title: GRO-JCW26_37 repeat 1

description: In vivo labeled total RNA of JCW28 strain at 37ºC. Replicate 1

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

source_name: Saccharomyces cerevisiae JCW26 (top2ts strain) at 37ºC

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 Ci/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Exponential growth in YPD at 30ºC. Then temperature was changed to 37ºC for 10 min.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

value: JCW26 (top2ts strain)


title: HYB3

status: Public on Feb 28 2010

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

hyb_protocol: according to manufacturer's protocol

scan_protocol: using Agilent Feature Extraction 8.5 Software

data_processing: Subtraction background correction and loess normalisation were applied to the data. Scan-date dependent biases were corrected by subtracting systematic noise across all arrays for each scan date

molecule: genomic DNA

organism: Homo sapiens

label_protocol: according to manufacturer's protocol

extract_protocol: genomic DNA isolated using proteinase-K treatment and phenol chloroform purification

tag: sample type

value: tumour

tag: treatment

value: Post-treatment (Paclitaxel)

tag: patient number

source_name: male pool

value: tissue


title: GRO-JCW26_37 repeat 2

status: Public on Feb 16 2010

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: In vivo labeled total RNA of JCW28 strain at 37ºC. Replicate 2

data_processing: Raw image quantization background subtracted.

molecule: total RNA

organism: Saccharomyces cerevisiae

tag: strain


title: Genomic DNA JCW25 strain

description: Random priming labeled DNA from JCW25 strain.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt’s, 0.5% SDS and 100 µg herring sperm DNA/ml.The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

source_name: Saccharomyces cerevisiae JCW25. Exponential growth in YPD at 30ºC

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol).The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

growth_protocol: Exponentian growth in YPD

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267-272

value: JCW25 (wt)


title: HYB2

value: Pre-treatment


title: TMP- JCW25_30 repeat 3

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 30ºC. Replicate 3

hyb_protocol: The arrays were pre-hybridized with 10 ml UltraHyb solution (Ambion) in a roller oven during 1 h at 46ºC. 33P-dCTP labeled DNA (5x106 dpm/ml) was then added and the hybridization conducted during 16 h at 46ºC. Arrays were washed at 65ºC, once in 2xSSC plus 0.1% SDS for 20 min, and twice in 0.2xSSC plus 0.1% SDS for 30 min.

source_name: JCW25 S. cerevisiae strain

label_protocol: Exonuclease resistant DNA chains were subjected to random priming with the Strip-EZ DNA kit (Ambion), which incorporates a modified dCTP nucleotide that produces easily strippable chains.

growth_protocol: Exponential growth in YPD at 30ºC

extract_protocol: Yeast cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier. Following proteinase K and RNAse I incubations, DNA fragments were extracted twice with phenol and once with phenol-chloroform, precipitated with EtOH, washed with 70% EtOH, and resuspended in 100 µl of water. Genomic DNA fragments were incubated with TMP (0.4 µg/ml) and irradiated (360 nm, at a dose of 1.2 kJ/m2/min during 120 seconds) to produce an amount of crosslinks comparable to that obtained in vivo (1 crosslink/10 kb). Crosslinked fragments were selected by exonuclease digestions: DNA samples were boiled for 2 min, chilled on ice, and then digested with excess Exonuclease I (NE BioLabs) during 4 hours. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess Exonuclease (NE BioLabs) during 6 hours. The reaction terminated by inactivation of the enzyme at 80ºC during 10 min.


title: TMP- JCW25_30 repeat 1

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 30ºC. Replicate 1


title: GRO-JCW26_37 repeat 3

description: In vivo labeled total RNA of JCW28 strain at 37ºC. Replicate 3


city: Rio de Janeiro

first: Marcelo

last: Ribeiro-Alves

state: RJ

address: Avenida Brasil 4365. Manguinhos.

department: Centro de Desenvolvimento Tecnológico em Saúde

country: Brazil

institute: Fundação Oswaldo Cruz

description: Biological replicate 5 of 6. Control thymic epithelial cell, untreated.

hyb_protocol: Hybridization of 15 h followed by washing was performed in an automated slide processor (ASP, Amersham Biosciences).

scan_protocol: The slides were scanned in a Generation III laser scanner (Amersham Biosciences).

data_processing: print-tip LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Bioconductor/R limma package was used.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 5

label_protocol: The cDNA complex probes were prepared by reverse transcription using 10 µg of total RNA from controls or CD49e silenced TECs which were labeled using CyScribe post-labeling kit (Amersham Biosciences, England), and oligo dT12–18 as a primer.

growth_protocol: TEC cells were cultured in 10% fetal bovine serum-supplemented RPMI 1640 medium at 37oC in a 5% CO2 atmosphere.

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

treatment_protocol: We transfected two siRNAs (Qiagen, Hilden, Germany), one scramble, this siRNA is not complementary to any gene in mammals, other siRNA, was designed to specifically silence the expression of integrin alpha5 subunit, CD49e-siRNA. Semi-confluent cultures of human TECs cell line were transiently transfected with 2.5 nM of CD49e-siRNA or scramble siRNA using Hiperfect reagent (Qiagen) in 24 well plates, following manufacturer’s instructions.Forty-eight hours after transfection we made RNA extraction for cDNA microarray.

tag: cell line

value: thymic epithelial cell line

value: no treatment

source_name: Jurkat, Hela, Hep-2 and U343

value: Jurkat, Hela, Hep-2 and U343 mix


title: GRO-JCW25_37 repeat 3

description: In vivo labeled total RNA of JCW25 strain at 37ºC. Replicate 3

source_name: Saccharomyces cerevisiae JCW25 (wt strain) at 37ºC


title: GRO-JCW25_37 repeat 1

description: In vivo labeled total RNA of JCW25 strain at 37ºC. Replicate 1


title: GRO-JCW25_37 repeat 2

description: In vivo labeled total RNA of JCW25 strain at 37ºC. Replicate 2


title: GRO-JCW28_37 repeat 3

source_name: Saccharomyces cerevisiae JCW28 (top1 top2ts strain) at 37ºC

value: JCW28 (top1 top2ts strain)


title: GRO-JCW28_37 repeat 1


title: GRO-JCW25_30 repeat 2

description: In vivo labeled total RNA of JCW25 strain at 30ºC. Replicate 2.


title: GRO-JCW25_30 repeat 3

description: In vivo labeled total RNA of JCW25 strain at 30ºC. Replicate 3.

source_name: Exponential growth in YPD at 30ºC


title: TMP- JCW25_37 repeat 2

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 37ºC. Replicate 2

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager

growth_protocol: Exponential growth in YPD at 30ºC. Then 10 min at 37ºC


title: GRO-JCW28_37 repeat 2


title: GRO-JCW25_30 repeat 1

description: In vivo labeled total RNA of JCW25 strain at 30ºC. Replicate 1.

growth_protocol: Exponential growth in YPD


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0054)

status: Public on Feb 14 2010

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

country: Canada

institute: Lady Davis Institute for Medical Research (JGH)

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Packard BioChip (QuantArray) and Axon 2000B (GenePix) scanners Images were quantified using Quantarray or GenePix Software.

data_processing: LOWESS normalization with background subtraction was applied to the data obtained from log2 of processed Red signal/processed Green signal. Gene Traffic Software (Iobion) was used for primary analysis.

source_name: CD4+ T-cells isolated from HTLV-1 infected patients

label_protocol: Direct Labelling protocol fron OCI-UHN, ImmunoArray2, http://www.microarrays.ca/info/protocols/DirectLabelling.pdf

extract_protocol: Total RNA extracted using Trizol or Rneasy (Qiagen) following manufacturer's instructions

tag: disease state

value: Neurological disorder tropical spastic paraparesis (HAM/TSP)

tag: source

value: Donor from Guyana

tag: cell type

value: HTLV-1 Infected PBMC cells

tag: gender

value: CD4+ T-Cells Isolated from HTLV-1 infected PBMC

source_name: Universal Human Reference RNA

value: reference RNA


title: Csac grown on glucose vs switchgrass for biomass loop

status: Public on Feb 15 2010

city: Raleigh

first: Amy

last: VanFossen

state: NC

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

country: USA

institute: NC State Unversity

description: Scatterplots were used to verify overall quality of the data making sure both channels are equal.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer:  27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC.

