII-stage oocytes, biological replicate 2


title: C. elegans N2_E. coli OP50_24h_Sample A


title: wild-type MII-stage oocytes, biological replicate 2


title: C. elegans N2_Y. pestis KIM5_24h_Sample C


title: C. elegans N2_Y. pestis KIM5_24h_Sample A


title: wild-type MII-stage oocytes, biological replicate 1


title: C. elegans N2_E. coli OP50_24h_Sample B


title: M202 at day 1, biological rep2

status: Public on Feb 04 2010

city: Riverside

first: Takeshi

last: Fukao

address: Department of Botany and Plant Sciences

institute: University of California, Riverside

description: Microarray data from aerial tissue of 1 d submerged M202

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized in the Affymetrix Hybridization Oven 640 for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G .

data_processing: The data were analyzed by use of the R program and Bioconductor packages. We used the GC-RMA method for normalization. MAS5 present calls were obtained in order to remove absent probe sets. We considered a gene as absent when it did not contain a P call in all replicates of at least one sample set.

organism: Oryza sativa

source_name: M202, submerged for 1 d

label_protocol: Biotinylated cRNA were prepared by use of One-Cycle Target Labeling and Control Reagents according to the standard Affymetrix protocol from 8 μg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Pregerminated seeds were transplanted into soiled pots (L x W x H: 10 cm x 10 cm x 8 cm; 25 plants/pot) and grown in a greenhouse for 14 d (30 degree C, natural light).

extract_protocol: Total RNA was extracted by using QIAGEN RNasy Plant Mini kit according to the manufacture's protocol.

treatment_protocol: Fourteen-d-old plants were completely submerged in deionized water (water level, 90 cm)  at 1 PM. Upon 24 h of treatment, aerial tissue was harvested and immediately frozen in liquid nitrogen.

value: aerial tissue

tag: germplasm

tag: genome/variation

value: Sub1A -

value: 14 d old

tag: treatment group

value: submerged


title: M202(Sub1) at day 1, biological rep2

description: Microarray data from aerial tissue of 1 d submerged M202(Sub1)

source_name: M202(Sub1), submerged for 1 d

value: Sub1A +


title: M202 at day 0, biological rep1

description: Microarray data from aerial tissue of non-submerged M202

source_name: M202, non-submerged

value: non-submerged


title: M202(Sub1) at day 0, biological rep2

description: Microarray data from aerial tissue of non-submerged M202(Sub1)

source_name: M202(Sub1), non-submerged


title: M202 at day 0, biological rep2


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 122)

city: Rochester

first: LIANG

last: WANG

state: MN

address: 200 FIRST ST SW

department: LAB MED PATH

institute: MAYO CLINIC

description: cell line from a patient with prostate cancer

scan_protocol: Illumina BeadArray reader

data_processing: We first transformed raw data generated from BeadStudio (Illumina, San Diego, CA) using a variance stabilization transformation algorithm and then normalized them using quantile normalization implemented in Bioconductor (www.bioconductor.org).

organism: Homo sapiens

label_protocol: 500ng of total RNA was labled using Illumina human-6 V2 BeadChip standard protocol

growth_protocol: We then grew all transformed cell lines in RPMI 1640 media supplemented with 15% fetal bovine serum, and 1% penicillin/streptomycin at 37°C in humidified incubators in an atmosphere of 5% CO2. Experimental series were set up by seeding 5-ml cultures in T25 flasks. Each culture was fed with 5ml of fresh media twice a week until the cell number reached ~106 in a T75 flask. The cells were harvested and suspended in 500 l of RNAlater and stored at -80°C for further processing.

extract_protocol: We extracted total RNA from each cell culture using miRNeasy Mini Kit (QIAGEN) under the manufacturer’s guidelines. This protocol could effectively recover both mRNA and miRNA. The integrity of these total RNAs was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Natural grown cell lines without any treatment

tag: cell line

tag: pathological grade

value: high grade


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 119)

hyb_protocol: Illumina human-6 V2 BeadChip standard protocol


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 123)


title: M202(Sub1) at day 1, biological rep1

tag: tissue


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 110)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 120)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 117)


title: M202 at day 1, biological rep1


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 125)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 116)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 114)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 115)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 111)


title: M202(Sub1) at day 0, biological rep1


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 109)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 108)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 124)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 113)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 112)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 105)

value: low grade


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 118)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 106)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 107)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 121)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 103)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 102)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 101)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 104)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 100)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 97)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 94)


title: Ctrl rep_6

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

hyb_protocol: Hybridization was done for 17 hours at 45oC at 60rpm according to the instructions in the Affymetrix Hybridization, Wash and Stain Kit. Fluidics station protocol FS450_0001 was used for the washing and staining

scan_protocol: GeneChip scanner 3000 7G was used for the scanning, and AGCC was used for image processing

data_processing:
Splicing analysis: Summarization Algorithm: Exon RMA16 Transcript Level; CoreProbeset Level; Affymetrix Exon Expression Chip Hu-Ex-1_0-st-v2; Normalization: Quantile
Gene Analysis: Summarization Algorithm: ExonRMA16; Meta probeset level: CORE Technology: Affymetrix.ExonExprChip.HuEx-1_0-st-v2; Normalization: None
The data in the VALUE column are log2 normalized values from GeneSpring X algorithm.

