title: Clone3200_LPI5_N+_8w_rep1

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

description: Gene expression data from a 8-week N experiment.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

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.

organism: Populus fremontii x Populus angustifolia

source_name: LPI5, normal nitrogen, 8-week

label_protocol: Affymetrix

growth_protocol: Rooted cuttings, 10-15 cm in height, were transferred into aerated nutrient solution containing 5 mM nitrogen.  Distilled water was added daily as needed to maintain a constant nutrient volume.  Nutrient solution was replaced weekly, and a pH of 5.8±0.3 was maintained by daily additions of 2N KOH or 2N HCl.

extract_protocol: CTAB protocol

treatment_protocol: Plants of ~1 m height were distributed into two large ebb and flow hydroponic tubs, one receiving 5 mM nitrogen (N+) and the other with 0.125 mM nitrogen (N-).  Plants were maintained as described in Growth Protocol for 8 weeks prior to sampling.

tag: clone


title: Leydig cells: DEHP-treated Sample 4 vs. Vehicle-treated Sample 2

status: Public on Feb 19 2009

type: RNA

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1).

data_processing: Data were analyzed under R (www.r-project.org) using the limma package of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {  okType<-x[,ControlType]==0  okFoundRed<-x[,rIsFound]==1  okFoundGreen<-x[,gIsFound]==1  okPixRed<-((x[,rNumPixOLHi]+x[,rNumPixOLLo])/x[,rNumPix])<=0.1  okPixGreen<-((x[,gNumPixOLHi]+x[,gNumPixOLLo])/x[,gNumPix])<=0.1  okBGRed1<-(x[,rMedianSignal]/x[,rBGMedianSignal])>=1.5  okBGRed2<-(x[,rMeanSignal]/x[,rBGMeanSignal])>=1.5  okBGRed3<-(x[,rMedianSignal]-x[,rBGMedianSignal])/x[,rBGPixSDev]>=2  okBGRed4<-(x[,rMeanSignal]-x[,rBGMeanSignal])/x[,rBGPixSDev]>=2  okBGGreen1<-(x[,gMedianSignal]/x[,gBGMedianSignal])>=1.5  okBGGreen2<-(x[,gMeanSignal]/x[,gBGMeanSignal])>=1.5  okBGGreen3<-(x[,gMedianSignal]-x[,gBGMedianSignal])/x[,gBGPixSDev]>=2  okBGGreen4<-(x[,gMeanSignal]-x[,gBGMeanSignal])/x[,gBGPixSDev]>=2  okSatRed<-x$rIsSaturated==0  okSatGreen<- x$gIsSaturated==0  okUnifRed<-x$rIsFeatNonUnifOL==0  okUnifGreen<-x$gIsFeatNonUnifOL==0  okUnifBGRed<-x$rIsBGNonUnifOL==0  okUnifBGGreen<-x$gIsBGNonUnifOL==0  okPopRed<-x$rIsFeatPopnOL==0  okPopGreen<-x$gIsFeatPopnOL==0  okPopBGRed<-x$rIsBGPopnOL==0  okPopBGGreen<-x$gIsBGPopnOL==0  okManualFlag<-x$IsManualFlag==0  okAbBGRed<-x$rIsWellAboveBG==1  okAbBGGreen<-x$gIsWellAboveBG==1  as.numeric(okType & okFoundRed & okFoundGreen & okPixRed & okPixGreen & ((okBGRed1 & okBGRed2 & okBGRed3 & okBGRed4) | (okBGGreen1 & okBGGreen2 & okBGGreen3 & okBGGreen4)) &  okSatRed & okSatGreen & okUnifRed & okUnifGreen & okUnifBGRed & okUnifBGGreen & okPopRed & okPopGreen & okPopBGRed & okPopBGGreen & okManualFlag & okAbBGRed & okAbBGGreen) }. Only the spots that had a weight of 1 on at least 6 microarrays corresponding to 3 dye-swap experiments were further analyzed. Additionally, we deleted the spots that were called present only on the 3 dye-swaps corresponding to a single DEHP-treated biological replicates. Local background was substracted on Cy3 and Cy5 data and a lowess normalization was applied to the log(Cy5/Cy3) data using the normalizeWithinArrays function.

molecule: total RNA

organism: Mus musculus

source_name: Laser capture microdissected Leydig cells from DEHP-treated mouse

label_protocol: For each sample, 1µg of amplified RNA was labelled using the Agilent Low Input Linear Amplification Labelling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Fourteen-week-old male C57BL/6J mice were purchased from Charles River (Les Oncins, France). Mice were acclimatized for four weeks, housed in polycarbonate cages at 22+2°C on a 12 hour light/dark cycle and allowed free access to water and food. In vivo studies were conducted under European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, the right testis of DEHP-treated or vehicle-treated C57BL/6J male mice were embedded in Tissue-Tek O.C.T. compound (Sankura Finetek, Torrance,CA) and snap frozen with isopentane cooled in liquid nitrogen. Sections of 10µm (Leica CM3050S cryostat) were mounted on microscope slides which were immediately fixed, stained with hematoxylin-eosin, dehydrated by sequential baths in ice-cold 70%, 95% and 100% ethanol and stored under vacuum. Laser capture microdissection of Leydig cells was performed with the Arcturus PixCell IIe (Arcturus, California, USA) using CapSure® Macro LCM Caps (Molecular Devices Corporation). To avoid contaminations, the laser power and duration was adjusted for each section (ranging from 50 to 70 mW and 0.6 to 0.8 ms respectively). Approximately 1500 laser shots were performed per tissue section. Total RNA was isolated from single caps obtained from independent mice using the PicoPure® RNA Isolation Kit (Molecular Devices Corporation) and was amplified for two rounds with RiboAmp® RNA Amplification Kit (Molecular Devices Corporation) according to the manufacturers instructions.

treatment_protocol: di-(2-ethylhexyl)-phthalate (DEHP) in solution into corn oil was administered at 200 mg/Kg/day for 21 days by daily gavage

tag: Strain

tag: Gender

value: male

tag: Age

value: 21 weeks

tag: Tissue

value: laser-capture microdissected Leydig cells

source_name: Laser capture microdissected Leydig cells from vehicle-treated mouse

treatment_protocol: Eighteen week-old mice were randomly divided into two groups (DEHP-treated and vehicle-treated, n=4 per group). di-(2-ethylhexyl)-phthalate (DEHP, 200 mg/Kg/day) in solution into corn oil (DEHP-treated group) or corn oil (vehicle-treated group) were administered for 21 days by daily gavage


title: T0 vs T2 second biological replica

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

description: Digestive gland responses to okadaic acid treatment, loop design

hyb_protocol: labelled cDNAs were hybridised in SSC 5X, Sarcosile 0.1%, Denhardt sol 1X overnight at 48°C, the slides were washed with decreasing stringency buffer untill SSC 0.05X.

scan_protocol: Bio-Rad Chip Reader, laser powers 100% and detector sensitivity varied to balance the two channel intensities spots were inspected and quantified with Bio-Rad Cheap Reader's software.

data_processing: Raw data was first background subtracted then normalized with the LOESS algorithm. Finally a quantile normalization was apply. R software was used implemented with LIMMA package

organism: Mytilus galloprovincialis

label_protocol: Total RNA was retro-transcribed using Superscript II Reverse Transcriptase (Invitrogen) with aminoallyl-dUTP and then labelled with Cy5 or Cy3 fluorescent dyes (GE Healthcare)

growth_protocol: Mussels were maintained in tanks provided with oxygen-pump and water-lively pump in sea water. To prevent additional environmental stress, the seasonal photoperiod (L 10-D 14) and water temperature (17°C) were maintained. Sea water was changed weekly and water salinity (37 PSU) was controlled daily.

extract_protocol: Total RNA extracted using RNAtidy G following manufacturer's instructions plus an additional LiCl precipitation

treatment_protocol: 6.5 µg of Okadaic acid (Sigma Chemical Co.) diluted in 1 mL ethanol every two days for a time span of 5 weeks

tag: treatment

value: Okadaic acid

tag: age

value: 1 week post treatment

tag: biological replica

tag: tissue

value: digestive gland

value: Control

value: 0 days post treatment


title: CUMC08

type: genomic

city: Houston

first: Federico

middle: A

last: Monzon

state: TX

address: 6565 Fannin St., MS205

department: Pathology

country: USA

institute: The Methodist Hospital Research Institute

hyb_protocol: Affymetrix Mapping 10K Xba 2.0 Assay

scan_protocol: Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue

label_protocol: Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)

extract_protocol: Deparaffinization followed by Qiagen DNeasy Blood and Tissue kit by manufacturer's instructions

tag: Sex:	M

tag: AgeDecade:	40-49

tag: Tumor Size:	8

tag: Furhman Nuclear Grade:	3

tag: TNM Stage:	pT2 Nx Mx

tag: LymphoVascular Invasion:	FALSE


title: Clone3200_LPI5_N-_8w_rep1

label: biotin

source_name: LPI5, low nitrogen, 8-week


title: T6 vs T0 second biological replica

value: 5 weeks post treatment


title: Leydig cells: DEHP-treated Sample 1 vs. Vehicle-treated Sample 2


title: Leydig cells: DEHP-treated Sample 4 vs. Vehicle-treated Sample 1


title: Leydig cells: DEHP-treated Sample 1 vs. Vehicle-treated Sample 1


title: Clone3200_LPI5_N+_8w_rep2


title: Clone3200_LPI5_N-_4w_rep1

description: Gene expression data from a 4-week N experiment.

source_name: LPI5, low nitrogen, 4-week

treatment_protocol: Plants of ~1 m height were distributed into two large ebb and flow hydroponic tubs, one receiving 5 mM nitrogen (N+) and the other with 0.125 mM nitrogen (N-).  Plants were maintained as described in Growth Protocol for 4 weeks prior to sampling.


title: Clone3200_LPI5_N+_4w_rep2

source_name: LPI5, normal nitrogen, 4-week


title: Clone3200_LPI5_N-_4w_rep2


title: Clone3200_LPI5_N-_8w_rep2


title: NtlChIP_gastrula_rep3

city: Cambridge

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).

scan_protocol: Slides were scanned using an Agilent scanner

data_processing:
Images were quantified using Genepix.
Data was analysed using Whitehead error model as described in Wardle et al 2006 (Genome Biology 7:R71).

organism: Danio rerio

source_name: Immunoprecipitated chromatin

growth_protocol: embryos grown to 75-85% epiboly

extract_protocol: Chromatin  immunoprecipitation assay

treatment_protocol: Embryos at 75%-85% epiboly were collected and used in  a ChIP assay to generate the Cy5 (ChIPed DNA) and Cy3 (whole cell input DNA) labelled probes for hybridisation to the gene arrays.

