title: D.rerio_embryo_CR vs Sth WT 24hpi C

status: Public on Mar 02 2009

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

institute: University of Leiden

description: D_rerio_embryo_CR vs Sth WT 24hpi_replica C

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The fold change was calculated by dividing the test intensity value by the reference value. If this number was less than one the (negative) reciprocal is listed.

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of PBS or bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma).

treatment_protocol: The zebrafish embryos injected at 27 hours post fertilization with either PBS, Salmonella typhimurium WT or Salmonella typhimurium Ra mutant were collected 2, 5, 8 or 24 hours post injection and immediately quenched in liquid nitrogen and stored at -80 ˚C prior to RNA extraction. This sample is a mixture of all RNA samples used in this infection study

tag: CR (common reference) is a mixture of all RNA samples from this infection study.

source_name: D.rerio_embryo_Sth WT 24hpi C

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 24 hours post injection.

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C.  Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: All injection experiments were performed using mixed egg clutches from three tanks of AB strain zebrafish. Embryos were staged at 27 hours post fertilization (hpf) by morphological criteria (Kimmel et al., 1995) and approximately 250 cfus of DsRed expressing S. typhimurium wild type bacteria were injected into the caudal vein close to the urogenital opening.

tag: Salmonella typhimurium wild type-injected zebrafish embryos at 24 hours post injection


title: D.rerio_embryo_CR vs Sth WT 24hpi A

type: RNA

country: Netherlands

description: D_rerio_embryo_CR vs Sth WT 24hpi_replica A

molecule: total RNA

extract_protocol: Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

source_name: D.rerio_embryo_Sth WT 24hpi A


title: D.rerio_embryo_CR vs Sth WT 8hpi A

description: D_rerio_embryo_CR vs Sth WT 8hpi_replica A

source_name: D.rerio_embryo_Sth WT 8hpi A

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 8 hours post injection.

tag: Salmonella typhimurium wild type-injected zebrafish embryos at 8 hours post injection


title: D.rerio_embryo_CR vs Sth WT 5hpi A

description: D_rerio_embryo_CR vs Sth WT 5hpi_replica A

source_name: D.rerio_embryo_Sth WT 5hpi A

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 5 hours post injection.

tag: Salmonella typhimurium wild type-injected zebrafish embryos at 5 hours post injection


title: D.rerio_embryo_CR vs Sth WT 8hpi C

description: D_rerio_embryo_CR vs Sth WT 8hpi_replica C

source_name: D.rerio_embryo_Sth WT 8hpi C


title: D.rerio_embryo_CR vs Sth WT 2hpi B

description: D_rerio_embryo_CR vs Sth WT 2hpi_replica B

source_name: D.rerio_embryo_Sth WT 2hpi B

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 2 hours post injection.

tag: Salmonella typhimurium wild type-injected zebrafish embryos at 2 hours post injection


title: D.rerio_embryo_CR vs Sth WT 8hpi B

description: D_rerio_embryo_CR vs Sth WT 8hpi_replica B

source_name: D.rerio_embryo_Sth WT 8hpi B


title: D.rerio_embryo_CR vs Sth Ra 24hpi B

description: D_rerio_embryo_CR vs Sth Ra 24hpi_replica B

source_name: D.rerio_embryo_Sth Ra 24hpi B

treatment_protocol: All injection experiments were performed using mixed egg clutches from three tanks of AB strain zebrafish. Embryos were staged at 27 hours post fertilization (hpf) by morphological criteria (Kimmel et al., 1995) and approximately 250 cfus of DsRed expressing S. typhimurium Ra mutant bacteria were injected into the caudal vein close to the urogenital opening.

tag: Salmonella typhimurium Ra mutant-injected zebrafish embryos at 24 hours post injection


title: D.rerio_embryo_CR vs Sth WT 5hpi C

description: D_rerio_embryo_CR vs Sth WT 5hpi_replica C

source_name: D.rerio_embryo_Sth WT 5hpi C


title: D.rerio_embryo_CR vs Sth WT 24hpi B

description: D_rerio_embryo_CR vs Sth WT 24hpi_replica B

source_name: D.rerio_embryo_Sth WT 24hpi B


title: D.rerio_embryo_CR vs Sth WT 5hpi B

description: D_rerio_embryo_CR vs Sth WT 5hpi_replica B

source_name: D.rerio_embryo_Sth WT 5hpi B


title: D.rerio_embryo_CR vs Sth WT 2hpi A

description: D_rerio_embryo_CR vs Sth WT 2hpi_replica A

source_name: D.rerio_embryo_Sth WT 2hpi A


title: D.rerio_embryo_CR vs Sth Ra 24hpi C

description: D_rerio_embryo_CR vs Sth Ra 24hpi_replica C

source_name: D.rerio_embryo_Sth Ra 24hpi C


title: D.rerio_embryo_CR vs Sth WT 2hpi C

description: D_rerio_embryo_CR vs Sth WT 2hpi_replica C

source_name: D.rerio_embryo_Sth WT 2hpi C


title: D.rerio_embryo_CR vs PBS 24hpi A

description: D_rerio_embryo_CR vs PBS 24hpi_replica A

source_name: D.rerio_embryo_PBS 24hpi A

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of PBS injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 24 hours post injection.

treatment_protocol: All injection experiments were performed using mixed egg clutches from three tanks of AB strain zebrafish. Embryos were staged at 27 hours post fertilization (hpf) by morphological criteria (Kimmel et al., 1995) and a volume of PBS was injected into the caudal vein close to the urogenital opening.

tag: PBS-injected zebrafish embryos at 24 hours post injection


title: D.rerio_embryo_CR vs Sth Ra 2hpi B

description: D_rerio_embryo_CR vs Sth Ra 2hpi_replica B

source_name: D.rerio_embryo_Sth Ra 2hpi B

tag: Salmonella typhimurium Ra mutant-injected zebrafish embryos at 2 hours post injection


title: D.rerio_embryo_CR vs PBS 8hpi B

description: D_rerio_embryo_CR vs PBS 8hpi_replica B

source_name: D.rerio_embryo_PBS 8hpi B

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of PBS injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 8 hours post injection.

tag: PBS-injected zebrafish embryos at 8 hours post injection


title: D.rerio_embryo_CR vs Sth Ra 2hpi A

description: D_rerio_embryo_CR vs Sth Ra 2hpi_replica A

source_name: D.rerio_embryo_Sth Ra 2hpi A


title: D.rerio_embryo_CR vs Sth Ra 2hpi C

description: D_rerio_embryo_CR vs Sth Ra 2hpi_replica C

source_name: D.rerio_embryo_Sth Ra 2hpi C


title: D.rerio_embryo_CR vs PBS 2hpi B

description: D_rerio_embryo_CR vs PBS 2hpi_replica B

source_name: D.rerio_embryo_PBS 2hpi B

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of PBS injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 2 hours post injection.

tag: PBS-injected zebrafish embryos at 2 hours post injection


title: D.rerio_embryo_CR vs PBS 8hpi C

description: D_rerio_embryo_CR vs PBS 8hpi_replica C

source_name: D.rerio_embryo_PBS 8hpi C


title: wt 70 days rep 2

status: Public on Mar 08 2009

city: Providence

first: Nicola

last: Neretti

state: RI

address: Box G-L158

country: USA

institute: Brown University

description: wt 70 days rep 2

hyb_protocol: DNA was made with random hexamer primers and Superscript II reverse transcriptase in the presence of Cy3 or Cy5 fluorescent-tagged dUTP. cDNA was hybridized to the arrays for 16 - 18 hours at 65°C in humidified incubation chambers. Cy3 was used for labeling the reference sample and Cy5 for experimental or control samples (Kevin P. White, Scott A. Rifkin, Patrick Hurban, David S. Hogness: Microarray Analysis of Drosophila Development During Metamorphosis, Science 1999, 284: 2179-2184).

scan_protocol: Scanned on a GenePix 4000B scanner

data_processing: Arrays were background adjusted and normalized via the LIMMA package of bioconducto with the following options: normexp, printtiploess, Gquantile

organism: Drosophila melanogaster

source_name: universal reference (pool of all RNA samples from wt control flies at all ages)

label_protocol: 2 μg of total RNA from each sample was amplified with T7 RNA polymerase (Promega) using one-round linear amplification protocol as described

growth_protocol: Flies were cultured on standard laboratory food as previously described (35). Indy206 flies heterozygous over Canton-S (Indy206/CS) and genetically matched heterozygous controls (2216/CS) were placed on cold block and head and thorax were dissected at age: 5, 10, 20, 30, 40, 50, 70 and 80.

extract_protocol: Three replicates of 15 males were homogenized in Trizol reagent (Invitrogen) and RNA was isolated by standard method of Chomczynski and Sacchi.

tag: head and thorax

source_name: wt

growth_protocol: Flies were cultured on standard laboratory food as previously described (Bross TG, Rogina B, & Helfand SL (2005) Behavioral, physical, and demographic changes in Drosophila populations through dietary restriction.  Aging cell 4(6):309-317). Indy206 flies heterozygous over Canton-S (Indy206/CS) and genetically matched heterozygous controls (2216/CS) were placed on cold block and head and thorax were dissected at age: 5, 10, 20, 30, 40, 50, 70 and 80.


