title: WT at LL4, rep2

source_name: Synechococcus wild type cells collected at hour 4 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL24, rep2

status: Public on Aug 01 2009

type: RNA

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

description: Gene expression data from Synechococcus elongatus PCC 7942

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings, divided by corresponding genomic DNA signals (genomic DNA sample), and global scaling as normalization method except for samples under DD conditions. The trimmed average target intensity of each array was arbitrarily set to 1000. For data under DD, genomic-DNA-divided value is shown.

label: biotin

molecule: total RNA

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Synechococcus wild type cells collected at hour 24 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (46 micromol/m^2/sec) or the dark

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: Genotype

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: WT at LL8, rep2

source_name: Synechococcus wild type cells collected at hour 8 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL48, rep1

source_name: Synechococcus wild type cells collected at hour 48 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at DD44, rep1

source_name: Synechococcus wild type cells collected at hour 44 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at LL36, rep1

source_name: Synechococcus wild type cells collected at hour 36 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL20, rep2

source_name: Synechococcus wild type cells collected at hour 20 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL44, rep1

source_name: Synechococcus wild type cells collected at hour 44 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL32, rep1

source_name: Synechococcus wild type cells collected at hour 32 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL28, rep1

source_name: Synechococcus wild type cells collected at hour 28 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL4, rep1


title: WT at LL8, rep1


title: WT at LL16, rep1

source_name: Synechococcus wild type cells collected at hour 16 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL20, rep1


title: WT at LL12, rep1

source_name: Synechococcus wild type cells collected at hour 12 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL24, rep1


title: WT at LL40, rep1

source_name: Synechococcus wild type cells collected at hour 40 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: CJD21/PMK-CAP1-CSE, untreated (expt 1)

status: Public on Jun 22 2009

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

country: USA

institute: University of Tennessee Health Science Center

description: First-generation custom C. albicans Affymetrix chip manufactured by NimbleGen.

hyb_protocol: The cRNA pellet was suspended in 10 μl of RNase-free water and 10 μg was fragmented at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45°C to C. albicans NimbleExpress GeneChip arrays (Affymetrix). Arrays were washed at 25°C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20. Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in GeneChip Operating System v2.0 (GCOS; Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250. The signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM – MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes, respectively.

data_processing: The scaled gene expression values from GCOS software were imported into GeneSpring 7.2 software (Agilent Technologies) for preprocessing and data analysis. Probesets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as the median expression for that gene across all chips in the study.

organism: Candida albicans

source_name: CAP1-deficient strain with hyperactive CAP1 allele introduced, untreated

label_protocol: First and second strand cDNA was synthesized from 15 μg total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and oligo-dT24-T7 primer (PrOligo) according to the manufacturer's instructions. cRNA was synthesized and labelled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray HighYield RNA Transcript Labelling Kit (ENZO Diagnostics). Double stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 μl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides, dithtiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37°C. The labeled cRNA was separated from unincorporated ribonucleotides with a CHROMA SPIN-100 column (Clontech) and ethanol precipitated at −20°C overnight.

extract_protocol: Cells were collected by centrifugation and cell pellets were frozen for at least 30min at -80 deg Celsius prior to RNA isolation. Total RNA was then isolated from cells using the hot phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cells were grown for 3hrs as before in YPD.

tag: strain

tag: experimental treatment

value: untreated


title: CJD21/PMK-CAP1-CSE, untreated (expt 2)

description: First-generation custom C. albicans Affymetrix chips manufactured by NimbleGen.

extract_protocol: Cells were collected by centrifugation and cell pellets were frozen at least 30min at -80 deg Celsius prior to RNA isolation.  RNA was then isolated using the hot phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was adjusted to 0.2 and cultures were allowed to grow an additional 3 hours as before in YPD.


title: CJD21/PMK + DMSO (expt 1)

description: second-generation custom C. albicans Affymetrix chips manufactured by Affymetrix.

data_processing: The scaled gene expression values from GCOS software were imported into GeneSpring 7.2 software (Agilent Technologies) for preprocessing and data analysis. Probesets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as the median expression for that gene across all chips in the study. Pairwise comparison of gene expression was performed for each matched experiment.

source_name: CAP1-deficient strain, DMSO-treated

extract_protocol: Cells were collected by centrifugation, and cell pellets were stored at -80 deg Celsius at least 30min until RNA was isolated.  Total RNA was isolated using the hot phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown an additional 3hrs as before in YPD.  DMSO was then added to the culture at the same volume as benomyl stock was added to benomyl-treated cultures, and cells were incubated for 30min as before.

value: DMSO, 30min


title: CJD21/PMK + Benomyl (expt 2)

description: first-generation custom C. albicans Affymetrix chips manufactured by NimbleGen.

source_name: CAP1-deficient strain, benomyl-treated

extract_protocol: Cells were collected by centrifugation, and cell pellets were stored at -80 deg Celsius at least 30min until RNA was isolated.  TOtal RNA was isolated using the hot phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown an additional 3hrs as before in YPD.  Benomyl was then added to the culture to a final concentration of 25 mcg/ml, and cells were incubated for 30min as before.