label: Biotin

source_name: Ctrl, peripheral blood

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit was used for the labeling of fragmented cDNA.

extract_protocol: Samples were treated with Ribo-minus Kit from Invitrogen according to the manufacturing instructions, cDNA was synthesized using Affymetrix GeneChip WT cDNA synthesis Kit. After cleaning of cDNA and in vitro transcription the second round first strand of cDNA was synthesized, cleaned and fragmented according to the manufacturer instructions.

tag: gender

value: male

tag: disease state


title: Ctrl rep_9


title: Ctrl rep_11

value: female


title: Ctrl rep_8


title: Ctrl rep_3


title: Ctrl rep_7


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 91)


title: Ctrl rep_10


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 98)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 99)


title: PD rep18

source_name: PD, peripheral blood

value: Parkinson's Disease


title: Ctrl rep_12


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 96)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 93)


title: PD rep17


title: Ctrl rep_5


title: Ctrl rep_4


title: PD rep14


title: Ctrl rep_2


title: PD rep16


title: PD rep13


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 95)


title: PD rep15


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 92)


title: PD rep12


title: PD rep11


title: PD rep7


title: PD rep6


title: PD rep9


title: PD rep8


title: PD rep2


title: MSC-HIP_donor6-85yrs_P10

type: genomic

city: Heidelberg

first: Simone

last: Bork

address: INF 410

department: Department of Medicine V

institute: University Hospital of Heidelberg

description:
alternatively named mesenchymal stem cells
MSC-HIP_85yrs

hyb_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA.

scan_protocol: The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.

data_processing: Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background normalized.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor6 (85 years old) - passage 10

label_protocol: Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo research Corporation, Orange, US). This step leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine. After bisulfate conversion each sample was whole genome amplified and enzymatically fragmented.

growth_protocol:
Human bone marrow samples were taken from the caput femoris from healthy donors (HIP) undergoing femoral head prosthesis.  All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. The mononuclear cell fraction was isolated by ficoll density fractionation and then taken into culture.
The culture conditions have been first described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625) and in our previous work (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use. MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

extract_protocol: Genomic DNA of 10(6) MSC was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.

treatment_protocol: Cells were harvested by trypsination after passage 10.

value: mesenchymal stromal cells from human bone marrow

tag: age

value: 85 year old human donor

tag: cell passage


title: PD rep5


title: MSC-HIP_donor1-79yrs_P2

description:
alternatively named mesenchymal stem cells
MSC-HIP_79yrs

data_processing: Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background  normalized.

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor1  (79 years old) - passage 2

growth_protocol:
Human bone marrow samples were taken from the caput femoris from elderly donors (HIP) undergoing femoral head prosthesis.  All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. The mononuclear cell fraction was isolated by ficoll density fractionation and then taken into culture.
The culture conditions have been first described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625) and in our previous work (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use. MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

treatment_protocol: Cells were harvested by trypsination after passage 2.

value: 79 year old human donor


title: MSC-HIP_donor8-85yrs_P8

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor8 (85 years old) - passage 8

treatment_protocol: Cells were harvested by trypsination after passage 8.


title: PD rep3


title: MSC-BM_donor277-21yrs_P11

description:
alternatively named mesenchymal stem cells
MSC-BM_21yrs

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor277 (21 years old) - passage 11

growth_protocol:
Human bone marrow samples were taken from the iliac crest (BM) of healthy donors . All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. The mononuclear cell fraction was isolated by ficoll density fractionation and then taken into culture.
The culture conditions have been first described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625) and in our previous work (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use. MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

treatment_protocol: Cells were harvested by trypsination after passage 11.

value: 21 year old human donor


title: MSC-BM_donor300-24yrs_P2

description:
alternatively named mesenchymal stem cells
MSC-BM_24yrs

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor300 (24 years old) - passage 2

value: 24 year old human donor


title: PD rep1


title: MSC-HIP_donor1-79yrs_P15

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor1  (79 years old) - passage 15

treatment_protocol: Cells were harvested by trypsination after passage 15.


title: Low N vs Medium N rep2 dye swap_A210

city: Urbana

first: Stephen

middle: Patrick

last: Moose

state: IL

address: 1201 W Gregory

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

description: Low N vs Medium N rep2 dye swap

hyb_protocol: Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Zea mays

source_name: IBMRI MO087 x IHP1

label_protocol: The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.

extract_protocol: Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse,  then Rneasy purification kit (Qiagen, Valencia, CA).