scan_protocol: Images were aquired with a scanarray 5000 (PE) scanner with 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards.

data_processing: Signals for each channel were obtained using ScanArray express and were background substrated using the median local intensity around the spot.

label: Cy™3 dye (GE Healthcare)

organism: Caldicellulosiruptor saccharolyticus

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70 degree C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix.  Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III  [Invitrogen]. dNTP mix:  3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) [Ambion], 6.8uL nuclease free water. Incubate at 46 degree C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65 degree C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 5,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate at room temp. for 1 min.  Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0.  Mix up and down with pipette for good mixing. Dissolve and mix thoroughly the Cy™ dye to be used with 20uL of DMSO. Typically Cy dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column  with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O.

growth_protocol: C. saccharolyticus was subcultured (overnight) 7 times on the substrate of interest in modified DSMZ 640 medium before inoculating 0.4-liter culture containing 0.5 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (cell density 3-5*10^-7)

extract_protocol: RNA Isolation Protocol: Collect all 400mL of  cells into precooled centrifuge tubes and cool down in a dry ice and ethanol back. Spin down 10 min at 6500 rpm at 4 ºC. Store pellets at -80 ºC (at least overnight). Resuspend in 1 ml Trizol and transfer to new eppindoff tube.  Then sonicate for 10 seconds and incubate for 5 min at room temperature. Add 0.2 ml chloroform, shake for 15 second and incubate for 5 min at room temperature. Spin down for 15 min at 10.000 rpm at 4 ºC. Transfer aqueous phase to new tube. Add an equal amount of 70% EtOH. Transfer the sample to an RNeasy spin column. Close lid and centrifuge for 15 sec at 10.000 RPM. After centrifugation, carefully remove the spin column form the collection tube so that the column does not contact the flow-through. Pipet the DNase I incubation mix (10 ul DNase I stock and 70 ul RDD buffer) directly onto the RNeasy membrane and incubate at room temperature for 15 min. Pipet 350 ul RW1 into the RNeasy column, incubate 5 min. and centrifuge 15s at 10,000 RPM. Wash with 700 ul RW1 and throw away the collection tube. Take a collection new tube and wash column twice with 500 ul RPE. Centrifuge the column 1 min at 10.000 RPM. Place the column onto a new tube and elute twice with 30 ul RNase free water, incubate for 5 min at room temperature. Store at -80°C.

value: whole cells

label: Cy™5 dye (GE Healthcare)


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0055)


title: Liver_WT_3

city: St. Lucia

first: Milena

last: Gongora

state: QLD

address: bld 80, services rd

country: Australia

institute: Institute for Molecular Biosciences

hyb_protocol: Illumina manufacturer's instructions

scan_protocol: Illumina manufacturer's instructions

data_processing: data was extracted with Bead Studio, then it was imported in R and read with the Lumi package, RMA-like background corrected with the affy package, quantile normalized with the Lumi package and then analysed with LIMMA. All these packages are part of Bioconductor.

label: Biotin

organism: Mus musculus

source_name: Liver from wildtype mice collected 24 hours after fasting

label_protocol: For labeling we followed Illumina TotalPrep RNA Amplification Kit

extract_protocol: Quiagen RNAeasy purification kit.

treatment_protocol: Mice were kept with access to food and water ad libitum with cycles of light and dark of 12 hours. Sacrifice of the animals and harvest of the tissues happened 24 hours after food withdrawal for the liver and 11 hours after food withdrawal for the adipose tissue. Tissues were cleaned from blood with cold PBS and rapidly frozen in liquid nitrogen. Then, we extracted RNA following RNAeasy RNA kit purification instructions. Once purified, total RNA was store at -80 until its analysis by microarray.

tag: genotype

value: WT

tag: tissue

value: Liver


title: AdiposeTissue_WT_2

source_name: Adipose tissue from wildtype mice collected 11 hours after fasting

value: Adipose


title: AdiposeTissue_KO_5

source_name: Adipose tissue from knockount mice collected 11 hours after fasting

value: Cav1 KO


title: Liver_KO_3

source_name: Liver from knockout mice collected 24 hours after fasting


title: AdiposeTissue_WT_4


title: Liver_KO_2


title: Csac grown on xylose vs glucose for biomass loop


title: Liver_WT_1


title: MEF_KO_3

source_name: MEFs primary line from knockout mice collected 24 hours after plating

value: MEFs


title: Csac grown on poplar vs xylose for biomass loop


title: MEF_KO_1


title: MEF_WT_3

source_name: MEFs primary line from wiltype mice collected 24 hours after plating


title: Liver_KO_1


title: MEF_WT_1


title: AdiposeTissue_KO_2


title: AdiposeTissue_WT_1


title: MEF_WT_2


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0052)


title: MEF_KO_2


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0053)


title: Csac grown on switchgrass vs poplar for biomass loop


title: AdiposeTissue_KO_3


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0051)


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0043)

value: Donor from Martinique

value: Male


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0049)


title: Healthy Donor , CD4+ T-cells from Healthy Donor (HISS0060)

source_name: CD4+ T-cells isolated from Healthy Donors

value: Healthy Donor

value: No infected, control PBMC cells

value: CD4+ T-Cells Isolated from Non Infected PBMC


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0041)


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0040)


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0031)


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0048)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0066)


title: Liver_WT_2


title: Neurological disorder tropical spastic paraparesis, CD4+ T-cells from HTLV-1 infected patient (HISS0021)

value: Female


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0063)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0067)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0065)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0061)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0064)


title: Healthy Donor, CD4+ T-cells from Healthy Donor (HISS0062)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0057)

value: Asymtomatic Carrier (AC)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0058)

value: Donor from Guyana


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0056)

value: HTLV-1 Infected PBMC cells


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0046)

value: CD4+ T-Cells Isolated from HTLV-1 infected PBMC


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0045)

value: reference RNA


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0042)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0047)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0015)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0013)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0044)


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0029)

value: Adult T-cell leukemia (ATL)


title: Asymtomatic Carrier, CD4+ T-cells from HTLV-1 infected patient (HISS0014)


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0018)


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0017)


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0010)

value: Donor from Antigua


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0022)


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0024)


title: PycA_Wild type replicate 2

status: Public on Feb 10 2010

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

description: replicate 2 of 4

hyb_protocol: The labelled cDNA were mixed together and hybridized onto prehybridized microarray slides as described in Marr et al., 2006.

scan_protocol: The slides were scanned using a ScanArray HT scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further processed using SAM (Flagged data are represented as null)

organism: Listeria monocytogenes

source_name: PycA mutant

label_protocol: 20 µg of total RNA from the pycA mutant was labelled with Cy5 dCTP and wild type RNA was labelled with Cy3 dCTP in replicate 1 and 3 and the dyes were swapped in replicates 2 and 4.

growth_protocol: The strains were grown in BHI to a mid log phase at 37°C

extract_protocol: Total RNA from the strains were isolated using the Rneasy kit from Qiagen (Qiagen, Germany).