value: benomyl, 25 mcg/ml, 30min


title: Log-phase wild-type bacteria grown at 37C

status: Public on Dec 22 2008

city: Beijing

first: Li

last: Zhu

address: 20 Dongdajie, Fengtai District

department: State Key Laboratory of Pathogens and Biosecurity

country: China

institute: Beijing Institute of Biotechnology

description: Log-phase wild-type bacteria grown at 37 degrees Celsius.

hyb_protocol: Available at manufacturer's website: www.nimblegen.com

organism: Shigella flexneri

source_name: Wild-type bacteria of log-phase cultures grown at 37C

growth_protocol: Wild-type bacteria were maintained on TSA plates at 30 degrees Celsius and cultured in LB broth at 37 degrees Celsius.

extract_protocol: use QIAGEN RNAeasy mini kit

treatment_protocol: Wild-type bacteria were cultured in LB broth into log-phase (OD=0.6) at 37 degrees Celsius.

tag: serotype

tag: genotype

value: wild-type

tag: growth phase

value: log-phase

tag: temperature


title: CJD21/PMK-CAP1 + DMSO (expt 3)

description: Arrays used were first-generation custom C. albicans Affymetrix chips manufactured by NimbleGen.

scan_protocol: The fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in GeneChip Operating System v2.0 (GCOS; Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250.

data_processing: The signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM – MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes, respectively.

source_name: CAP1-deficient strain with CAP1 reintroduced, DMSO-treated

extract_protocol: Cells were collected by centrifugation and cell pellets were frozen at -80 deg Celsius for at least 30min prior to RNA isolation.  RNA was isolated from cell pellets using the hot-phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density of the culture was then adjusted to 0.2 and allowed to grow as before for 3hrs in YPD.  DMSO was added to the culture (at the same volume that the benomyl stock was added in the benomyl-treated cultures) and cells were grown for 30min.

value: CJD21/PMK-CAP1 (wildtype CAP1 allele)


title: CJD21/PMK + Benomyl (expt 3)


title: CJD21/PMK-CAP1 + DMSO (expt 1)

description: Second-generation custom C. albicans Affymetrix chip manufactured by Affymetrix

extract_protocol: Cells were collected by centrifugation, and cell pellets were frozen at -80 deg Celsius for at least 30min prior to RNA isolation.  Total RNA was isolated using the hot phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown for an additional 3hrs as before in YPD.  DMSO was then added to the cultures at the same volume as benomyl stock was added to benomyl-treated cultures, and cultures were incubated for 30min as before.


title: CJD21/PMK-CAP1 + Benomyl (expt 1)

source_name: CAP1-deficient strain with CAP1 reintroduced, benomyl-treated

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown for an additional 3hrs as before in YPD.  Benomyl was then added to the cultures at a final concentration of 25 mcg/ml, and cultures were incubated for 30min as before.


title: CJD21/PMK-CAP1 + DMSO (expt 2)

description: Array is first-generation custom C. albicans Affymetrix chip manufactured by NimbleGen.

extract_protocol: Cells were collected by centrifugation.  Cell pellets were frozen at -80 deg Celsius for at least 30min, and RNA was isolated from the cells by the hot-phenol method.

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was adjusted to 0.2, and cells were grown as before in YPD for 3hrs.  DMSO was then added as a diluent control, and cells were incubated an additional 30min prior to harvest.


title: CJD21/PMK-CAP1, untreated (expt 1)

source_name: CAP1-deficient strain with CAP1 reintroduced, untreated

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density of the culture was then adjusted to 0.2 and allowed to grow as before for 3hrs in YPD.


title: CJD21/PMK + Benomyl (expt 1)

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown for an additional 3hrs as before in YPD.  Benomyl was then added to the cultures to a final concentration of 25 mcg/ml, and cultures were incubated for 30min as before.


title: CJD21/PMK-CAP1, untreated (expt C)

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown for an additional 3hrs as before in YPD.


title: CJD21/PMK-CAP1 + Benomyl (expt 3)

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density was adjusted to 0.2, and cells were grown as before in YPD for 3hrs.  Benomyl was then added to a final concentration of 25 mcg/ml, and cells were incubated an additional 30min prior to harvest.


title: CJD21/PMK-CAP1-CSE, untreated (expt C)


title: Stationary-phase mutant bacteria grown at 30C

description: Stationary-phase mutant bacteria grown at 30 degree

scan_protocol: Available at manufacturer's website: www.nimblegen.com

source_name: Mutant bacteria of stationary-phase cultures grown at 30C

growth_protocol: Mutant bacteria were maintained at TSA plates at 30 degree and cultured in LB broth at 30 degree

treatment_protocol: Mutant bacteria were cultured at 30 degree for 9 hours

value: shigella flexneri 2a str. 2457T:a virulence plasmid-free strain (delta pSF strain)

value: mutant

value: stationary-phase


title: Stationary-phase wild-type bacteria grown at 30C

description: Stationary-phase wild-type bacteria grown at 30 degrees Celsius.

data_processing: Available at manufacturer's website: www.nimblegen.com

source_name: Wild-type bacteria of stationary-phase cultures grown at 30C

growth_protocol: Wild-type bacteria were maintained on TSA plates at 30 degrees Celsius and cultured in LB broth at 30 degrees Celsius.

treatment_protocol: Wild-type bacteria were cultured at 30 degrees Celsius for 9 hours.


title: CJD21/PMK + DMSO (expt 3)