title: D.rerio_embryo_CR vs PBS 5hpi C

description: D_rerio_embryo_CR vs PBS 5hpi_replica C

source_name: D.rerio_embryo_PBS 5hpi C

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean sea salts) For the duration of PBS injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were harvested 5 hours post injection.

tag: PBS-injected zebrafish embryos at 5 hours post injection


title: EZH2 siRNA 1 with UMUC3

status: Public on Mar 11 2009

city: Los Angeles

first: Jeffrey

last: Friedman

state: CA

address: 1441 Eastlake Ave.

institute: USC/Norris Comprehensive Cancer Center

description: Note PMT1 settings

hyb_protocol: Illumina Human 6 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were extracted with Illumina BeadStudio software. Quantile normalization was performed.

organism: Homo sapiens

source_name: Bladder cancer cell line treated with EZH2 siRNA

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: Trizol

tag: UM-UC-3 cells transfected with EZH2 siRNA for 72 hours


title: ASJ_015

status: Public on Mar 31 2009

city: Paris

first: Julien

last: Laffaire

address: 10 rue Vauquelin

country: France

institute: ESPCI - CNRS UMR 7637

description: The level of expression of each gene was evaluated by calculating the mean ratio "signal/background" for each corresponding  spot from the 2 dye-swap experiments. Genes were considered to be expressed if their mean ratio was higher or equal to 1.2. Genes with mean ratio<1.2 in the 2 conditions were not used for further analysis.

hyb_protocol: RNG-MRC_MM25K_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dissecator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt's, 4X SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes 0.2X SSC and 5 minutess 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarrays images were obtained using ScanArray Gx scanner (perkin Elmer). Median signal and medin local background intensities were extracted from the images using Genepix 4.1 software (Axon Instruments).

data_processing: Filtered data were processed under R software for lowess fit normalization and  Analysis of variance (ANOVA).

organism: Mus musculus

source_name: Cerebellum P0 euploid

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5 µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).

extract_protocol: Total RNA was extracted from frozen individual cerebella and treated with DNAse using RNeasy Minikit (Qiagen) in accordance with the manufacturer's protocol. RNA quality and quantity were then checked on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

tag: Strain

value: B6EiC3SnF1/J A/a

tag: Genotype

value: euploid

tag: Stage

tag: Tissue

value: Cerebellum

source_name: Cerebellum P3 Ts1Cje

label_protocol: 5 µg of total RNA were reverse transcribed in the presence of 7.5 µM random hexamers (Pasteur Institute), 75 µM aa-dUTP (Sigma_Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (Amersham) according to the manufacturer's instructions. Labelled cDNA were then purified on Qiaquick PCR purification kit (Qiagen).


title: D.rerio_embryo_CR vs Sth Ra 24hpi A

description: D_rerio_embryo_CR vs Sth Ra 24hpi_replica A

tag: CR (common reference) is a mixture of all RNA samples from this infection study.

source_name: D.rerio_embryo_Sth Ra 24hpi A


title: D.rerio_embryo_CR vs PBS 2hpi A

description: D_rerio_embryo_CR vs PBS 2hpi_replica A

source_name: D.rerio_embryo_PBS 2hpi A


title: D.rerio_embryo_CR vs PBS 24hpi C

description: D_rerio_embryo_CR vs PBS 24hpi_replica C

source_name: D.rerio_embryo_PBS 24hpi C


title: D.rerio_embryo_CR vs Sth Ra 8hpi C

description: D_rerio_embryo_CR vs Sth Ra 8hpi_replica C

source_name: D.rerio_embryo_Sth Ra 8hpi C

tag: Salmonella typhimurium Ra mutant-injected zebrafish embryos at 8 hours post injection


title: D.rerio_embryo_CR vs Sth Ra 5hpi C

description: D_rerio_embryo_CR vs Sth Ra 5hpi_replica C

source_name: D.rerio_embryo_Sth Ra 5hpi C

tag: Salmonella typhimurium Ra mutant-injected zebrafish embryos at 5 hours post injection


title: D.rerio_embryo_CR vs Sth Ra 5hpi A

description: D_rerio_embryo_CR vs Sth Ra 5hpi_replica A

source_name: D.rerio_embryo_Sth Ra 5hpi A


title: D.rerio_embryo_CR vs Sth Ra 8hpi B

description: D_rerio_embryo_CR vs Sth Ra 8hpi_replica B

source_name: D.rerio_embryo_Sth Ra 8hpi B


title: D.rerio_embryo_CR vs Sth Ra 8hpi A

description: D_rerio_embryo_CR vs Sth Ra 8hpi_replica A

source_name: D.rerio_embryo_Sth Ra 8hpi A


title: D.rerio_embryo_CR vs PBS 5hpi B

description: D_rerio_embryo_CR vs PBS 5hpi_replica B

source_name: D.rerio_embryo_PBS 5hpi B


title: D.rerio_embryo_CR vs PBS 24hpi B

description: D_rerio_embryo_CR vs PBS 24hpi_replica B

source_name: D.rerio_embryo_PBS 24hpi B


title: D.rerio_embryo_CR vs Sth Ra 5hpi B

description: D_rerio_embryo_CR vs Sth Ra 5hpi_replica B

source_name: D.rerio_embryo_Sth Ra 5hpi B


title: D.rerio_embryo_CR vs PBS 5hpi A

description: D_rerio_embryo_CR vs PBS 5hpi_replica A

source_name: D.rerio_embryo_PBS 5hpi A


title: D.rerio_embryo_CR vs PBS 2hpi C

description: D_rerio_embryo_CR vs PBS 2hpi_replica C

source_name: D.rerio_embryo_PBS 2hpi C


title: D.rerio_embryo_CR vs PBS 8hpi A

description: D_rerio_embryo_CR vs PBS 8hpi_replica A

source_name: D.rerio_embryo_PBS 8hpi A


title: 5-Aza-CdR D7 B-rep1,rep2

status: Public on Mar 01 2009

first: Tina

last: Miranda

address: 1441 Eastlake Ave

institute: USC

description: The data was processed using beadstudio which averaged the two raw data files.  There is no normalization.

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The data was processed using Illumina Beadstudio which averaged the two raw data files.  There is no normalization.

source_name: MCF7 Cells

label_protocol: According to Illumina protocol

extract_protocol: Qiagen RNAEasy Kit

tag: MCF7 Cells treated with 1 uM 5-Aza-CdR for 24h.  Cells harvested on day 7


title: DZNep D7 A-rep1,rep2

hyb_protocol: According to Illumina Protocol.

scan_protocol: According to Illumina Protocol.

label_protocol: According to Illumina Protocol.

tag: MCF7 cells were treated with DZNep for 24h. Cells were harvested on Day 7


title: DZNep D1 A-rep1,rep2

tag: MCF7 cells were treated with DZNep and harvested after 24 h


title: DZNep D7 B-rep1,rep2


title: DZNep D1 B-rep1,rep2


title: 5-Aza-CdR D7 A-rep1,rep2


title: Control replicate 5

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

description: Trophozoites after long term axenic growth. Isolated mid-log phase.

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS scaling only- target 500

label: biotin

organism: Entamoeba histolytica

source_name: Trophozoites transfected with a control plasmid

label_protocol: Affymetrix single amplification

tag: Media

value: TYI + G418

tag: Long term axenic growth


title: Control replicate 4


title: Control replicate 1


title: Control replicate 2


title: EhMyb-dr OX replicate 2


title: 12 hr average vs. Mock, 12 hrs vs. miR-338, 12 hrs, b

city: Carlsbad

first: Aimee

last: Jackson

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: targets of miRNAs regulated by MYC in mouse ES cells

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.