tag: genotype/variation

value: pycA mutant

source_name: Wild type EGDe

value: wild type


title: PycA_Wild type replicate 3

description: replicate 3 of 4


title: Adult T-cell leukemia, CD4+ T-cells from HTLV-1 infected patient (HISS0023)


title: PycA_Wild type replicate 4

description: replicate 4 of 4


title: PycA_Wild type replicate 1

description: replicate 1 of 4


title: dikaryon vs monokaryon replicate 2

status: Public on Feb 01 2010

city: Bloomington

first: Claire

last: Burns

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description: Biological replicate 2 of 3

hyb_protocol: Microarray slides were blocked prior to hybridisation with 5xSSC, 0.1%SDS, 0.1mg.ml-1 BSA at 42oC for 45 min, after which slides were rinsed twice in room temperature 0.1xSSC for 5 min each, followed by a final 10s rinse in water.  Slides were dried by centrifugation for 1min in a Labnet C1303 slide spinner. Arrays were placed in Corning hybridization chambers and mSeries Lifterslips (Erie Scientific) placed over the array grids.  Labelled cDNAs were combined in 50μl with 30% deionized formamide (Ambion), 5xSSPE, 0.2% SDS, 1μg.μl-1 tRNA (Invitrogen), 40ng.μl-1 oligo dA (Invitrogen).  The hybridization mixture was heated at 100oC for 2min, cooled to 25oC, and applied to the microarray slide.  Slides were hybridised for 16 hours at 42oC, then washed for 5 min each in 1xSSC, 0.03%SDS (37oC), then 0.2xSSC (ambient temperature), and finally 0.1xSSC (ambient temperature).  Slides were dried by centrifugation, as previously, and scanned immediately.

scan_protocol: Microarray slides were scanned using a GenePix 4200A scanner (Molecular Devices).  PMT settings were adjusted so the dye channels were balanced, with a few saturated spots, to maximize data capture.  Spots were identified using GenePix Pro software (Molecular Devices) and manual inspection. Scans were quality assessed using the Basic Hybridization Analysis R script (http://cgb.indiana.edu/downloads/1). Spots were manually flagged to be excluded from analysis if there were areas of poor quality such as scratches or dust.  Spots were also flagged for omission, using GenePix software, if they fulfilled any of the following criteria: manually flagged, buffer only spots, spots not found, percentage of saturated pixels in both channels > 3, percentage of pixels above background plus 1 standard deviation in both channels < 60, spot pixels < 40.

data_processing: Data normalization and filtering were performed using the Bioconductor package (http://www.bioconductor.org/) within the R statistical framework (http://www.r-project.org/).  OLIN  [34] was used for intra-slide normalization and log2 transformation.  Data were included in further analysis if two of the four replicates for every timepoint were not flagged, or if all four of the replicates for any individual timepoint were not flagged.  Ratio values were exported for further analysis, with individual flagged ratio values omitted.  Statistical significance of changing expression was assessed using the one class timecourse function in Significance Analysis of Microarrays (SAM) software

label: Alexa fluor 647

organism: Coprinopsis cinerea

source_name: C. cinerea vegetative monokaryotic mycelia

label_protocol: 20ug of total RNA were reverse transcribed and labelled with Alexa fluor using the Invitrogen Superscript Indirect labeling kit.

growth_protocol: For each biological replicate, monokaryon C. cinerea wild-type strain OK7 and dikaryotic strain OK7xJava6 were gown in liquid YMG culture for 2 days, then harvested tohrough a Buchner funnel and frozen in liquid nitrogen.

extract_protocol: RNA was extracted from all the tissue collected using RNeasy Plant mini-prep kit.

value: Strain Okayama7

label: Alexa fluor 555

source_name: C. cinerea vegetative dikaryotic mycelia

value: Strain Java6 crossed with Okayama7


title: dikaryon vs monokaryon replicate 1

description: Biological replicate 1 of 3


title: Gill_tissue_K+12_rep3

description: Biological replicate 3 of 4

source_name: C. cinerea excised gill tissue, 12 hours after kayogamy

growth_protocol: For each biological replicate, monokaryon C. cinerea wild-type strains J6:5-4 and J6;5-5 were mated on YMG plates.  The resultant dikaryon was subcultured into fruiting tubes, grown at 37 for 2 dyas, then moved to 25 with a light regime of 8 hours dark, 16 hours light,

extract_protocol: At the pertiment timepoint, gill tissue from 7-10 mushrooms was separated form the mushroom stipe, and the veil removed.  Gill tissue was immediately frozen in liquid nitrogen. RNA was extracted from all the tissue collected using RNeasy Plant mini-prep kit.

treatment_protocol: no treatments

tag: Strain Java;5-5 crossed with Java;5-4

source_name: Mixture of RNA from timepoint samples K+3,K+6,K+9,K+12


title: Gill_tissue_K+9_rep4

description: Biological replicate 4 of 4

source_name: C. cinerea excised gill tissue, 9 hours after kayogamy


title: Gill_tissue_K+12_rep4

description: Biological replicate 4 of 4


title: Gill_tissue_K+9_rep3

description: Biological replicate 3 of 4


title: dikaryon vs monokaryon replicate 3

description: Biological replicate 3 of 3


title: Gill_tissue_K+9_rep2

description: Biological replicate 2 of 4


title: Gill_tissue_K+12_rep1

description: Biological replicate 1 of 4


title: Gill_tissue_K+6_rep2

description: Biological replicate 2 of 4

source_name: C. cinerea excised gill tissue, 6 hours after kayogamy


title: Gill_tissue_K+12_rep2

description: Biological replicate 2 of 4


title: Gill_tissue_K+3_rep4

description: Biological replicate 4 of 4

source_name: C. cinerea excised gill tissue, 3 hours after kayogamy


title: Gill_tissue_K+9_rep1

description: Biological replicate 1 of 4


title: Gill_tissue_K+3_rep3

description: Biological replicate 3 of 4


title: Gill_tissue_K+6_rep4

description: Biological replicate 4 of 4


title: Gill_tissue_K+6_rep3

description: Biological replicate 3 of 4


title: Gill_tissue_K+3_rep1

description: Biological replicate 1 of 4


title: Gill_tissue_K+3_rep2

description: Biological replicate 2 of 4


title: Gill_tissue_K+6_rep1

description: Biological replicate 1 of 4


title: day11b

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: no additional information

hyb_protocol: Because using cDNA, Agilent (Agilent, Santa Clara, USA) 8x15K CGH protocol was used, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing: Image analysis with GenePix Pro 6.0, data preprocessing in R with limma package: background subtraction with normexp and offset 50. Quantile-normalization for log2 intensities using both pai and ss probes of array.  Only pai probes were of interest of this study.

organism: Streptomyces turgidiscabies

source_name: potato scab lesion

label_protocol: cDNA synthesis, 5µg RNA, 2.5µg random hexamer primers and 3µl dNTP mix (Invitrogen, Carlsbad, USA) were added to total reaction volume of 9µl. 1.5µl 10XRT buffer (Stratagene, LaJolla, USA), 1.5µl 0.1M dithiotreitol, 1µl Cy3 or Cy5 (1mM each, GE Healthcare) and 2µl (100U) Stratascript RT (Strategene) were added and the reaction incubated at 37C for 4h. Reaction was stopped 0.75 µl 20mM EDTA (pH8.0). RNA was hybrolyzed by adding 7.5µl 0.1N NaOH and incubating for 15 min at 70C. Alkali was neutralized with 7.5µl of 0.1N HCI, Samples were purified, examined for incorporated label and DNA concentration.

growth_protocol: Bacteria were grown in 50ml of potato dextrose broth under shaking (120rpm) for 5 days, cells were spun down and resuspended in two 500ml volumes of minimal medium supplemented with 1% glucose. After 7 days of growth cells from 100ml aliquots were used for RNA extraction. Samples were collected after 1,2,3,4,7,11 days of growth.