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30deg Celsius with agitation.  Optical density was then adjusted to 0.2, and cultures were grown an additional 3hrs as before in YPD.  DMSO was then added to the culture at the same volume as benomyl was added to benomyl-treated cultures, and cells were incubated for 30min as before.


title: CJD21/PMK + DMSO (expt 2)


title: CJD21/PMK-CAP1 + Benomyl (expt 2)

treatment_protocol: Cultures were grown to saturation overnight in YPD at 30 deg Celsius with agitation.  Optical density of the culture was then adjusted to 0.2 and allowed to grow as before for 3hrs in YPD.  Benomyl was added to a final concentration of 25 mcg/ml, and cells were grown for 30min.


title: Log-phase wild-type bacteria grown at 30C

description: Log-phase wild-type bacteria grown at 30 degrees Celsius.

source_name: Wild-type bacteria of log-phase cultures grown at 30C

label_protocol: Available at manufacturer's website: www.nimblegen.com

treatment_protocol: Wild-type bacteria were cultured in LB broth into log-phase (OD=0.6) at 30 degrees Celsius.


title: CJD21/PMK-CAP1, untreated (expt 2)


title: Log-phase mutant bacteria grown at 30C

description: Log-phase mutant bacteria grown at 30 degree

source_name: Mutant bacteria of log-phase cultures grown at 30C

treatment_protocol: Mutant bacteria were cultured into log-phase (OD=0.6) at 30 degree


title: nirA637_strain_repressed_vs_induced

status: Public on Jan 01 2009

city: Vienna

first: Harald

last: Berger

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Applied Life Sciences, Vienna

description:
Four slides were analysed and condensed to one sample. Each slide contains  2 replicas of each oligo. Dye swaps were applied as follows:
1:GSM265039_1.txt	Cy3:r   Cy5:i;
2:GSM265039_2.txt	Cy3:r 	Cy5:i;
3:GSM265039_3.txt	Cy3:i 	Cy5:r;
4:GSM265039_4.txt	Cy3:i 	Cy5:r;
Here r stands for repressed (ammonium) and i for induced (nitrate)

hyb_protocol: The Cy-dye labeled cDNA probes (mix of Cy3 and Cy5) were hybridized according to the protocoll found at http://pfgrc.tigr.org/protocols.shtml.

scan_protocol: An Agilent DNA Microarray scanner G 25 65 B was used for obtaining TIFF files. These were processed using Agilent Feature extracton software version 9.1.

data_processing:
Data were analysed using the R/Bioconductor environment utilizing the package limma (Smyth, G.K. (2004), Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3) and the function duplicateCorrelation (Smyth, G.K. (2005), Bioinformatics 21(9), 2067-2075).
Non-processed median values were used for analysis.
The R/Bioconductor protocol:
>RG <- read.maimages(targets$FileName,source="generic", columns=col);
>RG$genes<-gene.names;
>MA<-normalizeWithinArrays(RG, method="loess");
>MA<-normalizeBetweenArrays(MA);
>design<- c(1,1,-1,-1);
>MA2 <- MA[MA$genes$Design.Strain=="FGSC A4", ];
>corfit <- duplicateCorrelation(MA2,design,ndups=2);
>fit <- lmFit(MA2,design,ndups=2,correlation=corfit$consensus);
>fit <- eBayes(fit);
(any operations dealing with sorting etc. were left out)

organism: Aspergillus nidulans

source_name: nirA637 pabaA1, ammonium (repressed)

label_protocol: The RNA samples were extracted with Trizol and labelled by incorporation of aminoallyl-dUTP followed by a coupling of the aminoallyl groups to either Cyanine-3 or Cyanine-5 (see protocolls at http://pfgrc.tigr.org/protocols.shtml).

growth_protocol: Wild Type  pabaA1 strain grown over night (16 hours) on minimal medium as descirbed by Cove (Cove, D.J. 1966, Biochim Biophys Acta 113:51-56) with 1% glucose as carbon and 10 mM ammonium as nitrogen source.

extract_protocol: Mycelia were harvested by filtration and quickly frozen in liquid nitrogen. For total RNA isolation, the mycelia were disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 0.8% agarose gel, stained with ethidium bromide, and then visualized with UV-light. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

treatment_protocol: Mycelia were washed with nitrogen free minimal media and incubated for 60 minutes on media containing 10 mM ammonium.

value: nirA637 pabaA1

tag: treatment

value: repressed, ammonium (10 mM)

source_name: nirA637 pabaA1, nitrate (induced)

treatment_protocol: Mycelia were washed with nitrogen free minimal media and incubated for 30 minutes on nitrogen free minimal media followed by addition of nitrate (10 mM) of additional 30 minutes.

value: induced, nitrate (10 mM)


title: Stationary-phase wild-type bacteria grown at 37C

description: Stationary-phase wild-type bacteria grown at 37 degrees Celsius.

source_name: Wild-type bacteria of stationary-phase cultures grown at 37C

treatment_protocol: Wild-type bacteria were cultured at 37 degrees Celsius for 9 hours.