tag: gastrula embryo

source_name: Whole cell chromatin


title: T0 vs T1 second biological replica

value: Okadaic acod

value: 3 days post treatment


title: T2 vs T4 second biological replica

value: 3 weeks post treatment


title: Clone3200_LPI5_N+_4w_rep1


title: T6 vs T2 first biological replica


title: T4 vs T6  first biological replica


title: Sertoli cells: Vehicle-treated Sample 3 vs. DEHP-treated Sample 2

data_processing: Data were analyzed under R (www.r-project.org) using the limma package of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {  okType<-x[,ControlType]==0  okFoundRed<-x[,rIsFound]==1  okFoundGreen<-x[,gIsFound]==1  okPixRed<-((x[,rNumPixOLHi]+x[,rNumPixOLLo])/x[,rNumPix])<=0.1  okPixGreen<-((x[,gNumPixOLHi]+x[,gNumPixOLLo])/x[,gNumPix])<=0.1  okBGRed1<-(x[,rMedianSignal]/x[,rBGMedianSignal])>=1.5  okBGRed2<-(x[,rMeanSignal]/x[,rBGMeanSignal])>=1.5  okBGRed3<-(x[,rMedianSignal]-x[,rBGMedianSignal])/x[,rBGPixSDev]>=2  okBGRed4<-(x[,rMeanSignal]-x[,rBGMeanSignal])/x[,rBGPixSDev]>=2  okBGGreen1<-(x[,gMedianSignal]/x[,gBGMedianSignal])>=1.5  okBGGreen2<-(x[,gMeanSignal]/x[,gBGMeanSignal])>=1.5  okBGGreen3<-(x[,gMedianSignal]-x[,gBGMedianSignal])/x[,gBGPixSDev]>=2  okBGGreen4<-(x[,gMeanSignal]-x[,gBGMeanSignal])/x[,gBGPixSDev]>=2  okSatRed<-x$rIsSaturated==0  okSatGreen<- x$gIsSaturated==0  okUnifRed<-x$rIsFeatNonUnifOL==0  okUnifGreen<-x$gIsFeatNonUnifOL==0  okUnifBGRed<-x$rIsBGNonUnifOL==0  okUnifBGGreen<-x$gIsBGNonUnifOL==0  okPopRed<-x$rIsFeatPopnOL==0  okPopGreen<-x$gIsFeatPopnOL==0  okPopBGRed<-x$rIsBGPopnOL==0  okPopBGGreen<-x$gIsBGPopnOL==0  okManualFlag<-x$IsManualFlag==0  okAbBGRed<-x$rIsWellAboveBG==1  okAbBGGreen<-x$gIsWellAboveBG==1  as.numeric(okType & okFoundRed & okFoundGreen & okPixRed & okPixGreen & ((okBGRed1 & okBGRed2 & okBGRed3 & okBGRed4) | (okBGGreen1 & okBGGreen2 & okBGGreen3 & okBGGreen4)) &  okSatRed & okSatGreen & okUnifRed & okUnifGreen & okUnifBGRed & okUnifBGGreen & okPopRed & okPopGreen & okPopBGRed & okPopBGGreen & okManualFlag & okAbBGRed & okAbBGGreen) }. Only the spots that had a weight of 1 on at least 6 microarrays corresponding to 3 dye-swap experiments were further analyzed. Local background was substracted on Cy3 and Cy5 data and a lowess normalization was applied to the log(Cy5/Cy3) data using the normalizeWithinArrays function.

source_name: Laser capture microdissected Sertoli cells-rich areas from vehicle-treated mouse

extract_protocol: Immediately following euthanasia, the right testis of DEHP-treated or vehicle-treated C57BL/6J male mice were embedded in Tissue-Tek O.C.T. compound (Sankura Finetek, Torrance,CA) and snap frozen with isopentane cooled in liquid nitrogen. Sections of 10µm (Leica CM3050S cryostat) were mounted on microscope slides which were immediately fixed, stained with hematoxylin-eosin, dehydrated by sequential baths in ice-cold 70%, 95% and 100% ethanol and stored under vacuum. Laser capture microdissection of Leydig cells was performed with the Arcturus PixCell IIe (Arcturus, California, USA) using CapSure® Macro LCM Caps (Molecular Devices Corporation). To avoid contaminations, the laser power and duration was adjusted for each section (ranging from 50 to 70 mW and 0.6 to 0.8 ms respectively). Approximately 5000 laser shots were performed per tissue section. Total RNA was isolated from single caps obtained from independent mice using the PicoPure® RNA Isolation Kit (Molecular Devices Corporation) and was amplified for two rounds with RiboAmp® RNA Amplification Kit (Molecular Devices Corporation) according to the manufacturers instructions.

treatment_protocol: corn oil was administered for 21 days by daily gavage

value: laser-capture microdissected Sertoli-cells rich areas (intermediate layer of the seminiferous tubule epithelium)

source_name: Laser capture microdissected Sertoli cells-rich areas from DEHP-treated mouse


title: Sertoli cells: Vehicle-treated Sample 4 vs. DEHP-treated Sample 3


title: Sertoli cells: Vehicle-treated Sample 2 vs. DEHP-treated Sample 1


title: Clone3200_LPI2_N-_4w_rep2

source_name: LPI2, low nitrogen, 4-week


title: T6 vs T0 first biological replica


title: T2 vs T4 first biological replica


title: NtlChIP_gastrula_rep2

label_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).


title: Clone3200_LPI2_N-_4w_rep1


title: Sertoli cells: Vehicle-treated Sample 1 vs. DEHP-treated Sample 4


title: Sertoli cells: DEHP-treated Sample 2 vs. Vehicle-treated Sample 3


title: NtlChIP_gastrula_rep3


title: T1 vs T2 first biological replica


title: NtlChIP_gastrula_rep1


title: Clone3200_LPI2_N+_4w_rep2

source_name: LPI2, normal nitrogen, 4-week


title: T0 vs T1 first biological replica


title: T1 vs T4 first biological replica


title: Clone3200_LPI2_N+_4w_rep1


title: Sertoli cells: DEHP-treated Sample 1 vs. Vehicle-treated Sample 2


title: T0 vs T2 first biological replica


title: Sertoli cells: DEHP-treated Sample 4 vs. Vehicle-treated Sample 1


title: Sertoli cells: DEHP-treated Sample 3 vs. Vehicle-treated Sample 4


title: Control Transfection, E2 Induction 1h, A

city: Geneva

first: Deo Prakash

last: Pandey

address: 30 Quai Ernest-Ansmert

department: Cell Biology

institute: University of Geneva

description: Gene expression analyses were carried out to identify genes regulated by 17-beta estradiol (E2) and Hydroxytamoxifen (OHT) through GPR30 in SKBR3 cells.

data_processing: Illumina Bead Studio, No background subtraction, No normalization

label: biotin UTP

label_protocol: As suggested by the manufacturer, Illumina for beadchip Illumina human-6 v2.0 expression beadchip, Illumina TotalPrep RNA Amplification Kit from Ambion, Catalog #IL1791

growth_protocol: SKBR3 cells were grown in RPMI-1640 media supplemented with 10% FCS and L-Glutamine. Cells were switched to media without serum 24 h before transfection.

extract_protocol: Total RNA was extracted using TriZOL.

treatment_protocol: SKBR3 cells were transfected in 10 cm plates at roughly 60% density with Fugene for 30 hours (3microl/microgram). Cells were induced for 1 h with respective treatment.

tag: Estrogen Receptor alpha and beta negative breast cancer cells


title: ExprProfile_w[m4]-Contr-A

status: Public on Feb 18 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Expression study

hyb_protocol: Hybridization was performed according to standard protocols available at http://microarrays.nki.nl/research/methods.html.

scan_protocol: Scanning was performed according to standard protocols available at http://microarrays.nki.nl/research/methods.html.

data_processing: Images of the expression arrays were analyzed using Agilent Feature Extraction Software version 9.5.1.1

organism: Drosophila melanogaster

source_name: male heads

label_protocol: Labeling was performed according to standard protocols available at http://microarrays.nki.nl/research/methods.html.

growth_protocol: Flies were raised at 25°C on standard cornmeal/molasses/agar medium.

extract_protocol: DNAse treatment and mRNA amplification were performed according to standard protocols available at http://microarrays.nki.nl/research/methods.html.

treatment_protocol: For Expression profiling: Fly heads were collected in Trizol and stored at -80C. Total RNA was isolated from 40 heads.

tag: w[m4]-Contr-A (EXPERIMENT)

tag: w[m4]-Contr-A (REFERENCE)


title: ExprProfile_w[m51b]

description: Expression study

tag: w[m51b] (EXPERIMENT)

tag: RS (REFERENCE)


title: ExprProfile_w[m4]-Su(var)3-9-B

description: Expression study

tag: w[m4]-B (EXPERIMENT)

tag: w[m4]-Contr-B (REFERENCE)


title: ExprProfile_w[m4]-Contr-B

description: Expression study

tag: w[m4]-Contr-B (EXPERIMENT)


title: ExprProfile_OregonRS

description: Expression study

tag: RS (EXPERIMENT)


title: wa_yw289-1_38_Normal_FF

city: Santa Clara

first: Yuker

last: Wang

state: CA

address: 3380 Central Expressway

institute: Affymetrix

hyb_protocol: George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan Forman, Yuker Wang, Martin Moorhead, and Malek Faham Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping p. 199-211; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

data_processing:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249-252; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.

For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246
Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.

source_name: normal tissue in fresh frozen form

label_protocol:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan
Forman, Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping
p. 199-211; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual",edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

extract_protocol: genomic DNA extracted from a fresh frozen block. It's a customer sample

tag: disease state

value: normal tissue

tag: sample

value: fresh frozen form

tag: tissue

value: Liver


title: ExprProfile_w[m4e]

description: Expression study

tag: w[m4e] (EXPERIMENT)


title: ExprProfile_w[m4]-Su(var)3-9-A

description: Expression study

tag: w[m4]-A (EXPERIMENT)


title: wa_yw289-1_36_Normal_FFPE

description:
George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
Yuker Wang, Martin Moorhead, and Malek Faham
Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination
p. 249-252; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

scan_protocol: George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan Forman, Yuker Wang, Martin Moorhead, and Malek Faham Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping p. 199-211; Cold Spring Harbor Lab "Genetic Variation: A Laboratory Manual", edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).

source_name: normal tissue in FFPE form

extract_protocol: genomic DNA extracted from a FFPE block. It's a customer sample

value: FFPE form


title: wa_yw289-1_29_Normal_FFPE


title: wa_yw289-1_27_Normal_FF


title: wa_yw289-1_34_Normal_FF


title: wa_yw289-1_25_Normal_FFPE


title: wa_yw289-1_11_Normal_FF


title: wa_yw289-1_19_Normal_FF


title: wa_yw289-1_17_Normal_FFPE


title: wa_yw289-1_15_Normal_FF


title: wa_yw289-1_21_Normal_FFPE


title: wa_yw289-1_13_Normal_FFPE


title: wa_yw289-1_23_Normal_FF


title: wa_yw289-1_02_Normal_FFPE


title: md_yw291_15_Normal_FFPE

value: Breast


title: wa_yw289-1_04_Normal_FF


title: wa_yw289-1_09_Normal_FFPE


title: Human placenta 001

city: New Haven, BASS 437

first: Michael

middle: R

last: Seringhaus

state: CT

address: 266 Whitney Ave

department: Molecular Biophysics & Biochemistry

institute: Yale University

description: Human placental RNA was applied.

hyb_protocol: Microarrays were hybridized with 2-3µg labeled cDNA in 360µl hybridization buffer (50mM MES, 0.5M NaCl, 10mM EDTA and 0.005% {V/V} Tween 20) for 20 hours at 50°C. Hybridizations were performed in disposable adhesive chambers (Grace Biolabs, Bend, OR) in a hybridization oven with constant agitation. After hybridization, the arrays were washed on an orbital platform in nonstringent buffer (6X SSPE, 0.01%[V/V] Tween-20) for 10 minutes at room temperature and then washed in a stringent buffer (100mM MES, 0.1M NaCl, 0.01% tween-20) for 30 minutes at 45°C. This was followed by a 5 minute wash in the non-stringent buffer and a 4 minute wash in 0.2X SSC. The arrays were then dried with an air duster.

scan_protocol: Fluorescence micrographs were acquired with an Axon 4200B laser scanner at 5µm resolution.

data_processing: Our normalization scale equates median log intensity of high-expression regions to 1.0, and median log intensity of non-coding regions (background) to 0.0 (Figure 2 a-d); thus, an oligo with intensity equal to that of a highly-expressed region will be assigned a score of ~1, while an intensity near baseline will score ~0. MM oligos were evaluated by taking the difference in normalized intensities (MM-PM). This value is expressed as a percentage of the total intensity range. (Thus, if the normalized PM probe intensity is 0.8, and the normalized MM intensity is 0.6, the MM-PM difference will be -0.2 on our normalized scale, which equates to 20% of the total normalized intensity range.)