value: at Anthesis

value: Earshoot

tag: nitrogen condition

value: Medium N

value: Low N


title: PD rep4


title: MSC-HIP_donor7-53yrs_P10

description:
alternatively named mesenchymal stem cells
MSC-HIP_53yrs

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor7 (53 years old) - passage 10

tag: cell type

value: 53 year old human donor


title: MSC-HIP_donor6-85yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor6 (85 years old) - passage 2


title: MSC-HIP_donor7-53yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor7 (53 years old) - passage 2


title: Low N vs High N rep3 dye swap_A211

description: Low N vs High N rep3 dye swap

source_name: IBMRI MO250 x IHP1

value: High N


title: MSC-BM_donor279-25yrs_P2

description:
alternatively named mesenchymal stem cells
MSC-BM_25yrs

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor279 (25 years old) - passage 2

value: 25 year old human donor


title: MSC-HIP_donor8-85yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor8 (85 years old) - passage 2


title: MSC-BM_donor279-25yrs_P11

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor279 (25 years old) - passage 11


title: MSC-BM_donor300-24yrs_P14

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor300 (24 years old) - passage 14

treatment_protocol: Cells were harvested by trypsination after passage 14.


title: MSC-BM_donor275-50yrs_P10

description:
alternatively named mesenchymal stem cells
MSC-BM_50yrs

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor275 (50 years old) - passage 10

value: 50 year old human donor


title: Low N vs High N rep3_A212

description: Low N vs High N rep3


title: MSC-BM_donor277-21yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor277 (21 years old) - passage 2


title: Low N vs High N rep3_B187

description: Low N vs High N rep3


title: Low N vs Medium N rep2_A209

description: Low N vs Medium N rep2


title: Low N vs High N rep3 dye swap_B188

description: Low N vs High N rep3 dye swap


title: Low N vs Medium N rep2_B185

description: Low N vs Medium N rep2


title: Low N vs Medium N rep2 dye swap_B186

description: Low N vs Medium N rep2 dye swap


title: MSC-BM_donor275-50yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor275 (50 years old) - passage 2

treatment_protocol: Cells were harvested by trypsination after passage 2


title: Low N vs High N rep2 dye swap_A200

description: Low N vs High N rep2 dye swap


title: Low N vs High N rep1 dye swap_A199

description: Low N vs High N rep1 dye swap

source_name: IBMRI MO009 x IHP1


title: Low N vs Medium N rep1 dye swap_B182

description: Low N vs Medium N rep1 dye swap


title: Tissue spatial point 4, biological rep2

city: Kansas City

first: Olivier

last: Pourquie

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

description: Gene expression data from the fourth spatiotemporal position along the axis

hyb_protocol: Each chip was hybridized to 13 μg fragmented cRNA. Arrays were hybridized according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned with a Affymetrix GeneChip Scanner 3000 7G at the Microarray Core Facility of the Stowers Institute for Medical Research

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Danio rerio

source_name: Zebrafish embryos paraxial mesoderm

label_protocol: Biotinylated cRNA were prepared by using Affymetrix GeneChip Expression 3'-Amplification Reagents for IVT Labeling kit.

growth_protocol: Wild type embryos from AB line were grown at 23C° untill 12-somite stage.

extract_protocol: Trizol extraction of total RNA was performed.

treatment_protocol: Embryos were manually dechorionated at room temperature (24C°). Selected embryos were transferred to a basket in L15 media. Embryos were manually dissected and the tissue sections were placed in the Trizol solution (Invitrogen) and frozen immediately on dry ice and stored at -80C°.

value: center PSM

tag: genotype

value: wild-type AB

value: 12-somite stage


title: Tissue spatial point 5, biological rep2

description: Gene expression data from the fifth spatiotemporal position along the axis

value: anterior PSM


title: Low N vs Medium N rep1_A198

description: Low N vs Medium N rep1


title: Low N vs Medium N rep1 dye swap_A196

description: Low N vs Medium N rep1 dye swap


title: Low N vs High N rep2_A208

description: Low N vs High N rep2


title: Tissue spatial point 4, biological rep1


title: Tissue spatial point 3, biological rep2

description: Gene expression data from the third spatiotemporal position along the axis

value: posterior PSM


title: Tissue spatial point 6, biological rep1

description: Gene expression data from the sixth spatiotemporal position along the axis

value: The last formed two somites


title: Tissue spatial point 5, biological rep1


title: Low N vs High N rep3 dye swap_A182

description: Low N vs High N rep3 dye swap

source_name: IBMRI MO340 X IHP1


title: Low N vs Medium N rep1_B181

description: Low N vs Medium N rep1


title: Low N vs High N rep3 dye swap_B163

description: Low N vs High N rep3 dye swap


title: Low N vs High N rep1_A197

description: Low N vs High N rep1


title: Low N vs High N rep1 dye swap_B180

description: Low N vs High N rep1 dye swap


title: Low N vs High N rep2_B184

description: Low N vs High N rep2


title: Low N vs High N rep2 dye swap_B183

description: Low N vs High N rep2 dye swap


title: Low N vs High N rep2 dye swap_A180

description: Low N vs High N rep2 dye swap

source_name: IBMRI MO289 X IHP1


title: Tissue spatial point 6, biological rep2


title: Low N vs High N rep3_B162

description: Low N vs High N rep3


title: Tissue spatial point 3, biological rep1


title: Tissue spatial point 2, biological rep2

description: Gene expression data from the second spatiotemporal position along the axis