title: Wild_Type_strain_repressed_vs_N-starved

description:
Four slides were analysed and condensed to one sample. Each slide contains  2 replicas of each oligo. Dye swaps were applied as follows:
1:GSM265038_2.txt	Cy3:r   Cy5:st;
2:GSM265038_3.txt	Cy3:st 	Cy5:r;
3:GSM265038_4.txt	Cy3:r 	Cy5:st;
4:GSM265038_1.txt	Cy3:st 	Cy5:r;
Here r stands for repressed (ammonium) and st for starved (nitrogen)

source_name: Wild Type pabaA1, ammonium (repressed)

value: wild type pabaA1

source_name: Wild Type pabaA1, starved (nitrogen)

treatment_protocol: Mycelia were washed with nitrogen free minimal media and incubated for 60 minutes on nitrogen free minimal media.

value: nitrogen starved


title: male chicken BC2 n°6558 (from the sire: BC1 n°1940)

status: Public on Sep 20 2008

city: Rennes

first: Sandrine

last: Lagarrigue

address: 65 rue de St Brieuc

country: France

institute: Agrocampus Rennes/ INRA

description:
Male broiler chicken fed ad libitum during 4 hours minimum.

For each gene, the fluorescence ratio represents the relative abundance of the hepatic mRNA of the animal of interest  compared with the RNA pool reference.

hyb_protocol: The microarray was hybridized for 8 h at 42°C with Cy5-labeled chicken cDNA sample  and an aliquot of the Cy3-labeled reference cDNA using automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a laser scanner (GenePix 4000A from Axon Instrument, CA) at 550 nM for Cy3 and 640 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Pre-processing and normalization of data were accomplished using the R-project statistical and Bioconductor environment (http://www.r-project.org) (http://www.bioconductor.org). For the normalization step, data were filtered according to 3 criterions based on 1) the genepix flag automatically performed by GenepixPro 4.0; 2) the SNR 3) the asymmetry spot (see Desert et al. 2008). The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized by “Lowess fitness”.

organism: Gallus gallus

label_protocol: Five µg of each mRNA sample were reverse-transcribed and Cy5 fluorescent-labeled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

growth_protocol: Standard broiler chicken growth protocol. Livers were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction.

extract_protocol: Total RNA was extracted from liver using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA)

tag: chicken type

value: broiler

tag: gender

value: male

tag: age

value: 9 weeks

tag: tissue

value: liver

source_name: Reference

label_protocol: Five µg of each mRNA sample were reverse-transcribed and Cy3 fluorescent-labeled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

tag: sample type

value: total liver RNA pool obtained from the 48 male broiler chickens (sire BC1 n°1940)


title: Wild_Type_strain_repressed_vs_induced

description:
Seven slides were analysed and condensed to one sample. Each slide contains  2 replicas of each oligo. Dye swaps were applied as follows:
1:GSM265037_1.txt	Cy3:r 	Cy5:i;
2:GSM265037_2.txt	Cy3:i 	Cy5:r;
3:GSM265037_3.txt	Cy3:r 	Cy5:i;
4:GSM265037_4.txt	Cy3:r 	Cy5:i;
5:GSM265037_5.txt	Cy3:r 	Cy5:i;
6:GSM265037_6.txt	Cy3:i 	Cy5:r;
7:GSM265037_7.txt	Cy3:i 	Cy5:r;
Here r stands for repressed (ammonium) and i for induced (nitrate)

data_processing:
Data were analysed using the R/Bioconductor environment utilizing the package limma (Smyth, G.K. (2004), Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3) and the function duplicateCorrelation (Smyth, G.K. (2005), Bioinformatics 21(9), 2067-2075).
Non-processed median values were used for analysis.
The R/Bioconductor protocol:
>RG <- read.maimages(targets$FileName,source="generic", columns=col);
>RG$genes<-gene.names;
>MA<-normalizeWithinArrays(RG, method="loess");
>MA<-normalizeBetweenArrays(MA);
>design<- c(1,-1,1,1,1,-1,-1);
>MA2 <- MA[MA$genes$Design.Strain=="FGSC A4", ];
>corfit <- duplicateCorrelation(MA2,design,ndups=2);
>fit <- lmFit(MA2,design,ndups=2,correlation=corfit$consensus);
>fit <- eBayes(fit);
(any operations dealing with sorting etc. were left out)

source_name: Wild Type pabaA1, nitrate (induced)

treatment_protocol: Mycelia were washed with nitrogen free minimal media and incubated for 30 minutes on nitrogen free minimal media followed by addition of 10 mM nitrate and incubation for additional 30 minutes.


title: male chicken BC2 n°6549  (from the sire: BC1 n°1940)

extract_protocol:
Total RNA was extracted  from liver using TRIzol reagent according to the
manufacturer’s instructions (Invitrogen, Carlsbad, CA)


title: male chicken BC2 n°6403  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6553  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6532  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6548  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6537 (from the sire: BC1 n°1940)


title: A549 LV H1term pool vs. A549 LV p53 1026

status: Public on Apr 01 2009

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Microarray analysis has been useful for identifying the targets of many transcription factors. However, gene expression changes in response to transcription factor perturbation reveal both direct transcriptional targets and secondary gene regulation. By integrating RNA interference, gene expression profiling, and chromatin immunoprecipitation technologies, we identified a set of 32 direct transcriptional targets of the tumor suppressor p53. Of these 32 genes, 11 are not currently associated with the core p53 pathway. From among these novel pathway members, we focused on understanding the connection between p53 and SULF2, which encodes an extracellular heparan sulfate 6-O-endosulfatase that modulates the binding of growth factors to their cognate receptors and that has been shown to function as a tumor suppressor. Genetic and pharmacologic perturbation of p53 directly influences SULF2 expression, and similar to silencing of TP53, RNA interference-mediated suppression of SULF2 results in an impaired senescence response of cells to genotoxic stress. Thus, our integrated genomic approach has led to the identification of a novel mediator of p53 network biology.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Homo sapiens