extract_protocol: RNAeasy kit (Qiagen)

tag: growth replicate

value: B

tag: time

value: day 11


title: Gill_tissue_K-3_rep4

description: Biological replicate 4 of 4

source_name: C. cinerea excised gill tissue, 3 hours before kayogamy


title: Gill_tissue_K_rep2

description: Biological replicate 2 of 4

source_name: C. cinerea excised gill tissue, at kayogamy


title: Gill_tissue_K-3_rep3

description: Biological replicate 3 of 4


title: Gill_tissue_K_rep4

description: Biological replicate 4 of 4


title: Gill_tissue_K_rep1

description: Biological replicate 1 of 4


title: Gill_tissue_K_rep3

description: Biological replicate 3 of 4


title: melanoma cell line 501Mel

city: Cambridge

first: Michael

last: Berger

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Instititute

description: gene expression data, microarray-derived

hyb_protocol: cRNA were hybridized according to the standard Affymetrix protocol

scan_protocol: data were scanned according to standard protocols

data_processing: data were processed using the aroma.affymetrix package in Bioconductor. RMA (robust multichip average) was applied in combination with quantile normalization to generate gene centric expression values.

label: biotin

source_name: melanoma cell line 501Mel

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

growth_protocol: Cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

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

treatment_protocol: cells were grown under standard conditions (no treatment)

tag: melanoma type

value: cell line 501Mel


title: day7b

description: no additional information

value: day 7


title: day3b

description: no additional information

value: day 3


title: day2b

description: no additional information

value: day 2


title: day2a

description: no additional information

value: A


title: day1a

description: no additional information

value: day 1


title: day3a

description: no additional information


title: day4

description: no additional information

value: day 4


title: day7a

description: no additional information


title: Gill_tissue_K-3_rep2

description: Biological replicate 2 of 4


title: day0

description: no additional information

value: day 0


title: day1b

description: no additional information


title: Lymphoblastoid B cell line_IARC 304

city: New York

first: Katia

last: Basso

state: NY

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: Gene expression data from lymphoblastoid cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

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.

source_name: EBV-immortalized lymphoblastoid cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's indications.

treatment_protocol: Cells were lysated in Trizol Reagent (Invitrogen) and frozen

value: EBV-immortalized lymphoblastoid B cell

value: IARC 304


title: Follicular lymphoma_FL.E.29

description: Gene expression data from follicular lymphoma

source_name: Follicular lymphoma bioptic tissue

treatment_protocol: The frozen tissue was homogeneized in Trizol reagent.

value: Follicular lymphoma biopsy


title: day11a

description: no additional information


title: Lymphoblastoid B cell line_RD

value: RD


title: Lymphoblastoid B cell line_DAIKIKI

value: DAIKIKI


title: Lymphoblastoid B cell line_NC 6

value: NC 6


title: Gill_tissue_K-3_rep1

description: Biological replicate 1 of 4


title: Lymphoblastoid B cell line_CB33


title: Follicular lymphoma_FL.E.28


title: Follicular lymphoma_FL.E.27


title: Follicular lymphoma_FL.E.25


title: Follicular lymphoma_FL.E.26


title: 251186836552

city: Angers

first: Celine

last: Fassot-Lucht

address: Rue Haute de Reculée

department: BNMI

country: France

institute: INSERM U1083

description:
216-cy3 vs 220-cy5
Date:2005/10/03

hyb_protocol: Agilent : 750.0 ng at 60 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : loess, Background norm. : Kooperberg, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Rattus norvegicus

label_protocol: cRNA Agilent

extract_protocol: Trizol

tag: label

tag: extract

tag: sample

tag: subject

value: CMO 216

value: thoracic aorta

tag: origin

value: control mother

value: DMO 220

value: diabetic mother


title: 251186836387

description:
194-cy3 vs 190-cy5
Date:2005/10/03

value: DMO 194

value: CMO 190


title: Follicular lymphoma_FL.E.22


title: 251186836385

description:
193-cy3 vs 189-cy5
Date:2005/10/03

value: DMO 193

value: CMO 189


title: 251186836384

description:
189-cy3 vs 193-cy5
Date:2005/10/03


title: Follicular lymphoma_FL.E.24


title: Follicular lymphoma_FL.E.19


title: Follicular lymphoma_FL.E.21


title: Follicular lymphoma_FL.E.20


title: 251186836553

description:
220-cy3 vs 216-cy5
Date:2005/10/03


title: 251186836551

description:
199-cy3 vs 192-cy5
Date:2005/10/03

value: DMO 199

value: CMO 192


title: 251186836550

description:
192-cy3 vs 199-cy5
Date:2005/10/03


title: Follicular lymphoma_FL.E.17


title: 251186836549

description:
197-cy3 vs 191-cy5
Date:2005/10/03

value: DMO 197

value: CMO 191


title: 251186836388

description:
191-cy3 vs 197-cy5
Date:2005/10/03


title: Follicular lymphoma_FL.E.11

value: Follicular lymphoma biopsy


title: Follicular lymphoma_FL.E.15


title: Follicular lymphoma_FL.E.12


title: Follicular lymphoma_FL.E.14


title: Follicular lymphoma_FL.E.10


title: Follicular lymphoma_FL.E.08


title: Follicular lymphoma_FL.E.13


title: ddm1-12_1135_rep3

city: Vienna

first: Ortrun

last: Mittelsten Scheid

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

hyb_protocol: Nottingham Arabidopsis Stock Centre (NASC) standard method

data_processing: R/BioC using RMA

organism: Arabidopsis thaliana

source_name: ddm1-12, whole seedling, 17dpg

growth_protocol: Standard growth protocol on plates containing GM medium, long day condition, 21°C, 17 days

extract_protocol: Qiagen Rneasy

value: whole seedling

tag: line


title: Follicular lymphoma_FL.E.05


title: Follicular lymphoma_FL.E.06


title: Follicular lymphoma_FL.E.03


title: Follicular lymphoma_FL.E.02


title: Follicular lymphoma_FL.E.07


title: Follicular lymphoma_FL.E.01


title: ddm1-12_1135_rep2

scan_protocol: Nottingham Arabidopsis Stock Centre (NASC) standard method


title: hog1-7_774_rep1

source_name: hog1-7, whole seedling, 17dpg

label_protocol: Nottingham Arabidopsis Stock Centre (NASC) standard method


title: hog1-7_774_rep2


title: ddm1-12_1135_rep1


title: Follicular lymphoma_FL.B.09


title: Follicular lymphoma_FL.E.09


title: hog1-7_774_rep3


title: Follicular lymphoma_FL.E.04


title: Follicular lymphoma_FL.E.16


title: Follicular lymphoma_FLB 08


title: C2S1_wt_rep2

source_name: wt, whole seedling, 17dpg

value: Wild type


title: Follicular lymphoma_FLB 07


title: Follicular lymphoma_FLB 06


title: Follicular lymphoma_FLB 05


title: C2S1_wt_rep3


title: Follicular lymphoma_FLB 04


title: Follicular lymphoma_FLB 02


title: Follicular lymphoma_FLB 01


title: C2S1_wt_rep1


title: Follicular lymphoma_FLB 03


title: Gata3_Cdx2_null_9

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

description: Gata3 overexpression in Cdx2 null cells replicate 3

hyb_protocol: as per facility protocols

scan_protocol: Gene Chips were scanned using the Hewlett-Packard Gene Array Scanner G2500A.

data_processing: The data were analyzed with Expression Console (Affymetrix) using the quartile normalization and PLIER algorithm

source_name: Gata3 overexpression in Cdx2 null cells

label_protocol: as per facility protocols

growth_protocol: To create stably transformed lines, 1-3 x 107 ES cells were electroporated with 20-30 µg plasmid (pCAG-mCdx2ER-ires-puror (Niwa et al., 2005), pCAG-hCdx2ERT2-ires-puror, or pCAG-hGata3ERT2-ires-puror), and seeded on two 10 cm gelatinized plates.  Cells were fed with plasmid selection medium (ES medium + 1.2 µg/mL puromycin) until colonies were visible by eye.  Colonies were picked and individually expanded on gelatin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A second clean up step was done using the RNEasy kit from QIAGEN according to manufactures instructions

treatment_protocol: To induce transgene activity, cells were treated with induction medium (TS medium + 1 µg/mL tamoxifen (Sigma)).  For microarray analysis, ES cells were seeded at densities of 2 x 105 cells per gelatinized 35-mm well in ES medium, switched to induction medium the following day, and fed daily for the indicated time period.