source_name: Mouse ES cells

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: 12 hr average

tag: Mock, 12 hrs vs. miR-338, 12 hrs, b


title: 5-Aza-CdR D1 B-rep1,rep2

tag: MCF7 Cells treated with 1 uM 5-Aza-CdR and harvested after 24 h


title: Control replicate 3


title: 24 hr average vs. Mock,  24 hrs vs. miR-m429, 24 hrs, b

tag: 24 hr average

tag: Mock,  24 hrs vs. miR-m429, 24 hrs, b


title: 5-Aza-CdR D1 A-rep1,rep2


title: 12 hr average vs. Mock, 12 hrs vs. miR-302a*, 12 hrs, b

tag: Mock, 12 hrs vs. miR-302a*, 12 hrs, b


title: 24 hr average vs. Mock,  24 hrs vs. miR-302a, 24 hrs, b

tag: Mock,  24 hrs vs. miR-302a, 24 hrs, b


title: Untreated A-rep1,rep2

tag: Untreated MCF7 cells


title: 12 hr average vs. Mock, 12 hrs vs. miR-141, 12 hrs, b

tag: Mock, 12 hrs vs. miR-141, 12 hrs, b


title: 24h Average vs. Mock,  24 hrs vs. miR-302a*, 24 hrs, a

tag: 24h Average

tag: Mock,  24 hrs vs. miR-302a*, 24 hrs, a


title: Untreated B-rep1,rep2

tag: Untreated MCF7 Cells


title: 24 hr average vs. Mock,  24 hrs vs. miR-338, 24 hrs, b

tag: Mock,  24 hrs vs. miR-338, 24 hrs, b


title: 24 hr average vs. Mock,  24 hrs vs. miR-302a*, 24 hrs, b

tag: Mock,  24 hrs vs. miR-302a*, 24 hrs, b


title: 24h Average vs. Mock,  24 hrs vs. miR-141, 24 hrs, a

tag: Mock,  24 hrs vs. miR-141, 24 hrs, a


title: 24 hr average vs. Mock,  24 hrs vs. miR-200, 24 hrs, b

tag: Mock,  24 hrs vs. miR-200, 24 hrs, b


title: 12 hr average vs. Mock, 12 hrs vs. miR-m429, 12 hrs, b

tag: Mock, 12 hrs vs. miR-m429, 12 hrs, b


title: 24h Average vs. Mock,  24 hrs vs. miR-302a, 24 hrs, a

tag: Mock,  24 hrs vs. miR-302a, 24 hrs, a


title: 12 hr average vs. Mock, 12 hrs vs. miR-302a, 12 hrs, b

tag: 12 hr average

tag: Mock, 12 hrs vs. miR-302a, 12 hrs, b


title: 24 hr average vs. Mock,  24 hrs vs. miR-141, 24 hrs, b

tag: 24 hr average

tag: Mock,  24 hrs vs. miR-141, 24 hrs, b


title: 12 hr average vs. Mock, 12 hrs vs. miR-200, 12 hrs, b

tag: Mock, 12 hrs vs. miR-200, 12 hrs, b


title: 24h Average vs. Mock,  24 hrs vs. miR-m429, 24 hrs, a

tag: Mock,  24 hrs vs. miR-m429, 24 hrs, a


title: 24h Average vs. Mock,  24 hrs vs. miR-200, 24 hrs, a

tag: Mock,  24 hrs vs. miR-200, 24 hrs, a


title: 24h Average vs. Mock,  24 hrs vs. miR-338, 24 hrs, a

tag: Mock,  24 hrs vs. miR-338, 24 hrs, a


title: EhMyb-dr OX replicate 1

tag: Strain

tag: Media

tag: Long term axenic growth


title: knockout replicate 2_dye swap

status: Public on Feb 28 2009

city: Greenwood

first: traci

last: pawlowski

state: SC

address: 125 Gregor Mendel Circle

department: research

institute: Greenwood Genetic Ctr

description: dye swap, two of 4 KO

hyb_protocol: Agilent hybridization protocol for 17 hours at 65 degrees Celcius

scan_protocol: Agilent scanner G2505B, 10 micron resolution extracted with Agilent Feature Extraction v 8.0 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: whole brain P1 knockout

label_protocol: Agilent low RNA input linear amplification kit with Cy3 or Cy5-CTP according to maunfacturer instructions

extract_protocol: Total RNA was extracted from frozen slices of whole brain using the Qiagen Rneasy kit according to manufacturer instructions followed by Dnase with the Ambion Turbo Dnase-free kit

tag: C57BL/6 x 129;male; postnatal day 1

source_name: whole brain P1 control


title: knockout replicate 1_dye swap

description: dye swap, one of 4 KO


title: knockout replicate 3_dye swap

description: dye swap, three of 4 KO


title: knockout replicate 4_dye swap

description: dye swap, four of 4 KO


title: knockout replicate 1

description: biological replicate, one of 4 KO


title: AGTR2 knockout replicate 4

source_name: whole brain E15 Knockout

source_name: whole brain E15 control replicate one


title: knockout replicate 4

description: biological replicate, four of 4 KO


title: AGTR2 knockout replicate 6 dye-swap

source_name: whole brain E15 control replicate five


title: AGTR2 knockout replicate 3

source_name: whole brain E15 control replicate two


title: AGTR2 knockout replicate 8 dye-swap

source_name: whole brain E15 control replicate three


title: AGTR2 knockout replicate 7

source_name: whole brain E15 control replicate six


title: knockout replicate 2

description: biological replicate, two of 4 KO


title: AGTR2 knockout replicate 7 dye-swap


title: AGTR2 knockout replicate 2


title: AGTR2 knockout replicate 5 dye-swap

source_name: whole brain E15 control replicate four


title: Ref vs control rep2

status: Public on Feb 27 2009

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

description: The hybridization here was ref (pool of control) vs control reps

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments).

data_processing: The BioArray Software Environment Database (BASE 1.2.12, http://www.islab.ua.ac.be/base/) was used for storage, further evaluation and succeeding statistical analysis of the microarray datasets. After a local background correction, spots with a foreground larger than the mean local background +2 standard deviations for one or both colours were selected for further analysis. The Log2 transformed Cy3/Cy5 ratio data were normalized by implementation of a Locally Weighed Scatterplot Smoothing (Lowess) (Yang et al., 2002) step, which is an intensity-based method.

organism: Daphnia magna

source_name: D.magna control 96h old

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 7µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 150 pmol labelled target was vacuum dried.

extract_protocol:
Approximately 45 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

tag: Tissue

value: whole body extracts (45 organisms);

tag: Age

value: 96h old;

source_name: Ref sample composed of control RNA samples

tag: Exposure


title: D.magna exposed to a Ni and Cd mixture for 96h rep2

description: The hybridization here was ref (pool of control) vs a nickel/cadmium mixture

source_name: D.magna exposed to 0.5mg/L nickel + 0.05mg/L cadmium for 96h

value: 0.5mg/L nickel & 0.05mg/L cadmium


title: D.magna exposed to a Ni and Pb mixture for 96h rep3

description: The hybridization here was ref (pool of control) vs a nickel/lead mixture

source_name: D.magna exposed to 0.5mg/L nickel + 0.5mg/L lead for 96h

value: 0.5mg/L nickel & 0.5mg/L lead


title: AGTR2 knockout replicate 8


title: AGTR2 knockout replicate 6


title: AGTR2 knockout replicate 5


title: AGTR2 knockout replicate 1 dye-swap


title: AGTR2 knockout replicate 1

source_name: whole brain E15 control replicate 6


title: AGTR2 knockout replicate 2 dye-swap

source_name: whole brain E15 control replicate 2


title: knockout replicate 3

description: biological replicate, three of 4 KO


title: D.magna exposed to a Ni and Cd mixture for 96h rep3


title: Ref vs control rep3


title: D.magna exposed to a Ni and Cd mixture for 96h rep1


title: Ref vs control rep1


title: D.magna exposed to a Ni and Pb mixture for 96h rep1


title: D.magna exposed to a Ni and Pb mixture for 96h rep2


title: D.magna exposed to 2mg/L nickel for 96h rep3

description: The hybridization here was ref (pool of control) vs nickel exposed (2mg/L)

source_name: D.magna exposed to 2mg/L nickel for 96h

value: 2mg/L nickel chloride


title: D.magna exposed to 2mg/L nickel for 96h rep2


title: D.magna exposed to 2mg/L nickel for 96h rep1


title: D.magna exposed to 1mg/L nickel for 96h rep2

description: The hybridization here was ref (pool of control) vs nickel exposed (1mg/L)

source_name: D.magna exposed to 1mg/L nickel for 96h

value: 1mg/L nickel chloride


title: D.magna exposed to 1mg/L nickel for 96h rep1


title: D.magna_0.125 mg/L nickel_96h_rep3

description: The hybridization here was ref (pool of control) vs nickel exposed (0.125mg/L)

source_name: D.magna exposed to 0.125mg/L nickel for 96h

value: 0.125mg/L nickel chloride


title: D.magna exposed to 1mg/L nickel for 96h rep3


title: D.magna_0.5 mg/L nickel_96h_rep3

description: The hybridization here was ref (pool of control) vs nickel exposed (0.5mg/L)

source_name: D.magna exposed to 0.5mg/L nickel for 96h

value: 0.5mg/L nickel chloride


title: D.magna_0.125 mg/L nickel_96h_rep2

value: whole body extracts (45 organisms)

value: 96h old


title: D.magna_0.5 mg/L nickel_96h_rep2


title: D.magna_0.5 mg/L nickel_96h_rep1


title: D.magna_0.125 mg/L nickel_96h_rep1

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006).  In brief, 7µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA.  The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature.  Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA).  The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 150 pmol labelled target was vacuum dried.

extract_protocol:
Approximately 45 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance.  For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt4

status: Public on Feb 09 2009

city: Bethesda

first: Tomoshige

last: Kino

state: MD

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

description: Biological Replicates 2-3 comparing Brx haploinsufficient and WT mice, labeling switch

hyb_protocol: Array 900 protocol (Genisphere):Two hybridizations are involved; the cDNA and the fluorescent 3DNA reagent are hybridized on the chip in succession. Routine washing is performed between the hybridizations.

scan_protocol: Scanned on a Perkin Elmer Life Sciences ScanArray Express microarray scanner.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of (processed Red signal/processed Green signal). Agilent software was used. The normalized values are converted to log2 (treated/control) ratios as shown in the VALUE column below to enable easy Sample-to-Sample comparisons.

source_name: Total RNA from wild type mouse spleen

label_protocol: Array 900 protocol (Genisphere) for indirect labeling of 2ug RNA: The 5' end of the special RTdT primer used in reverse transcription is complementary to the 3DNA capture reagent (containing approximately 850 fluorescent dyes, Cy3 or Cy5 labeled). In this method, the fluorescent dye is not incorporated during the cDNA preparation avoiding inefficient hybridization; in addition, because each bound cDNA is detected by a single 3DNA molecule, the signal generated from each message is largely independent of base composition or length of the transcript.