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: conditions

value: A549 LV H1term pool

tag: cell line

tag: agent

value: shRNA TP53


title: male chicken BC2 n°5646 (from the sire: BC1 n°1940)


title: male chicken BC2 n°5662  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6413  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6546  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6380  (from the sire: BC1 n°1940)


title: male chicken BC2 n°6406 (from the sire: BC1 n°1940)


title: male chicken BC2 n°6387 (from the sire: BC1 n°1940)


title: male chicken BC2 n°6536 (from the sire: BC1 n°1940)


title: male chicken BC2 n°5656 (from the sire: BC1 n°1940)


title: male chicken BC2 n°5635  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5645 (from the sire: BC1 n°1940)


title: male chicken BC2 n°6385 (from the sire: BC1 n°1940)


title: male chicken BC2 n°5633  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5663  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5630  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5643 (from the sire: BC1 n°1940)


title: male chicken BC2 n°6388  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5640 (from the sire: BC1 n°1940)


title: male chicken BC2 n°6420 (from the sire: BC1 n°1940)


title: male chicken BC2 n°5616  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4131  (from the sire: BC1 n°1940)

data_processing:
The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Pre-processing and normalization of data were accomplished using the R-project statistical and Bioconductor environment (http://www.r-project.org) (http://www.bioconductor.org).

Data filtering: the first step was to select the genes considered as expressed in liver (roughly 60% expected) regarding to a good contrast between spot and background intensities (SNR (Signal to Noise Ratio) defined superior to 2). Among the 20461 genes on microarray, we selected 11590 genes (57%) and eliminated one microarray (n°5643) for which the average SNR was equal to 1.5. Second, we removed 377 genes for which minimum of 20% of spots among the 45 microarrays  did not respect the 2 criteria: i)  absence of the genepix flag (automatically performed by GenepixPro 4.0) and ii) a symmetry of the spot. A total of 11213 genes were finally selected. Third we targeted the isolated “bad” spots not conformed to the two criteria in order not to take into account during the normalization procedure: 2.8% of spots were concerned.

Data normalization: the Cy5/Cy3 ratio used was expressed as the Log2 of the ratio of median pixel intensity of the two red and green spots. Median Log2 ratio values were then normalized (ratio centered on zero) by Lowess fitness. Only the array spots conforming to the filtering step were used for the normalization.


title: male chicken BC2 n°4142  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4141  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4130  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4133 (from the sire: BC1 n°1940)


title: male chicken BC2 n°4108  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5617  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4107  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4112  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4120  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4111  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4122  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4101  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4116 (from the sire: BC1 n°1940)


title: male chicken BC2 n°4109  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4123  (from the sire: BC1 n°1940)


title: male chicken BC2 n°4114  (from the sire: BC1 n°1940)


title: male chicken BC2 n°5618  (from the sire: BC1 n°1940)


title: MPI-598

status: Public on Jun 17 2008

city: Regensburg

first: Stefan

last: Bentink

state: Bayern

address: Josef Engertstr. 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

description: Mature aggressive B-cell lymphoma

hyb_protocol: Affymetrix hybridization was carried with U133A GeneChips according to the manufacturer’s recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter.

scan_protocol: After hybridization of night (16 hours, 45 C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

label: Biotin

source_name: Frozen tissue

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation.

extract_protocol: RNA was isolated using RNeasy Mini Kit (both from QIAGEN).The concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed by analysis of an aliquot in the Agilent BioAnalyzer.

tag: Unique Identifier

tag: Age at diagnosis

tag: Sex of patient

tag: Consensus morphological diagnosis from expert hematopathologists

value: DLBCL

tag: Immunohistochemistry

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):0

tag: Cytogenetics

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

tag: ArrayCGH

value: Complexity/relative number of genomic gains and losses:NA

tag: Cytogenetics/arryCGH

value: MYC-break with simple or complex karyotype:MYC.neg

tag: Ann Arbour Stage

tag: Gene expression

value: Diagnosis according to mBL gene expression signature:non-mBL

tag: Germinal center like/ activated B-cell like signature

value: unclassified

tag: mBL index (>0.95 => mBL)


title: MPI-597

description: Mature aggressive B-cell lymphoma

value: male

value: Proportion of positive tumor cells BCL2 (>1 => pos):2

value: Percentage Ki-67 of positive tumor cells (proliferative index):80

value: Percentage of positive tumor cells BCL6 (>1 => pos):NA

value: Breakpoint at BCL6-locus detected:pos

value: ABC


title: MPI-594

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Signal intensity BCL2:1

value: Complexity/relative number of genomic gains and losses:3


title: MPI-581

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Percentage Ki-67 of positive tumor cells (proliferative index):50

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:13

value: GCB


title: MPI-567

description: Mature aggressive B-cell lymphoma

value: male

value: FL

value: Proportion of positive tumor cells CD10 (>1 => pos):NA

value: Proportion of positive tumor cells BCL2 (>1 => pos):2

value: Percentage Ki-67 of positive tumor cells (proliferative index):70

value: Complexity/relative number of genomic gains and losses:0

value: MYC-break with simple or complex karyotype:MYC.neg

value: I

value: Diagnosis according to mBL gene expression signature:intermediate


title: MPI-530

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):80

value: Complexity/relative number of genomic gains and losses:4


title: MPI-571

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Percentage Ki-67 of positive tumor cells (proliferative index):60