tag: Cdx2 null ES cells expressing human Gata3 T2ER fusion


title: Ramos siBCL6_4

description: Gene expression data from Burkitt  lymphoma cell line transduced with lentivirus expressing a siRNA targeting BCL6

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U95Av2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

growth_protocol: Cells were lysated in Trizol Reagent (Invitrogen) and frozen

treatment_protocol: The cells were infected with lentiviral particles expressing a commercial siRNA (TRC0000013606, Sigma) targeting BCL6

value: Burkitt lymphoma cell line


title: Ramos siBCL6_2

source_name: Burkitt lymphoma cell line transduced with lentivirus expressing a siRNA targeting BCL6


title: Ramos siBCL6_3


title: R1_control

description: R1 differentiated controls

source_name: R1 differentiated controls

tag: R1 control ES cells


title: Ramos siCTR_1

description: Gene expression data from Burkitt  lymphoma cell line transduced with lentivirus expressing a control siRNA

treatment_protocol: The cells were infected with lentiviral particles expressing a commercial control siRNA (SHC002, Sigma)


title: Gata3_Cdx2_null_11

description: Gata3 overexpression in Cdx2 null cells replicate 1


title: Ramos siBCL6_1


title: Ramos siCTR_2

source_name: Burkitt lymphoma cell line transduced with lentivirus expressing a control siRNA


title: Ramos siCTR_4


title: Ramos siCTR_3


title: Cdx2_E1

description: Cdx2 overexpression replicate 1

source_name: Cdx2 overexpression

tag: R1 ES cells expressing mouse Cdx2 T2ER fusion


title: Gata3_F2

description: Gata3 overexpression line replicate 4

source_name: Gata3 overexpression line

tag: R1 ES cells expressing human Gata3 T2ER fusion


title: Gata3_D3

description: Gata3 overexpression line replicate 3


title: Gata3_Cdx2_null_3

description: Gata3 overexpression in Cdx2 null cells replicate 2


title: TS 6.5 day 0

description: gene expression data of undifferentiated TS cells

source_name: undifferentiated TS cells

growth_protocol: TS cells were grown feeder free with 30% feeder conditioned medium, RPMI, FGF4 and heparin as per Tanaka et al , 1998 PMID:9851926

treatment_protocol: To differentiate TS cell FGF4 heparin and feeder conditioned medium were all withdrawn from the media.

tag: 129S6 genetic background


title: Cdx2_H2

description: Cdx2 overexpression replicate 2


title: Gata3_H4

description: Gata3 overexpression line replicate 1


title: TS 6.5 day 1

description: gene expression data of TS cells differentiated day 1

source_name: TS cells differentiated day 1


title: TS 6.5 day 2

description: gene expression data of TS cells differentiated day 2

source_name: TS cells differentiated day 2


title: TS 6.5 day 4

description: gene expression data of TS cells differentiated day 4

source_name: TS cells differentiated day 4


title: TS 6.5 day 3

description: gene expression data of TS cells differentiated day 3

source_name: TS cells differentiated day 3


title: Gata3_A3

description: Gata3 overexpression line replicate 2


title: TS 3.5 day 5

description: gene expression data of TS cells differentiated day 5

source_name: TS cells differentiated day 5


title: TS 6.5 day 5


title: TS 6.5 day 6

description: gene expression data of TS cells differentiated day 6

source_name: TS cells differentiated day 6


title: TS 3.5 day 6


title: TS 3.5 day 0


title: TS 3.5 day 4


title: TS 3.5 day 3


title: TS 3.5 day 2


title: Follicular lymphoma_FL.E.18

source_name: Follicular lymphoma bioptic tissue

tag: cell type


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_5

city: Southampton

first: Gail

last: Taylor

address: Bassett Crescent East

country: United Kingdom

institute: University of Southampton

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 3_rep_6 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 1_rep_2 and flash frozen in liquid nitrogen for storage at -80 oC.

hyb_protocol: Purified dye coupled cDNA Cy3 and Cy5 were eluted into the same eppendorf tube total eluate containing 200 µl of Cy3-and-Cy5 coupled cDNA was concentrated down to 25 µl in a spin concentrator (Eppendorf Concentrator 5301, Eppendorf, Cambridge, UK). The dye-labelled cDNA target (25 µl) was denatured by the addition of 50 µl formamide, 25 µl of hybridisation buffer (Amersham, UK) was added and the sample heated at 95 ºC for 1 minute and then chilled on ice. PICME microarray slides were  pre-hybridised, in a coplin staining jar, containing pre-hybridisation buffer (50 % (v/v) formamide 5X SSC, 0.1 % SDS (w/v) (Fisher, Leicestershire, UK) and 0.1 mg ml-1BSA (Sigma-Aldrich, Dorset, UK.) in a water bath at 42 ºC, for approximately 1 hour. Slides were then washed by placing directly into a bath containing wash buffer III (0.2xSSC) for 5 minutes. Followed by a further 5 minute wash in fresh wash buffer III, then followed by the following washes; 30 seconds in H2O (milliQ, Elga, Maxima, York, UK), 60 seconds in boiling H2O (milliQ), and a 4 ºC soak in 100 % ethanol (approximately 1 minute) prior to drying by centrifugation (3000 x g for 1 minute). At no stage were slides allowed to dry prior to the final centrifugation step. Hybridisation, and post-hybridsation slide washing, was carried out using an HS400 hybridisation station (Tecan, Reading, UK). The pre-hybridised slides were washed for 1 min in pre-hybridisation buffer. Each target (100 µl) was then added to the respective slide. Microarray hybridisation was carried out at 42 ºC for 16 hours with a low agitation frequency. Slides were then washed with wash buffers (WB) in the following order: WB I (0.1X SSC, 0.2 % SDS), WB II (0.1X SSC, 0.2 % SDS), WB III (0.2X SSC), H2O (milliQ) and finally 100 % ethanol. Slides were then dried in a stream of pure N2 gas.

scan_protocol: The hybridised slides were scanned on a Genetix Aquire scanner (Genetix, Hampshire, UK) at 5 μm resolution. PMT settings were adjusted to equalise the channel intensities and were typically between 60 to 80 %, with no more than a difference of 10% gain between channels. The TIFF images were analysed using GenePixPro 5.1 (Axon Instruments, Union City, California). Spots were flagged as “bad” if the median signal intensity was equal to 65535 or if less than 200. Images were also checked manually and miss-called spots were manually flagged as bad.

data_processing: The data were loaded into the R statistical package (http://www.r-project.org/) and the LIMMA package [http://bioinf.wehi.edu.au/limma/] was used to perform background correction and normalization. A combination of custom functions and functions from within the LIMMA package were used to produce pre- and post-normalized quality control plots to ensure data quality. Background subtraction was achieved by removing the local median background intensity from the spot foreground median intensity. Background corrected data were then normalized using a print-tip LOWESS normalization, and spots with a ‘bad’ flag had a negative weighting factor of 0.1 applied to them. A cross-slide normalization was also applied to ensure consistency of scale. Normalized data were then filtered based on A value [(log2 R + log2 G)/2] to remove spots with low intensities in both channels (the threshold value for A was set to 8.0, equating to a raw intensity of 256). These pre-normalised data were imported into GeneSpring GX (Version 7.3.1, Silicon Genetics, Redwood City, CA) to facilitate visual interpretation of results and the production of annotated lists of differentially expressed ESTs. A dye-swap normalization was applied where required followed by a ‘Divide by Control’ normalization to produce ratio values. All spots flagged as “bad” were excluded.