extract_protocol: Total RNA extracted using Qiagen RNAeasy Medi columns

value: 3 weeks, Strain:C57BL/6, Tissue:spleen

source_name: Total RNA from Brx Haploinsuffient mouse spleen


title: E18.5 pylorus Nkx3.2 wildtype (274.06WTPS)

city: College Station

first: Warren

middle: Eugene

last: Zimmer

state: TX

address: 310b J. Reynolds Medical Building

department: Systems Biology and Translational Medicine

institute: Texas A&M Health Science Center

description: gene expression data from distal stomach from Nkx3.2 wt littermate

hyb_protocol: Labeled cRNA was applied to the Codelink genome arrays (GPL2897) for 18 hrs and washed, stained using the Codelink protocol and reagents

scan_protocol: Arrays were scanned on an Axon 4000B scanner.

data_processing: Array images were processed using codelink software, and global median normalization used to generate normalized expression values.

source_name: Pylorus tissue Nkx3.2 wild type littermate

label_protocol: 2 ug total RNA was used to generat biotin-labeled cRNA using a codelink iExpress kit.

growth_protocol: Heterozygous (Bapx1 CRE/+) animals were bred and embryos collected at E18.5 days.  Genotyping was obtained from yolk sac DNA and segregated embryos into KO, WT,Het.

extract_protocol: Total RNA was extracted using a kit, Rneasy from Qiagen. RNA purity was assessed by Agilent 2100 Bioanalyzer.

treatment_protocol: Gi tract was removed and the distal segment of the stomach locaoized.  This region was excised along with 1-2 mm of tissue before and behind the pyloric stricture.

tag: Mouse 129SvJ X C57Bl6

tag: Genotype Nkx3.2 +/+


title: E18.5 pylorus Nkx3.2 knockout (278.10KOPS)

description: gene expression data from distal stomach from Nkx3.2 knockout mouse

source_name: Pylorus tissue Nkx3.2 knockout

tag: Genotype Nkx3.2 CRE/CRE


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt3

description: Biological Replicates 1-3 comparing Brx haploinsufficient and WT mice, labeling switch


title: E18.5 pylorus Nkx3.2 wildtype (278.06WTPS)


title: E18.5 pylorus Nkx3.2 knockout (274.04KOPS)


title: E18.5 pylorus Nkx3.2 wildtype (5804WTPS)


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt1

description: Biological Replicates 1-3 comparing WT and Brx haploinsufficient mice


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt5

description: Biological Replicates 3-3 comparing WT and Brx haploinsufficient mice


title: CMH_NP5

city: Utrecht

first: Nagesha

middle: A S

last: Rao

state: Utrecht

department: Veterinary sciences

institute: Utrecht University

description: Progesterone-induced mammary hyperplasia, 5 out of 8

hyb_protocol: Microarray slides were washed for 1 min in 2x SSC containing 0.05% Sodium dodecyl sulphate (SDS) at room temperature (RT), incubated in 0.25% sodium borohydride and 0.25% SDS in 2x SSC for 30 min at 420C  and then rinsed 5 times in double distilled water at RT.  Slides were incubated for 45 minutes at 420C in pre-warmed pre-hybridization buffer (2X) consisting of 10xSSC, 25% formamide, 0.1% SDS and 1% BSA. Slides were washed 5 times in water followed by 5 times in isopropanol at RT and air dried. To 40 µl containing 2.5 µg of each Cy3 and Cy5 labeled RNA 40 µl hybridization buffer was added consisting of 50% formamide, 0.2% SDS and 200 µg/ml sheared herring sperm DNA. The mixture was heated at 95°C for 5 min, centrifuged for 2 min at 12,000xg and hybridized to the slides at 420C for 16 hours using hybridization chambers (Corning Life Sciences) in a water bath. After hybridization, slides were washed three times: first a low-stringency wash for 4 min at RT in 1xSSC and 0.2% SDS, next a high-stringency wash in 0.1% SDS and 0.2% SDS for 4 min and finally 2 washes in 0.1xSSC at room temperature. Slides were blown dry using compressed nitrogen.

scan_protocol: Slides were scanned using an Agilent G2565AA DNA microarray scanner (100% laser power, 30% photomultiplier tube).

data_processing: Image analysis was carried out using Imagene 5.0 software (Biodiscovery Inc). Data were normalized based on Lowess print-tip normalization by using the gene spots to calculate the Lowess line for each sub grid and then applying these lines to all spots.

organism: Canis lupus familiaris

label_protocol: Total RNA was isolated from cells which were grown to near confluence and is used for cRNA synthesis. About 2 µg total RNA was reverse transcribed using Superscript II reverse transcriptase and T7 promoter coupled poly T primers (5' GGCCAGTGAATTGTAATACGACTCACCTATAGGGAGG CGGT). After second strand synthesis, cDNA products were purified using QIAquick PCR Purification Kit and transcribed using the T7 Megascript kit (Ambion) using a UTP to 5-(3-aminoallyl)-UTP ratio of 1/3.5. The RNeasy mini kit (Qiagen) was used to clean the resulting cRNA. Three µg cRNA  was coupled to Cy3 or Cy5 fluorophores. Labeled cRNA was cleaned using ChromaSpin-30 columns and cRNA samples with specific activity of 2-5% dye-labeled nucleosides were used for microarray hybridization

extract_protocol: Total RNA was isolated using Qiagen RNA isolation (mini) kit and DNase treatment kit

source_name: Reference pool

tag: Equal quantity of cRNA derived from individual samples used in this study.


title: CMH_NP7

description: Progesterone-induced mammary hyperplasia, 3 out of 8


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt2

description: Biological Replicates 2-3 comparing WT and Brx haploinsufficient mice


title: E18.5 pylorus Nkx3.2 knockout (5805KOPS)


title: CMH_NP9

description: Progesterone-induced mammary hyperplasia, 2 out of 8


title: CMH_NP3

description: Progesterone-induced mammary hyperplasia, 8 out of 8


title: CMH_NP10

description: Progesterone-induced mammary hyperplasia, 1 out of 8


title: CMH_NP1T

description: Progesterone-induced mammary hyperplasia, 7 out of 8


title: Comparison of spleens from WT and Brx haploinsufficient mice_expt6

description: Biological Replicates 3-3 comparing Brx haploinsufficient and WT mice, labeling switch


title: CMH_NP11d

description: Progesterone-induced mammary hyperplasia, 6 out of 8


title: CMH_NP8

description: Progesterone-induced mammary hyperplasia, 4 out of 8


title: normal_VP2

description: Normal, 1 out of 8

tag: Normal.


title: normal_VP9

description: Normal, 7 out of 8


title: normal_VP7

description: Normal, 6 out of 8


title: normal_VP4

description: Normal, 3 out of 8


title: normal_VP6

description: Normal, 5 out of 8


title: normal_VP3

description: Normal, 2 out of 8


title: normal_VP1

description: Normal, 8 out of 8


title: CMC_T18d

description: Spontaneous tumor, 13 out of 21

tag: Ductal adenocarcinoma complex.


title: CMC_T14

description: Spontaneous tumor, 8 out of 21

tag: Carcinoma.


title: CMC_T17

description: Spontaneous tumor, 11 out of 21

tag: Normal-like carcinoma.


title: CMC_T18

description: Spontaneous tumor, 12 out of 21


title: CMC_T15

description: Spontaneous tumor, 9 out of 21


title: CMC_T16

description: Spontaneous tumor, 10 out of 21

tag: Proliferation of connective tissue.


title: Hippocampus PND7.  Mother (1M) not dosed

status: Public on Jan 31 2009

city: Research Triangle Park

first: Jennifer

last: Fostel

state: NC

institute: NIEHS

description: Gene expression data from Hippocampus from pup on PND7.  Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7

hyb_protocol: Chips were incubated at 42  degree C for ≥ 16 h, washed with a series of non-stringent (25  degree C) and stringent (50  degree C) solutions and the fluorescent signal amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in a GeneChip® Scanner 3000 and expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix).

data_processing: Data were analyzed with RMAExpress (rmaexpress.bmbolstad.com) with background adjustment and quantile adjustment preprocessing, and the values log-transformed

label: Biotin

organism: Rattus norvegicus

label_protocol: Ten microgram of total RNA was used to generate cDNA, which in turn was used to make double-stranded cDNA. The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides to generate cRNA which was purified and quantified, then fragmented prior to loading onto the chips.

growth_protocol: The animals were housed individually in standard plastic hanging cages with sterilized pine shavings as bedding. Food (Purina lab chow) and water were provided ad libitum. We have previously reported that this rat chow (4.7 ppb) and water (1.4 ppb) have low levels of PCBs.