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg


title: MPI-531

description: Mature aggressive B-cell lymphoma

value: male

value: Proportion of positive tumor cells BCL2 (>1 => pos):3

value: Complexity/relative number of genomic gains and losses:3

value: MYC-break with simple or complex karyotype:MYC.neg

value: Diagnosis according to mBL gene expression signature:non-mBL

value: unclassified


title: MPI-578

description: Mature aggressive B-cell lymphoma

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):1

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):50

value: Percentage of positive tumor cells BCL6 (>1 => pos):1


title: MPI-592

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Complexity/relative number of genomic gains and losses:2

value: Diagnosis according to mBL gene expression signature:intermediate

value: GCB


title: MPI-236

status: Public on Jun 07 2006

city: Berlin

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

description: Mature aggressive B-cell lymphoma

tag: Relapse

value: no

tag: Age

tag: Sex

value: male

value: present

value: absent

value: III

tag: Lesions

value: nodal

value: dead

tag: Radiotherapy

value: yes

tag: RITUXIMAB

tag: Chemotherapy

value: other

value: non-mBL

value: Test


title: MPI-243

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: MYC-negative

value: unclassified

value: Training


title: MPI-246

description: Mature aggressive B-cell lymphoma


title: MPI-251

description: Mature aggressive B-cell lymphoma

value: female

value: alive

value: CHOP-like


title: MPI-415

description: Mature aggressive B-cell lymphoma

tag: Unique Identifier

tag: Age at diagnosis

tag: Sex of patient

value: male

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):85

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):1

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:6

value: MYC-break with simple or complex karyotype:MYC.neg

value: Diagnosis according to mBL gene expression signature:non-mBL

value: ABC


title: MPI-388

description: Mature aggressive B-cell lymphoma

value: female

tag: Consensus morphological diagnosis from expert hematopathologists

value: DLBCL

tag: Immunohistochemistry

value: Proportion of positive tumor cells CD10 (>1 => pos):NA

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):60

value: Percentage of positive tumor cells BCL6 (>1 => pos):0

tag: Cytogenetics

value: IgH-BCL2 Fusion:pos

value: Complexity/relative number of genomic gains and losses:2

value: unclassified


title: MPI-250

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: present

value: absent

value: MYC-negative

value: II

value: nodal

value: dead

value: yes

value: CR

value: CHOP-like

value: intermediate

value: Test


title: MPI-247

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: IV

value: nodal + extranodal

value: PR

value: other

value: non-mBL

value: Training


title: MPI-249

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: present

value: absent

value: GCB


title: MPI-224

description: Mature aggressive B-cell lymphoma

value: unk

value: female

value: MYC-negative

value: unclassified


title: MPI-232

description: Mature aggressive B-cell lymphoma


title: MPI-239

description: Mature aggressive B-cell lymphoma

value: dead

value: ABC

value: Test


title: MPI-244

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: IV

value: nodal + extranodal


title: MPI-213

description: Mature aggressive B-cell lymphoma

value: alive

value: non-mBL


title: MPI-284

description: Mature aggressive B-cell lymphoma

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):90

value: Percentage of positive tumor cells CD5 (>1 => pos):1

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

tag: ArrayCGH

value: Complexity/relative number of genomic gains and losses:7

tag: Cytogenetics/arryCGH

value: MYC-break with simple or complex karyotype:MYC.neg

tag: Ann Arbour Stage

value: Diagnosis according to mBL gene expression signature:intermediate


title: MPI-225

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: DLBCL

value: present

value: absent

value: MYC-negative

value: intermediate

value: GCB

value: Training

value: no


title: MPI-216

description: Mature aggressive B-cell lymphoma

value: II

value: nodal

value: dead

value: CRu

value: CHOP-like

value: Test


title: MPI-215

description: Mature aggressive B-cell lymphoma

value: female

value: III

value: alive

value: yes

value: CR

value: non-mBL

value: ABC


title: MPI-223a

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: present

value: absent

value: MYC-negative

value: PR


title: MPI-219

description: Mature aggressive B-cell lymphoma

value: unk

value: aggressive B-NHL.unclassifiable

value: unclassified

value: Training

value: no


title: male chicken BC2 n°4113  (from the sire: BC1 n°1940)

tag: chicken type

value: broiler

tag: gender

tag: age

value: 9 weeks

tag: tissue

value: liver

tag: sample type

value: total liver RNA pool obtained from the 48 male broiler chickens (sire BC1 n°1940)