organism: Populus x canadensis

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in CONTROL CO2 in plot 3 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.

label_protocol:
100 µg of total RNA in a 0.5 ml eppendorf tube was denatured with 2 µl of anchored oligo(dt)20 primer by heating at 65 º for 10 minutes then chilling on ice (max. 1 minute). A reverse transcription master mix was prepared. This consisted of 6 µl 5x -RT-buffer (first strand buffer), 3 µl of 10mM DTT, 1 µl of 50x dNTP mix (a mix of dA, dC and dG, and aa-dUTP and dTTP in a ratio of 4:1 aa-dUTP:dTTP) (Amersham UK; except aa-dUTP, Sigma UK), 1 µl RNase inhibitor and 2 µl of Superscript™ reverse transcriptase. The master mix was made in bulk such that 13 µl was added to each oligo (dt)20 primed RNA sample for overnight cDNA synthesis at 48 ºC. After overnight synthesis the reverse transcription reaction was inhibited by addition of 10 µl 0.5 M EDTA and any remaining RNA degraded by the addition of 10 µl 1 M NaOH and heating at 65 ºC for 15 minutes. The remaining cDNA was then neutralised with 50 µl of 1M HEPES (pH 7.5).
cDNA was purified using a Qiagen PCR purification kit, (Qiagen, Crawley, UK). The cDNA clean up was carried out according to the manufacturer’s instructions for the purification of single- or double-stranded DNA, with the following exceptions. A phosphate-ethanol wash buffer (PWB: pH 8.0, 5 mM KPO4; http://pga.tigr.org/sop/M004_1a.pdf) was used instead of buffer PE and two PWB steps were included. cDNA was then eluted via two elutions each with 30 µl of 0.1 M NaHCO3 (pH 9.0), 1 µl of cDNA (60 µl total) was then taken for spectrometric quantification. The purified cDNA (59 µl total) was taken and 35 µl 100 mM sodium acetate (pH 5.2) added. Under minimal light, purified cDNA was added to an aliquot of Cy3 CyDye™ ester (Amersham, Buckinghamshire, UK). The sample was gently agitated and then left in the dark at room temperature for 2 hours. Dye coupled cDNA was purified using Qiagen PCR purification kit. The Cy3 labelled cDNA was purified according to the manufacturer’s protocol with the following exceptions. An additional buffer PE wash step was included and two repeated elution steps were carried out.

growth_protocol: Trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control plots of the POP/EUROFACE experimental site http://www.unitus.it/euroface/. Throughout the entire experiment all plants were drip irrigated at six to ten mm per day. Between October 2001 and February 2002, following three years growth, the entire plantation was coppiced. Following the coppice one half of each plot (the sub-plot) representing all the clones was provided weekly with a combined NPK fertiliser (20:6:6 N:P:K + micro-elements, 212 kg ha-1) for 16 weeks through the drip irrigation system. During the growing season of 2003 and 2004 this combined fertiliser was replaced with an ammonium nitrate nutrient treatment for twenty weeks (2003) and twenty two weeks (2004) (34:0:0, N:P:K, 290 kg ha-1). The material used here were grown in the unfertilised sub-plot.

extract_protocol: Total RNA was extracted using the protocol of Chang et al., (1993) with the following modifications, 2.67 % β-Mercapto-ethanol was added to the CTAB extraction buffer instead of spermidine. After the overnight 4 ºC LiCl precipitation and re-suspension in SSTE two additional CHISAM (chloroform:isoamylalcohol, 24:1) extractions were performed. The RNA pellet was re-suspended in 20 µl of DEPC treated H2O. RNA quantity was checked (NanoDrop® ND-1000 Spectrophotometer, Wilmington, DE, USA.) and RNA quality checked (Agilent 2100 bioanaylser, Agilent Technologies, USA).

treatment_protocol:
Trees were grown within the control plots of the POP/EUROFACE infrastructure.
Between October 2001 and February 2002, following three years growth, the entire plantation was coppiced.

tag: synonym

tag: growth protocol

value: ambient CO2

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in ELEVATED CO2 in plot 1 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.

label_protocol:
100 µg of total RNA in a 0.5 ml eppendorf tube was denatured with 2 µl of anchored oligo(dt)20 primer by heating at 65 º for 10 minutes then chilling on ice (max. 1 minute). A reverse transcription master mix was prepared. This consisted of 6 µl 5x -RT-buffer (first strand buffer), 3 µl of 10mM DTT, 1 µl of 50x dNTP mix (a mix of dA, dC and dG, and aa-dUTP and dTTP in a ratio of 4:1 aa-dUTP:dTTP) (Amersham UK; except aa-dUTP, Sigma UK), 1 µl RNase inhibitor and 2 µl of Superscript™ reverse transcriptase. The master mix was made in bulk such that 13 µl was added to each oligo (dt)20 primed RNA sample for overnight cDNA synthesis at 48 ºC. After overnight synthesis the reverse transcription reaction was inhibited by addition of 10 µl 0.5 M EDTA and any remaining RNA degraded by the addition of 10 µl 1 M NaOH and heating at 65 ºC for 15 minutes. The remaining cDNA was then neutralised with 50 µl of 1M HEPES (pH 7.5).
cDNA was purified using a Qiagen PCR purification kit, (Qiagen, Crawley, UK). The cDNA clean up was carried out according to the manufacturer’s instructions for the purification of single- or double-stranded DNA, with the following exceptions. A phosphate-ethanol wash buffer (PWB: pH 8.0, 5 mM KPO4; http://pga.tigr.org/sop/M004_1a.pdf) was used instead of buffer PE and two PWB steps were included. cDNA was then eluted via two elutions each with 30 µl of 0.1 M NaHCO3 (pH 9.0), 1 µl of cDNA (60 µl total) was then taken for spectrometric quantification. The purified cDNA (59 µl total) was taken and 35 µl 100 mM sodium acetate (pH 5.2) added. Under minimal light, purified cDNA was added to an aliquot of Cy5 CyDye™ ester (Amersham, Buckinghamshire, UK). The sample was gently agitated and then left in the dark at room temperature for 2 hours. Dye coupled cDNA was purified using Qiagen PCR purification kit. The Cy5 labelled cDNA was purified according to the manufacturer’s protocol with the following exceptions. An additional buffer PE wash step was included and two repeated elution steps were carried out.

growth_protocol: Trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the FACE infrastructure at the POP/EUROFACE experimental site http://www.unitus.it/euroface/. Throughout the entire experiment all plants were drip irrigated at six to ten mm per day. Between October 2001 and February 2002, following three years growth, the entire plantation was coppiced, and the fumigation was continued in March 2002 for the re-growth. Following the coppice one half of each plot (the sub-plot) representing all the clones was provided weekly with a combined NPK fertiliser (20:6:6 N:P:K + micro-elements, 212 kg ha-1) for 16 weeks through the drip irrigation system. During the growing season of 2003 and 2004 this combined fertiliser was replaced with an ammonium nitrate nutrient treatment for twenty weeks (2003) and twenty two weeks (2004) (34:0:0, N:P:K, 290 kg ha-1). The material used here were grown in the unfertilised sub-plot.

treatment_protocol:
Immediately after planting, material was exposed to an elevated CO2 atmosphere of 550 ppm via the FACE infrastructure. This CO2 enrichment continued for five years from bud-burst (March) until bud-set (October) and during the sixth year of growth (2004) CO2 fumigation continued until November.
Between October 2001 and February 2002, following three years growth, the entire plantation was coppiced, and the fumigation was continued in March 2002 for the re-growth. During the first three year growing cycle the CO2 fumigation measured at 1 min intervals was within 20 % of the target concentration for 80 % of the time as detailed in Tricker et al., (2004). In 2003 the mean [CO2] within the FACE plots was 535.9 ± 20.4 and within 20 % of the target concentration of 550 ppm for 72.2 % of the time and this reduced to 70 % for 2004.

value: elevated CO2


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_9

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED CO2 plot 4_rep_1 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 2_rep_4 and flash frozen in liquid nitrogen for storage at -80 oC.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in ELEVATED CO2 in plot 4 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in CONTROL CO2 in plot 2 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_8

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED plot 4_rep_4 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 3_rep_2 and flash frozen in liquid nitrogen for storage at -80 oC.

value: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214)


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_7

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 2_rep_2 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control plots receiving ambient co2 at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED CO2 plot 1_rep_3 and flash frozen in liquid nitrogen for storage at -80 oC.