extract_protocol: RNA was extracted using an adapted Trizol/RNeasy minicolumn protocol (Invitrogen). Briefly, tissues (cerebellum or hippocampus) were homogenized in 1 ml Trizol, 0.2 ml chloroform added, tubes centrifuged, the aqueous layer removed to a clean, sterile tube, 500 microliter ice cold isopropanol added and RNA precipitated overnight at − 20 degreesC. Samples were centrifuged, pellets washed 2 times with 75% ethanol to remove excess salts, dried briefly and RNA re-solubilized in RNase-free H2O. Contaminating DNA was removed with the Ambion DNA-free kit; RNA quality was verified by Agilent bioanalyzer analysis using a RNA 6000 nanochip and RNA stored at − 80 degrees C

treatment_protocol: A commercial PCB mixture, Aroclor 1254 (Lot # 124-191; purity > 99%) was purchased from AccuStandard, Inc (New Haven, CT). This lot of Aroclor 1254 has been characterized before with respect to its congener content (Kodavanti et al., 2001). The dosing solutions were prepared in corn oil. In each cohort, at least 15 dams per group were given Aroclor 1254 (0 or 6 mg/kg) in corn oil (2 ml/kg) by oral gavage starting from gestational day (GD) 6 through postnatal day (PND) 21. Dams were left undisturbed on PND1. The rats were weighed and dosed once a day between 8:00 and 10:00 AM. Beginning on GD22, rats were checked twice daily (AM and PM) for births, and the date that birth was first discovered was designated as PND0. All dams (> 90% success of pregnancy) gave birth within few hours apart and the litter size varied between 7 and 15 pups. On PND4, litters were culled to 4 each, male and female pups/litter. On PNDs 7 and 14, one male pup from each litter was randomly selected for genomic analysis.

tag: strain

value: Long Evans

tag: Sex

value: male


title: CMC_T8

description: Spontaneous tumor, 19 out of 21

tag: Multifocal mammary adenoma.


title: Hippocampus PND7.  Mother (12M) dosed

description: Gene expression data from Hippocampus from pup on PND7.  Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: CMC_T4

description: Spontaneous tumor, 15 out of 21


title: CMC_T12

description: Spontaneous tumor, 7 out of 21

tag: Solid carcinoma.


title: Hippocampus PND7.  Mother (18M) dosed

description: Gene expression data from Hippocampus from pup on PND7.  Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: Hippocampus PND7.  Mother (13M) not dosed

description: Gene expression data from Hippocampus from pup on PND7.  Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7


title: Hippocampus PND7.  Mother (7M) not dosed

description: Gene expression data from Hippocampus from pup on PND7.  Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7


title: CMC_BT4

description: Spontaneous tumor, 4 out of 21

tag: Benign - 50% percent epithelium.


title: Hippocampus PND14.  Mother (18M) dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: CMC_BT2

description: Spontaneous tumor, 2 out of 21

tag: Complex adenoma.


title: CMC_T6

description: Spontaneous tumor, 17 out of 21


title: CMC_T10

description: Spontaneous tumor, 5 out of 21

tag: Ductal papillary simple adenocarcinoma.


title: CMC_T11

description: Spontaneous tumor, 6 out of 21

tag: Adenocarcinoma simple.


title: Hippocampus PND7.  Mother (15M) dosed

description: Gene expression data from Hippocampus from pup on PND7.  Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: CMC_T5

description: Spontaneous tumor, 16 out of 21


title: CMC_BT3

description: Spontaneous tumor, 3 out of 21

tag: Lipoma, benign tumor of fat mass.


title: CMC_T7

description: Spontaneous tumor, 18 out of 21

tag: Papillary adenocarcinoma complex.


title: CMC_T3

description: Spontaneous tumor, 14 out of 21


title: CMC_T9

description: Spontaneous tumor, 20 out of 21


title: CMC_T13

description: Spontaneous tumor, 21 out of 21

tag: Anaplastic carcinoma.


title: Hippocampus PND14.  Mother (15M) dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: Hippocampus PND14.  Mother (1M) not dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND7.  Mother (7M) not dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7


title: Hippocampus PND14.  Mother (13M) not dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14


title: Hippocampus PND14.  Mother (12M) dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND7.  Mother (15M) dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: Cerebellum PND7.  Mother (18M) dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: Cerebellum PND7.  Mother (13M) not dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7


title: Cerebellum PND14.  Mother (7M) not dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND14.  Mother (13M) not dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (13M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND7.  Mother (1M) not dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 7


title: Cerebellum PND7.  Mother (12M) dosed

description: Gene expression data from Cerebellum from pup on PND7.  Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 7


title: Cerebellum PND14.  Mother (15M) dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (15M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND14.  Mother (12M) dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (12M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND14.  Mother (18M) dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (18M) dosed with 6 mg/kg/day of Aroclor 1254, from gestation day 6 to postnatal day 14


title: Cerebellum PND14.  Mother (1M) not dosed

description: Gene expression data from Cerebellum from pup on PND14.  Mother (1M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14


title: IN5-B (Internode 5)

city: corvallis

first: palitha

last: dharmawardhana

state: OR

address: 321 richarson hall,OSU

institute: OSU

hyb_protocol: Nimblegen Inc. microarray processing pipeline

data_processing: Normalized with RMA algorithm within Nimblescan software

organism: Populus trichocarpa

source_name: Internode 5

growth_protocol: Trees growing in field condition

extract_protocol: Total RNA isolated using Qiagen RNeasy kit with on column DNAse treatment

treatment_protocol: No treatment

tag: Individual 5

tag: Internode 5


title: S. roseum two-component analysis

type: genomic

city: Taipei

first: Ralph

last: Kirby

address: Li-Nong Road

country: Taiwan

institute: National Yang-Ming University

description: Kirby et al (2008) Antonie van Leewenhoek 94 173-186

hyb_protocol: The two DNA pools to be compared were mixed and applied to an array in a hybridization mixture that contained 3.68X SSC, 0.18% SDS, and 1μg yeast tRNA (total 16.3μl), which had been heated at 100oC for 5 min before being applied to array. Hybridization took place under a glass coverslip sealed by glue in a humidified Omnislide (Thermo Hybaid) at 60oC for twelve to fourteen hours.

scan_protocol: The slides were washed, dried and scanned for fluorescence using a GenePix TM 4000B scanner (Axon instruments).

data_processing: The average signal intensity and local background measurements were obtained for each spot on each array using GenePixPro software. The dataset was screened for aberrant spots and these were eliminated from the analysis after manual checking. Most genes are present in duplicate on the arrays and the signal from each pair of spots was inputted into the computer program available from ScanAlyze (Eisen et al., 1998; Gollub et al., 2003). The data was then processed into a mean log2 Cy3/Cy5 ratio format. The dataset was normalized for each array separately and outputted to Excel where after checking the alignment of the datasets from each array, a mean signal for each common gene was calculated. Based on Bentley et al., 2002, the mean signal and standard deviation for the core region of genes from SCO2050 to SCO5800 was calculated. The standard deviation was used to set a cut-off for gene absence at 2SD below the core mean. The ratio given are the normalized log2 ratio representing test organism/Streptomyces coelicolor ratio.

molecule: genomic DNA

organism: Streptomyces coelicolor A3(2)

source_name: Streptomyces coelicolor

label_protocol: Four to six micrograms of sonicated genomic DNA were used as template and this was denatured in the presence of 12 μl of 72% GC-content random hexamers in a total volume of 25μl at 100oC for ten minutes. The mixture was then snap-cooled on ice before adding the remaining reaction components: 1.5 μl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech), 4μl Klenow fragment (NEB #212), 5μl Klenow buffer, 0.5μl dNTP (4mM dATP, 4mM dTTP, 10mM dGTP, and 0.2mM dCTP), and 14μl ddH2O. The random primed labeling reaction was carried out for two to three hours at 37oC. Buffer exchange, purification and concentration of the DNA products was accomplished by three cycles of diluting the reaction mixture in 0.5ml TE buffer (10mM Tris and 1mM EDTA PH 8.0) and filtering though a Microcon-30 microconcentrators (Millipore).

extract_protocol: Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995) and had been sonicated to <2Kb.

tag: Streptomyces coelicolor A3(2) (SCP1+) 104

organism: Streptosporangium roseum

source_name: Streptosporangium roseum

tag: Streptosporangium roseum ATCC12428


title: IN4-A (Internode 4)

scan_protocol: Nimblegen Inc. microarray processing pipeline

source_name: Internode 4

tag: Individual 4

tag: Internode 4


title: S. rochei two-component analysis

organism: Streptomyces rochei

source_name: Streptomyces rochei

tag: Streptomyces rochei ATCC10739


title: S. aureofaciens two-component analysis

organism: Kitasatospora aureofaciens

source_name: Streptomyces aureofaciens

tag: Streptomyces aureofaciens ATCC10762


title: S. bikiniensis two-component analysis

organism: Streptomyces bikiniensis

source_name: Streptomyces bikiniensis

tag: Streptomyces bikiniensis ATCC11062


title: S. fradiae two-component analysis

organism: Streptomyces fradiae

source_name: Streptomyces fradiae

tag: Streptomyces fradiae ATCC10745


title: IN4-B (Internode 4)

label_protocol: Nimblegen Inc. microarray processing pipeline


title: S. maritimus two-component analysis

organism: Streptomyces maritimus

source_name: Streptomyces maritimus

tag: Streptomyces maritimus (Yang Ming)


title: IN2-A (Internode 2)

source_name: Internode 2

tag: Individual 2

tag: Internode 2


title: IN5-A (Internode 5)


title: IN3-A (Internode 3)