title: MPI-205

description: Mature aggressive B-cell lymphoma

tag: Relapse

tag: Age

tag: Sex

value: III

tag: Lesions

value: nodal + extranodal

value: alive

tag: Radiotherapy

value: non-mBL

value: Test


title: MPI-196

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: present

value: absent

value: II

tag: RITUXIMAB

value: CR

tag: Chemotherapy

value: CHOP-like


title: MPI-208

description: Mature aggressive B-cell lymphoma

value: unk

value: MYC-negative

value: unclassified

value: no


title: MPI-201

description: Mature aggressive B-cell lymphoma

value: Training


title: MPI-204

description: Mature aggressive B-cell lymphoma

value: male

value: dead

value: yes

value: CRu


title: MPI-199

description: Mature aggressive B-cell lymphoma

value: I

value: extranodal

value: alive

value: non-mBL

value: ABC

value: Test


title: MPI-194

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: present

value: absent

value: III

value: nodal

value: Progress


title: MPI-200

description: Mature aggressive B-cell lymphoma

value: no

value: MYC-negative

value: CR

value: CHOP-like

value: unclassified

value: Training


title: MPI-195

description: Mature aggressive B-cell lymphoma

value: male

value: I

value: extranodal

value: dead

value: yes


title: MPI-191

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: other

value: non-mBL


title: MPI-206

description: Mature aggressive B-cell lymphoma

value: present

value: absent

value: III

value: nodal + extranodal

value: PR

value: Test


title: MPI-192

description: Mature aggressive B-cell lymphoma

value: no

value: MYC-negative

value: nodal

value: alive

value: Progress

value: CHOP-like

value: ABC


title: MPI-193

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: intermediate

value: GCB

value: Training


title: MPI-179

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: present

value: absent

value: non-mBL


title: MPI-185

description: Mature aggressive B-cell lymphoma

value: Test

value: no


title: MPI-180

description: Mature aggressive B-cell lymphoma

value: III

value: nodal

value: yes


title: MPI-186

description: Mature aggressive B-cell lymphoma

value: MYC-negative

value: unclassified


title: MPI-184

description: Mature aggressive B-cell lymphoma

value: I

value: extranodal

value: dead

value: CR

value: CHOP-like


title: MPI-178

description: Mature aggressive B-cell lymphoma

value: unk

value: female

value: atypical BL

value: ABC

value: Training


title: MPI-177

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: present

value: absent

value: non-mBL


title: MPI-182

description: Mature aggressive B-cell lymphoma

value: male

value: aggressive B-NHL.unclassifiable

value: no


title: MPI-183

description: Mature aggressive B-cell lymphoma

value: MYC-negative

value: III

value: nodal

value: Progress

value: other


title: MPI-188

description: Mature aggressive B-cell lymphoma

value: IV

value: nodal + extranodal

value: dead

value: CHOP-like

value: unclassified


title: MPI-175

description: Mature aggressive B-cell lymphoma

value: female

value: atypical BL

value: II

value: yes

value: intermediate

value: GCB

value: Training


title: MPI-174

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: DLBCL

value: present

value: absent

value: MYC-negative

value: non-mBL

value: ABC

value: no


title: MPI-159

description: Mature aggressive B-cell lymphoma

value: IV

value: nodal + extranodal

value: dead

value: Progress

value: CHOP-like

value: Test


title: MPI-143

description: Mature aggressive B-cell lymphoma

value: I

value: extranodal

value: alive

value: CR

value: intermediate

value: GCB


title: MPI-164

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: present

value: absent

value: other

value: Training


title: MPI-167

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: MYC-negative

value: III

value: nodal

value: PR

value: non-mBL

value: ABC


title: MPI-145

description: Mature aggressive B-cell lymphoma

value: II

value: alive

value: yes

value: CR

value: CHOP-like

value: unclassified

value: Test


title: MPI-287

description: Mature aggressive B-cell lymphoma

tag: Unique Identifier

tag: Age at diagnosis

tag: Sex of patient

tag: Consensus morphological diagnosis from expert hematopathologists

value: aggressive B-NHL.unclassifiable

tag: Immunohistochemistry

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):2

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):90

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:0

value: MYC-break with simple or complex karyotype:MYC.neg

tag: Gene expression

value: Diagnosis according to mBL gene expression signature:non-mBL

tag: Germinal center like/ activated B-cell like signature

value: GCB

tag: mBL index (>0.95 => mBL)