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_6

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 3_rep_4 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control plots receiving ambient co2 at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED CO2 plot 4_rep_6 and flash frozen in liquid nitrogen for storage at -80 oC.


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_2

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 2_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED CO2 plot 1_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in CONTROL plot 2 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in ELEVATED CO2 plot 1 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_4

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 2_rep_3 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ELEVATED CO2 plot 4_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_1

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from elevated CO2 plot 4_rep_2 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control plots receiving ambient co2 at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from ambient CO2 plot 2_rep_6 and flash frozen in liquid nitrogen for storage at -80 oC.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in CONTROL CO2 in plot 1 of the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.


title: P. x euramericana_time_course(e[CO2] 18th_Oct / e[CO2]_31st_Aug)_rep_1

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from Elevated CO2 plot_4_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1].

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in ELEVATED CO2 at the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.

label_protocol:
100 µg of total RNA in a 0.5 ml eppendorf tube was denatured with 2 µl of anchored oligo(dt)20 primer by heating at 65 º for 10 minutes then chilling on ice (max. 1 minute). A reverse transcription master mix was prepared. This consisted of 6 µl 5x -RT-buffer (first strand buffer), 3 µl of 10mM DTT, 1 µl of 50x dNTP mix (a mix of dA, dC and dG, and aa-dUTP and dTTP in a ratio of 4:1 aa-dUTP:dTTP) (Amersham UK; except aa-dUTP, Sigma UK), 1 µl RNase inhibitor and 2 µl of Superscript™ reverse transcriptase. The master mix was made in bulk such that 13 µl was added to each oligo (dt)20 primed RNA sample for overnight cDNA synthesis at 48 ºC. After overnight synthesis the reverse transcription reaction was inhibited by addition of 10 µl 0.5 M EDTA and any remaining RNA degraded by the addition of 10 µl 1 M NaOH and heating at 65 ºC for 15 minutes. The remaining cDNA was then neutralised with 50 µl of 1M HEPES (pH 7.5).
cDNA was purified using a Qiagen PCR purification kit, (Qiagen, Crawley, UK). The cDNA clean up was carried out according to the manufacturer’s instructions for the purification of single- or double-stranded DNA, with the following exceptions. A phosphate-ethanol wash buffer (PWB: pH 8.0, 5 mM KPO4; http://pga.tigr.org/sop/M004_1a.pdf) was used instead of buffer PE and two PWB steps were included. cDNA was then eluted via two elutions each with 30 µl of 0.1 M NaHCO3 (pH 9.0), 1 µl of cDNA (60 µl total) was then taken for spectrometric quantification. The purified cDNA (59 µl total) was taken and 35 µl 100 mM sodium acetate (pH 5.2) added. Under minimal light, purified cDNA was added to an aliquot of Cy3 CyDye™ ester (Amersham, Buckinghamshire, UK). The sample was gently agitated and then left in the dark at room temperature for 2 hours. Dye coupled cDNA was purified using Qiagen PCR purification kit. The Cy3 labelled cDNA was purified according to the manufacturer’s protocol with the following exceptions. An additional buffer PE wash step was included and two repeated elution steps were carried out

tag: date

value: 18th October 2004

extract_protocol: Total RNA was extracted using the protocol of Chang et al., (1993) with the following modifications, 2.67 % β-Mercapto-ethanol was added to the CTAB extraction buffer instead of spermidine. After the overnight 4 ºC LiCl precipitation and re-suspension in SSTE two additional CHISAM (chloroform:isoamylalcohol, 24:1) extractions were performed. The RNA pellet was re-suspended in 20 µl of DEPC treated H2O. RNA quantity was checked (NanoDrop® ND-1000 Spectrophotometer, Wilmington, DE, USA.) and RNA quality checked (Agilent 2100 bioanaylser, Agilent Technologies, USA). RNA was extracted individually from pre-senescent (31 August 2004) leaves and then pooled. The pool from elevated CO2 consisted of seven samples (four from plot one and three from plot four). The pool from ambient CO2 consisted of seven samples (four from plot two and three from plot three). In each pool 100 µg of total RNA was established using 14.3 µg of total RNA from each replicate leaf.

value: 31 August 2004


title: P. x euramericana_time_course(a[CO2] 18th_Oct / a[CO2]_31st_Aug)_rep_2

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control (ambient co2) plots within the infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003)
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control (ambient co2) plots within the infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from control (ambient CO2)_plot_3_rep_2 and flash frozen in liquid nitrogen for storage at -80 oC.

source_name: Populus x euramericana Dode (Guiner) (P. deltoides Bart. Ex Marsh. X P. nigra L., genotype I-214) Growing in the CONTROL (AMBIENT CO2) plots at the POP/EUROFACE site Viterbo Italy http://www.unitus.it/euroface/.


title: P. x euramericana_time_course(a[CO2] 18th_Oct / a[CO2]_31st_Aug)_rep_1

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control (ambient co2) plots within the infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from control (ambient CO2)_plot_2_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the control (ambient co2) plots within the infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003).


title: TS 3.5 day 1

description: gene expression data of TS cells differentiated day 1


title: P. x euramericana_senescent_leaf_(e[CO2] / a[CO2])_rep_3

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 2_rep_1 and flash frozen in liquid nitrogen for storage at -80 oC.
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from CONTROL plot 1_rep_4 and flash frozen in liquid nitrogen for storage at -80 oC.


title: MS25_P16_V58_4_A3_12H_OHT

city: Mannheim

first: Tobias

last: Czymai

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Dermatology

institute: University Medical Center Mannheim, University of Heidelberg

description: Primary HUVECs cells infected with pBP-FoxO3.A3.ER vector and treated with OHT for 12h.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.1, from SAS. Gene expression profiling was performed using arrays of human genome 133 2.0 -type from Affymetrix. A Custom CDF Version 11 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: Primary HUVECs infected with pBP-FoxO3.A3.ER vector +12h OHT

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

growth_protocol: primary HUVEC purchased from Lonza and cultured as previously described (Viemann et al, 2007).

extract_protocol: Total RNA was isolated from cells by spin column based technique using “RNeasy Mini Kit” (Qiagen)

value: Primary HUVECs

tag: infection

value: pBP-FoxO3.A3.ER vector

tag: agent

value: OHT


title: P. x euramericana_time_course(e[CO2] 18th_Oct / e[CO2]_31st_Aug)_rep_2

description:
CH1: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1].
CH2: populus x euramericana dode (guiner) (i bart. ex marsh. x p. nigra l., genotype i-214) leaf material. trees were planted in the spring of 1999 as hard wood cuttings at 1m spacing and inside the face infrastructure at the pop/euroface experimental site http: //www.unitus.it/euroface/. Four replicate leaves per sub-plot were sampled and flash frozen into liquid nitrogen, on 31 August 2004, and prior to visible senescence but around the time of bud-set as given by Calfapietra et al., (2003) [1]. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were selected. On the 14th September 2004 twenty trees from within each experimental plot were taken. The tenth leaf down the dominant stem (which represented the first fully expanded mature leaf of maximum size) from a reference leaf of 30 mm in length (leaf one) were labelled on the main-stem above the petiole. All labelled leaves were a uniform height (approx 0.3 m) from the canopy top across all treatments and not shaded by the canopy. On 18th October 2004 the labelled leaf was sampled from Elevated CO2 plot_1_rep_5 and flash frozen in liquid nitrogen for storage at -80 oC.