source_name: Internode 3

tag: Individual 3

tag: Internode 3


title: S. hydrogenans two-component analysis

organism: Streptomyces exfoliatus

source_name: Streptomyces hydrogenans

tag: Streptomyces hydrogenans ATCC19631


title: S. venezuaelae two-component analysis

organism: Streptomyces venezuelae

source_name: Streptomyces venezuelae

tag: Streptomyces venezuelae ATCC23951


title: S. cattelya two-component analysis

organism: Streptantibioticus cattleyicolor

source_name: Streptomyces cattleya

tag: Streptomyces cattleya ATCC35852


title: IN9-A (Internode 9)

source_name: Internode 9

tag: Individual 9

tag: Internode 9


title: IN9-B (Internode 9)


title: S. lipmanii two-component analysis

tag: Streptomyces coelicolor A3(2) (SCP1+) 104

organism: Streptomyces microflavus

source_name: Streptomyces lipmanii

tag: Streptomyces lipmanii ATCC27357


title: IN3-B (Internode 3)


title: S. tanashiensis two-component analysis

organism: Streptomyces tanashiensis

source_name: Streptomyces tanashiensis

tag: Streptomyces tanashiensis ATCC23967


title: IN2-B (Internode 2)


title: S. virginiae two-component analysis

organism: Streptomyces virginiae

source_name: Streptomyces virginiae

tag: Streptomyces virginiae ATCC12630


title: S. antibioticus two-component analysis

source_name: Streptomyces coelicolor

organism: Streptomyces antibioticus

source_name: Streptomyces antibioticus

tag: Streptomyces antibioticus ATCC8663


title: S. clavuligerus two-component analysis

organism: Streptomyces clavuligerus

source_name: Streptomyces clavuligerus

tag: Streptomyces clavuligerus ATCC27064


title: S. griseus two-component analysis

organism: Streptomyces griseus

source_name: Streptomyces griseus

tag: Streptomyces griseus ATCC31031


title: Hippocampus PND14.  Mother (7M) not dosed

description: Gene expression data from Hippocampus from pup on PND14.  Mother (7M) dosed with 0 Aroclor 1254, from gestation day 6 to postnatal day 14

organism: Rattus norvegicus

tag: strain

tag: Sex


title: CMC_BT1

description: Spontaneous tumor, 1 out of 21

organism: Canis lupus familiaris

source_name: Reference pool

tag: Equal quantity of cRNA derived from individual samples used in this study.

tag: Benign mixed tumor.


title: TONSIL2 (ref-hyb)

status: Public on Jan 22 2009

city: Houston

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: human normal tonsil sample 2

hyb_protocol: Microarray hybridizations were carried out using Agilent Human custom 4x44K oligonucleotide microarrays in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Scanned on an Agilent microarray scanner.  Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: The LogRatio data (transformed from log10 to log2) in the Agilent Feature extraction output file was used, which contained LOWESS normalized, background subtracted data obtained from log-transformation of processed Red signal/processed Green signal. Agilent software was used. Probes with more than 70% flagged arrays were filtered out. Other flagged probes were KNN imputed.

organism: Homo sapiens

source_name: Stratagene Human Universal Reference

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.

extract_protocol: total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

tag: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: human normal tonsil

tag: site

value: tonsil

tag: normal tissue


title: T172 (ref-hyb)

description: Human head and neck squamous cell carcinoma sample 8

value: oropharynx

tag: tumor tissue


title: TONSIL10 (ref-hyb)

description: human normal tonsil sample 10


title: TONSIL1 (self-hyb)

description: human normal tonsil sample 1

hyb_protocol: Microarray hybridizations were carried out using Agilent Human custom 4x44K oligonucleotide microarrays in an Robbins Scientific hybridization oven with 850ng of Cy3-labeled experimental sample and 850ng of Cy5-labeled experimental sample using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

data_processing: The red (cy5) and green (cy3) background-subtracted signals in the Agilent Feature extraction output files were used as raw signals for each channel. LOWESS normalizations were performed across arrays for each channel and across channels for each array (for dye-bias correction). The mean of the two channels of each array was taken as the combined signal.

label: Cy3, Cy5


title: T181 (ref-hyb)

description: Human head and neck squamous cell carcinoma sample 5


title: T172 (self-hyb)

source_name: Human head and neck squamous cell carcinoma


title: TONSIL3 (ref-hyb)

description: human normal tonsil sample 3


title: TONSIL8 (ref-hyb)

description: human normal tonsil sample 8


title: HNO2-0346B (self-hyb)

description: Human head and neck squamous cell carcinoma sample 7


title: TONSIL6 (ref-hyb)

description: human normal tonsil sample 6


title: HNO2-0346B (ref-hyb)


title: TONSIL1 (ref-hyb)

description: human normal tonsil sample 1


title: TONSIL4 (ref-hyb)

description: human normal tonsil sample 4


title: HNO4-604B (self-hyb)

description: Human head and neck squamous cell carcinoma sample 4


title: TONSIL5 (self-hyb)

description: human normal tonsil sample 5


title: HNO4-357B (self-hyb)

description: Human head and neck squamous cell carcinoma sample 3


title: TONSIL5 (ref-hyb)

description: human normal tonsil sample 5


title: TONSIL4 (self-hyb)

description: human normal tonsil sample 4


title: normal_VP5

description: Normal, 4 out of 8

tag: Normal.


title: HNO4-0331B (ref-hyb)

description: Human head and neck squamous cell carcinoma sample 1


title: HNO4-357B (ref-hyb)


title: T181 (self-hyb)


title: HNO4-604B (ref-hyb)


title: T190 (ref-hyb)

description: Human head and neck squamous cell carcinoma sample 6


title: TONSIL2 (self-hyb)

description: human normal tonsil sample 2


title: TONSIL6 (self-hyb)

description: human normal tonsil sample 6


title: T190 (self-hyb)


title: TONSIL10 (self-hyb)

description: human normal tonsil sample 10


title: HNO2-0254 (ref-hyb)

description: Human head and neck squamous cell carcinoma sample 2


title: TONSIL8 (self-hyb)

description: human normal tonsil sample 8


title: HNO2-0254 (self-hyb)


title: HNO4-0331B (self-hyb)


title: 23Months_5

status: Public on Jan 18 2009

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: rat hippocampal CA1, 23 month old, replicate 5

hyb_protocol: Standard Affimetrix

scan_protocol: Affy

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

label: Standard Affymetrix

source_name: rat hippocampal CA1, 23 month old

label_protocol: Standard Affymetrix

extract_protocol: Standard Affymetrix

tag: Rat hippocampus CA1

tag: Fisher 344 Rat

tag: Male


title: 23Months_8

description: rat hippocampal CA1, 23 month old, replicate 8


title: 23Months_3

description: rat hippocampal CA1, 23 month old, replicate 3


title: 23Months_10

description: rat hippocampal CA1, 23 month old, replicate 10


title: 23Months_14

description: rat hippocampal CA1, 23 month old, replicate 14


title: 23Months_11

description: rat hippocampal CA1, 23 month old, replicate 11


title: 23Months_6

description: rat hippocampal CA1, 23 month old, replicate 6


title: 23Months_7

description: rat hippocampal CA1, 23 month old, replicate 7


title: 23Months_15

description: rat hippocampal CA1, 23 month old, replicate 15


title: 23Months_13

description: rat hippocampal CA1, 23 month old, replicate 13


title: 12Months_5

description: rat hippocampal CA1, 12 month old, replicate 5

source_name: rat hippocampal CA1, 12 month old


title: 9Months_7

description: rat hippocampal CA1, 9 month old, replicate 7

source_name: rat hippocampal CA1, 9 month old


title: 12Months_1

description: rat hippocampal CA1, 12 month old, replicate 1


title: 23Months_4

description: rat hippocampal CA1, 23 month old, replicate 4


title: 12Months_4

description: rat hippocampal CA1, 12 month old, replicate 4


title: 12Months_2

description: rat hippocampal CA1, 12 month old, replicate 2


title: 9Months_4

description: rat hippocampal CA1, 9 month old, replicate 4


title: 23Months_1

description: rat hippocampal CA1, 23 month old, replicate 1


title: 12Months_8

description: rat hippocampal CA1, 12 month old, replicate 8


title: 12Months_9

description: rat hippocampal CA1, 12 month old, replicate 9


title: 12Months_6

description: rat hippocampal CA1, 12 month old, replicate 6


title: 12Months_3

description: rat hippocampal CA1, 12 month old, replicate 3


title: 12Months_7

description: rat hippocampal CA1, 12 month old, replicate 7


title: 9Months_5

description: rat hippocampal CA1, 9 month old, replicate 5


title: 9Months_6

description: rat hippocampal CA1, 9 month old, replicate 6


title: 9Months_8

description: rat hippocampal CA1, 9 month old, replicate 8


title: 9Months_9

description: rat hippocampal CA1, 9 month old, replicate 9


title: TONSIL3 (self-hyb)