title: MPI-146

description: Mature aggressive B-cell lymphoma

value: unk

value: male

value: DLBCL

value: present

value: absent

value: MYC-negative

value: non-mBL

value: ABC

value: Training

value: no


title: MPI-152

description: Mature aggressive B-cell lymphoma

value: female

value: II

value: nodal + extranodal

value: alive

value: yes

value: Progress

value: CHOP-like

value: Test


title: MPI-126

description: Mature aggressive B-cell lymphoma

value: male

value: III

value: dead

value: PR

value: intermediate


title: MPI-131

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: present

value: absent

value: MYC-negative


title: MPI-151

description: Mature aggressive B-cell lymphoma

value: no

value: IV

value: nodal

value: CRu

value: non-mBL

value: unclassified


title: MPI-141

description: Mature aggressive B-cell lymphoma

value: extranodal

value: alive

value: CR

value: CHOP-like

value: Test


title: MPI-133

description: Mature aggressive B-cell lymphoma

value: male

value: II

value: dead

value: PR

value: ABC


title: MPI-132

description: Mature aggressive B-cell lymphoma

value: unk

value: DLBCL

value: present

value: absent

value: MYC-negative

value: I


title: MPI-107

description: Mature aggressive B-cell lymphoma

value: female

value: intermediate

value: unclassified

value: Training

value: no


title: MPI-110

description: Mature aggressive B-cell lymphoma

value: alive

value: non-mBL

value: Test


title: MPI-106

description: Mature aggressive B-cell lymphoma

value: IV

value: nodal

value: dead

value: Progress

value: CHOP-like


title: MPI-111

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: present

value: III

value: CRu


title: MPI-115

description: Mature aggressive B-cell lymphoma

value: female

value: absent

value: MYC-negative

value: ABC


title: MPI-130

description: Mature aggressive B-cell lymphoma

value: no

value: nodal + extranodal

value: alive

value: yes


title: MPI-093

description: Mature aggressive B-cell lymphoma

value: unk

value: aggressive B-NHL.unclassifiable

value: intermediate

value: GCB

value: Training


title: MPI-108

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: non-mBL


title: MPI-088

description: Mature aggressive B-cell lymphoma

value: present


title: MPI-135

description: Mature aggressive B-cell lymphoma

value: female

value: III

value: nodal

value: dead

value: CHOP-like

value: Test


title: MPI-083

description: Mature aggressive B-cell lymphoma

value: no

value: absent

value: MYC-negative

value: I

value: extranodal

value: CRu

value: ABC


title: MPI-076

description: Mature aggressive B-cell lymphoma

value: CR

value: ALL-like

value: unclassified

value: Training


title: MPI-098

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: present

value: IV

value: nodal + extranodal

value: alive

value: yes

value: PR

value: non-mBL


title: MPI-124

description: Mature aggressive B-cell lymphoma

value: no

value: female

value: absent

value: MYC-negative

value: II

value: nodal

value: CHOP-like

value: intermediate

value: Test


title: MPI-118

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: dead

value: CRu

value: ABC


title: MPI-100

description: Mature aggressive B-cell lymphoma

value: unk

value: present


title: MPI-069

description: Mature aggressive B-cell lymphoma

value: I

value: alive

value: yes

value: CR

value: non-mBL

value: unclassified


title: MPI-063

description: Mature aggressive B-cell lymphoma

value: no

value: female

value: absent

value: MYC-negative

value: other

value: Training


title: MPI-073

description: Mature aggressive B-cell lymphoma

value: DLBCL


title: MPI-062

description: Mature aggressive B-cell lymphoma

value: male


title: 10-3, photosynthetic, 10 W/m2

status: Public on Jul 19 2003

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: Rhodobacter sphaeroides 2.4.1, Laramie

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

organism: Cereibacter sphaeroides 2.4.1

source_name: photosynthetic conditions (10W/m2 white light illumination, no oxygen); no salt stress

label_protocol: according to Affymetrix protocol

growth_protocol: Cells are grown at anoxic photosynthetic (10 W/m2 illumination) conditions without salt stress

extract_protocol: RNA isolated with bead beater + RNeasy kits

tag: strain


title: MPI-041

description: Mature aggressive B-cell lymphoma

value: aggressive B-NHL.unclassifiable

value: nodal

value: CRu

value: CHOP-like

value: intermediate

value: GCB

value: Test


title: MPI-040

description: Mature aggressive B-cell lymphoma

value: present

value: III

value: dead

value: Progress

value: non-mBL

value: ABC


title: 10-2

status: Public on Mar 11 2003

description: Rhodobacter sphaeroides 2.4.1, Laramie


title: MPI-050

description: Mature aggressive B-cell lymphoma

value: no

value: female

value: absent

value: MYC-negative

value: alive

value: other

value: unclassified


title: MPI-011

description: Mature aggressive B-cell lymphoma

value: unk

value: aggressive B-NHL.unclassifiable

value: Training


title: MPI-047

description: Mature aggressive B-cell lymphoma

value: male

value: DLBCL

value: II

value: nodal


title: MPI-059

description: Mature aggressive B-cell lymphoma

value: present

value: I

value: yes

value: CR

value: CHOP-like

value: intermediate

value: GCB


title: MPI-013

description: Mature aggressive B-cell lymphoma

value: no

value: absent

value: MYC-negative

value: III

value: nodal + extranodal

value: dead

value: non-mBL

value: ABC


title: 10-1

description: Rhodobacter sphaeroides 2.4.1, Laramie


title: MPI-064

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: other

value: Training


title: MPI-012

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: present

value: unclassified

value: Test


title: MPI-045

description: Mature aggressive B-cell lymphoma

value: II

value: nodal

value: alive

value: PR

value: CHOP-like


title: MPI-029

description: Mature aggressive B-cell lymphoma

value: no

value: absent

value: MYC-negative

value: III

value: yes

value: CR


title: MPI-007

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: nodal + extranodal

value: intermediate

value: GCB


title: MPI-009

description: Mature aggressive B-cell lymphoma

value: present

value: dead

value: other

value: non-mBL

value: ABC

value: Test


title: MPI-014

description: Mature aggressive B-cell lymphoma

value: no

value: male

value: Training


title: MPI-015

description: Mature aggressive B-cell lymphoma

value: absent

value: MYC-negative

value: II

value: alive


title: MPI-021

description: Mature aggressive B-cell lymphoma

value: female

value: DLBCL

value: yes

value: CR

value: CHOP-like

value: unclassified


title: MPI-008

description: Mature aggressive B-cell lymphoma

value: present

value: nodal

value: PR


title: MPI-148

description: Mature aggressive B-cell lymphoma

value: atypical BL

value: IV

value: nodal + extranodal

value: ALL-like

value: intermediate

value: GCB

value: Test