value: right side flanking tailbud


title: Low N vs High N rep2 dye swap_B160

description: Low N vs High N rep2 dye swap


title: Low N vs High N rep1_B179

description: Low N vs High N rep1


title: Low N vs High N rep3_A181

description: Low N vs High N rep3


title: Tissue spatial point 2, biological rep1

value: left side flanking tailbud


title: Low N vs High N rep2_B159

description: Low N vs High N rep2


title: Low N vs High N rep2_A179

description: Low N vs High N rep2


title: Low N vs High N rep1 dye swap_A178

description: Low N vs High N rep1 dye swap

source_name: IBMRI MO264 X IHP1


title: Low N vs High N rep1 dye swap_B158

description: Low N vs High N rep1 dye swap


title: Low N vs High N rep1_A177

description: Low N vs High N rep1


title: Tissue spatial point 1, biological rep2

description: Gene expression data from the first spatiotemporal position along the axis

value: center tailbud


title: Low N vs High N rep1_B156

description: Low N vs High N rep1

value: at Anthesis


title: Tissue spatial point 1, biological rep1


title: RIIIS/J_Male_Nuc_Acc

status: Public on Feb 03 2010

city: Chapel Hill

first: Samantha

middle: Katherine

last: Segall

address: 120 Mason Farm Road

institute: UNC- Chapel Hill

hyb_protocol: cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol

scan_protocol: standard Affymetrix procedures using the GeneChip 3000 scanner

data_processing: data were processed using the gcRMA algorithm, as described in Wu. Z et al. 2004

source_name: pooled tissue, Nucleus Accumbens, 8-10 week old, male, (n=3)

label_protocol: RNA was amplified and labeled using the Affymetrix one-cycle target labeling kit.

growth_protocol: Eight to ten week old male mice of each strain were purchased from the Jackson Laboratory (Bar Harbor, ME, USA).  The mice were habituated for one week prior to tissue collection. Animals were housed in an SPF barrier colony. Animals were maintained on a 12-h light: 12-h dark cycle, housed in groups of 2Ð4 in standard high efficiency particulate air-filtered polycarbonate mouse cages containing a layer of Bed-o-cob bedding and one cotton nestlet. Food (Pico rodent chow 20; Purina, St Louis, MO, USA) and water were made available ad libitum.

extract_protocol: After dissection, tissues were immediately frozen on dry ice and stored in a -80 freezer until RNA preparation.  Tissues were pulverized to a fine powder while frozen to obtain a mixture of homogeneous tissue.  A small (~10mg) aliquot was homogenized using a rotor-stator (Omni TH polytron) homogenizer in Trizol (Invitrogen) and total RNA purified with RNeasy columns (Qiagen).

value: male

value: Nucleus Accumbens

tag: strain

value: RIIIS/J


title: SWR/J_Male_Nuc_Acc

value: SWR/J


title: SJL/J_Male_Nuc_Acc

value: SJL/J


title: NOD/LtJ_Male_Nuc_Acc

value: NOD/LtJ


title: P/J_Male_Nuc_Acc

value: P/J


title: PL/J_Male_Nuc_Acc

value: PL/J


title: SM/J_Male_Nuc_Acc

value: SM/J


title: CBA/J_Male_Nuc_Acc

value: CBA/J


title: MA/MyJ_Male_Nuc_Acc

value: MA/MyJ


title: NZW/LacJ_Male_Nuc_Acc

value: NZW/LacJ


title: FVB/NJ_Male_Nuc_Acc

value: FVB/NJ


title: NON/LtJ_Male_Nuc_Acc

value: NON/LtJ


title: KK/HlJ_Male_Nuc_Acc

value: KK/HlJ


title: DBA/2J_Male_Nuc_Acc


title: C57BR/cdJ_Male_Nuc_Acc


title: C58/J_Male_Nuc_Acc


title: C57BL/6J_Male_Nuc_Acc


title: BTBR_T+_tf/J_Male_Nuc_Acc


title: BUB/BnJ_Male_Nuc_Acc

value: BUB/BnJ


title: WSB/EiJ_Male_Nuc_Acc

value: WSB/EiJ


title: CE/J_Male_Nuc_Acc

value: male

value: CE/J


title: PL/J_Male_Frontal_Cortex

source_name: pooled tissue, Prefrontal Cortex, 8-10 week old, male, (n=3)