description: human normal tonsil sample 3


title: 23Months_9

description: rat hippocampal CA1, 23 month old, replicate 9


title: 9Months_2

description: rat hippocampal CA1, 9 month old, replicate 2


title: 9Months_3

description: rat hippocampal CA1, 9 month old, replicate 3


title: 9Months_1

description: rat hippocampal CA1, 9 month old, replicate 1


title: 6Months_9

description: rat hippocampal CA1, 6 month old, replicate 9

source_name: rat hippocampal CA1, 6 month old


title: 6Months_7

description: rat hippocampal CA1, 6 month old, replicate 7


title: 6Months_2

description: rat hippocampal CA1, 6 month old, replicate 2


title: 6Months_1

description: rat hippocampal CA1, 6 month old, replicate 1


title: 6Months_3

description: rat hippocampal CA1, 6 month old, replicate 3


title: 3Months_2

description: rat hippocampal CA1, 3 month old, replicate 2

source_name: rat hippocampal CA1, 3 month old


title: 3Months_6

description: rat hippocampal CA1, 3 month old, replicate 6


title: 3Months_7

description: rat hippocampal CA1, 3 month old, replicate 7


title: 3Months_9

description: rat hippocampal CA1, 3 month old, replicate 9


title: 6Months_8

description: rat hippocampal CA1, 6 month old, replicate 8


title: 6Months_4

description: rat hippocampal CA1, 6 month old, replicate 4


title: 3Months_8

description: rat hippocampal CA1, 3 month old, replicate 8


title: 3Months_1

description: rat hippocampal CA1, 3 month old, replicate 1


title: 3Months_5

description: rat hippocampal CA1, 3 month old, replicate 5


title: brain 5

city: Baltimore

first: rafael

last: irizarry

institute: Johns Hopkins University

description: Gene expression data obtained from post-mortem brain (pre-frontal cortex)

hyb_protocol: cRNA was fragmented and 10ug hybridized to an Affymetrix U133A or U133A Plus 2.0 arrays for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: The data were processed with RMA (Bioconductor, R). Brain (U133A) and liver (U133A_Plus 2.0) data was processed together but only probes common to both arrays were used in the analysis. The data from tumor and matched normal colon samples was analyzed independently from the brain and liver samples.

source_name: normal brain

label_protocol: Preparation of biotinylated cRNA was performed according to the standard (one-cycle) Affymetrix U133A 2.0 sample preparation protocol, starting with 1ug of total RNA

growth_protocol: no growth

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

treatment_protocol: no treatment

tag: Tissue

value: normal brain


title: 6Months_6

description: rat hippocampal CA1, 6 month old, replicate 6


title: brain 4


title: 3Months_3

description: rat hippocampal CA1, 3 month old, replicate 3


title: brain 1


title: brain 3


title: 6Months_5

description: rat hippocampal CA1, 6 month old, replicate 5


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep6

status: Public on Jan 15 2009

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

description: Biological replicate 6 of 6.

hyb_protocol: Purified cDNA was denatured at 95 °C for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacturer’s manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software. The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

organism: Candida parapsilosis

source_name: Candida parapsilosis cells grown in normoxic conditions (21% oxygen) in SD medium

label_protocol: Twenty-four micrograms of total RNA was used for cDNA labeling. Briefly RNA samples were incubated with 100 pmol of anchor oligonucleotide deoxyriboslthymine (Invitrogen) at 70°C for 10 min, after which following reaction reagents were added including 1 X First strand buffer, 6.67 mM dATP, dTTP, and dGTP; 2mM dCTP; 100 mM dithiothreitol; 2 µl Superscript II reverse transcriptase (Invitrogen). 37.5 µM Cy5-dCTP were then added into the mixture in dark. The mixture were left at 42°C for two hours followed by adding additional 2 µl Superscript II reverse transcriptase, and reaction was continued for one more hour. 50 µg ml-1 RNase A and 0.05 unit µl RNase H were added and the reaction was incubated for 30 min at 37°C.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C in normoxic (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic condtions (1% 02, 99% N2) in a dedicated chamber (In vivo 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch1 represents the normoxic sample.

extract_protocol: RNA was isolated using a RiboPure Yeast kit (Ambion).

tag: Age

value: 3 h

tag: Growth condition

value: normoxic

tag: Medium

value: SD

tag: Strain

source_name: Candida parapsilosis cells grown in hypoxic conditions (1% oxygen) in SD medium

label_protocol: Twenty-four micrograms of total RNA was used for cDNA labeling. Briefly RNA samples were incubated with 100 pmol of anchor oligonucleotide deoxyriboslthymine (Invitrogen) at 70°C for 10 min, after which following reaction reagents were added including 1 X First strand buffer, 6.67 mM dATP, dTTP, and dGTP; 2mM dCTP; 100 mM dithiothreitol; 2 µl Superscript II reverse transcriptase (Invitrogen). 37.5 µM Cy3-dCTP were then added into the mixture in dark. The mixture were left at 42°C for two hours followed by adding additional 2 µl Superscript II reverse transcriptase, and reaction was continued for one more hour. 50 µg ml-1 RNase A and 0.05 unit µl RNase H were added and the reaction was incubated for 30 min at 37°C.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C in normoxic (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic conditions (1% 02, 99% N2) in a dedicated chamber (In vivo 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch2 represents the hypoxic sample.

value: hypoxic


title: brain 2


title: 3Months_4

description: rat hippocampal CA1, 3 month old, replicate 4


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep5

description: Biological replicate 5 of 6.


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep4

description: Biological replicate 4 of 6.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C in normoxic (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic conditions (1% 02, 99% N2) in a dedicated chamber (In vivo 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch1 represents the hypoxic sample.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C in normoxic (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic condtions (1% 02, 99% N2) in a dedicated chamber (In vivo 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch2 represents the normoxic sample.


title: Candida_parapsilosis_Biofilm_rep4

description: Biological replicate 4 of 4.

hyb_protocol: Microarray slides were prehybridized with in 5X SSC, 0.1% SDS, 10 mg ml-1 BSA for 1 h at 42ºC, washed 3 times in water, 1 time in isopropanol and dried. Incorporation of Cy3 and Cy5 dyes into cDNA targets was quantified by measuring the absorbance of each sample at 260 nm, 550 nm or 650 nm. Samples were used if incorporation was greater than 15 pmol. The labeled cDNAs were concentrated by drying under vacuum, resuspended and pooled in 45 ul of hybridization buffer (1X DigEasy (Roche) containing 0.5 mg ml-1 bakers yeast tRNA (Invitrogen) and 0.5 mg ml-1 salmon sperm DNA (Sigma)). The mixture was denatured at 95ºC for 2 min, quickly cooled on ice, applied to the DNA microarray and covered with a 24 mm x 60 mm coverslip. Slides were placed in a hybridization chamber (Corning, Palo Alto, CA) and incubated at 42ºC for approximately 16 h. The slides were washed in 1 X SSC at 42ºC until the coverslip fell off, and then washed 3 times for 10 min in 1 X SSC, 0.1% SDS at 42ºC, 3 times 5 min in 1 X SSC at 42ºC, and finally rinsed in 0.2 X SSC at room temperature. The slides were dried by centrifugation at 1000 rpm for 5 min.

source_name: Planktonic Candida parapsilosis cells grown in SD medium

label_protocol: Reverse transcription, cDNA labeling and probe purification were carried out using 1 an Atlas Powerscript Fluoresecent labeling kit (Takara) according to the manufacturer’s instructions, starting with 5 µg of total RNA.

growth_protocol: Flasks containing 50 ml of the same medium used for the biofilm were inoculated at A600 of 0.2 from an overnight culture. Cells were grown at 37°C with orbital shaking to an A600 of 1.

extract_protocol: RNA was isolated using an RNeasy kit (Qiagen). The quality and concentration of the isolated RNA was analyzed using an Agilent 2100 Bioanalyzer.

tag: Planktonic cells

source_name: Candida parapsilosis biofilm cells grown in SD medium

growth_protocol: Biofilm growth in continuous flow was carried out in a microfermentor system as described in Garcia-Sanchez et al. {, 2004}. Briefly, this consists of a glass vessel with a 40 ml incubation chamber with tubes allowing entry and evacuation and continuous medium flow. Air under pressure is supplied to allow medium to flow through the chamber. The continuous flow allows cells to grow as a biofilm on a slide positioned in the chamber and minimizes planktonic growth. Thermanox slides (Nunc) were first immersed in an inoculum of the appropriate culture at A600 of 1 for 1 h at 37°C to allow adherence, and were then transferred to the microfermentor system. Experiments were performed at 37°C and biofilm was sampled after 50h growth.

tag: Biofilm cells


title: Candida_parapsilosis_Biofilm_rep2

description: Biological replicate 2 of 4.


title: Candida_parapsilosis_Biofilm_rep3

description: Biological replicate 3 of 4.


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep3

description: Biological replicate 3 of 6.