molecule: polyA RNA

source_name: human placenta

label_protocol: Following reverse transcription the products were heated at 95°C for 5 minutes to denature the RNA:DNA hybrids and heat inactivate the reverse transcriptase, after which the RNA template was hydrolysed by incubating in 0.2M NaOH at 65°C for 15 minutes. The reaction was then neutralized in 0.3M HEPES (pH 7.0). Reverse transcription products from 10 separate reactions were produced in this manner and pooled to reduce technical variability between samples. The cDNAs were precipitated in ethanol with 3M sodium acetate and resuspended in 0.1m NaHCO3 to facilitate coupling reactive groups of the amino allyl dUTPs. Following incubation at room temperature for 2 hours, the labeled cDNAs were purified with CyScribe GFX glass fiber spin columns (Amersham Bioscience, Piscataway, NJ) and isopropanol precipitated.

extract_protocol: Poly(A)+ RNA human placenta tissue pooled from 2-3 individuals was obtained from Ambion (Austin, TX). First strand cDNA was generated from 5µg RNA for each reaction with (RnaseH-)M-MLV reverse transcriptase, primed with equimolar concentrations of oligo(dT)18 and random decamers. The reactions were carried out at 42°C for 2 hours in the presence of 0.5mM dATP, 0.5mM dCTP, 0.5mM dGTP, 0.15mM dTTP and 0.15mM amino allyl dUTP to facilitate the secondary labeling of an amine reactive fluorescent conjugate.

tag: human placenta


title: wa_yw289-1_31_Normal_FF


title: md_yw291_16_Normal_FFPE


title: md_yw291_13_Normal_FFPE


title: md_yw291_11_Normal_FFPE


title: wa_yw289-1_05_Normal_FFPE


title: Human placenta 002

description: Human placental RNA was applied.


title: wa_yw289-1_07_Normal_FF


title: md_yw291_05_Normal_FFPE


title: md_yw291_02_Normal_FFPE


title: md_yw291_04_Normal_FFPE


title: md_yw291_03_Normal_FFPE


title: md_yw291_07_Normal_FFPE


title: md_yw291_08_Normal_FFPE


title: md_yw291_10_Normal_FFPE


title: md_yw291_14_Normal_FFPE


title: Human placenta 003

description: Human placental RNA was applied.


title: md_yw291_40_Normal_FFPE


title: md_yw291_37_Normal_FFPE


title: md_yw291_35_Normal_FFPE


title: md_yw291_33_Normal_FFPE


title: md_yw291_36_Normal_FFPE


title: kd_yw286-1_09_Normal_FFPE

value: Kidney


title: md_yw291_01_Normal_FFPE


title: md_yw291_39_Normal_FFPE


title: md_yw291_32_Normal_FFPE


title: md_yw291_34_Normal_FFPE


title: kd_yw292_14_Normal_FFPE


title: kd_yw286-1_08_Normal_FFPE


title: kd_yw286-1_05_Normal_FFPE


title: kd_yw292_18_Normal_FFPE


title: kd_yw292_10_Normal_FFPE


title: hv_yw285-2_42_Normal_FFPE


title: hv_yw285-1_08_Normal_FFPE


title: kd_yw292_12_Normal_FFPE


title: cr_yw292_24_Normal_FFPE

value: Colorectal


title: kd_yw286-1_06_Normal_FFPE


title: hv_yw285-1_10_Normal_FFPE


title: hv_yw285-1_06_Normal_FFPE


title: hv_yw285-1_09_Normal_FFPE


title: kd_yw286-1_10_Normal_FFPE


title: hv_yw285-1_07_Normal_FFPE


title: kd_yw286-1_11_Normal_FFPE


title: kd_yw292_16_Normal_FFPE


title: cr_yw292_27_Normal_FFPE


title: cr_yw292_34_Normal_FFPE


title: cr_yw292_30_Normal_FFPE


title: cr_yw292_33_Normal_FFPE


title: cr_yw292_23_Normal_FFPE


title: cr_yw292_22_Normal_FFPE


title: cr_yw292_28_Normal_FFPE


title: cr_yw292_32_Normal_FFPE


title: cr_yw292_31_Normal_FFPE


title: cr_yw292_26_Normal_FFPE


title: ch_yw285-2_48_Normal_FFPE


title: ch_yw285-2_08_Normal_FF


title: ch_yw285-2_01_Normal_FF


title: ch_yw285-2_10_Normal_FF


title: cr_yw292_21_Normal_FFPE


title: cr_yw292_25_Normal_FFPE


title: ch_yw285-1_41_Normal_FFPE


title: ch_yw285-2_04_Normal_FF


title: ch_yw285-2_05_Normal_FF


title: ch_yw285-1_40_Normal_FFPE


title: ch_yw285-2_09_Normal_FF


title: ch_yw285-2_07_Normal_FF


title: cr_yw292_20_Normal_FFPE


title: cr_yw292_19_Normal_FFPE


title: ch_yw285-1_36_Normal_FFPE


title: ch_yw285-2_37_Normal_FFPE


title: ch_yw285-1_39_Normal_FFPE


title: cr_yw292_29_Normal_FFPE


title: ch_yw285-1_23_Normal_FFPE


title: ch_yw285-2_03_Normal_FF


title: ch_yw285-2_22_Normal_FF

value: Colon


title: ch_yw285-2_06_Normal_FF

value: Bladder


title: wa_yw289-1_28_Tumor_FFPE

source_name: primary tumor in FFPE form

value: primary tumor


title: ch_yw285-1_45_Normal_FFPE


title: wa_yw289-1_32_Tumor_FFPE


title: ch_yw285-1_38_Normal_FFPE


title: ch_yw285-1_43_Normal_FFPE


title: wa_yw289-1_35_Tumor_FFPE


title: ch_yw285-1_21_Normal_FFPE


title: wa_yw289-1_33_Tumor_FF

source_name: primary tumor in fresh frozen form


title: ch_yw285-2_02_Normal_FF


title: wa_yw289-1_37_Tumor_FF


title: wa_yw289-1_03_Tumor_FF


title: wa_yw289-1_30_Tumor_FF


title: wa_yw289-1_26_Tumor_FF


title: wa_yw289-1_24_Tumor_FFPE


title: wa_yw289-1_06_Tumor_FF


title: wa_yw289-1_16_Tumor_FFPE


title: wa_yw289-1_18_Tumor_FF


title: wa_yw289-1_20_Tumor_FFPE


title: wa_yw289-1_14_Tumor_FF


title: wa_yw289-1_10_Tumor_FF


title: md_yw291_30_Tumor_FFPE


title: wa_yw289-1_22_Tumor_FF


title: wa_yw289-1_12_Tumor_FFPE


title: wa_yw289-1_01_Tumor_FFPE


title: md_yw291_23_Tumor_FFPE


title: md_yw291_27_Tumor_FFPE


title: wa_yw289-1_08_Tumor_FFPE


title: md_yw291_24_Tumor_FFPE


title: md_yw291_43_Tumor_FFPE


title: md_yw291_45_Tumor_FFPE


title: md_yw291_22_Tumor_FFPE


title: md_yw291_47_Tumor_FFPE


title: md_yw291_48_Tumor_FFPE


title: md_yw289-1_47_Tumor_FFPE


title: md_yw291_46_Tumor_FFPE


title: md_yw291_44_Tumor_FFPE


title: md_yw291_42_Tumor_FFPE


title: md_yw291_41_Tumor_FFPE


title: md_yw285-2_25_Tumor_FFPE


title: md_yw289-1_45_Tumor_FFPE


title: md_yw289-1_48_Tumor_FFPE


title: md_yw289-1_42_Tumor_FFPE


title: md_yw285-2_35_Tumor_FFPE


title: md_yw289-1_43_Tumor_FFPE


title: md_yw289-1_40_Tumor_FFPE


title: md_yw289-1_46_Tumor_FFPE


title: md_yw289-1_39_Tumor_FFPE


title: md_yw285-2_27_Tumor_FFPE


title: md_yw289-1_41_Tumor_FFPE


title: md_yw289-1_44_Tumor_FFPE


title: md_yw285-2_29_Tumor_FFPE


title: md_yw285-2_33_Tumor_FFPE


title: md_yw285-2_28_Tumor_FFPE


title: md_yw285-2_26_Tumor_FFPE


title: md_yw285-2_34_Tumor_FFPE


title: md_yw285-2_32_Tumor_FFPE


title: md_yw285-2_31_Tumor_FFPE


title: md_yw285-2_30_Tumor_FFPE


title: kd_yw292_17_Tumor_FFPE


title: kd_yw292_11_Tumor_FFPE


title: kd_yw292_02_Tumor_FFPE


title: md_yw285-2_36_Tumor_FFPE


title: kd_yw292_07_Tumor_FFPE


title: kd_yw292_03_Tumor_FFPE


title: kd_yw292_05_Tumor_FFPE


title: kd_yw292_04_Tumor_FFPE


title: kd_yw292_06_Tumor_FFPE


title: kd_yw292_08_Tumor_FFPE


title: kd_yw292_15_Tumor_FFPE


title: kd_yw292_09_Tumor_FFPE


title: hv_yw285-1_01_Tumor_FFPE


title: kd_yw292_01_Tumor_FFPE


title: hv_yw285-2_45_Tumor_FFPE


title: kd_yw292_13_Tumor_FFPE


title: cr_yw292_42_Tumor_FFPE


title: cr_yw292_48_Tumor_FFPE


title: hv_yw285-2_41_Tumor_FFPE


title: hv_yw285-1_05_Tumor_FFPE


title: cr_yw286_40_Tumor_FFPE


title: cr_yw286_28_Tumor_FFPE


title: cr_yw292_46_Tumor_FFPE


title: cr_yw292_45_Tumor_FFPE


title: cr_yw292_44_Tumor_FFPE


title: cr_yw286_25_Tumor_FFPE


title: cr_yw292_41_Tumor_FFPE


title: hv_yw285-1_03_Tumor_FFPE


title: cr_yw292_43_Tumor_FFPE


title: hv_yw285-1_02_Tumor_FFPE


title: cr_yw286_31_Tumor_FFPE


title: cr_yw292_38_Tumor_FFPE


title: cr_yw286_30_Tumor_FFPE


title: cr_yw286_27_Tumor_FFPE


title: cr_yw286_26_Tumor_FFPE


title: cr_yw273-2_20_Tumor_FF


title: cr_yw273-2_10_Tumor_FF


title: cr_yw273-2_22_Tumor_FF


title: cr_yw273-2_08_Tumor_FF


title: cr_yw273-2_07_Tumor_FF


title: cr_yw286_39_Tumor_FFPE


title: cr_yw273-2_09_Tumor_FF


title: cr_yw273-2_21_Tumor_FF


title: cr_yw273-2_13_Tumor_FF


title: cr_yw273-2_14_Tumor_FF


title: cr_yw273-2_16_Tumor_FF


title: cr_yw273-2_19_Tumor_FF


title: cr_yw273-2_15_Tumor_FF


title: cr_yw273-2_18_Tumor_FF


title: cr_yw273-2_06_Tumor_FF


title: ch_yw285-1_26_Tumor_FFPE


title: ch_yw285-2_23_Tumor_FF


title: ch_yw285-2_17_Tumor_FF


title: cr_yw273-2_11_Tumor_FF


title: ch_yw285-1_31_Tumor_FFPE


title: ch_yw285-2_20_Tumor_FF


title: ch_yw285-1_20_Tumor_FFPE


title: ch_yw285-1_34_Tumor_FFPE


title: ch_yw285-2_15_Tumor_FF


title: cr_yw273-2_17_Tumor_FF


title: ch_yw285-2_21_Tumor_FF


title: ch_yw285-1_28_Tumor_FFPE


title: siScramble1, biological rep 1

city: Rehovot

first: Michal

last: pardo

state: Rehovot

address: P.O.Box 12

country: Israel

institute: Hebrew university

description: Gene expression data from cells transfected with no gene recognition scramble plasmid