value: Frontal Cortex


title: A/J_Male_Nuc_Acc

value: Nucleus Accumbens

value: A/J


title: SM/J_Male_Frontal_Cortex


title: SWR/J_Male_Frontal_Cortex

value: SWR/J


title: SJL/J_Male_Frontal_Cortex

value: SJL/J


title: 129S1/SvImJ_Male_Nuc_Acc


title: BALB/cByJ_Male_Nuc_Acc

value: BALB/cByJ


title: P/J_Male_Frontal_Cortex

value: P/J


title: C3H/HeJ_Male_Nuc_Acc


title: NZW_LacJ_Male_Frontal_Cortex


title: AKR/J_Male_Nuc_Acc

value: AKR/J


title: NOD/LtJ_Male_Frontal_Cortex

value: NOD/LtJ


title: MRL_MpJ_Male_Frontal_Cortex

value: MRL/MpJ


title: MA/MyJ_Male_Frontal_Cortex

value: MA/MyJ


title: SSArray10

first: Thierry

last: Janssens

address: de Boelelaan 1085

department: Ecological Sciences

institute: VU  University Amsterdam

description: Pool of approximately thirty animals of F.candida

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma (2.9.2) package in the R (2.18.3) software environment (http://www.r-project.org/), which consisted of normexp background correction (set off = 30), global loess normalization and between array normalization (Aquantile).

source_name: Cladosporium cladosporoides diet

label_protocol: 500 ng input was used for amplification and labeling with the Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

treatment_protocol: fed to the diet mentioned in source name

value: Berlin

value: 28 days

source_name: Mixed diet 2


title: CBA/J_Male_Frontal_Cortex

value: CBA/J


title: KK/HlJ_Male_Frontal_Cortex

value: KK/HlJ


title: I/LnJ_Male_Nuc_Acc

value: male

value: I/LnJ


title: I/LnJ_Male_Frontal_Cortex

value: Frontal Cortex


title: DBA/2J_Male_Frontal_Cortex


title: NON/LtJ_Male_Frontal_Cortex

value: NON/LtJ


title: RIIIS/J_Male_Frontal_Cortex

value: RIIIS/J


title: SSArray9

source_name: Aspergillus nidulans WT diet


title: CE/J_Male_Frontal_Cortex

value: CE/J


title: C58/J_Male_Frontal_Cortex


title: NZO/HILtJ_Male_Frontal_Cortex

value: NZO/HILtJ


title: SSArray4

source_name: Mixed diet 1


title: WSB/EiJ_Male_Frontal_Cortex

value: WSB/EiJ


title: SSArray7

source_name: Aspergillus nidulans  ΔLaeA diet


title: SSArray2


title: SSArray6


title: C57BR/cdJ_Male_Frontal_Cortex


title: BTBR_T+_tf/J_Male_Frontal_Cortex


title: SSArray8


title: FVB/NJ_Male_Frontal_Cortex

value: FVB/NJ


title: BUB/BnJ_Male_Frontal_Cortex

value: BUB/BnJ


title: SSArray5


title: C57BL/6J_Male_Frontal_Cortex


title: AKR/J_Male_Frontal_Cortex

value: AKR/J


title: C3H/HeJ_Male_Frontal_Cortex


title: OSRISARRAY16

source_name: solvent control

treatment_protocol: exposed for 2 days in a jar containing LUFA 2.2 soil spiked with the compound from source

value: 25 days old

source_name: 3,5-dichloroaniline 76.8 μmole/kg soil (EC50)


title: OSRISARRAY14

source_name: pentachloroaniline 163.8 μmole/kg soil (EC50)

source_name: aniline 77.7 μmole/kg soil (EC50)


title: SSArray1


title: OSRISARRAY13

source_name: 2,3,5,6-tetrachloroaniline 120.3 μmole/kg soil (EC50)


title: 129S1/SvImJ_Male_Frontal_Cortex


title: A/J_Male_Frontal_Cortex

value: A/J


title: OSRISARRAY15

source_name: 1,2,3,4-tetrachlorobenzene 163.8 μmole/kg soil (EC50)

value: Berlin

source_name: 4-chloroaniline 74.8 μmole/kg soil (EC50)


title: stellate_sympathetic_ganglia_8-weeks-TAC_A

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

description: The whole procedure was carried out according to the Affymetrix standard protocol (Eukaryotic Sample and Array Processing).

hyb_protocol: 10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

scan_protocol: The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

source_name: stellate sympathetic ganglia, 8 weeks TAC

label_protocol: Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

extract_protocol: Total RNA from bothh stellate sympathetic ganglia of one animal was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany).

value: Male


title: OSRISARRAY12

source_name: 2,3,4-trichloroaniline 101.8 μmole/kg soil (EC50)


title: OSRISARRAY21


title: BALB/cByJ_Male_Frontal_Cortex

value: BALB/cByJ


title: stellate_sympathetic_ganglia_sham_C

source_name: stellate sympathetic ganglia, sham


title: OSRISARRAY11


title: OSRISARRAY8


title: stellate_sympathetic_ganglia_sham_B


title: OSRISARRAY7


title: Zebrafish embryo, MBT, rep. 3

city: Oslo

first: Håvard

last: Aanes

state: Oslo

address: Ullevålsveien 72

department: Biochemistry

country: Norway

institute: Norwegian School of Veterinary Science

description: Gene expression in 3.5 hpf embryos

hyb_protocol: Arrays were hybridized (Agilent Hybridization kit, cat. No 5188-5242) for 17 hours (65 °C) and washed before scanning as per the protocol recommended by Agilent  (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Ver.5.7, March 2008).