title: MS25_P18_V58_H212R_12H_0HT

description: Primary HUVECs cells infected with mutated vector pBP-FoxO3.A3.ER.H212R and treated with OHT.

source_name: Primary HUVECs infected with pBP-FoxO3.A3.ER.H212R vector +12h OHT

value: pBP-FoxO3.A3.ER.H212R vector (mutated)


title: MS25_P15_V58_4_A3

description: Primary HUVECs cells infected with pBP-FoxO3.A3.ER vector.

source_name: Primary HUVECs infected with pBP-FoxO3.A3.ER vector


title: MS25_P14_V58_4_LV_12H_OHT

description: Primary HUVECs cells infected with empty pBabe puro vector and treated with 4OHT for 12h.

source_name: Primary HUVECs infected with empty pBabe puro vector +12h OHT

value: empty pBabe puro vector


title: MS25_P13_V58_4_LV

description: Primary HUVECs cells infected with empty pBabe puro vector.

source_name: Primary HUVECs infected with empty pBabe puro vector


title: MS25_P17_V58_4_H212R

description: Primary HUVECs cells infected with mutated vector pBP-FoxO3.A3.ER.H212R

source_name: Primary HUVECs infected with pBP-FoxO3.A3.ER.H212R vector


title: MS25_P11_V58_5_H212R


title: MS25_P12_V58_5_H212R_12H_0HT


title: MS25_P8_V58_5_LV_12H_OHT


title: MS25_P7_V58_5_LV


title: MS25_P9_V58_5_A3


title: MS25_P6_V58_H212_12h_0HT


title: MS25_P4_V58_3_12H_0HT


title: 13685789-5573-CONCY3-PHACY5

status: Public on Jan 31 2010

city: Jouy en Josas

first: Yu

last: GAO

address: INRA, BAT440

department: Animal Genetics

institute: GABI-GIS

description: The peripheral blood mononuclear cells (PBMCs) from Large White pigs (male) (~50 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature

hyb_protocol: The CyDye-labelled cDNA samples were evaporated and were resuspended at a final concentration of 2.5 pmol/ul in cDNA/long oligonucleotide hybridization buffer. In total, 28 SLA-RI/NRSP8-13K chips were used in this experiment. Microarray hybridization was performed using coring hybridization system. Slides were presocked and prehybridized using Corning “Pronto! Universal Hybridization Solutions and Kits” (Product #40026) to unbound amino groups before hybridization. Hybridization was carried out for 16 h in the dark at 42oC in sealed Corning Hybridization Cassettes (Product #2551) submerged in a water bath. The slides were washed according to a commercial protocol (Corning, Product #40026) and dried by centrifugation at 1600 rpm for 2 min.

scan_protocol: Scanned on a GenePix 4000B scanner. Images were quantified using GenePix Pro software V6.0.

data_processing: After data pre-processing within-array global loess normalisation, the empirical eBayes method in Limma, which computed moderated t-statistics, moderated F-statistics, and log-odds of differential expression, was applied to identify the significance of differential expression at each culture condition.

organism: Sus scrofa

label_protocol: Cy3 or Cy5 was incorporated into each total RNA sample (5 ug) using ChipShotTM Direct Labeling System (Promega) and the CyDye-labelled cDNA was purified by ChipShotTM.

growth_protocol: PBMCs from seven Large White male pigs (~50 kg) were isolated by Ficoll-Hypaque density gradient certrifugation at room temperature. The PBMCs were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated FCS (fetal calf serum), 2 mmol/L L-glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin. In our experimental conditions, 5x106 cells were incubated for 24 hours in culture medium supplemented with 1 µg/ml LPS or a mixture of PMA at10 ng/ml and ionomycin at 1 ug/ml. For mock-stimulation, cells were maintained in the culture medium for 24 hours. After 24h, PBMCs were further centrifuged for 10 min at 4000 rpm and harvested for RNA extraction.

extract_protocol: Total RNA was extracted from cells using RNeasy Midi Kit (Qiagen, USA)

value: PBMC

value: mock

value: PMA/ionomycin


title: MS25_P5_V58_3_H212R


title: MS25_P1_V58_3_LV


title: MS25_P3_V58_A3


title: MS25_P10_V58_5_A3_12H_OHT


title: 13691599-5571-CONCY3-PHACY5


title: 13691620-5573-PHACY3-CONCY5


title: MS25_P2_V58_3_LV_OHT


title: 13685787-5563-PHACY3-CONCY5


title: 13691603-5571-PHACY3-CONCY5


title: 13691612-5572-PHACY3-CONCY5


title: 13691606-5621-CONCY3-PHACY5


title: 13685782-5563-CONCY3-PHACY5


title: 13691614-5572-CONCY3-PHACY5


title: 13685776-5624-CONCY3-PHACY5


title: 13691609-5621-PHACY3-CONCY5


title: 13685777-5624-PHACY3-CONCY5


title: 13685773-5622-PHACY3-CONCY5


title: 13685771-5622-CONCY3-PHACY5


title: 13691617-5573-LPSCY3-CONCY5

value: LPS


title: 13691618-5573-CONCY3-LPSCY5


title: 13685790-5572-CONCY3-LPSCY5


title: HapMap normal cell line NA19137

description: hybridized to Affy SNP 6.0

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Probe-level intensities were scaled so that the sample-specific median value is 1000.
For further data processing details, please see: The Cancer Genome Atlas Research Network (2008) Nature, 455:1061-1068.

source_name: HapMap normal cell line NA19137

label_protocol: Standard Affymetrix protocol.

growth_protocol: melanoma cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

extract_protocol: DNA was extracted from melanomas as described in Lin et al, Cancer Research (2008), 68:664-673. DNA from HapMap normal samples was obtained from Coriell cell repository

treatment_protocol: cells were grown under standard conditions

tag: disease status

value: normal


title: 13691597-5571-CONCY3-LPSCY5


title: 13691615-5572-LPSCY3-CONCY5


title: 13691596-5571-LPSCY3-CONCY5


title: 13685783-5563-LPSCY3-CONCY5


title: 13685781-5563-CONCY3-LPSCY5


title: 13691607-5621-LPSCY3-CONCY5


title: HapMap normal cell line NA19153

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA19153


title: 13685775-5624-LPSCY3-CONCY5


title: HapMap normal cell line NA19194

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA19194


title: HapMap normal cell line NA19099

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA19099


title: HapMap normal cell line NA18871

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18871


title: HapMap normal cell line NA18508

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18508


title: HapMap normal cell line NA12144

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA12144


title: 13685774-5624-CONCY3-LPSCY5


title: HapMap normal cell line NA18504

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18504


title: 13685772-5622-LPSCY3-CONCY5


title: 13691605-5621-CONCY3-LPSCY5


title: 13685770-5622-CONCY3-LPSCY5


title: STZ6

status: Public on Jan 30 2010

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
4256337002_F
Replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization using BeadStudio software.

source_name: STZ-treated retina

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: treatment

value: Streptozotocin


title: STZ5

description:
4256337002_E
Replicate 5


title: HapMap normal cell line NA19142

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA19142


title: HapMap normal cell line NA18912

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18912


title: STZ4

description:
4256337002_D
Replicate 4


title: HapMap normal cell line NA18870

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18870


title: HapMap normal cell line NA18863

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA18863


title: STZ3

description:
4256337002_C
Replicate 3


title: Control6

description:
4256337010_F
Replicate 6

source_name: Un-treated retina

value: control


title: HapMap normal cell line NA19143

description: hybridized to Affy SNP 6.0

source_name: HapMap normal cell line NA19143