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Scramble control knocked down cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 150ng total RNA (GeneChip® Whole Transcript Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Cells were grown in DMEM with supplemented with 10% (w/v) fetal calf serum, 50 ug/ml gentamycin, 100 ug/ml kanamycin and 1% (w/v) glutamine at 37°C in a humidified atmosphere consisting of 95% air and 5% CO2.

extract_protocol: Trireagent extraction of total RNA was performed according to the manufacturer's instructions, followed by RNA clean up with Qiagene kit.

tag: cell type

value: origin from AML-12


title: ch_yw285-1_30_Tumor_FFPE


title: ch_yw285-2_14_Tumor_FF


title: siScramble2, biological rep 2


title: ch_yw285-2_18_Tumor_FF

value: Colon/Rectum


title: siMnSOD2, biological rep 2

description: Gene expression data from cells knocked down for MnSOD

source_name: MnSODknocked down cells


title: siScramble3, biological rep 3


title: ch_yw285-1_32_Tumor_FFPE


title: ch_yw285-2_11_Tumor_FF


title: ch_yw285-2_12_Tumor_FF


title: siMnSOD1, biological rep 1


title: ch_yw285-2_13_Tumor_FF


title: ch_yw285-1_35_Tumor_FFPE


title: ch_yw285-1_29_Tumor_FFPE


title: ch_yw285-2_16_Tumor_FF


title: ch_yw285-1_33_Tumor_FFPE


title: MKO1_minHGF

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA, employing the empirical Bayes approach for background adjustment.

source_name: liver; c-Met knockout mouse; unstimulated

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: C-MetloxP/loxP animals were first crossed with albumin/AFP promoter/enhancer13 (Alfp-Cre) or albumin promoter-Cre transgenic animals (Alb-Cre). The Alfp-Cre animals express Cre-recombinase during embryonal development, while Alb-Cre mice start to express Cre 2 weeks after birth.

extract_protocol: Total RNA was extracted from cryopreserved liver tissue by using peqGold RNAPure (PeqLab, Erlangen, Germany).

treatment_protocol: For gene array analysis c-MetDhepa and c-MetloxP/loxP controls were stimulated for 2 hours with 2µg recombinant mouse HGF.Three animals per group were treated in parallel, before and after i.p. injection of recombinant HGF or NaCl.

tag: Backgroud:C57/BL6, Gender:male, Age:8-10 weeks


title: ch_yw285-2_24_Tumor_FF


title: ch_yw285-1_25_Tumor_FFPE


title: siMnSOD3, biological rep 3


title: MKO2_plusHGF

source_name: liver; c-Met knockout mouse; stimulated with HGF


title: MKO3_plusHGF


title: MKO1_plusHGF


title: cr_yw286_32_Tumor_FFPE


title: MKO2_minHGF


title: CTRL2_plusHGF

source_name: liver; control mouse; stimulated with HGF


title: CTRL1_plusHGF


title: HP1-DamID_w[m4]-Contr

description: DamID experiment

hyb_protocol: Hybridizations were done using standard protocols (see http://microarrays.nki.nl/download/protocols.html) on a custom designed, 4x44K Agilent microarray.

scan_protocol: Microarrays were scanned in the Agilent scanner and Agilent Feature Extraction Software version 9.5.1.1 was used to quantify images.

data_processing: DamID data were normalized using R-packages limma (Smyth 2005) and vsn (Huber et al. 2002). Raw data files were loaded in R and the weight of control spots was set to zero to exclude them from the results. We did not apply background correction to the data. Data was normalized between different arrays (method=”vsn”).

label_protocol: Each experiment consisted of 4 hybridizations using biologically independent samples. 1 g of amplified methylated gDNA from the experimental or reference sample were labeled in a 20 ul volume with ULS Cy-dyes according to standard protocols (see http://microarrays.nki.nl/download/protocols.html).

extract_protocol: We made minor modifications to the DamID protocol so that we could make chromatin profiles using 5 heads as input material. Detailed protocols of the DamID procedure are available at http://research.nki.nl/vansteensellab/.

treatment_protocol: The male heads were decapitated using a razor blade and stored at -80°C.

tag: HP1-Dam (EXPERIMENT)

tag: Dam (REFERENCE)


title: CTRL3_plusHGF


title: CTRL3_minHGF

source_name: liver; control mouse; unstimulated


title: MKO3_minHGF


title: CTRL2_minHGF


title: ch_yw285-1_19_Tumor_FFPE


title: Patient 5 MIRA-tumor vs MIRA-normal

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: patient 5

hyb_protocol: According to Agilent aCGH protocol (http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=52010 )

scan_protocol: An Axon GenePix4000B scanner was used with the following settings: 100% power, 5 µm 2 lines to average and PMT gain for each channel adjusted for each array.

data_processing: No Background correction, Lowess Normalization within each array, no between array normalization

label_protocol: Agilent aCGH protocol was followed and 2 µg of amplified MIRA-enriched fragments were labeled for each sample; tumor: cy5; input: cy3.

extract_protocol: Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947

tag: Normal DNA from 5

tag: DCIS Breast cancer


title: HP1-DamID_w[m51b]

description: DamID experiment


title: HP1-DamID_w[m4]-Su(var)3-9

description: DamID experiment


title: HP1-DamID_OregonRS

description: DamID experiment


title: 333_tumour_ovary

status: Public on Feb 17 2009

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

description: Hybridized to Affymetrix GeneChip Mapping 100K Set Array (50K_Xba240_SNP).

hyb_protocol: DNA was XbaI restriction digested, adapter ligated, PCR amplified, fragmented, labelled and hybridized to a 50K SNP XbaI array according to the manufacturer's instructions.

scan_protocol: Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Copy number normalization, batch correction and smoothing steps were performed using GISTIC as described in Beroukhim et al., 2007 (PMID 18077431) and Etemadmoghadam et al., in press.
Copy number ratio was generated by normalizing each tumor sample to the mean of normal reference samples with similar baseline signal intensity profiles to minimize systematic noise resulting from undetermined experimental factors. We used the 5 closest references, measured by Euclidean distance between each normal and tumor signal profile. Additional normal (diploid) data (which supplement the 16 reference samples available from the current submission) were obtained from the Broad Institute, Boston (Beroukhim et al., 2007; GSE9635) and from the Affymetrix 100K HapMap Trio Dataset (available from https://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx).

source_name: Tumor, ovary

label_protocol: The mapping array assays were performed according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Fresh-frozen (LN2) tissue collected at surgery.

extract_protocol: Genomic DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: DNA was extracted from whole tumor tissue for samples with ≥ 80% neoplastic cells. For samples with < 80% overall tumor cells, needle dissection of serial tumor sections was performed to enrich for the epithelial fraction prior to DNA extraction. Needle-dissected samples were stained with cresyl-violet to facilitate morphological distinction between tumor and stromal elements.

tag: Primary tumour

tag: Gender

value: F

tag: Stage

value: IIIB

tag: Histology

value: Ser/PapSer

tag: Grade


title: 528_tumour_ovary

value: IIIC


title: 355_tumour_ovary

value: IV


title: CTRL1_minHGF


title: HP1-DamID_w[m4e]

description: DamID experiment


title: Patient 1 MIRA-tumor vs MIRA-normal

description: patient 1

tag: Normal DNA from 3


title: Patient 4 MIRA-tumor vs MIRA-normal

description: patient 4

tag: Normal DNA from 4


title: Patient 6 MIRA-tumor vs MIRA-normal

description: patient 6

tag: Normal DNA from 132


title: 327_tumour_ovary

value: unknown


title: 300_tumour_ovary


title: 308_tumour_ovary

value: IIIA


title: 329_tumour_ovary


title: 309_tumour_ovary

value: Endo


title: 282_tumour_ovary

value: Undiff


title: Yeast poly-A RNA 001

description: Yeast poly-A RNA was applied.

hyb_protocol: Before hybridization, cRNA was fragmented to an average size of 50-200bp by incubating in 5X RNA fragmentation buffer (200mM Tris acetate, pH8.1, 100mM KOAc and 150mM MgOAc) at 950C for 35 minutes. Fragmentation was checked on an agarose gels. Microarrays were hybridized with 10-12µg of cRNA in 55µL in the presence of 40% formamide, 1mM Tris, 0.1mM EDTA, 5X SSC and 0.1% SDS for 18 hours at 420C. Before application to the array, samples were heated to 950C for 5 minutes, then at 450C until ready for hybridization(Max 5-30minutes). Hybridization was performed in a MAUI station.

scan_protocol: After hybridization, arrays were washed in 0.2% SDS and 0.2X SSC for 2 minutes at 420C and placed in nonstringent buffer (6X SSPE, 0.01%{V/V}Tween 20) until ready for the next wash in 0.2X SSC at room temperature for one  minute. After washing arrays were stained with streptavidin-cy3 conjugate from Amersham Pharmacia for 25 minutes at room temperature followed by a quick rinse in 0.2X SSC and signals were amplified by antibody amplification mix(Antistreptavidin and goat IgG) for 25 minutes. Staining and amplification was repeated for 10 more minutes after a quick rinse in 0.2X SSC. This was followed by holding the arrays in nonstringent hold buffer until ready for wash in 0.2X SSC for one minute followed by 30 seconds wash in 0.05X SSC.

organism: Saccharomyces cerevisiae

source_name: yeast poly-A RNA

label_protocol: The labeling was performed using Eberwine procedure to amplify the starting material. RNA was converted to double stranded cDNA using Gibco BRL(Rockville, MD) superscript choice system and an oligo (dT) primer containing the T7 RNA polymerase  promoter (Proligo LLC)  [5'GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dT)24-3']. Briefly, 10µg total RNA or 2µg poly(A)+ RNA was incubated with 5X first strand buffer, 0.1M DTT, 10mM each dNTPs, 5pmol primer for 60 minutes at 420C. Second strand synthesis was accomplished by incubation with 40U DNA polymerase I, 2U of Escherichia coli RNase H, 10mM ea dNTPs and 10U of Escherichia coli DNA ligase in 5X second strand buffer for 2 hours at 160C. The double strand cDNA synthesis was terminated by incubating with 10U of T4 DNA polymerase for 5 minutes at 160C. Double stranded cDNA was purified using phenol chloroform extraction and ethanol precipitated, washed with 80% ethanol and resuspended in 3.25µL of water. Invitrotranscription (IVT) was used to produce biotin labeled cRNA from the cDNA using the Ambion (Austin, TX) MEGA script T7 kit. Briefly, 1µg double stranded cDNA was incubated with  7.5mM ATP and  GTP , 5.625mM CTP and  UTP  and 1.875mM bio-11-CTP and  bio-16-UTP (Enzo or Perkin Elmer) in 1X transcription buffer and 1X T7 enzyme mix at 370C for 5 hours. Invitrotranscribed biotin labeled cRNA was purified on RNeasy mini columns (Qiagen) according to manufacturer's protocol. cRNA was quantified by absorbance at 260nm.

growth_protocol: Yeast strain BY4741(leu2_0 ura3_0 met15_0 his3_1) was grown at 30C to mid exponential phase (OD 600=1.0) in YPAD rich medium.

extract_protocol: Total RNA was extracted from Ribopure Yeast kit (Ambion, Austin, TX) and treated for 30 min at 370 C with RNAse free DNase I (Ambion).