scan_protocol: Arrays were scanned using Agilent Technologies Scanner G2505B US45103038 with 5 microns resolution (scan protocol GE1-v5_95_Feb07). Scan area: 61 x 21.6 mm. Grid name: 021643_D_F_20081005. Using the 16 bit tif images generated, feature extraction was performed using Feature Extraction Software 9.5.3 (Agilent Technologies, Inc., CA, USA), with background detrend (FeatNCRange, LoPass) and Multiplicative Detrend.

data_processing: The gProcessed signals from feature extraction were imported into the R-environment (http://cran.r-project.org/). The two groups were normalized separately, using quantile normalization (Bolstad, 2003). The genes of interest were extracted from the dataset. Where there were multiple probes for a single transcript or replicate probes, these were aggregated using the median value (only the genes of interest). These merged intensity values were then log2-transformed and mean and standard deviation were calculated.

source_name: Whole embryo

label_protocol: Total RNA (400 ng) and spike-in control RNA was converted to cDNA, followed by cRNA synthesis and amplification, and then purification of cRNA using Agilent's Quick Amp labeling Kit (Product Cat. No: 5190_0442). We followed the protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Ver.5.7, March 2008; Manual Pat Number:G4140-90040). This method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- labeled CTP which generates cy3 labeled fluorescent cRNA.

growth_protocol: The zebrafish was kept in 28 degrees under standard procedures (zebrafish.no).

extract_protocol: 100 embryos at the time were crushed in a mortar with liquid nitrogen. 2 ml trizol (Triazol reagent fom Invitrogen, CA, U.S.A) was added and the content was transferred to a 15 ml tube and incubated 5 min at RT. 400 μl chloroform was added, embryos were shaken by hand for 15 seconds and further incubated 2-3 min at RT.  The lysate was centrifuged (10000 rpm, 10 min, 4ºC), the upper phase was transferred to a new tube, 1 μL glycogen added and RNA was precipitated with 1 mL isopropanol for 10 min at RT before centrifugation (10000 rpm, 10 min, 4ºC) the supernatant was discarded and the pellet washed with 75 % ice-cold ethanol. The samples were then dissolved and treated with DNase and RNeasy (Qiagen; 74104/6).

treatment_protocol: 0 hpf embryos (unfertilized eggs) were collected immediatly after spawning and snap-frozen in dry-ice ethanol bath and stored at -80 oC. MBT embryos were incubated at 28ºC for 3.5 h prior to harvest and snap-freezing.

tag: developmental stage

value: 3.5 hpf

value: Whole embryo


title: Zebrafish embryo, MBT, rep. 4

description: Gene expression in 3.5 hpf embryos


title: stellate_sympathetic_ganglia_8-weeks-TAC_C


title: stellate_sympathetic_ganglia_sham_A


title: OSRISARRAY6

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).


title: daf-2(e1370) xbp-1 vs daf-2(e1370)_4

city: Ramat Gan

first: sivan

last: korenblit

address: Ramat Gan

department: life sciences

country: Israel

institute: Bar-Ilan University

description: total RNA from day 1 animals

hyb_protocol: Arrays were hybridised using the Hi-RPM hybridization kit according to manufacturer's instructions. Protocols available from www.agilent.com.

scan_protocol: Scanning was performed on G2565BA DNA Scanner and feature extraction was made by FE software Version 9.5 (Agilent) using extraction protocol GE2-v5_95_Feb07.

data_processing: Lowess normalization and analysis was performed in GeneSpring (Agilent Technologies). Arrays were first filtered to remove features which were at or below average background signal.

label_protocol: Arrays labelled using the Agilent QuickAmp Kit according to manufacturer's instructions. Protocols available from www.agilent.com.

growth_protocol: Eggs were synchronized by bleaching, grown at 20 degrees and harvested as day-1 adults (after 72 hours for e1368 mutants, after 96 hours for e1370 mutants).

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

value: day 1


title: Zebrafish embryo, MBT, rep. 1

description: Gene expression in 3.5 hpf embryos


title: Zebrafish embryo, MBT, rep. 2

description: Gene expression in 3.5 hpf embryos


title: daf-2(e1370) xbp-1 vs daf-2(e1370)_3

description: total RNA from day 1 animals


title: CD34+ cells_C [Exon-Level core analysis, Affymetrix Expression Console v1.1]

city: montpellier

first: tondeur

last: sylvie

address: 80 avenue augustin fliche

department: hopital saint eloi

country: France

institute: IRB

description: CD34+ cells_C

hyb_protocol: Hybridization was processed according manufacturer's intructions (http://www.affymetrix.com/products/arrays/specific/exon.affx)

scan_protocol: Probe arrays were scanned using the Affymetrix GCOS 3000 7G and the Gene-Chip Operating Software v.1.4 to obtain the .CEL files

data_processing: Expression signal values and p-values were obtained from .cel files for each probeset using the Robust Microarray Analysis (RMA) Exon-Level core analysis with Affymetrix Expression Console v1.1

source_name: mobilized CD34+ cells from cytapheresis

label_protocol: Ribosomal RNA reduction, first and double strand cDNA synthesis, cRNA synthesis, second round single-strand (ss) cDNA synthesis, ss-cDNA fragmentation and labelling were processed following the manufacturers instructions (http://www.affymetrix.com/products/arrays/specific/exon.affx).