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep2

description: Biological replicate 2 of 6.

growth_protocol: Overnight cultures of C. parapsilosis CLIN214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C at normoxia (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic condtions (1% 02, 99% N2) in a dedicated chamber (in Vivo2 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch2 represents the normoxic sample.


title: Candida_parapsilosis_Biofilm_rep1

description: Biological replicate 1 of 4.


title: Candida_parapsilosis_Normoxia_Vs_Hypoxia_rep1

description: Biological replicate 1 of 6.

growth_protocol: Overnight cultures of C. parapsilosis CLIB214 were diluted to a A600 of 0.2 in 300 ml of SD at 37°C in normoxic (atmosphere oxygen) conditions for 3 hours. Two 100 ml aliquots were removed, the cells were collected by centrifugation, and re-suspended in media pre-conditioned at the relevant concentration of oxygen. One flask was incubated in normoxic conditions (21% oxygen) in a standard orbital shaker, and the other was incubated in hypoxic condtions (1% 02, 99% N2) in a dedicated chamber (In vivo 400 workstation). Both cultures were incubated at 37°C at 200 rpm. Ch1 represents the hypoxic sample.


title: Populus balsamifera_Female_Catkin_midday_1

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

description: Affymetrix protol: Fluidics script: EukGE-WS2v5

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization

scan_protocol: Affymetrix protocol: GeneChip® Scanner 3000 7G Affymetrix 00-0073

data_processing: MAS5.0, scaled to 500

organism: Populus balsamifera

source_name: Populus balsamifera, female catkin, midday

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay

growth_protocol: Catkins were collected from mature P. balsamifera trees grown by Alberta Pacific Forest Industries Inc. in a field trial in Grassland, AB, Canada on April 30, 2007. Material was flash frozen in liquid nitrogen and then stored at -80°C until RNA was extracted.

extract_protocol: Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-116.

tag: Female Catkin

tag: Alberta Pacific Forest Industries

tag: Field trial in Grassland, AB, Canada

tag: Collected April 30, 2007


title: Populus balsamifera_Male_Catkin_midday_3

source_name: Populus balsamifera, Male catkin, midday

tag: Male Catkin


title: Populus balsamifera_Female_Catkin_midday_3

source_name: Populus balsamifera, Female catkin, midday


title: Populus balsamifera_1006_differentiating_xylem_midday_1

source_name: Populus balsamifera, clone 1006, differentiating xylem, midday

growth_protocol: Plant material was collected from clonally-propagated, 8-week-old Populus balsamifera saplings (1006, Alberta Pacific Forest Industries Inc., Boyle, AB, Canada) grown in a climate-controlled growth chamber. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C. All tissues were collected at midday. All tissues were collected from saplings without water limitations. Differentiating xylem was collected from the bottom 6 inches of the stem by peeling off the bark and immediately scraping the surface of the exposed wood into micro collection tubes containing liquid nitrogen. Flash frozen plant tissue was stored at -80°C until RNA was extracted.

tag: Differentiating xylem – bottom 15 cm of stem - peel off  bark and immediately scrape the surface of the exposed wood into micro collection tubes containing liquid nitrogen

tag: Alberta Pacific Forest Industries clone 1006

tag: Clonally-propagated, 8-week-old Populus balsamifera saplings

tag: Differentiating xylem collected in the middle of the light period


title: Populus balsamifera_1006_differentiating_xylem_midday_2

tag: Differentiating xylem – bottom 15 cm of stem - peel off bark and immediately scrape the surface of the exposed wood into micro collection tubes containing liquid nitrogen


title: Populus balsamifera_1006_mature_leaf_midday_2

source_name: Populus balsamifera, clone 1006, mature leaf, midday

growth_protocol: Plant material was collected from clonally-propagated, 8-week-old Populus balsamifera saplings (1006, Alberta Pacific Forest Industries Inc., Boyle, AB, Canada) grown in a climate-controlled growth chamber. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C. All tissues were collected at midday. All tissues were collected from saplings without water limitations. Mature leaf samples include the first fully expanded leaf including petiole. Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

extract_protocol: Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-11

tag: Mature leaf, including petiole - from 3 individuals

tag: Leaves collected in the middle of the light period


title: Populus balsamifera_1006_mature_leaf_midday_1


title: Populus balsamifera_Male_Catkin_midday_2


title: Populus balsamifera_1006_mature_leaf_midday_3


title: Populus balsamifera_1006_differentiating_xylem_midday_3


title: Populus balsamifera_1006_root_midday_3

source_name: Populus balsamifera, clone 1006, root, midday

growth_protocol: Plant material was collected from clonally-propagated, 8-week-old Populus balsamifera saplings (1006, Alberta Pacific Forest Industries Inc., Boyle, AB, Canada) grown in a climate-controlled growth chamber. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C. All tissues were collected at midday. All tissues were collected from saplings without water limitations. Root samples include the distal 15cm of well-rinsed roots mass. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

tag: Distal 15cm of well-rinsed root mass

tag: Roots collected in the middle of the light period


title: Populus balsamifera_1006_root_midday_2


title: Populus balsamifera_Female_Catkin_midday_2


title: Populus balsamifera_1006_young_leaf_midday_2

source_name: Populus balsamifera, clone 1006, young leaf, midday

growth_protocol: Plant material was collected from clonally-propagated, 8-week-old Populus balsamifera saplings (1006, Alberta Pacific Forest Industries Inc., Boyle, AB, Canada) grown in a climate-controlled growth chamber. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C. All tissues were collected at midday, except for the “dark” samples, which were collected at midnight. All tissues were collected from saplings without water limitations. Young leaf samples include the first leaf, with its petiole, that was completely uncurled, but was still shiny and much smaller than the mature leaves. Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

tag: Young leaf, including petiole - from 3 individuals


title: Populus balsamifera_1006_young_leaf_midday_1

source_name: Young leaf


title: Populus balsamifera_20071015_Etiolated_seedling_6d_1

description: Affymetrix protocol: Fluidics script: EukGE-WS2v5

hyb_protocol: Affymetrix protocol: Eukaryotic sample and array processing: Eukaryotic target hybridization

source_name: 6 day old Populus balsamifera seedlings germinated in continuous darkness for 6 days

label_protocol: Affymetrix protocol: Eukaryotic sample and array processing: One-cycle target labeling assay

growth_protocol: Seedlings were germinated in a continuously dark growth chamber on wetted filter paper in petri plates with a constant temperature of 21°C. They were grown in this way for 6 days. On the 6th day, whole seedlings were collected and were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted. Each sample comprises pooled material from 20 individuals.

extract_protocol: Trizol method (Invitrogen, Burlington, ON, Canada)

tag: Whole seedling - 20 individuals

tag: Seedlot number 20071015

tag: 6 days post germination

tag: Continuous light


title: Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_3

source_name: 6 day old Populus balsamifera seedlings germinated in continuous darkness for 5 days, followed by 3 hours of light

growth_protocol: Seedlings were germinated in a continuously dark growth chamber on wetted filter paper in petri plates with a constant temperature of 21°C. They were grown in this way for five days. On the 6th day, plates were transfered to a light growth chamber for 3 hours. At this time whole seedlings were collected and were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted. Each sample comprises pooled material from 20 individuals.

tag: Continuous darkness for 5 days, transfered to light on sixth day for 3 hours


title: Populus balsamifera_20071015_Etiolated_seedling_6d_2


title: Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_2


title: Populus balsamifera_20071015_Etiolated_seedling_6d_3


title: Populus balsamifera_1006_young_leaf_midday_3


title: Populus balsamifera_1006_root_midday_1


title: Populus balsamifera_Male_Catkin_midday_1

tag: Alberta Pacific Forest Industries

tag: Field trial in Grassland, AB, Canada

tag: Collected April 30, 2007


title: Populus balsamifera_20071015_Seedling_continuous_light_6d_3

source_name: Populus balsamifera seedlings, 6 days old, contiuous light

growth_protocol: Seedlings were germinated in a continuous light growth chamber on wetted filter paper in petri plates with a constant temperature of 21°C. They were grown in this way for five days. On the 6th day, whole seedlings were collected and were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted. Each sample comprises pooled material from 20 individuals.


title: Populus balsamifera_20071015_Seedling_continuous_light_6d_2


title: Populus balsamifera_20071015_Etiolated_seedling_6d_transfered_to_light_3h_1


title: S6-ko 29d Spleen -2

status: Public on Jan 09 2009

city: South San Francisco

first: Adam

middle: S

last: Adler

address: 1 DNA Way

institute: Genentech

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77698.gif
Tissue type: 29 day spleen

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 4710; Software: type: feature extraction; Performer: Adam,,Adler

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mus musculus

source_name: WT 29d Spleen

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

extract_protocol: not provided

tag: WT 29d Spleen

source_name: S6-ko 29d Spleen -2

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen)

tag: S6-ko 29d Spleen -2


title: SIRT6null_3weekpups_liver11

description:
Simple annotation: Transcription, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76632.gif
Tissue type: 21 day liver

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 5080; Software: type: feature extraction; Performer: Tiara,,Kawahara

source_name: wildtype tissue (pool of 3 wt littermates)

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 21d Liver; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Tiara,,Kawahara

source_name: SIRT6 null tissue

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 21d Liver; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara

tag: SIRT6 null tissue


title: S6-ko 29d Thymus -1

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77701.gif
Tissue type: 29 day thymus

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 780, 4540; Software: type: feature extraction; Performer: Adam,,Adler

source_name: WT 29d Thymus

label_protocol: not provided

tag: WT 29d Thymus

source_name: S6-ko 29d Thymus -1

tag: S6-ko 29d Thymus -1


title: SIRT6null_3weekpups

description:
Simple annotation: Transcription, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76631.gif
Tissue type: 21 day liver

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 4640; Software: type: feature extraction; Performer: Tiara,,Kawahara

tag: wildtype tissue (pool of 3 wt littermates)