tag: yeast poly-A RNA


title: Yeast poly-A RNA 002

description: Yeast poly-A RNA was applied.


title: Yeast poly-A RNA 003

description: Yeast poly-A RNA was applied.


title: 280_tumour_ovary


title: Patient 2 MIRA-tumor vs MIRA-normal

description: patient 2

tag: Normal DNA from 1


title: 289_tumour_ovary


title: 240_tumour_ovary


title: 231_tumour_ovary


title: 261_tumour_ovary


title: 246_tumour_ovary


title: 277_tumour_ovary


title: 260_tumour_ovary


title: 291_tumour_ovary

value: Germ


title: 241_tumour_ovary


title: 215_tumour_ovary


title: 170_tumour_ovary


title: 120_tumour_ovary


title: 196_tumour_ovary


title: 156_tumour_ovary


title: 126_tumour_Fallopian

source_name: Tumor, Fallopian tube

value: I


title: 92_tumour_ovary


title: 150_tumour_ovary


title: 3_tumour_ovary

value: Unknown


title: 78_tumour_ovary


title: 17_tumour_ovary

value: LMP


title: 97_tumour_Fallopian


title: 70_tumour_ovary


title: 79_tumour_ovary


title: 56_tumour_ovary


title: 65_tumour_ovary


title: 49_tumour_ovary


title: 64_tumour_ovary


title: 71_tumour_ovary


title: 42_tumour_ovary


title: 40_tumour_ovary


title: 26_tumour_ovary


title: 15_tumour_ovary


title: 70088_tumour_ovary


title: 70148_tumour_ovary


title: 70049_tumour_ovary


title: 58_tumour_ovary


title: 31_tumour_ovary


title: 70048_tumour_peritoneum

source_name: Tumor, peritoneum


title: 70047_tumour_ovary


title: 60228_tumour_ovary


title: 70094_tumour_ovary


title: 60174_tumour_ovary


title: Patient 3 MIRA-tumor vs MIRA-normal

description: patient 3

tag: Normal DNA from 57


title: 60180_tumour_ovary


title: 60065_tumour_ovary


title: 70003_tumour_ovary


title: 60214_tumour_ovary


title: 60139_tumour_ovary


title: 60164_tumour_ovary


title: 70054_tumour_ovary


title: 34_tumour_ovary


title: 51080_tumour_peritoneum


title: 60318_tumour_ovary


title: 51053_tumour_ovary


title: 60148_tumour_ovary


title: 51005_tumour_ovary


title: 44078_tumour_ovary


title: 44428_tumour_ovary


title: 44242_tumour_ovary


title: 51016_tumour_peritoneum


title: 44306_tumour_ovary


title: 41079_tumour_ovary


title: 44186_tumour_ovary


title: 44313_tumour_ovary


title: 34090_tumour_ovary


title: 23178_tumour_ovary


title: 23162_tumour_ovary


title: 44219_tumour_ovary


title: 34202_tumour_peritoneum


title: 41023_tumour_ovary


title: 41324_tumour_peritoneum


title: 34125_tumour_ovary


title: 23084_tumour_ovary


title: 44164_tumour_ovary


title: 34066_tumour_ovary


title: 23074_tumour_Fallopian


title: 23053_tumour_ovary


title: 541_tumour_ovary


title: 23030_tumour_ovary


title: 22031_tumour_ovary


title: 22057_tumour_ovary


title: 22023_tumour_ovary


title: 27006_tumour_ovary


title: 552_tumour_Fallopian


title: 525_tumour_ovary


title: Control KC vs Notch activated KC replicate 4 dye swap

first: Sarah

last: Bray

department: PDN

institute: University  of Cambridge

description: control KC vs Notch activated KC replicate 4 dye swap

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.pdf)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/scanning2.pdf)

data_processing: Spot finding and quantitation via the Dapple package.

source_name: KC E

label_protocol: Reverse transcription and direct labelling for cDNA and oligo arrays (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.pdf)

growth_protocol: KC cells were grown at 25C in Schneider's Drosophila Medium (Invitrogen) supplemented with 10% fetal calf serum, 100ug/ml streptamycin and 100 units/ml penicilin and with 10ug/ml insulin (Sigma). Cultures were split and replated in fresh medium approximately 12-18 hours prior to activation.

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.pdf).

treatment_protocol: Notch activation was achieved by exposing cells to 2mM EDTA in PBS for 30 minutes. Control cells were pre-treated with PBS alone.

tag: Notch activated KC Drosophila cells [EDTA treated]

source_name: Kc

growth_protocol: KC were grown at 25C in Schneider's Drosophila Medium (Invitrogen) supplemented with 10% fetal calf serum, 100ug/ml streptamycin and 100 units/ml penicilin and with 10ug/ml insulin (Sigma). Cultures were split and replated in fresh medium approximately 12-18 hours prior to activation.

extract_protocol: Medium scale Trizol extraction (http://www.flychip.org.uk/protocols/gene_expression/medium_extraction.php).

tag: Control KC Drosophila cells [no EDTA]


title: Control KC vs Notch activated KC replicate 6 dye swap

description: control KC vs Notch activated KC replicate 6 dye swap


title: 20031_tumour_ovary

value: II


title: 32048_tumour_ovary


title: 533_tumour_ovary


title: Control KC vs Notch activated KC replicate 5 dye swap

description: control KC vs Notch activated KC replicate 5 dye swap


title: Control KC vs Notch activated KC replicate 3

description: control KC vs Notch activated KC replicate 3


title: 34019_tumour_ovary


title: 22029_tumour_ovary


title: Control KC vs Notch activated KC replicate 2

description: control KC vs Notch activated KC replicate 2


title: 546_tumour_ovary

value: III


title: 502_tumour_ovary


title: Control KC vs Notch activated KC replicate 1

description: control KC vs Notch activated KC replicate 1


title: 44417_tumour_ovary


title: 500_tumour_ovary


title: 23026_tumour_ovary


title: 575_tumour_ovary


title: DFK-167 pre-treated Notch activated DmD8 vs Notch activated DmD8 replicate 5 dye swap

source_name: D8 E

growth_protocol: DmD8 cells were grown at 25C in Schneider's Drosophila Medium (Invitrogen) supplemented with 10% fetal calf serum, 100ug/ml streptamycin and 100 units/ml penicilin and with 10ug/ml insulin (Sigma). Cultures were split and replated in fresh medium approximately 12-18 hours prior to activation.

treatment_protocol: Notch activation was achieved by exposing cells to 2mM EDTA in PBS for 30 minutes. Control cells were pre-treated with PBS alone. In experiments with gamma-secretase inhibitor, cells were incubated with 300um DFK-167 overnight and then activated by EDTA.

source_name: D8 DFK

tag: DFK-167 pre-treated Notch activated DmD8 Drosophila cells [EDTA treated]


title: 496_tumour_ovary


title: 22037_tumour_ovary


title: 484_tumour_ovary


title: DFK-167 pre-treated Notch activated DmD8 vs Notch activated DmD8 replicate 3

tag: Notch activated DmD8 Drosophila cells [EDTA treated]


title: DFK-167 pre-treated Notch activated DmD8 vs Notch activated DmD8 replicate 1


title: 379_tumour_ovary


title: 434_tumour_ovary


title: DFK-167 pre-treated Notch activated DmD8 vs Notch activated DmD8 replicate 4 dye swap


title: 153_tumour_ovary


title: DFK-167 pre-treated Notch activated DmD8 vs Notch activated DmD8 replicate 2


title: 488_tumour_ovary


title: Control DmD8 vs Notch activated DmD8 replicate 1

source_name: D8 PBS

tag: Control DmD8 Drosophila cells [no EDTA]


title: Control DmD8 vs Notch activated DmD8 replicate 2


title: Control DmD8 vs Notch activated DmD8 replicate 3


title: Control DmD8 vs Notch activated DmD8 replicate 5 dye swap


title: Control DmD8 vs Notch activated DmD8 replicate 4 dye swap


title: 474_tumour_ovary


title: P. infestans, four days post inoculation of potato, biological replicate 2 of 2

status: Public on Feb 16 2009

first: Brian

last: Haas

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: RNA samples were prepared and submitted to NimbleGen for full microarray expression services, including cDNA preparation, Cy3 labeling, hybridizations, and scans.

hyb_protocol: Labeled cDNA was hybridized to the microarrays for 16 hours at 42°C.

scan_protocol: The arrays were washed, dried, and scanned at 5μm resolution using a GenePix 4000B microarray scanner.

data_processing: Probe signal intensities were quantile normalized, and target probe intensities were computed as a Tukey biweight of the corresponding probe intensities.  Probe intensity normalizations and target intensity computations were limited to those probes corresponding to P. infestans sequences, and limited to probe sequences found minimally repetitive (matching the P. infestans genome sequence at most five times using SSAHA).

organism: Phytophthora infestans

source_name: Phytophthora infestans infected potato leaves

label_protocol: Double-stranded cDNA was random-prime labeled with Cy3-nonamers.

extract_protocol: P. infestans zoospores stage was induced by adding cold water to the culture and incubating for 2-3 hours at 4ºC. Each potato leave was infected with 4 drops containing Zoospores and incubated at 18ºC in containers with a wet paper towel to promote humidity. Infected leaf discs were collected at 2, 3, 4 and 5 days post inoculation, and ground in liquid nitrogen.  Powder tissue was homogenized with RLT buffer containing ß-mercaptoethanol from Qiagen (Cat.No. 74904) and total RNA was extracted according to manufacture’s protocol.

tag: Infected leaf discs were collected at four days post inoculation.


title: P. infestans, five days post inoculation of potato, biological replicate 1 of 2

tag: Infected leaf discs were collected at five days post inoculation.


title: 381_tumour_ovary

tag: Primary tumour

tag: Gender


title: 152_tumour_ovary

tag: Stage

tag: Histology


title: P. infestans, two days post inoculation of potato, biological replicate 2 of 2

tag: Infected leaf discs were collected at two days post inoculation.


title: P. infestans, RS agar, biological replicate 2 of 2

source_name: Phytophthora infestans mycelia grown in RS agar

extract_protocol: Mycelia was harvested with a sterile blade, grinded in liquid nitrogen and frozen. Powder tissue was homogenized with RLT buffer containing ß-mercaptoethanol from Qiagen (Cat.No. 74904) proceeding with manufacture’s protocol to harvest total RNA.

tag: Mycelia of P. infestans T30-4 grown on RS agar for 10-12 days.


title: P. infestans, four days post inoculation of potato, biological replicate 1 of 2


title: P. infestans, three days post inoculation of potato, biological replicate 1 of 2

tag: Infected leaf discs were collected at three days post inoculation.


title: P. infestans, five days post inoculation of potato, biological replicate 2 of 2


title: 374_tumour_ovary

tag: Grade


title: Rectum IL18ko Stress

status: Public on Feb 14 2009

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Stress Science

country: Japan

institute: Institue for Health Biosciences, The University of Tokushima Graduate School

description: The data from each "spot ID" of rectum mucosa of 5 isolated IL18ko mice were subdivided by those of colonic mucosa of 5 control WT mice for all present spots.