extract_protocol: Blood samples were collected by venipuncture from 4 healthy subjects in PAXgene collection tubes (PreAnalytix/Qiagen, Courtaboeuf, France) after informed consent. Total RNA was then extracted with PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France), including DNase I treatment. Hematopoietic stem cells provided from 3 patients suffering multiple myeloma and undergoing autologous stem cell transplantation after informed consent. CD34+ cells were sorted by flow cytometry. RNA purity and integrity was assessed by capillary electrophoresis using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and the 2100 Expert software.

value: mobilized CD34+ cells from cytapheresis


title: stellate_sympathetic_ganglia_8-weeks-TAC_B


title: OSRISARRAY3

city: Amsterdam


title: OSRISARRAY5


title: OSRISARRAY1


title: Zebrafish, Egg, rep. 2

description: Gene expression in unfertilized eggs

source_name: Egg

value: 0 hpf

value: Egg


title: daf-2(e1368) xbp-1 vs daf-2(e1368)_1

description: total RNA from day 1 animals


title: OSRISARRAY17


title: OSRISARRAY20


title: Zebrafish, Egg, rep. 1

description: Gene expression in unfertilized eggs


title: daf-2(e1368) xbp-1 vs daf-2(e1368)_4

description: total RNA from day 1 animals


title: CD34+ cells_B [Exon-Level core analysis, Affymetrix Expression Console v1.1]

description: CD34+ cells_B


title: CD34+ cells_A [Exon-Level core analysis, Affymetrix Expression Console v1.1]

description: CD34+ cells_A


title: Zebrafish, Egg, rep. 3

description: Gene expression in unfertilized eggs


title: daf-2(e1370) xbp-1 vs daf-2(e1370)_2

description: total RNA from day 1 animals


title: daf-2(e1368) xbp-1 vs daf-2(e1368)_3

description: total RNA from day 1 animals


title: daf-2(e1368) xbp-1 vs daf-2(e1368)_2

description: total RNA from day 1 animals


title: SSArray3

source_name: Mixed diet 2

value: 28 days


title: Whole_Blood_C [Exon-Level core analysis, Affymetrix Expression Console v1.1]

source_name: whole blood cells (leucocytes, platelets and reticulocytes)


title: Whole_Blood_D [Exon-Level core analysis, Affymetrix Expression Console v1.1]

value: whole blood cells (leucocytes, platelets and reticulocytes)


title: daf-2(e1370) xbp-1 vs daf-2(e1370)_1

description: total RNA from day 1 animals


title: UF936_Root-Rep1

status: Public on Feb 02 2010

city: Gainesville

first: Matias

last: Kirst

institute: University of Florida

description: Gene expression measured from RNA extracted from root samples collected from individual UF936

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42C overnight (16-20h).

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

data_processing:
Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).
Data was quantile normalized using the Bioconductor Package (Gentleman et al. 2004, Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: R80) in R programming environment (v. 2.4.1; www.r-project.org) and Log2 transformed.

organism: Populus trichocarpa x Populus deltoides

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, root tissue

label_protocol: RNA extracted from each individual in the progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerâ??s protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37C.

extract_protocol: At harvest, the main plant organs (stems, roots, leaves and sylleptic branches) were collected separately. Stems were further dissected into secondary xylem tissue and phloem/bark/immature xylem. Leaf, secondary xylem, and root tissue from two biological replicates of each genotype were selected for gene expression analysis. All tissue was flash-frozen in liquid nitrogen immediately after harvest and stored at -80 Celsius (C) prior to lyophilization and subsequent RNA isolation. RNA was isolated by a standard protocol described previously (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116).

value: root

tag: environmental conditions

value: 25mM supplemental N, long day conditions


title: UF941_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF941

value: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny


title: UF939_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF939


title: UF929_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF929


title: UF934_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF934


title: Whole_Blood_B [Exon-Level core analysis, Affymetrix Expression Console v1.1]


title: UF931_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF931


title: UF927_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF927


title: UF926_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF926


title: Whole_Blood_A [Exon-Level core analysis, Affymetrix Expression Console v1.1]