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).

data_processing: Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value for data points labeled as Present. Then the data from each "spot ID" of channel 1 was subdivided by channel 2.

source_name: Rectum, IL18ko, stress

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at Agilent's website. Labeled cRNAs were generated from 400 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).

extract_protocol: The mucosal tissues from the rectum were incubated immediately after the collection with RNAlater stabilization reagent for 24 hours and stored at -80℃ until analysis. The rectum was considered as ranged in 7 mm total length from the anus. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).

treatment_protocol: Five brother mice were group-housed in one cage after weaning until 10-12 weeks age. Then, 3 of them were separated individually in an independent cage for the isolation stress. 16 days after the isolation stress, they were sacrificed under anesthetized with diethyl ether at 10:00 AM.

tag: Strain; C57BL/6J, Type; IL18 knock out, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the rectum, The time of sacrifice; 16 days after the isolation stress. Equivalent amount of total RNA from rectum mucosa of 5 isolated IL18ko mice were mixed equally and used for microarray.


title: P. infestans, V8 agar, biological replicate 2 of 2

source_name: Phytophthora infestans mycelia grown in V8 agar

tag: Mycelia of P. infestans T30-4 grown on V8 agar for 10-12 days.


title: Seed_35DAP

type: SAGE

anchor: NlaIII

city: Giessen

first: Christian

last: Obermeier

address: Heinrich-Buff-Ring 26-32

department: Plant Breeding

country: Germany

institute: Justus Liebig University

description: LongSAGE library o B. napus seeds of the variety 'Express 617' harvested 35 days after pollination (35 DAP)

organism: Brassica napus

source_name: Brassica napus 'Express 617' seeds

extract_protocol: Total RNA was extracted from seeds using RNA Reagent (Invitrogen) and purified from DNA residues by incubation with RQ1 RNAse-free DNAse (Promega), according to the manufacturer’s recommendations.

tag: Plants of the homozygous male-sterile winter oilseed rape maternal line ‘MSL-Express’ were cultivated under controlled growth chamber conditions and manually fertilised with pollen from plants of the isogenic male-fertile line ‘Express 617’. Pods were harvested weekly from the main racemes of pollinated plants at time points 14 days up to 70 days after pollination (DAP).


title: Rectum WT Stress

description: The data from each "spot ID" of rectum mucosa of 5 isolated WT mice were subdivided by those of colonic mucosa of 5 control WT mice for all present spots.

source_name: Rectum, WT, stress

tag: Strain; C57BL/6J, Type; WT, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the rectum, The time of sacrifice; 16 days after the isolation stress. Equivalent amount of total RNA from rectum mucosa of 5 control mice were mixed equally and used for microarray.


title: P. infestans, RS agar, biological replicate 1 of 2


title: Colon WT stress

description: The data from each "spot ID" of colonic mucosa of 5 stressed WT mice were subdivided by those of 5 control WT mice for all present spots.

source_name: Colon, WT, stress

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at Agilent's website. Labeled cRNAs were generated from 400 ng of total RNA using Agilentâ??s Low RNA Input Linear Amplification Kit (P/N 5188-5339).

extract_protocol: The mucosal tissues from the colon were incubated immediately after the collection with RNAlater stabilization reagent for 24 hours and stored at -80℃ until analysis. The colon was considered as localized at middle portion, between 2.5 cm and 3.5 cm from the ileocecum. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).

tag: Strain; C57BL/6J, Type; WT, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the colon, The time of sacrifice; 16 days after the isolation stress. Equivalent amount of total RNA from colonic mucosa of 5 stressed mice were mixed equally and used for microarray.


title: P. infestans, Pea agar, biological replicate 2 of 2

source_name: Phytophthora infestans mycelia grown in Pea agar

tag: Mycelia of P. infestans T30-4 grown on Pea agar for 10-12 days.


title: rpoS_6 Rep AVG

city: new york

first: Galadriel

last: Hovel-Miner

state: NY

department: Microbiology

institute: Columbia University

description: LM1376 is an rpoS transposon insertion mutant (Hales & Shuman 1999)

hyb_protocol: UV cross-linked slides were pre-hybridized in 5x SSC, 0.1% SDS, and 0.1mg/mL BSA for 45 min at 37°C. Slides were then rinsed in 0.1 x SSC and dried. Labeled cDNA was added to hybridization solution (40% formamide, 5x SSC, 0.1% SDS, 10mM Tris HCl pH 7.5, 1mg/mL human placental DNA) and hybridized to microarrays in hybridization chambers (GraceBio Inc, Bend, OR) at 37°C overnight with rotation. Slides were washed twice with 5x SSC 0.1% SDS, 0.1x SSC 0.1% SDS, rinsed shortly with 0.01x SSC and dried with high-pressure air using dust remover.

scan_protocol: Slides were scanned with 5-µm resolution using ScanArray Express Microarray Scanner (Perkin Elmer Inc, Wellesley, MA) and spot analysis was performed using Pro Scan Array Express software (Perkin Elmer Inc, Wellesley, MA).

data_processing: Raw signal intensities were corrected for dye labeling effects within and between all slides using normalize.lowess() R-function implemented in Bioconductor affy microarray analysis package.

label: Alexa 546, Alexa 647

organism: Legionella pneumophila

source_name: Strain rpoS log phase, Strain rpoS stat phase

label_protocol: RNA samples (20μg) were reverse-transcribed with Superscript II Plus RNase H- reverse transcriptase (Invitrogen, Carlsbad, CA), random primers and mixture of dNTPs containing aminoallyl-modified dUTP (Sigma-Aldrich, St Louis, MO). RNA templates were removed by alkaline hydrolysis and aminoallyl-cDNA were purified using the QiaQuick PCR purification kit (QIAGEN Inc, Valencia, CA) and coupled with Alexa Fluor 546 or 647 dyes (Invitrogen, Carlsbad, CA).

growth_protocol: L. pneumophila strains were grown in AYE liquid media to OD 0.8, log phase, or OD>3.0, stat phase, and then sujected to RNA extraction.

extract_protocol: Bacteria from liquid culture were pelleted by 30 seconds of centrifugation at 14,000 rpm and total RNA was extracted with using the RNeasy kit (QIAGEN Inc, Valencia, CA)

treatment_protocol: No treatment applied before RNA extraction

tag: strain

tag: reference condition

value: rpoS log

tag: test condition

value: rpoS stat

source_name: Strain rpoS stat phase, Strain rpoS log phase


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-8

status: Public on Feb 15 2009

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: The experiments were repeated four times with samples from different experiments, as biological replicates.

hyb_protocol: Labeled samples were mixed and then hybridized to microarray for 15 h at 60°C. The slides were washed at room temperature in three wash steps: 2 x SSC, 0.5% SDS; 0.5 x SSC; and 0.05 x SSC for 5 min each with gentle shaking.

scan_protocol: The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA). Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.

data_processing: Hybridization intensities for each microarray element were measured using ScanAlyze 4.24 (available at http://genome-www4.stanford.edu/MicroArray/SMD/restech.html). The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad, 2003) and signals from spots from different experiments were statistically analyzed using Significance Analysis of Microarrays using the one class response (SAM, http://www-stat.stanford.edu/~tibs/SAM/), cut at a false discovery rate < 10% (Tusher, 2001).

organism: Arabidopsis thaliana

source_name: WT Arabidopsis plants

label_protocol: The experimental (mutant) and reference (wild type) RNA samples were reverse-transcribed and directly labeled with Cy5-dUTP fluorescent dye (GE Healthcare), using random hexamer primers (Invitrogen). Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen).

growth_protocol: WT Arabidopsis plants were grown in greenhouse conditions at 25 ºC under fluorescent lamps (Grolux, Sylvania and Cool White, Philips) with an intensity of 150 μmol m-2 s-1 using a 16 h light/8 h dark photoperiod. Flower samples were collected from 6-week-old plants.

extract_protocol: Total RNA from 6-week-old flowers was extracted using Tri reagent (Sigma).

tag: genotype

value: WT

tag: age

value: 6 weeks

source_name: Ap3::u-ATP9 transgenic Arabidopsis plants

label_protocol: The experimental (mutant) and reference (wild type) RNA samples were reverse-transcribed and directly labeled with Cy3-dUTP fluorescent dye (GE Healthcare), using random hexamer primers (Invitrogen). Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen).

growth_protocol: Transgenic line Ap3::u-ATP9 was obtained by transformation with recombinant pZP212 plasmids carrying the u-ATP9 gene under the control of apetala 3 (Ap3) promoters as described (Gomez-Casati, 2002). Selection of transgenic plants was performed in Murashige-Skoog agar medium (Sigma) containing 30 ug/ml of kanamycin. After two weeks, plants were transferred to soil and grown in greenhouse conditions at 25 ºC under fluorescent lamps (Grolux, Sylvania and Cool White, Philips) with an intensity of 150 μmol m-2 s-1 using a 16 h light/8 h dark photoperiod. Flower samples were collected from 6-week-old plants.

value: transgenic line Ap3::u-ATP9


title: Seed_23DAP

description: LongSAGE library of B. napus seeds of the variety 'Express 617' harvested 23 days after pollination (23 DAP)


title: JR32_6 Rep AVG

description: JR32 is a restriction-negative mutant of L. pneumophila st. Philadelphia-1

source_name: Strain JR32 stat phase, Strain JR32 log phase

value: JR32 stat

value: JR32 log

source_name: Strain JR32 log phase, Strain JR32 stat phase


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-2


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-7

source_name: A9::u-ATP9 transgenic Arabidopsis plants

growth_protocol: Transgenic line A9::u-ATP9 was obtained by transformation with recombinant pZP212 plasmids carrying the u-ATP9 gene under the control of A9 promoters as described (Gomez-Casati, 2002). Selection of transgenic plants was performed in Murashige-Skoog agar medium (Sigma) containing 30 ug/ml of kanamycin. After two weeks, plants were transferred to soil and grown in greenhouse conditions at 25 ºC under fluorescent lamps (Grolux, Sylvania and Cool White, Philips) with an intensity of 150 μmol m-2 s-1 using a 16 h light/8 h dark photoperiod. Flower samples were collected from 6-week-old plants.

value: transgenic line A9::u-ATP9


title: P. infestans, Pea agar, biological replicate 1 of 2


title: HCC 113

status: Public on Feb 13 2009

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Pair matched to 113N

hyb_protocol: The hybridization was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA).

scan_protocol: The arrays were scanned by ScanArray scanner (Perkin-Elmer)

data_processing: Background subtraction and LOWESS normalization of log2 ratio (Cy5/Cy3) using sma R package

source_name: Human placental RNA (reference)

label_protocol: The probe preparation was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA) with 20mg of total RNA.

extract_protocol: Total RNA was isolated from frozen tissue according to the manufacturer’s instructions (Qiagen), and quality of the total RNA was judged based on the ratio of 28S/18S RNA after agarose gel electrophoresis.

tag: tissue

value: placenta

source_name: HCC 113T

value: hepatocellular carcinoma


title: HCC 124

description: Pair matched to 124N

source_name: HCC 124T


title: HCC 132

description: Pair matched to 132N

source_name: HCC 132T


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-9


title: P. infestans, three days post inoculation of potato, biological replicate 2 of 2

source_name: Phytophthora infestans infected potato leaves


title: HCC 118

description: Pair matched to 118N

source_name: HCC 118T


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-4


title: Colon IL18ko Stress

description: The data from each "spot ID" of colonic mucosa of 5 isolated IL18ko mice were subdivided by those of 5 control WT mice for all present spots.

source_name: Colon, IL18ko, stress

tag: Strain; C57BL/6J, Type; IL18 knock out, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the colon, The time of sacrifice; 16 days after the isolation stress. Equivalent amount of total RNA from colonic mucosa of 5 isolated IL18ko mice were mixed equally and used for microarray.


title: HCC 127

description: Pair matched to 127N

source_name: HCC 127T


title: Rectum WT Control

description: The data from each "spot ID" of rectum mucosa of 5 control WT mice were subdivided by those of colonic mucosa of 5 control WT mice for all present spots.

source_name: Rectum, WT, control

treatment_protocol: Five brother mice were group-housed in one cage after weaning until 10-12 weeks age. Then, the control 2 in the above 5 mice were sacrificed under anesthetized with diethyl ether at 10:00 AM.

tag: Strain; C57BL/6J, Type; WT, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the rectum, The time of sacrifice; When 3 of 5 group-housed mice were separated individually in an independent cage for the isolation stress, the remaining 2 were sacrificed before the isolation stress as control. Equivalent amount of total RNA from rectum mucosa of 5 control mice were mixed equally and used for microarray.


title: Colon IL18ko Control

description: The data from each "spot ID" of colonic mucosa of 5 control IL18ko mice were subdivided by those of 5 control WT mice for all present spots.

source_name: Colon, IL18ko, control

tag: Strain; C57BL/6J, Type; IL18 knock out, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the colon, The time of sacrifice; When 3 of 5 group-housed mice were separated individually in an independent cage for the isolation stress, the remaining 2 were sacrificed before the isolation stress as control. Equivalent amount of total RNA from colonic mucosa of 5 control IL18ko mice were mixed equally and used for microarray.


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-5


title: Rectum IL18ko Control

description: The data from each "spot ID" of rectum mucosa of 5 control IL18ko mice were subdivided by those of colonic mucosa of 5 control WT mice for all present spots.

source_name: Rectum, IL18ko, control

tag: Strain; C57BL/6J, Type; IL18 knock out, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the rectum, The time of sacrifice; When 3 of 5 group-housed mice were separated individually in an independent cage for the isolation stress, the remaining 2 were sacrificed before the isolation stress as control. Equivalent amount of total RNA from rectum mucosa of 5 control IL18ko mice were mixed equally and used for microarray.


title: P. infestans, two days post inoculation of potato, biological replicate 1 of 2

tag: Infected leaf discs were collected at two days post inoculation.


title: Normalization control, Colon WT control

description: The data from each "spot ID" of colonic mucosa of 5 control WT mice were subdivided by those of 5 control WT mice for all present spots.

data_processing: Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value for data points labeled as Present. Then the data from each "spot ID" was subdivided by own.

source_name: Colon, WT, control

tag: Strain; C57BL/6J, Type; WT, Gender; Male, Age; 10-12 wks, Tissue; Mucosal tissues from the colon, The time of sacrifice; When 3 of 5 group-housed mice were separated individually in an independent cage for the isolation stress, the remaining 2 were sacrificed before the isolation stress as control. Equivalent amount of total RNA from colonic mucosa of 5 control mice were mixed equally and used for microarray.


title: HCC 98

description: Pair matched to 98N

source_name: HCC 98T


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-3

source_name: WT Arabidopsis plants


title: HCC 106

description: Pair matched to 106N

source_name: HCC 106T


title: HCC 97

description: Pair matched to 97N

source_name: HCC 97T


title: HCC 94

description: Pair matched to 94N

source_name: HCC 94T


title: HCC 92

description: Pair matched to 92N

source_name: Human placental RNA (reference)

source_name: HCC 92T


title: 424_tumour_ovary

description: Hybridized to Affymetrix GeneChip Mapping 100K Set Array (50K_Xba240_SNP).

source_name: Tumor, ovary

tag: Primary tumour

tag: Gender

value: F

tag: Stage

value: IV

tag: Histology

value: Ser/PapSer

tag: Grade


title: HCC 87

description: Pair matched to 87N

source_name: HCC 87T


title: HCC 81

description: Pair matched to 81N

source_name: HCC 81T


title: HCC 63

description: Pair matched to 63N

source_name: HCC 63T


title: HCC 75

description: Pair matched to 75N

source_name: HCC 75T


title: HCC 50

description: Pair matched to 50N

source_name: HCC 50T


title: HCC 95

description: Pair matched to 95N

source_name: HCC 95T


title: HCC 93

description: Pair matched to 93N

source_name: HCC 93T


title: HCC 78

description: Pair matched to 78N

source_name: HCC 78T


title: HCC 44

description: Pair matched to 44N

source_name: HCC 44T


title: HCC 72

description: Pair matched to 72N

source_name: HCC 72T


title: HCC 62

description: Pair matched to 62N

source_name: HCC 62T


title: HCC 89

description: Pair matched to 89N

source_name: HCC 89T


title: HCC 91

description: Pair matched to 91N

source_name: HCC 91T


title: HCC 55

description: Pair matched to 55N

source_name: HCC 55T


title: HCC 70

description: Pair matched to 70N

source_name: Human placental RNA (reference)

source_name: HCC 70T


title: HCC 79

description: Pair matched to 79N

source_name: HCC 79T


title: HCC 71

description: Pair matched to 71N

source_name: HCC 71T


title: P. infestans, V8 agar, biological replicate 1 of 2

source_name: Phytophthora infestans mycelia grown in V8 agar

tag: Mycelia of P. infestans T30-4 grown on V8 agar for 10-12 days.


title: HCC 59

description: Pair matched to 59N

source_name: HCC 59T


title: HCC 54

description: Pair matched to 54N

source_name: HCC 54T


title: HCC 46

description: Pair matched to 46N

source_name: HCC 46T


title: HCC 77

description: Pair matched to 77N

source_name: HCC 77T


title: HCC 45

description: Pair matched to 45N

source_name: HCC 45T


title: HCC 61

description: Pair matched to 61N

source_name: HCC 61T


title: HCC 83

description: Pair matched to 83N

source_name: HCC 83T


title: HCC 43

description: Pair matched to 43N

source_name: HCC 43T


title: HCC 41

description: Pair matched to 41N

source_name: HCC 41T


title: Mitochondrial dysfunction effects in Arabidopsis thaliana-1

source_name: WT Arabidopsis plants

source_name: Ap3::u-ATP9 transgenic Arabidopsis plants


title: HCC 37

description: Pair matched to 37N

source_name: HCC 37T


title: HCC 38

description: Pair matched to 38N

source_name: Human placental RNA (reference)

source_name: HCC 38T


title: HCC 28

description: Pair matched to 28N

source_name: HCC 28T


title: HCC 13

description: Pair matched to 13N

source_name: HCC 13T


title: HCC 20

description: Pair matched to 20N

source_name: HCC 20T


title: HCC 10

description: Pair matched to 10N

source_name: HCC 10T


title: HCC 39

description: Pair matched to 39N

source_name: HCC 39T


title: HCC 5

description: Pair matched to 5N

source_name: HCC 5T


title: HCC 15

description: Pair matched to 15N

source_name: HCC 15T


title: HCC 31

description: Pair matched to 31N

source_name: HCC 31T


title: HCC 25

description: Pair matched to 25N

source_name: HCC 25T


title: HCC 26

description: Pair matched to 26N

source_name: HCC 26T


title: HCC 27

description: Pair matched to 27N

source_name: HCC 27T


title: Adjacent Tissue 127

description: Pair matched to 127T

source_name: Adjacent liver tissue 127N

value: liver


title: HCC 22

description: Pair matched to 22N

source_name: HCC 22T


title: HCC 2

description: Pair matched to 2N

source_name: HCC 2T


title: HCC 3

description: Pair matched to 3N

source_name: HCC 3T


title: HCC 33

description: Pair matched to 33N

source_name: Human placental RNA (reference)

source_name: HCC 33T


title: Adjacent Tissue 124

description: Pair matched to 124T

source_name: Adjacent liver tissue 124N


title: HCC 14

description: Pair matched to 14N

source_name: HCC 14T


title: Adjacent Tissue 132

description: Pair matched to 132T

source_name: Adjacent liver tissue 132N


title: Adjacent Tissue 113

description: Pair matched to 113T

source_name: Adjacent liver tissue 113N


title: Adjacent Tissue 118

description: Pair matched to 118T

source_name: Adjacent liver tissue 118N


title: HCC 35

description: Pair matched to 35N

source_name: HCC 35T


title: Adjacent Tissue 106

description: Pair matched to 106T

source_name: Adjacent liver tissue 106N


title: Adjacent Tissue 95

description: Pair matched to 95T

source_name: Adjacent liver tissue 95N


title: Adjacent Tissue 81

description: Pair matched to 81T

source_name: Adjacent liver tissue 81N


title: Adjacent Tissue 72

description: Pair matched to 72T

source_name: Adjacent liver tissue 72N


title: Adjacent Tissue 83

description: Pair matched to 83T

source_name: Adjacent liver tissue 83N


title: Adjacent Tissue 71

description: Pair matched to 71T

source_name: Adjacent liver tissue 71N


title: Adjacent Tissue 87

description: Pair matched to 87T

source_name: Adjacent liver tissue 87N


title: Adjacent Tissue 97

description: Pair matched to 97T

source_name: Adjacent liver tissue 97N


title: Adjacent Tissue 70

description: Pair matched to 70T

source_name: Adjacent liver tissue 70N


title: Adjacent Tissue 75

description: Pair matched to 75T

source_name: Human placental RNA (reference)

source_name: Adjacent liver tissue 75N


title: Adjacent Tissue 79

description: Pair matched to 79T

source_name: Adjacent liver tissue 79N


title: Adjacent Tissue 50

description: Pair matched to 50T

source_name: Adjacent liver tissue 50N


title: Adjacent Tissue 77

description: Pair matched to 77T

source_name: Adjacent liver tissue 77N


title: Adjacent Tissue 92

description: Pair matched to 92T

source_name: Adjacent liver tissue 92N


title: Adjacent Tissue 59

description: Pair matched to 59T

source_name: Adjacent liver tissue 59N


title: Adjacent Tissue 91

description: Pair matched to 91T

source_name: Adjacent liver tissue 91N


title: Adjacent Tissue 63

description: Pair matched to 63T

source_name: Adjacent liver tissue 63N


title: Adjacent Tissue 78

description: Pair matched to 78T

source_name: Adjacent liver tissue 78N


title: Adjacent Tissue 62

description: Pair matched to 62T

source_name: Adjacent liver tissue 62N


title: Adjacent Tissue 55

description: Pair matched to 55T

source_name: Adjacent liver tissue 55N


title: Adjacent Tissue 89

description: Pair matched to 89T

source_name: Adjacent liver tissue 89N


title: Adjacent Tissue 93

description: Pair matched to 93T

source_name: Adjacent liver tissue 93N


title: Adjacent Tissue 54

description: Pair matched to 54T

source_name: Adjacent liver tissue 54N


title: Adjacent Tissue 61

description: Pair matched to 61T

source_name: Adjacent liver tissue 61N


title: Adjacent Tissue 94

description: Pair matched to 94T

source_name: Adjacent liver tissue 94N


title: Adjacent Tissue 46

description: Pair matched to 46T

source_name: Human placental RNA (reference)

source_name: Adjacent liver tissue 46N


title: Adjacent Tissue 45

description: Pair matched to 45T

source_name: Adjacent liver tissue 45N


title: Adjacent Tissue 33

description: Pair matched to 33T

source_name: Adjacent liver tissue 33N


title: Adjacent Tissue 31

description: Pair matched to 31T

source_name: Adjacent liver tissue 31N


title: Adjacent Tissue 37

description: Pair matched to 37T

source_name: Adjacent liver tissue 37N


title: Adjacent Tissue 35

description: Pair matched to 35T

source_name: Adjacent liver tissue 35N


title: Adjacent Tissue 28

description: Pair matched to 28T

source_name: Adjacent liver tissue 28N


title: Adjacent Tissue 26

description: Pair matched to 26T

source_name: Adjacent liver tissue 26N


title: Adjacent Tissue 38

description: Pair matched to 38T

source_name: Adjacent liver tissue 38N


title: Adjacent Tissue 25

description: Pair matched to 25T

source_name: Adjacent liver tissue 25N


title: Adjacent Tissue 22

description: Pair matched to 22T

source_name: Adjacent liver tissue 22N


title: Adjacent Tissue 43

description: Pair matched to 43T

source_name: Adjacent liver tissue 43N


title: Adjacent Tissue 27

description: Pair matched to 27T

source_name: Adjacent liver tissue 27N


title: Adjacent Tissue 39

description: Pair matched to 39T

source_name: Adjacent liver tissue 39N


title: Adjacent Tissue 14

description: Pair matched to 14T

source_name: Adjacent liver tissue 14N


title: Adjacent Tissue 20

description: Pair matched to 20T

source_name: Adjacent liver tissue 20N


title: Adjacent Tissue 41

description: Pair matched to 41T

source_name: Human placental RNA (reference)

source_name: Adjacent liver tissue 41N


title: Adjacent Tissue 36

description: Pair matched to 36T

source_name: Adjacent liver tissue 36N


title: Adjacent Tissue 13

description: Pair matched to 13T

source_name: Adjacent liver tissue 13N


city: Gdansk

first: Katarzyna

last: Majak

address: Debinki 1

department: Department of Anatomy and Neurobiology

country: Poland

institute: Medical University of Gdansk

description: basolateral_amygdala__epileptogenic_unpaired_group__replicate_B

hyb_protocol: Biotynylated cRNA probe was hybridized to Rat Genome 230 2.0 Gene Chip (Affymetrix) according to protocols recommended by the manufacturer and used in the Finnish DNA-Microarray Centre (http://microarrays.btk.fi/index.php?id=874).

scan_protocol: Scanning of Rat Genome 230 2.0 Gene Chip was performed in the Finnish DNA-Microarray Centre (http://microarrays.btk.fi/index.php?id=874).

data_processing: Expression data (31099 distinct probesets) from Rat Genome 230-2.0 arrays (Affymetrix) were pre-processed using MAS 5.0 software (Affymetrix).

organism: Rattus norvegicus

source_name: basolateral amygdala of the rat, epileptogenesis unpaired group

label_protocol: aRNAs from two (of four) rats belonging to this experimental group were pooled (3 μg aRNA from each animal). The array experiments were conducted in the Finnish DNA-Microarray Centre, Centre for Biotechnology, University of Turku, Finland. For microarray analysis,  5 μg of the pooled aRNA was first converted to cDNA using the one-cycle protocol (Affymetrix, Santa Clara,CA, USA), then to biotinylated cRNA.

growth_protocol:
Amygdala stimulation model (Nissinen et al., 2000):
epileptogenic (E) animals = stimulated, responded with "good" status epilepticus (at least 40HAFDs within first 3h of SE), not expressing spontaneous seizures through the whole study.
Fear conditioning:
unpaired group;
Animals received 5 habituation session to the fear conditioning apparatus lasting 10 min, starting on day 5 (2 sessions on day 5 and 6 and 1 session on day 7) after stimulation (induction of SE). On 8th day after stimulation:
unpaired (U) = twice received: 2min in apparatus → footshock (1.5mA, 1s)¬→ tone (75dB for 20 sec).

extract_protocol:
RNA isolation and amplification:
Total cellular RNA was isolated using the PicoPure RNA isolation kit (#KIT0204, Molecular Devices, Sunnyvale, CA, USA) according to the protocol provided by the manufacturer. The quantity of isolated RNA was measured using NanoDrop-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). Thereafter, 30 ng of total cellular RNA from each rat underwent 2 rounds of amplification using the MessageAmp II aRNA kit (#AM1751, Ambion, Austin, TX, USA), according to protocol provided by the manufacturer (in vitro transcription time was 14 h in both rounds). The quality of amplified aRNA was assessed on 1.5% agarose gel after each round of amplification.

treatment_protocol:
Laser-capture microdissection of the lateral and basal nuclei of the amygdala
for molecular profiling:
Three hours after termination of the fear conditioning procedure animals were
decapitated and the ipsilateral temporal lobe was dissected and embedded in Tissue- TekO.C.T. Compund (Sakura Finetek, McGaw Park, IL, USA), frozen on dry ice, and stored at -80oC. Then cryomolds containing the temporal lobe were cut into 7 μm thick serial sections and collected on Slides for Membrane-based Laser
Microdissection (#11505158, Leica Microsystems, Germany). The slides were then
stained with 1% cresyl violet (for protocol see www.ambion.com) and the lateral and basal nuclei of the amygdala (basolateral amygdala), delineated according to the description of Pitkänen and coworkers (1997), were dissected using Leica AS LMD Laser Microdissection System (Leica Microsystems). For each animal, around 60-70 sections containing basolateral amygdala were collected and used for laser-microdissection.

tag: Protocol

value: epileptogenic in amygdala stimulation model;

value: unpaired in fear conditioning learning.


title: Adjacent Tissue 15

description: Pair matched to 15T

source_name: Adjacent liver tissue 15N


title: epileptogenic_paired_group__replicate_A

description: basolateral_amygdala__epileptogenic_paired_group__replicate_A

source_name: basolateral amygdala of the rat, epileptogenesis paired group

growth_protocol:
Amygdala stimulation model (Nissinen et al., 2000):
epileptogenic (E) animals = stimulated, responded with "good" status epilepticus (at least 40HAFDs within first 3h of SE), not expressing spontaneous seizures through the whole study.
Fear conditioning:
paired group;
Animals received 5 habituation session to the fear conditioning apparatus lasting 10 min, starting on day 5 (2 sessions on day 5 and 6 and 1 session on day 7) after stimulation (induction of SE). On 8th day after stimulation:
paired (P) = twice received: 2min in apparatus → tone (75dB for 20 sec) co-terminated by footshock (1.5mA, 1s).

value: paired in fear conditioning learning.


description: basolateral_amygdala__epileptogenic_unpaired_group__replicate_A


title: control_paired_group__replicate_B

description: basolateral_amygdala__control_paired_group__replicate_B

source_name: basolateral amygdala of the rat, control paired group

growth_protocol:
Amygdala stimulation model (Nissinen et al., 2000):
control (C) animals = operated, not stimulated.
Fear conditioning:
paired group;
Animals received 5 habituation session to the fear conditioning apparatus lasting 10 min, starting on day 5 (2 sessions on day 5 and 6 and 1 session on day 7) after stimulation (induction of SE). On 8th day after stimulation:
paired (P) = twice received: 2min in apparatus → tone (75dB for 20 sec) co-terminated by footshock (1.5mA, 1s)

value: control in amygdala stimulation model;


title: epileptogenic_paired_group__replicate_B

description: basolateral_amygdala__epileptogenic_paired_group__replicate_B


title: control_paired_group__replicate_A

description: basolateral_amygdala__control_paired_group__replicate_A


title: Adjacent Tissue 10

description: Pair matched to 10T

source_name: Adjacent liver tissue 10N


title: Adjacent Tissue 5

description: Pair matched to 5T

source_name: Adjacent liver tissue 5N


title: control_unpaired_group__replicate_B

description: basolateral_amygdala__control_unpaired_group__replicate_B

source_name: basolateral amygdala of the rat, control unpaired group

growth_protocol:
Amygdala stimulation model (Nissinen et al., 2000):
control (C) animals = operated, not stimulated.
Fear conditioning:
unpaired group;
Animals received 5 habituation session to the fear conditioning apparatus lasting 10 min, starting on day 5 (2 sessions on day 5 and 6 and 1 session on day 7) after stimulation (induction of SE). On 8th day after stimulation:
unpaired (U) = twice received: 2min in apparatus → footshock (1.5mA, 1s)→ tone (75dB for 20 sec).

treatment_protocol:
Laser-capture microdissection of the lateral and basal nuclei of the amygdala
for molecular profiling:
Three hours after termination of the fear conditioning procedure animals were
decapitated and the ipsilateral temporal lobe was dissected and embedded in Tissue- TekO.C.T. Compund (Sakura Finetek, McGaw Park, IL, USA), frozen on dry ice, and stored at -80oC. Then cryomolds containing the temporal lobe were cut into 7 μm thick serial sections and collected on Slides for Membrane-based Laser
Microdissection (#11505158, Leica Microsystems, Germany). The slides were then
stained with 1% cresyl violet (for protocol see www.ambion.com) and the lateral and basal nuclei of the amygdala (basolateral amygdala), delineated according to the description of Pitkänen and coworkers (1997), were dissected using Leica AS LMD Laser Microdissection System (Leica Microsystems). For each animal, around 60-70 sections containing basolateral amygdala were collected and used for laser- microdissection.


title: Adjacent Tissue 98

description: Pair matched to 98T

source_name: Adjacent liver tissue 98N


title: mstm_wt_2 rep1

city: Augusta

first: Han

last: Zhang

department: IMMAG

institute: Medical College of Georgia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using Mean/median scaling normalization and Welch t test  with Array Track v3.3

source_name: Gastric mucosa from wild type mice

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

extract_protocol: Total RNA was isolated using a Perfect RNA Tissue kit (5 Prime Inc., Gaithersburg, MD) following manufacturer's instructions.

tag: wild type


title: control_unpaired_group__replicate_A

description: basolateral_amygdala__control_unpaired_group__replicate_A

treatment_protocol:
Laser-capture microdissection of the lateral and basal nuclei of the amygdala
for molecular profiling:
Three hours after termination of the fear conditioning procedure animals were
decapitated and the ipsilateral temporal lobe was dissected and embedded in Tissue- TekO.C.T. Compund (Sakura Finetek, McGaw Park, IL, USA), frozen on dry ice, and stored at -80oC. Then cryomolds containing the temporal lobe were cut into 7 μm thick serial sections and collected on Slides for Membrane-based Laser
Microdissection (#11505158, Leica Microsystems, Germany). The slides were then
stained with 1% cresyl violet (for protocol see www.ambion.com) and the lateral and basal nuclei of the amygdala (basolateral amygdala), delineated according to the description of Pitkänen and coworkers (1997), were dissected using Leica AS LMD Laser Microdissection System (Leica Microsystems). For each animal, around 60-70 sections containing basolateral amygdala were collected and used for laser-
microdissection.


title: mstm_KO_6 rep3

source_name: Gastric mucosa from Lasp1 knockout

tag: Lasp1 knockout


title: mstm_wt_3 rep2


title: mstm_KO_4 rep2


title: Pre BR soleus muscle biopsy: Nu_L2Spre_1

status: Public on Feb 12 2009

city: OTTAWA

first: Angele

last: CHOPARD

state: ONTARIO

address: 451 Smyth road

department: Faculty of Medicine

country: Canada

institute: University of Ottawa

description: Pre BR soleus muscle biopsy

hyb_protocol: Each individual cRNA sample was Cy3-labeled and mixed with an equal amount of Cy5-labeled reference sample (pool of equal quantities of cRNA from 18 Pre-BR Soleus or 23 Pre-BR Vastus Lateralis biopsies). The mixture was pre-incubated with human Cot-I DNA (Gibco-BRL), yeast tRNA, and polyA RNA, and hybridized onto duplicate microarrays.

scan_protocol: All hybridized arrays were scanned by fluorescence confocal microscopy (Scan array 4000XL, GSI-Lumonics) anda images were quantified using Genepix Pro 5.1.0.19 Extraction Software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal. Home made (MADSCAN) software was used.

source_name: Pre BR soleus muscle biopsy

label_protocol: 500 ng total RNA was prepared for hybridization using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion). According to the manufacturer, total RNA was reverse transcribed with an oligo-dT primer containing a T7 RNA polymerase promoter, and then converted into double-stranded cDNA. cDNA was used in an in vitro transcription (IVT) reaction in presence of amino-allyl nucleotides. After column purification, the IVT reaction yielded 30-100 µg aminoallyl cRNA. IVT products were labeled either with cyanine 3 or cyanine 5, and fragmented with RNA Fragmentation Reagents (Ambion) into lengths around 100 bases before hybridization.

extract_protocol: Total RNA was extracted from frozen samples with a polytron homogeneizer and the RNeasy Fibrous Tissue Mini kit (Qiagen).

value: soleus muscle biopsy

source_name: reference


title: Adjacent Tissue 3

description: Pair matched to 3T

source_name: Adjacent liver tissue 3N