title: UF924_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF924


title: UF923_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF923


title: UF919_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF919


title: UF921_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF921


title: UF922_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF922


title: UF911_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF911


title: UF91_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF91


title: UF917_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF917


title: UF913_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF913


title: UF912_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF912


title: UF916_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF916


title: UF906_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF906


title: UF883_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF883


title: UF915_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF915


title: UF894_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF894


title: UF886_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF886


title: UF882_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF882


title: UF891_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF891


title: UF920_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF920


title: UF877_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF877


title: UF873_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF873


title: UF871_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF871


title: UF897_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF897


title: UF867_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF867


title: UF914_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF914


title: UF869_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF869


title: UF881_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF881


title: UF879_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF879


title: UF902_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF902


title: UF865_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF865


title: UF863_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF863


title: UF861_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF861


title: UF888_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF888


title: UF859_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF859


title: UF840_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF840


title: UF848_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF848


title: UF844_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF844


title: UF847_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF847


title: UF850_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF850


title: UF824_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF824


title: UF856_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF856


title: UF820_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF820


title: UF833_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF833


title: UF812_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF812


title: UF816_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF816


title: UF814_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF814


title: UF803_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF803


title: UF807_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF807


title: UF802_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF802


title: UF810_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF810


title: UF808_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF808


title: UF836_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF836


title: UF806_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF806


title: UF805_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF805


title: UF800_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF800


title: UF720_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF720


title: UF748_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF748


title: UF723_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF723


title: UF755_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF755


title: UF734_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF734


title: UF705_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF705


title: UF61_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF61


title: UF700_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF700


title: UF715_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF715


title: UF710_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF710


title: UF718_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF718


title: UF69_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF69


title: UF62_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF62


title: UF717_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF717


title: UF884_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF884


title: UF724_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF724


title: UF590_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF590


title: UF722_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF722


title: UF79_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF79


title: UF703_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF703


title: UF66_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF66


title: UF701_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF701


title: UF706_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF706


title: UF7_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF7


title: UF58_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF58


title: UF579_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF579


title: UF547_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF547


title: UF552_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF552


title: UF561_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF561


title: UF539_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF539


title: UF533_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF533


title: UF513_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF513


title: UF570_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF570


title: UF468_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF468


title: UF529_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF529


title: UF491_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF491


title: UF532_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF532


title: UF490_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF490


title: UF457_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF457


title: UF481_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF481


title: UF544_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF544


title: UF546_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF546


title: UF526_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF526


title: UF489_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF489


title: UF477_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF477


title: UF500_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF500


title: UF503_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF503


title: UF456_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF456


title: UF493_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF493


title: UF453_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF453


title: UF909_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF909


title: UF441_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF441


title: UF436_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF436


title: UF435_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF435


title: UF409_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF409


title: UF419_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF419


title: UF392_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF392


title: UF381_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF381


title: UF407_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF407


title: UF383_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF383


title: UF396_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF396


title: UF372_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF372


title: UF402_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF402


title: UF309_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF309


title: UF300_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF300


title: UF380_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF380


title: UF320_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF320


title: UF40_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF40


title: UF32_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF32


title: UF325_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF325


title: UF352_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF352


title: UF35_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF35


title: UF326_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF326


title: UF298_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF298


title: UF437_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF437


title: UF846_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF846


title: UF292_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF292


title: UF285_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF285


title: UF293_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF293


title: UF287_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF287


title: UF266_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF266


title: UF269_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF269


title: UF284_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF284


title: UF254_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF254


title: UF272_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF272


title: UF565_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF565


title: UF229_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF229


title: UF240_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF240


title: UF215_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF215


title: UF231_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF231


title: UF223_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF223


title: UF241_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF241


title: UF939_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF939

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, leaf tissue

value: leaf


title: UF201_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF201


title: UF224_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF224


title: UF209_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF209


title: UF237_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF237


title: UF941_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF941


title: UF936_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF936


title: UF22_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF22


title: UF934_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF934


title: UF217_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF217


title: UF214_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF214


title: UF931_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF931


title: UF919_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF919


title: UF923_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF923


title: UF929_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF929


title: UF924_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF924


title: UF913_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF913


title: UF922_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF922


title: UF927_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF927


title: UF925_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF925


title: UF917_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF917


title: UF912_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF912


title: UF911_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF911


title: UF920_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF920


title: UF902_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF902


title: UF909_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF909


title: UF916_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF916


title: UF921_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF921


title: UF906_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF906


title: UF907_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF907


title: UF926_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF926


title: UF897_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF897


title: UF915_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF915


title: UF91_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF91


title: UF914_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF914


title: UF894_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF894


title: UF891_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF891


title: UF892_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF892


title: UF280_Root-Rep1

description: Gene expression measured from RNA extracted from root samples collected from individual UF280


title: UF882_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF882


title: UF877_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF877


title: UF883_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF883


title: UF879_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF879


title: UF886_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF886


title: UF888_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF888


title: UF865_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF865


title: UF856_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF856


title: UF873_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF873


title: UF848_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF848


title: UF871_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF871


title: UF861_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF861


title: UF867_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF867


title: UF852_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF852


title: UF863_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF863


title: UF869_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF869


title: UF836_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF836


title: UF850_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF850


title: UF859_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF859