title: RWPE-1 cells cultured 5 days in GFR Matrigel. Rep 1

status: Public on Dec 06 2010

type: RNA

city: Turku

first: Matthias

last: Nees

address: Itäinen Pitkäkatu 4C

department: Medical Biotechnology

country: Finland

institute: VTT Technical Research Centre of Finland

description: replicate 1

hyb_protocol: Samples were hybridized to Illumina’s Sentrix HumanRef-8 v3 Expression BeadChips, at 58 °C overnight according to Illumina Whole-Genome Gene Expression Direct Hybridization Guide.

scan_protocol: Chips were scanned with Illumina BeadArray Reader.

data_processing: Raw microarray data were quantile-normalized and log2 transformed using the Beadarray R package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: GFR Matrigel 3D culture

label_protocol: Total RNA was amplified with Ambion's Illumina TotalPrep RNA Amplification kit (Ambion). In vitro transcription reaction was performed overnight to yield sufficiently biotinylated cRNA. The cRNA concentrations where checked with Nanodrop ND-1000 and cRNA quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: All cells were propagated at 37˚C in standard cell culture conditions (5% CO2, 95% humidity). Non-transformed cells and their derivatives (EP156T, RWPE-1, PrEC and RWPE-2/w99) were cultured in Keratinocyte Serum-Free Medium (KSFM) supplemented with 2% (v/v) fetal bovine serum, 12.5 mg/l bovine pituitary extract (BPE) and 1.25 µg/l EGF. All transformed cells (PC-3, PC-3M, ALVA31, DU145, LNCaP, 22rv1)were cultured in RPMI-1640 supplemented with 10% (v/v) fetal bovine serum.

extract_protocol: 3D prostasphere cultures were washed with ice-cold PBS, membranes excised with a scalpel, and gels (plus prostaspheres) transferred into 6-well plates. The gels were mixed vigorously with 5 mM EDTA in PBS, transferred into Falcon tubes, and incubated on a tabletop rocker for 45 minutes, to detach prostaspheres from Matrigel. Free prostaspheres were sedimented by centrifugation and lysed with RLT buffer (Qiagen). Cells propagated in monolayer were lysed at 90% confluence, directly on 10cm cell culture dishes, with RLT buffer. RNA was extracted with QIAGEN RNeasy Mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Monolayer cultures were propagated in 10 cm cell culture dishes. 3D prostaspheres were cultured in Millicell hanging cell culture inserts with 1.0 µm PET transparent membranes (Millipore) on 6-well plates (Costar). The membranes were pre-coated with matrigel/medium mix (1:1) and incubated at 37˚C for 1 hour, to prevent cells from growing as a monolayer on the membrane. Cell suspension was mixed 1:4 with matrigel and transferred onto the coated membrane, polymerized overnight at 37˚C. Fresh medium was added every other day.

tag: cell line

tag: organ

value: Prostate

tag: cell line origin

value: Non-transformed prostate epithelial cells immortalized by human papilloma virus 18 (HPV-18)

tag: days in 3d


title: Primary prostate epithelial cells (PrEC) cultured in monolayer. Rep 1

description: replicate 1

source_name: Monolayer culture

value: PrEC

value: Non-transformed prostate epithelial primary cells


title: PC-3M cells cultured 4 days in GFR Matrigel. Rep 2

description: replicate 2

value: Prostate adenocarcinoma, highly metastatic variant of PC-3


title: PC-3 cells cultured 4 days in GFR Matrigel. Rep 2

description: replicate 2

value: Prostate adenocarcinoma, bone metastasis


title: PrEC cells cultured 5 days in GFR Matrigel. Rep 1

description: replicate 1


title: PrEC cells cultured 12 days in GFR Matrigel. Rep 1

description: replicate 1


title: PrEC cells cultured 12 days in GFR Matrigel. Rep 2

description: replicate 2


title: PrEC cells cultured 5 days in GFR Matrigel. Rep 2

description: replicate 2


title: EP156T cells cultured 5 days in GFR Matrigel. Rep 1

description: replicate 1

value: Non-transformed prostate epithelial cells immortalized with pBabe-hTERT-puro retroviral vector


title: EP156T cells cultured 5 days in GFR Matrigel. Rep 2

description: replicate 2


title: Primary prostate epithelial cells (PrEC) cultured in monolayer. Rep 2

description: replicate 2


title: EP156T cells cultured in monolayer. Rep 2

description: replicate 2


title: PC-3M cells cultured in monolayer. Rep 2

description: replicate 2


title: RWPE-2/w99 cells cultured in monolayer. Rep 2

description: replicate 2

value: Transformed prostate epithelial RWPE-1 derivative cloned in soft agar to select cells that show high expression of Ki-ras


title: RWPE-1 cells cultured in monolayer. Rep 1

description: replicate 1


title: RWPE-1 cells cultured 5 days in GFR Matrigel. Rep 2

description: replicate 2


title: PC-3M cells cultured 4 days in GFR Matrigel. Rep 1

description: replicate 1


title: PC-3M cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: PC-3M cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: ALVA31 cells cultured in monolayer. Rep 1

description: replicate 1

value: Prostate adenocarcinoma


title: PC-3 cells cultured 4 days in GFR Matrigel. Rep 1

description: replicate 1


title: PC-3M cells cultured in monolayer. Rep 1

description: replicate 1


title: DU145 cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2

value: Prostate adenocarcinoma, brain metastasis


title: RWPE-2/w99 cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: 22rv1 cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2

value: Prostate primary carcinoma, androgen independent line derived from CWR22 xenograft model


title: EP156T cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: EP156T cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: EP156T cells cultured in monolayer. Rep 1

description: replicate 1


title: RWPE-1 cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: RWPE-1 cells cultured in monolayer. Rep 2

description: replicate 2


title: RWPE-2/w99 cells cultured in monolayer. Rep 1

description: replicate 1


title: RWPE-1 cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: LNCaP cells cultured in monolayer. Rep 2

description: replicate 2

value: LNCaP

value: Prostate adenocarcinoma, left supraclavicular lymph node metastasis


title: ALVA31 cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: LNCaP cells cultured in monolayer. Rep 1

description: replicate 1


title: ALVA31 cells cultured in monolayer. Rep 2

description: replicate 2


title: DU145 cells cultured in monolayer. Rep 1

description: replicate 1


title: 22rv1 cells cultured in monolayer. Rep 2

description: replicate 2


title: DU145 cells cultured in monolayer. Rep 2

description: replicate 2


title: RWPE-2/w99 cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: DU145 cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: PC-3 cells cultured 15 days in GFR Matrigel. Rep 1

description: replicate 1


title: 22rv1 cells cultured in monolayer. Rep 1

description: replicate 1


title: 22rv1 cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: Adult brain, Dnmt1 Dnmt3a double knockout (DKO), replicate 2

status: Public on Dec 03 2010

city: Los Angeles

first: jian

last: feng

state: CA

address: 695 Charles E Young Dr

department: Human Genetics

country: USA

institute: UCLA

description: Replicate 2 of 4.

hyb_protocol: Following exactly the Agilent company protocol.  In brief, labelled cRNA was mixed with Agilent 10x Control targets and Agilent 25x Fragmentation Buffer. This was incubated at 37C for 30 min and the reaction was stopped by the addition of 2x Agilent hybridization buffer. This mix was hybridized to arrays for 17 hours at 65C at 4rpms. Arrays were washed as per Agilent protocol and scanned immediately.

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 8.5).

data_processing: The resultant data were retrieved by Agilent feature extraction software 8.5 and analyzed by FOCUS software with default settings.

organism: Mus musculus

source_name: Control brain

label_protocol: Following exactly the Agilent company protocol with dye Cy3 (for control) or Cy5 (for DKO) by Agilent Low Input Linear Amplification Kit. 750ng of RNA was labelled for each channel.

growth_protocol: All mice were housed under normal conditions.

extract_protocol: Total RNA was extracted by Trizol and cleaned up with the Qiagen RNeasy kit.

treatment_protocol: No special treament was given.

tag: tissue

value: cortex and hippocampus

tag: strain

tag: genotype

value: wild type

tag: age

value: 2.5 months

source_name: DKO brain

value: Dnmt1 Dnmt3a double knockout


title: Adult brain, Dnmt1 Dnmt3a double knockout (DKO), replicate 4

description: Replicate 4 of 4.


title: PC-3 cells cultured 8 days in GFR Matrigel. Rep 1

description: replicate 1

value: Prostate


title: LNCaP cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: LNCaP cells cultured 11 days in GFR Matrigel. Rep 2

description: replicate 2


title: Preadipocytes+PBMC experiment 4

city: Houston

first: Jacob

last: Couturier

state: TX

address: 6431 Fannin St., MSB 2.112

institute: University of Texas Medical School at Houston

description: Experimental replicate 4 of 4

hyb_protocol: Cy3- and Cy5-labeled were combined and hybridized overnight for 17hrs at 65degC to an Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of hybridized Agilent Oligo Microarrays were detected using Agilent's DNA microarray scanner.

data_processing: Agilent Feature Extraction Software was used to read and process microarray image files, including background subtraction and normalization.

source_name: Preadipocytes+Media 4

label_protocol: 250ng of cDNA were used as template for Cy3 labeling via Miltenyi Biotec's undisclosed protocol.

extract_protocol: Samples were lysed and shipped to Miltenyi Biotec for RNA amplification and cDNA generation as part of company's Agilent microarray services.

tag: cell type

value: Human subcutaneous preadipocytes

tag: tissue type

value: Human subcutaneous adipose tissue

source_name: Preadipocytes+PBMC 4

label_protocol: 250ng of cDNA were used as template for Cy5 labeling via Miltenyi Biotec's undisclosed protocol.


title: ALVA31 cells cultured 11 days in GFR Matrigel. Rep 1

description: replicate 1


title: PC-3 cells cultured 15 days in GFR Matrigel. Rep 2

description: replicate 2


title: PC-3 cells cultured 13 days in GFR Matrigel. Rep 2

description: replicate 2


title: PDSAg_2

status: Public on Dec 01 2010

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

country: Germany

institute: HelmholtzZentrum

description: Gene expression data from independent T cell lines from PDSAg treated rats.

hyb_protocol: We used standard Affymetrix procedures for hybridization

scan_protocol: Reactions were performed essentially according to the Affymetrix protocol.

data_processing: The resultant CEL files were analyzed using the ChipInspector software V.0.92 (CI; Genomatix Software GmbH, Munich, Germany).  Log2 normalized ChipInspector results provided as a supplementary file on the Series record.

organism: Rattus norvegicus

source_name: T cell line from PDSAg_2

label_protocol: 20µg of total RNA were reverse-transcribed and used for biotinylation employing the GeneChip Expression 3' amplification one-cycle target labeling and control kit (Affymetrix, Sunnydale, CA).

growth_protocol: Inbred rats were purchased from Janvier (Le Genest St. Isle, France) and were used in all experiments.

extract_protocol: Total RNA was isolated by the method of Chomczynski and Sacci. RNA quality was characterized using a RNA6000 Nanochip (Agilent).

value: LEW RT1l

value: T cell lines

tag: disease model

value: Experimental autoimmune uveitis (EAU)

tag: eau-inducing antigen

value: S-antigen peptide PDSAg


title: Ad-Progerin EC gene expression N3

status: Public on Dec 02 2010

city: Boston

first: Belinda

last: Yap

state: MA

address: 77 Avenue Louis Pasteur, NRB 752

department: Pathology

institute: Brigham and Women's Hospital, Harvard Medical School

description: Transcriptional profiling was performed with endothelial cells infected with Ad-Progerin or Ad-Null in order to assess the changes in endothelial functional phenotype as a result of progerin expression

hyb_protocol: ABI protocol

scan_protocol: ABI protocol

data_processing: ABI 1700 chemiluminescent microarray system and analyzer.  Post-processing of data with Lowess regression and Z-pool variances was performed with custom statistical software

label: Digoxigenin

source_name: Ad-Progerin EC

label_protocol: Digoxigenin labeling of the cDNA products (ABI protocol)

growth_protocol: Medium-199, 20% FBS, 2 mM L-Glutamine, 50 ug/ml endothelial cell growth supplement, 100 ug/ml heparin, 100 units/ml penicillin plus 100 ug/ml streptomycin

extract_protocol: 40 ug of total RNA, extracted from pooled source using Trizol (Invitrogen) and RNeasy Purification Kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Approximately 10 million endothelial cells were infected with Ad-Progerin at MOI of 300 for 4 days

value: primary human umbilical vein endothelial cells


title: VMC Patient 60

status: Public on Dec 04 2010

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: VMC Patient 60

label_protocol: standard Affymetrix protocol

extract_protocol: Qiagen Rneasy

tag: gender

value: female

tag: ethnicity

value: caucasian

tag: adenoma type

value: Tubulovillous

tag: location

value: Left


title: Preadipocytes+PBMC experiment 1

description: Experimental replicate 1 of 4

source_name: Preadipocytes+Media 1

source_name: Preadipocytes+PBMC 1


title: PDSAg_1

data_processing: The resultant CEL files were analyzed using the ChipInspector software V.0.92 (CI; Genomatix Software GmbH, Munich, Germany).  Log2 normalized ChipInspector results are provided as a supplementary file on the Series record.

source_name: T cell line from PDSAg_1


title: PC-3 cells cultured 13 days in GFR Matrigel. Rep 1

description: replicate 1

value: Prostate adenocarcinoma, bone metastasis


title: PC-3 cells cultured in monolayer. Rep 2

description: replicate 2


title: PC-3 cells cultured 8 days in GFR Matrigel. Rep 2

description: replicate 2


title: PC-3 cells cultured in monolayer. Rep 1

description: replicate 1


title: VMC Patient 61

source_name: VMC Patient 61

value: male

value: Adenoma

value: Sigmoid


title: NHE2 small intestine null vs. wild type

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min.  For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.  The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.  To test for differentially expressed genes, a hierarchical Bayes procedure, IBMT (Sartor et al., BMC Bioinf, 2006) was used.

label: Cy3, Cy5

source_name: total RNA from NHE2 KO small intestine

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

growth_protocol: Mice had access to normal chow and water ad libitum, and were aged to 8 weeks old.

extract_protocol: Total RNA was extracted from small intestine using Tri-Reagent as per the manufacturer's instructions.

tag: genetic background

value: inbred FVBN

value: small intestine

value: NHE2 null

source_name: total RNA from wild type small intestine

value: wild type


title: VMC Patient 58

source_name: VMC Patient 58


title: VMC Patient 59

source_name: VMC Patient 59

value: Villous adenoma


title: VMC Patient 56

source_name: VMC Patient 56

value: Right


title: Bovine isolate 4

type: genomic

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

description: Dye-swap

hyb_protocol: Genomic DNA from C. difficile 630 was used as a reference DNA for all hybridizations. Dye swaps were performed to test dye-incorporation bias. The microarray slides were prehybridized using a solution containing 25% formamide, 5x SSC (1x SSC consists of 0.15M NaCl with 0.015M sodium citrate), 0.2% (w/v) sarcosyl, and 10 mg/ml bovine serum albumin at 42 °C for 1 h. The slides were then washed in MilliQ water and blow dried using compressed nitrogen gas. Equivalent amounts of labeled probes from reference and tested strains were pooled, lyophilized, and resuspended in 70 µl of hybridization buffer (25% formamide, 5x SSC, 0.2% sodium dodecyl sulfate (SDS), 1 mg/ml salmon sperm DNA, and 1 mg/ml yeast tRNA). The probes were then denatured at 99 °C for 5 min, centrifuged briefly at 13,800 x g and applied to the microarray under a 22 x 60mm LifterSlip (Erie Scientific Co.). Hybridizations were performed at 42 °C for 16 h in a sealed humidified hybridization chamber (Corning). Following the hybridization, excess hybridization solution and unbound probes were washed away during four washing steps including 5 min in 2x SSC, 1% SDS at 42 °C and 5 min in 0.1% SSC at room temperature for three times. The slides were then dried and scanned immediately.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments).

data_processing: The Cy3 and Cy5 signals and the local background intensities were quantified using GenePix Pro 6.1 software. The local background value was subtracted from the intensity of each spot. Spots were examined manually, and poor spots were flagged for elimination from the analysis. All subsequent data analyses were performed by using Microsoft Excel and a genomotyping analysis software GACK to determine present/divergent genes.

molecule: genomic DNA

organism: Clostridioides difficile

source_name: Bovine isolate 4

label_protocol: Three micrograms of genomic DNA from each strain was fragmented by DraI digestion at 37°C for 3 h and cleaned up with QIAquick PCR purification kit (Qiagen). Fragmented DNA was then labeled with 10 µg of exo-resistant random primers (Fermentas), 25 U of Klenow fragment (New England Biolabs), dNTP mix (0.12 mM each dATP, dCTP, and dGTP and 0.03 mM dTTP), and 0.1 mM of either Cy3- or Cy5-dUTP (Amersham Biosciences). Probes were purified from unincorporated dyes using the QIAquick PCR purification kit (Qiagen). Labeled DNA sample yields and dye incorporation efficiencies were determined using spectrometry.

extract_protocol: Genomic DNA was isolated from C. difficile by using DNeasy Blood and Tissue Mini Kit (Qiagen) as described in the manufacturer’s protocol for gram-positive bacteria.

tag: source

value: Bovine isolate

source_name: Reference strain 630

value: Reference strain 630


title: Dog isolate 3

description: Dye-swap

source_name: Dog isolate 3

value: Dog isolate


title: Dog isolate 2

description: Dye-swap

source_name: Dog isolate 2


title: VMC Patient 57

source_name: VMC Patient 57

value: female

value: not specified

value: Recto-sigmoid


title: Bovine isolate 5

description: Dye-swap

source_name: Bovine isolate 5


title: Dog isolate 1

description: Dye-swap

source_name: Dog isolate 1


title: Adult brain, Dnmt1 Dnmt3a double knockout (DKO), replicate 1

description: Replicate 1 of 4.

source_name: Control brain

value: cortex and hippocampus

value: 2.5 months

source_name: DKO brain

value: Dnmt1 Dnmt3a double knockout


title: Human isolate 1

description: Dye-swap

source_name: Human isolate 1

value: Human isolate


title: Adult brain, Dnmt1 Dnmt3a double knockout (DKO), replicate 3

description: Replicate 3 of 4.


title: Liver Non-Tumor Tissue LCS-241B

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Hybridization Protocol Other: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Scanning Protocol for HT Arrays Other: GeneChips were scanned using GeneChip® HT Array Plate Scanner by Affymetrix.

data_processing:
Data Processing Protocol
Calculation Method: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

label_protocol:
Biotinylated cRNA Labeling for HT Arrays
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, For HT Array Plates Using the GeneChip® Array Station, P/N 702063 Rev. 2, Affymetrix).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was isolated from microdissected fresh frozen tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Tissue

value: Liver Non-Tumor Tissue

tag: Disease state

value: Hepatocellular carcinoma (HCC)

tag: Individual


title: Liver Tumor Tissue LCS-046A

description: No additional information.

value: Liver Tumor Tissue


title: Liver Tumor Tissue LCS-200A

description: No additional information.


title: Liver Tumor Tissue LCS-197A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-166B

description: No additional information.


title: Preadipocytes+PBMC experiment 3

description: Experimental replicate 3 of 4

source_name: Preadipocytes+Media 3

value: Human subcutaneous preadipocytes

value: Human subcutaneous adipose tissue

source_name: Preadipocytes+PBMC 3


title: Liver Tumor Tissue LCS-216A

description: No additional information.


title: Liver Tumor Tissue LCS-161A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-014B

description: No additional information.


title: Ad-Progerin EC gene expression N2

source_name: Ad-Progerin EC

value: primary human umbilical vein endothelial cells


title: Ad-Null EC gene expression N2

source_name: Ad-Null EC

treatment_protocol: Approximately 10 million endothelial cells were infected with Ad-Null at MOI of 300 for 4 days


title: Ad-Null EC gene expression N3


title: R14_3

description: Gene expression data from independent T cell lines from R14 treated rats.

source_name: T cell line from R14_3

value: LEW RT1l

value: T cell lines

value: Experimental autoimmune uveitis (EAU)

value: R14 (a peptide derived from interphotoreceptor retinoid-binding protein)


title: Preadipocytes+PBMC experiment 2

description: Experimental replicate 2 of 4

source_name: Preadipocytes+Media 2

source_name: Preadipocytes+PBMC 2


title: Liver Non-Tumor Tissue LCS-150B

description: No additional information.


title: Liver Tumor Tissue LCS-158A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-140B

description: No additional information.


title: R14_2

source_name: T cell line from R14_2


title: Liver Non-Tumor Tissue LCS-290B

description: No additional information.


title: Ad-Null EC gene expression N1


title: Ad-Progerin EC gene expression N1


title: R14_1

source_name: T cell line from R14_1


title: Liver Non-Tumor Tissue LCS-093B

description: No additional information.


title: PDSAg_3

source_name: T cell line from PDSAg_3

value: S-antigen peptide PDSAg


title: Human isolate 2

description: Dye-swap

source_name: Human isolate 2

source_name: Reference strain 630

value: Reference strain 630


title: Dog isolate 4

description: Dye-swap

source_name: Dog isolate 4

value: Dog isolate


title: Liver Tumor Tissue LCS-273A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-259B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-072B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-248B

description: No additional information.


title: Liver Tumor Tissue LCS-269A

description: No additional information.


title: Liver Tumor Tissue LCS-238A

description: No additional information.


title: Liver Tumor Tissue LCS-072A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-231B

description: No additional information.


title: Liver Tumor Tissue LCS-231A

description: No additional information.


title: Bovine isolate 2

description: Dye-swap

source_name: Bovine isolate 2

value: Bovine isolate


title: Bovine isolate 1

description: Dye-swap

source_name: Bovine isolate 1


title: Bovine isolate 3

description: Dye-swap

source_name: Bovine isolate 3


title: Liver Tumor Tissue LCS-201A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-216B

description: No additional information.


title: Liver Tumor Tissue LCS-172A

description: No additional information.


title: Liver Tumor Tissue LCS-263A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-162B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-196B

description: No additional information.


title: Liver Tumor Tissue LCS-097A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-104B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-289B

description: No additional information.


title: Liver Tumor Tissue LCS-290A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-273B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-142B

description: No additional information.


title: Liver Tumor Tissue LCS-289A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-097B

description: No additional information.


title: Liver Tumor Tissue LCS-138A

description: No additional information.


title: TCDD C1 5days versus Reference 5days (dye swap)

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: Biological replicate 3 dye swap

hyb_protocol: 1µg of labelled nucleic acid was hybridized at 67 degree_C during 17 hours

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using Genepix pro 6.0

data_processing: Lowess normalization. Only spots with SNR > 2 were considered

source_name: Reference 5days

label_protocol: One microgram of total RNA was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes, following a dye swap experimental plan.  Fluorescent probes were purified using Rneasy minikit (Qiagen)

extract_protocol: Total RNA were extracted using Rneasy Mini Kit following manufacturer's instructions

source_name: TCDD C1 5days


title: TCDD A1 5days versus Reference 5days (dye swap)

description: Biological replicate 1 dye swap

source_name: TCDD A1 5days


title: TCDD D1 5days versus Reference 5days (dye swap)

description: Biological replicate 4 dye swap

source_name: TCDD D1 5days


title: Liver Non-Tumor Tissue LCS-263B

description: No additional information.


title: Liver Tumor Tissue LCS-251A

description: No additional information.


title: TCDD E1 28days versus Reference 28days

description: Biological replicate 3

source_name: Reference 28days

source_name: TCDD E1 28days


title: Liver Non-Tumor Tissue LCS-269B

description: No additional information.


title: Liver Tumor Tissue LCS-207A

description: No additional information.


title: TCDD C2 28days versus Reference 28days (dye swap)

description: Biological replicate 2 dye swap

source_name: TCDD C2 28days


title: TCDD E1 28days versus Reference 28days (dye swap)

description: Biological replicate 3 dye swap


title: TCDD B2 28days versus Reference 28days (dye swap)

description: Biological replicate 1 dye swap

source_name: TCDD B2 28days


title: Liver Tumor Tissue LCS-116A

description: No additional information.


title: Liver Tumor Tissue LCS-196A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-107B

description: No additional information.


title: Liver Tumor Tissue LCS-107A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-139B

description: No additional information.


title: TCDD B1 5days versus Reference 5days (dye swap)

description: Biological replicate 2 dye swap

source_name: TCDD B1 5days


title: Liver Tumor Tissue LCS-142A

description: No additional information.


title: TCDD B2 28days versus Reference 28days

description: Biological replicate 1


title: Liver Tumor Tissue LCS-016A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-138B

description: No additional information.


title: TCDD C2 28days versus Reference 28days

description: Biological replicate 2


title: Liver Tumor Tissue LCS-031A

description: No additional information.


title: Liver Tumor Tissue LCS-139A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-137B

description: No additional information.


title: Liver Tumor Tissue LCS-266A

description: No additional information.


title: Liver Tumor Tissue LCS-240A

description: No additional information.


title: Liver Tumor Tissue LCS-173A

description: No additional information.


title: Liver tissue of six healthy donors  Normal1

description: No additional information.

scan_protocol: Scanning Protocol Other: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

label_protocol:
Biotinylated cRNA Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, P/N 702232 Rev. 2, Affymetrix).

value: Liver tissue of six healthy donors


title: Liver Non-Tumor Tissue LCS-424B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-426B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-109B

description: No additional information.


title: TCDD C1 5days versus Reference 5days

description: Biological replicate 3


title: Liver Non-Tumor Tissue LCS-243B

description: No additional information.


title: Liver Tumor Tissue LCS-109A

description: No additional information.


title: TCDD D1 5days versus Reference 5days

description: Biological replicate 4


title: Liver Tumor Tissue LCS-106A

description: No additional information.


title: TCDD B1 5days versus Reference 5days

description: Biological replicate 2


title: TCDD A1 5days versus Reference 5days

description: Biological replicate 1


title: Liver Tumor Tissue LCS-415A

description: No additional information.


title: Liver Tumor Tissue LCS-137A

description: No additional information.


title: Liver Tumor Tissue LCS-167A

description: No additional information.


title: Liver Tumor Tissue LCS-028A

description: No additional information.


title: Liver Tumor Tissue LCS-406A

description: No additional information.


title: Liver Tumor Tissue LCS-050A

description: No additional information.


title: Liver Tumor Tissue LCS-032A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-056B

description: No additional information.


title: Liver Tumor Tissue LCS-426A

description: No additional information.


title: Liver Tumor Tissue LCS-285A

description: No additional information.


title: Liver tissue of six healthy donors  Normal2

description: No additional information.

value: Liver tissue of six healthy liver donors


title: Liver Non-Tumor Tissue LCS-110B

description: No additional information.


title: Liver Tumor Tissue LCS-147A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-146B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-208B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-165B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-415B

description: No additional information.


title: Liver Tumor Tissue LCS-165A

description: No additional information.


title: Liver Tumor Tissue LCS-424A

description: No additional information.


title: Liver Tumor Tissue LCS-056A

description: No additional information.


title: Liver Tumor Tissue LCS-401A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-406B

description: No additional information.


title: Liver Tumor Tissue LCS-208A

description: No additional information.


title: Liver Tumor Tissue LCS-146A

description: No additional information.


title: Liver Tumor Tissue LCS-403A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-400B

description: No additional information.


title: Liver Tumor Tissue LCS-110A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-403B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-401B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-247B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-051B

description: No additional information.


title: opr3 systemic wounding

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

description: opr3 systemic wounding

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 7G.

data_processing: RMA via the PARTEK software

label: Biotin

organism: Arabidopsis thaliana

source_name: opr3 systemic wounding

label_protocol:
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix), in the Weizmann Institute microarray unit

growth_protocol:
Plants were grown under white light in a 10-h-light/14-h-dark cycle (short day ) at 21°C.
6 weeks old plants

extract_protocol: Extraction of total RNA was performed using RNeasy plant Mini Kit (Qiagen) according to the manufacture's protocol.

treatment_protocol:
Wounding treatment
Half of the rosette leaves of six weeks old WT  plants were wounded by clamping a tweezers across the midvein. RNA was extracted from control  leaves 2 h after wounding, and was subject to affymetrix ATH1 chip.

tag: opr3 mutant systemic wounding


title: Liver Tumor Tissue LCS-088A

description: No additional information.


title: Liver Tumor Tissue LCS-243A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-393B

description: No additional information.


title: Liver Tumor Tissue LCS-051A

description: No additional information.


title: Liver Tumor Tissue LCS-393A

description: No additional information.


title: Liver Tumor Tissue LCS-400A

description: No additional information.


title: Liver Tumor Tissue LCS-346A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-346B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-347B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-157B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-260B

description: No additional information.


title: Liver Tumor Tissue LCS-247A

description: No additional information.


title: wt systemic wounding

description: wt systemic wounding

source_name: wt systemic wounding

tag: wt plants systemic wounding


title: Liver Tumor Tissue LCS-343A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-027B

description: No additional information.


title: Liver Tumor Tissue LCS-347A

description: No additional information.


title: opr3 control

description: opr3 control

source_name: opr3 control

treatment_protocol: control

tag: opr3 mutants control


title: Liver Non-Tumor Tissue LCS-012B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-148B

description: No additional information.


title: wt control

description: wt control

source_name: wt control

tag: wt arabidopsis leaves


title: Liver Non-Tumor Tissue LCS-343B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-344B

description: No additional information.


title: Liver Tumor Tissue LCS-344A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-066B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-121B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-025B

description: No additional information.


title: Liver Tumor Tissue LCS-260A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-048B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-223B

description: No additional information.


title: Liver Tumor Tissue LCS-341A

description: No additional information.


title: Liver Tumor Tissue LCS-339A

description: No additional information.


title: Liver Tumor Tissue LCS-012A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-339B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-341B

description: No additional information.


title: Liver Tumor Tissue LCS-333A

description: No additional information.


title: Liver Tumor Tissue LCS-048A

description: No additional information.


title: Liver Tumor Tissue LCS-126A

description: No additional information.


title: Liver Tumor Tissue LCS-157A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-333B

description: No additional information.


title: Liver Tumor Tissue LCS-068A

description: No additional information.


title: Liver Tumor Tissue LCS-148A

description: No additional information.


title: Liver Tumor Tissue LCS-066A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-068B

description: No additional information.


title: Liver Tumor Tissue LCS-254A

description: No additional information.


title: Liver Tumor Tissue LCS-121A

description: No additional information.


title: Liver Tumor Tissue LCS-248A

description: No additional information.


title: Liver Tumor Tissue LCS-025A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-254B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-039B

description: No additional information.


title: Liver Tumor Tissue LCS-027A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-022B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-076B

description: No additional information.


title: Liver Tumor Tissue LCS-076A

description: No additional information.


title: Liver Tumor Tissue LCS-039A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-036B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-192B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-063B

description: No additional information.


title: Liver Tumor Tissue LCS-029A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-268B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-117B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-100B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-277B

description: No additional information.


title: Liver Tumor Tissue LCS-268A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-222B

description: No additional information.


title: Liver Tumor Tissue LCS-054A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-054B

description: No additional information.


title: Liver Tumor Tissue LCS-019A

description: No additional information.


title: Liver Tumor Tissue LCS-005A

description: No additional information.


title: Liver Tumor Tissue LCS-100A

description: No additional information.


title: Liver Tumor Tissue LCS-228A

description: No additional information.


title: Liver Tumor Tissue LCS-063A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-267B

description: No additional information.


title: Liver Tumor Tissue LCS-192A

description: No additional information.


title: Liver Tumor Tissue LCS-267A

description: No additional information.


title: Liver Tumor Tissue LCS-117A

description: No additional information.


title: Liver Tumor Tissue LCS-222A

description: No additional information.


title: Liver Tumor Tissue LCS-277A

description: No additional information.


title: Liver Tumor Tissue LCS-189A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-016B

description: No additional information.


title: Liver Tumor Tissue LCS-022A

description: No additional information.


title: Liver Tumor Tissue LCS-175A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-228B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-285B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-050B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-032B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-064B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-240B

description: No additional information.


title: Liver Tumor Tissue LCS-270A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-182B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-028B

description: No additional information.


title: Liver Tumor Tissue LCS-182A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-173B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-167B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-270B

description: No additional information.


title: Liver Tumor Tissue LCS-002A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-236B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-266B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-038B

description: No additional information.


title: Liver Tumor Tissue LCS-236A

description: No additional information.


title: Liver Tumor Tissue LCS-064A

description: No additional information.


title: Liver Tumor Tissue LCS-038A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-197B

description: No additional information.


title: Liver Tumor Tissue LCS-036A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-145B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-195B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-031B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-206B

description: No additional information.


title: Liver Tumor Tissue LCS-145A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-200B

description: No additional information.


title: Liver Tumor Tissue LCS-206A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-161B

description: No additional information.


title: Liver Tumor Tissue LCS-195A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-071B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-204B

description: No additional information.


title: Liver Tumor Tissue LCS-204A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-219B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-194B

description: No additional information.


title: Liver Tumor Tissue LCS-170A

description: No additional information.


title: Liver Tumor Tissue LCS-219A

description: No additional information.


title: Liver Tumor Tissue LCS-194A

description: No additional information.


title: Liver Tumor Tissue LCS-071A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-108B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-084B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-170B

description: No additional information.


title: Liver Tumor Tissue LCS-011A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-215B

description: No additional information.


title: Liver Tumor Tissue LCS-084A

description: No additional information.


title: Liver Tumor Tissue LCS-250A

description: No additional information.


title: Liver Tumor Tissue LCS-261A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-011B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-198B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-193B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-129B

description: No additional information.


title: Liver Tumor Tissue LCS-215A

description: No additional information.


title: Liver Tumor Tissue LCS-198A

description: No additional information.


title: Liver Tumor Tissue LCS-166A

description: No additional information.


title: Liver Tumor Tissue LCS-193A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-043B

description: No additional information.


title: Liver Tumor Tissue LCS-021A

description: No additional information.


title: Liver Tumor Tissue LCS-044A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-174B

description: No additional information.


title: Liver Tumor Tissue LCS-129A

description: No additional information.


title: Liver Tumor Tissue LCS-043A

description: No additional information.


title: Liver Tumor Tissue LCS-174A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-021B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-041B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-044B

description: No additional information.


title: Liver Tumor Tissue LCS-041A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-284B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-261B

description: No additional information.


title: Liver Tumor Tissue LCS-284A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-203B

description: No additional information.


title: Liver Tumor Tissue LCS-178A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-178B

description: No additional information.


title: Liver Tumor Tissue LCS-108A

description: No additional information.


title: Liver Tumor Tissue LCS-119A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-184B

description: No additional information.


title: Liver Tumor Tissue LCS-203A

description: No additional information.


title: Liver Tumor Tissue LCS-034A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-119B

description: No additional information.


title: Liver Tumor Tissue LCS-143A

description: No additional information.


title: Liver Tumor Tissue LCS-278A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-199B

description: No additional information.


title: Liver Tumor Tissue LCS-163A

description: No additional information.


title: Liver Tumor Tissue LCS-199A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-278B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-034B

description: No additional information.


title: Liver Tumor Tissue LCS-089A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-143B

description: No additional information.


title: Liver Tumor Tissue LCS-259A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-163B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-264B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-089B

description: No additional information.


title: Liver Tumor Tissue LCS-184A

description: No additional information.


title: Liver Tumor Tissue LCS-010A

description: No additional information.


title: Liver Tumor Tissue LCS-075A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-047B

description: No additional information.


title: Liver Tumor Tissue LCS-264A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-075B

description: No additional information.


title: Liver Tumor Tissue LCS-047A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-061B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-291B

description: No additional information.

value: AN B


title: Liver Non-Tumor Tissue LCS-282B

description: No additional information.

value: Liver Non-Tumor Tissue


title: Liver Non-Tumor Tissue LCS-090B

description: No additional information.

value: Hepatocellular carcinoma (HCC)


title: Liver Non-Tumor Tissue LCS-156B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-279B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-172B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-253B

description: No additional information.


title: Liver Tumor Tissue LCS-282A

description: No additional information.

value: Liver Tumor Tissue


title: Liver Tumor Tissue LCS-151A

description: No additional information.


title: Liver Tumor Tissue LCS-090A

description: No additional information.


title: Liver Tumor Tissue LCS-049A

description: No additional information.


title: Liver Tumor Tissue LCS-156A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-049B

description: No additional information.


title: Liver Tumor Tissue LCS-008A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-151B

description: No additional information.


title: Liver Tumor Tissue LCS-279A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-008B

description: No additional information.


title: Liver Tumor Tissue LCS-281A

description: No additional information.


title: Liver Tumor Tissue LCS-291A

description: No additional information.

value: AN A


title: Liver Non-Tumor Tissue LCS-134B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-224B

description: No additional information.


title: Liver Tumor Tissue LCS-093A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-078B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-009B

description: No additional information.


title: Liver Tumor Tissue LCS-253A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-057B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-201B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-147B

description: No additional information.


title: Liver Tumor Tissue LCS-078A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-131B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-179B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-074B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-160B

description: No additional information.


title: Liver Tumor Tissue LCS-009A

description: No additional information.


title: Liver Tumor Tissue LCS-057A

description: No additional information.


title: Liver Tumor Tissue LCS-224A

description: No additional information.


title: Liver Tumor Tissue LCS-074A

description: No additional information.


title: Liver Tumor Tissue LCS-241A

description: No additional information.


title: Liver Tumor Tissue LCS-160A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-094B

description: No additional information.


title: Liver Tumor Tissue LCS-179A

description: No additional information.


title: Liver Tumor Tissue LCS-094A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-249B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-171B

description: No additional information.


title: Liver Tumor Tissue LCS-045A

description: No additional information.


title: Liver Tumor Tissue LCS-134A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-020B

description: No additional information.


title: Liver Tumor Tissue LCS-171A

description: No additional information.


title: Liver Tumor Tissue LCS-131A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-045B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-191B

description: No additional information.


title: Liver Tumor Tissue LCS-245A

description: No additional information.


title: Liver Tumor Tissue LCS-191A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-281B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-245B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-164B

description: No additional information.


title: Liver Tumor Tissue LCS-249A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-033B

description: No additional information.


title: Liver Tumor Tissue LCS-223A

description: No additional information.


title: Liver Tumor Tissue LCS-061A

description: No additional information.


title: Liver Tumor Tissue LCS-020A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-213B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-169B

description: No additional information.


title: Liver Tumor Tissue LCS-033A

description: No additional information.


title: Liver Tumor Tissue LCS-164A

description: No additional information.


title: Liver Tumor Tissue LCS-213A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-149B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-234B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-265B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-015B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-040B

description: No additional information.


title: Liver Tumor Tissue LCS-234A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-190B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-210B

description: No additional information.


title: Liver Tumor Tissue LCS-040A

description: No additional information.


title: Liver Tumor Tissue LCS-169A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-069B

description: No additional information.


title: Liver Tumor Tissue LCS-256A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-118B

description: No additional information.


title: Liver Tumor Tissue LCS-265A

description: No additional information.


title: Liver Tumor Tissue LCS-210A

description: No additional information.


title: Liver Tumor Tissue LCS-062A

description: No additional information.


title: Liver Tumor Tissue LCS-018A

description: No additional information.


title: Liver Tumor Tissue LCS-149A

description: No additional information.


title: Liver Tumor Tissue LCS-118A

description: No additional information.


title: Liver Tumor Tissue LCS-042A

description: No additional information.


title: Liver Tumor Tissue LCS-183A

description: No additional information.


title: Liver Tumor Tissue LCS-069A

description: No additional information.


title: Liver Tumor Tissue LCS-015A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-144B

description: No additional information.


title: Liver Tumor Tissue LCS-275A

description: No additional information.


title: Liver Tumor Tissue LCS-153A

description: No additional information.


title: Liver Tumor Tissue LCS-180A

description: No additional information.


title: Liver Tumor Tissue LCS-024A

description: No additional information.


title: Liver Tumor Tissue LCS-212A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-209B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-065B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-262B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-152B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-237B

description: No additional information.


title: Liver Tumor Tissue LCS-262A

description: No additional information.


title: Liver Tumor Tissue LCS-073A

description: No additional information.


title: Liver Tumor Tissue LCS-230A

description: No additional information.


title: Liver Tumor Tissue LCS-209A

description: No additional information.


title: Liver Tumor Tissue LCS-144A

description: No additional information.


title: Liver Tumor Tissue LCS-065A

description: No additional information.


title: Liver Tumor Tissue LCS-211A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-067B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-211B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-073B

description: No additional information.


title: Liver Tumor Tissue LCS-237A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-227B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-046B

description: No additional information.


title: Liver Tumor Tissue LCS-152A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-205B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-159B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-272B

description: No additional information.


title: Liver Tumor Tissue LCS-067A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-230B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-158B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-274B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-283B

description: No additional information.


title: Liver Tumor Tissue LCS-104A

description: No additional information.


title: Liver Tumor Tissue LCS-272A

description: No additional information.


title: Liver Tumor Tissue LCS-159A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-132B

description: No additional information.


title: Liver Tumor Tissue LCS-274A

description: No additional information.


title: Liver Tumor Tissue LCS-283A

description: No additional information.


title: Liver Tumor Tissue LCS-132A

description: No additional information.


title: Liver Tumor Tissue LCS-162A

description: No additional information.


title: Liver Tumor Tissue LCS-150A

description: No additional information.


title: Liver Tumor Tissue LCS-205A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-275B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-286B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-177B

description: No additional information.


title: Liver Tumor Tissue LCS-014A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-023B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-238B

description: No additional information.


title: Liver Tumor Tissue LCS-177A

description: No additional information.


title: Liver Tumor Tissue LCS-086A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-120B

description: No additional information.


title: Liver Tumor Tissue LCS-023A

description: No additional information.


title: Liver Tumor Tissue LCS-120A

description: No additional information.


title: Liver Tumor Tissue LCS-227A

description: No additional information.


title: Liver Tumor Tissue LCS-035A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-185B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-154B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-042B

description: No additional information.


title: Liver Tumor Tissue LCS-286A

description: No additional information.


title: Liver Tumor Tissue LCS-140A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-086B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-018B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-188B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-180B

description: No additional information.


title: Liver Tumor Tissue LCS-188A

description: No additional information.


title: Liver Tumor Tissue LCS-154A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-062B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-136B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-130B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-035B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-024B

description: No additional information.


title: Liver Tumor Tissue LCS-185A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-212B

description: No additional information.


title: Liver Tumor Tissue LCS-136A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-125B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-183B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-153B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-127B

description: No additional information.


title: KKTa_isolated glomeruli_Chow

city: Tokyo

first: Maki

last: Murakoshi

address: 2-1-1, Hongo, Bunkyo-ku

department: Division of Nephrology, Department of Internal Medicine

country: Japan

institute: Juntendo University School of Medicine

description: Mice fed with a normal chow diet.

hyb_protocol: Twenty ug fragmented cRNA was hybridized with GeneChip Mouse Genome 430 2.0 Array (Affymetrix) at 45 C for 16h.

scan_protocol: The chips were washed, stained with srteptavidin phycoerythrin and scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Scanned images were converted to signal intensity using GeneChip Operating software (Affymetrix).

source_name: KKTa, isolated glomeruli

label_protocol: Total RNA was converted to cDNA using Superscript 2 reverse transcriptase, and biotin-labeled cRNA was synthesized from the cDNA by in vitro transcription as described (Two-cycle Target Labeling and Control Reagents, Affymetrix)

extract_protocol: Total RNA was isolated using Qiagen RNeasy Mini Kit.

tag: strain

value: KKTa

value: male

tag: age

value: 20 weeks

tag: diet

value: normal fat diet


title: Liver Non-Tumor Tissue LCS-135B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-122B

description: No additional information.


title: Liver Tumor Tissue LCS-127A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-123B

description: No additional information.


title: Liver Tumor Tissue LCS-007A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-007B

description: No additional information.


title: Liver Tumor Tissue LCS-125A

description: No additional information.


title: Liver Tumor Tissue LCS-123A

description: No additional information.


title: KKTa_isolated glomeruli_HFD

description: Mice fed with a high-fat diet.

extract_protocol: Total RNA was isolated using Qiagen RNeasy Mini Kit

value: high-fat diet


title: Liver Non-Tumor Tissue LCS-105B

description: No additional information.


title: Liver Tumor Tissue LCS-130A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-099B

description: No additional information.


title: Liver Tumor Tissue LCS-122A

description: No additional information.


title: Liver Tumor Tissue LCS-135A

description: No additional information.


title: Liver Tumor Tissue LCS-105A

description: No additional information.


title: Liver Tumor Tissue LCS-091A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-103B

description: No additional information.


title: Liver Tumor Tissue LCS-096A

description: No additional information.


title: Liver Tumor Tissue LCS-099A

description: No additional information.


title: Liver Tumor Tissue LCS-004A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-095B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-091B

description: No additional information.


title: Liver Tumor Tissue LCS-085A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-102B

description: No additional information.


title: Liver Tumor Tissue LCS-102A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-101B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-083B

description: No additional information.


title: Liver Tumor Tissue LCS-095A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-085B

description: No additional information.


title: Liver Non-Tumor Tissue LCS-079B

description: No additional information.


title: Liver Tumor Tissue LCS-079A

description: No additional information.


title: Liver Non-Tumor Tissue LCS-092B

description: No additional information.


title: Liver Tumor Tissue LCS-092A

description: No additional information.


title: Liver Tumor Tissue LCS-101A

description: No additional information.


title: Liver Tumor Tissue LCS-103A

description: No additional information.


title: Liver Tumor Tissue LCS-083A

description: No additional information.


title: Prefrontal cortex KO

city: Tokushima

first: Yuta

last: Yamamoto

address: 3-18-15 Kuramoto-cho

department: Stress Science

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

description: An equal amount of RNA from 5 mice was pooled and used for microarray analysis.

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 10.0.2. 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 75 percentile scaled using the 75 percentile of signal intensity value for data points labeled as Present.

source_name: Prefrontal cortex KO

label_protocol: 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: After systemic perfusion with cold phosphate-buffered saline through the heart using a syringe attached to a 21-G needle, whole mouse brains were removed. Coronal sections (1 mm thickness) of mouse brain were prepared on ice. The prefrontal cortex was sliced between 2.5 and 3.5 mm posterior to bregma. Total RNA was immediately prepared from these samples using an RNeasy kit (Qiagen, Hilden, Germany). The quality of purified RNA was assessed by an Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: genotype

value: IL-18 KO

value: Male

value: 12 wks

tag: tissue

value: Prefrontal cortex


title: Striatum WT

source_name: Striatum WT

value: WT

tag: gender

value: Striatum


title: Striatum KO

source_name: Striatum KO


title: Olfactory bulb WT

source_name: Olfactory bulb WT

value: Olfactory bulb


title: Hypothalamus WT

source_name: Hypothalamus WT

value: Hypothalamus


title: Amygdala KO

source_name: Amygdala KO

value: Amygdala


title: Hippocampus WT

source_name: Hippocampus WT

value: Hippocampus


title: Hippocampus KO

source_name: Hippocampus KO


title: Lung FFPE A-1

status: Public on Nov 25 2010

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

description: LN_RD129_1 ffpetL

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console using RMA-sketch quantile as normalization method.

source_name: Formalin-fixed paraffin-embedded tissue, lung tumor

label_protocol: Purified RNA was subjected to whole-transcriptome amplification using the WT-Ovation FFPE system. For RNA extracted from frozen or FFPE sections, 10 ng or 50 ng of input RNA, respectively, was used to generate amplified Ribo-SPIA product. All clean-up steps were performed with RNAClean magnetic beads (Agencourt Biosciences). Five micrograms of WT-Ovation product were used to fragment and label using the FL-Ovation Biotin V2 labeling module and labeled product was hybridized to Affymetrix Human U133 Plus 2.0 (Wilm’s and kidney quadsets) or U133Av2 (lung and colon quadsets) GeneChips following manufacturer’s recommendations (Affymetrix, Santa Clara, CA).

growth_protocol: NA.

extract_protocol: Agencourt FormaPure kit.

treatment_protocol: NA.

value: lung tumor

tag: fixation

value: FFPE

tag: block age (at extraction in years)

tag: biological replicate

tag: donor

value: G tumor


title: Amygdala WT

source_name: Amygdala WT


title: Olfactory bulb KO

source_name: Olfactory bulb KO


title: Prefrontal cortex WT

source_name: Prefrontal cortex WT


title: MSC GFP rep1

city: Taipei

first: Shih-Hwa

last: Chiou

address: No. 201, Sec. 2, Shih-Pai Road

country: Taiwan

institute: Vghtpe

description: MSC expression GFP rep1

hyb_protocol: Affymetrix SOP

scan_protocol: Affymetrix SOP

data_processing: Affymetrix Expression Console (RMA)

source_name: MSC GFP

label_protocol: Affymetrix SOP

extract_protocol: standard protocol of TRIzol

treatment_protocol: Expression GFP

tag: cell type

value: mesenchymal stem cells (MSC)


title: Lung FFPE A-3

description: LN_RD129_3 ffpetL


title: Lung FFPE B-1

description: LN_RD133_1 ffpenL

source_name: Formalin-fixed paraffin-embedded tissue, lung

value: lung

value: G NAT


title: Hypothalamus KO

source_name: Hypothalamus KO


title: Lung FFPE A-2

description: LN_RD129_2 ffpetL


title: Lung FFPE B-2

description: LN_RD133_2 ffpenL


title: Lung FF B-3

description: LN_RD125_4 fnL

source_name: Fresh-frozen tissue, lung

extract_protocol: Qiagen RNEasy kit.

value: FF


title: MSC GFP rep2

description: MSC expression GFP rep2


title: MSC PGC-1 alpha rep2

description: MSC expression PGC-1 alpha rep2

source_name: MSC PGC-1 alpha

treatment_protocol: Expression PGC-1 alpha


title: MSC PGC-1 alpha rep1

description: MSC expression PGC-1 alpha rep1


title: Lung FFPE B-4

description: LN_RD133_4 ffpenL


title: Lung FF B-2

description: LN_RD125_3 fnL


title: Lung FFPE B-3

description: LN_RD133_3 ffpenL


title: Lung FFPE A-4

description: LN_RD129_4 ffpetL


title: Lung FF B-1

description: LN_RD125_2 fnL


title: Colon FFPE B-3

source_name: Formalin-fixed paraffin-embedded tissue, colon tumor

extract_protocol: Roche Hign Pure RNA paraffin kit.

value: colon tumor

value: F tumor


title: Lung FF A-3

description: LN_RD123_3 ftL

source_name: Fresh-frozen tissue, lung tumor


title: Colon FF D-3

source_name: Fresh-frozen tissue, colon tumor


title: Lung FF A-1

description: LN_RD123_1 ftL


title: Colon FF D-4


title: Colon FFPE B-1


title: Lung FF A-2

description: LN_RD123_2 ftL


title: Colon FF D-1


title: Colon FFPE A-1

source_name: Formalin-fixed paraffin-embedded tissue, colon

value: colon

value: F NAT


title: Colon FFPE B-2


title: Colon FF D-2


title: Colon FF C-1

description: 911 #9

extract_protocol: Ambion ToTALLY kit.

value: E tumor


title: Colon FFPE A-2


title: Colon FF C-4

description: 914 #12


title: Colon FFPE A-3


title: Colon FF C-2

description: 912 #10


title: Colon FF C-3

description: 913 #11


title: Wilms' FF F-1

description: L754-A-HG-U133_Plus_2-01-1 (S06-965N-Frozen)

source_name: Fresh-frozen tissue, kidney

extract_protocol: Trizol/Qiagen RNEasy kit.

value: kidney

value: B normal


title: Colon FF B-2

description: 908 #6

value: D tumor


title: Colon FF B-4

description: 910 #8


title: Colon FF B-3

description: 909 #7


title: Wilms' FF C-1

description: L751-A-HG-U133_Plus_2-01-1 (S07-1035W-Frozen)

source_name: Fresh-frozen tissue, kidney tumor

value: Wilms' Tumor

value: C tumor


title: Colon FFPE A-4


title: Colon FF B-1

description: 907 #5


title: Colon FF A-3

description: 905 #3

source_name: Fresh-frozen tissue, colon

value: D NAT


title: Colon FF A-4

description: 906 #4


title: Liver Non-Tumor Tissue LCS-096B

description: No additional information.

tag: Tissue

value: Liver Non-Tumor Tissue

tag: Disease state

value: Hepatocellular carcinoma (HCC)


title: Wilms' FF B-1

description: L750-A-HG-U133_Plus_2-01-1 (S99-2051N-Frozen)

value: A normal


title: Wilms' FF B-2

description: L750-A-HG-U133_Plus_2-02-1 (S99-2051N-Frozen)


title: Colon FF A-2

description: 904 #2


title: Wilms' FF E-1

description: L753-A-HG-U133_Plus_2-01-1 (S06-965W-Frozen)

value: B tumor


title: Wilms' FF A-1

description: L749-A-HG-U133_Plus_2-01-1 (S99-2051W-Frozen)

value: A tumor


title: Wilms' FFPE E-1

description: L747-A-HG-U133_Plus_2-01-1 (S06-965W-FFPE)

source_name: Formalin-fixed paraffin-embedded tissue, kidney tumor

value: FFPE


title: Colon FF A-1

description: 903 #1

value: FF


title: Wilms' FFPE F-1

description: L748-A-HG-U133_Plus_2-01-1 (S06-965N-FFPE)

source_name: Formalin-fixed paraffin-embedded tissue, kidney


title: Wilms' FFPE D-1

description: L746-A-HG-U133_Plus_2-01-1 (S07-1035N-FFPE)

value: C normal


title: Wilms' FFPE B-2

description: L744-A-HG-U133_Plus_2-02-1 (S99-2051N-FFPE)


title: Wilms' FFPE A-2

description: L743-A-HG-U133_Plus_2-02-1 (S99-2051W-FFPE)


title: Wilms' FFPE A-1

description: L743-A-HG-U133_Plus_2-01-1 (S99-2051W-FFPE)


title: Wilms' FFPE C-1

description: L745-A-HG-U133_Plus_2-01-1 (S07-1035W-FFPE)


title: Wilms' FF A-2

description: L749-A-HG-U133_Plus_2-02-1 (S99-2051W-Frozen)


title: Wilms' FFPE B-1

description: L744-A-HG-U133_Plus_2-01-1 (S99-2051N-FFPE)


title: Wilms' FF D-1

description: L752-A-HG-U133_Plus_2-01-1 (S07-1035N-Frozen)


title: 1.5mM t60g_t0r

status: Public on Nov 01 2010

city: Wageningen

first: Clint

last: van Melis

address: Bomenweg 2

department: Agro- & Food Science Group

country: Netherlands

institute: Wageningen University and Research centre

description: No extra description

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 14579

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 1.5mM undissociated sorbic acid. Sample was taken after 60 minutes.

value: Bc ATCC 14579

treatment_protocol: Dormant spores were used as t0 samples


title: untreated(Control) - biological replicate 1

status: Public on Oct 31 2010

city: Singapore

first: Peter

last: Nissom

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

description: Biological replicate 1 of 2. Control, untreated, harvested after 4h incubation.

hyb_protocol: Labeled miRNA targets and hybridization buffer were added, and samples were applied to microarrays and hybridized at 42C for 16 hrs, using Telechem hybridization chambers.

scan_protocol: Scanned on an Axon 4000B and analysed using  Axon Genepix 4.0

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

source_name: Bone marrow derived macrophages (BMDM)-Wild type

label_protocol: 500ng of miRNA were labeled using LABELIT® kit (Mirus, USA) according to manufacturer's protocol.

growth_protocol: Non-adherant bone-marrow cells (2x106 cells) were plated into 6-well plates(Nuncleon, Denmark) in 2ml of DMEM complemented with 10% FCS and 20% (v/v) L929-conditioned medium as a source of MCSF and placed in the incubator at 37C, 5% CO2 humified atmosphere. 1ml of medium was replaced from each well and replenished with fresh medium supplemented with 20% L929-conditioned medium every 2 days. At day 7, the cells formed an adherent monolayer which resembled macrophages in their morphology and showed 98% purity by F4/80 staining in FACS. At this stage, cells were washed with complete medium and ready for treatment.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, miRNA extracted using microcon YM-100 fractionation followed by isopropanol precipitation.

treatment_protocol: Medium only (Untreated)

tag: Bone marrow derived macrophages (BMDM)

value: 6 weeks

value: C56/Bl6 mice

source_name: Bone marrow derived macrophages (BMDM)-Dcr1 hypomorphic

value: C57BL/5; Dcr1 hypomorphic mice


title: Lipid A treated (4h) - biological replicate 2

description: Biological replicate 2 of 2. DICER knockout, treated, harvested after 4hr treatment.

source_name: Bone marrow derived macrophages (BMDM)

treatment_protocol: Treated in vitro with 100ng/ml Lipid A(LPA) for 4h


title: 1.5mM t10g_t0r

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 1.5mM undissociated sorbic acid. Sample was taken after 10 minutes.


title: 0mM t120r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0mM undissociated sorbic acid. Sample was taken after 120 minutes.


title: 1.5mM t60r_t0g

description: No extra description


title: 0mM t60r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0mM undissociated sorbic acid. Sample was taken after 60 minutes.


title: 1.5mM t30g_t0r

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 1.5mM undissociated sorbic acid. Sample was taken after 30 minutes.


title: 0.75mM t10g_t0r

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0.75mM undissociated sorbic acid. Sample was taken after 10 minutes.


title: 1.5mM t30r_t0g

description: No extra description


title: Lipid A treated (2h) - biological replicate 2

description: Biological replicate 2 of 2. DICER knockout, treated, harvested after 2hr treatment.

treatment_protocol: Treated in vitro with 100ng/ml Lipid A(LPA) for 2h


title: 1.5mM t10r_t0g

description: No extra description


title: 0mM t120g_t0r

description: No extra description


title: 0.75mM t30r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0.75mM undissociated sorbic acid. Sample was taken after 30 minutes.


title: 0.75mM t120g_t0r

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0.75mM undissociated sorbic acid. Sample was taken after 120 minutes.


title: 1.5mM t120r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 1.5mM undissociated sorbic acid. Sample was taken after 120 minutes.


title: untreated(Control) - biological replicate 2

description: Biological replicate 2 of 2. Control, untreated, harvested after 4h incubation.


title: 0mM t10r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0mM undissociated sorbic acid. Sample was taken after 10 minutes.


title: 0.75mM t30g_t0r

description: No extra description


title: 0mM t30r_t0g

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0mM undissociated sorbic acid. Sample was taken after 30 minutes.


title: 0.75mM t60g_t0r

description: No extra description

treatment_protocol: Dormant spores germinated under in buffered BHI (100mM, pH5.5) containing 0.75mM undissociated sorbic acid. Sample was taken after 60 minutes.


title: 1.5mM t120g_t0r

description: No extra description


title: 0.75mM t10r_t0g

description: No extra description


title: 0.75mM t60r_t0g

description: No extra description


title: 0mM t30g_t0r

description: No extra description


title: 0mM t10g_t0r

description: No extra description


title: Lipid A treated (4h) - biological replicate 1

description: Biological replicate 1 of 2. DICER knockout, treated, harvested after 4hr treatment.


title: Lipid A treated (2h) - biological replicate 1

description: Biological replicate 1 of 2. DICER knockout, treated, harvested after 2hr treatment.


title: wild type DMSO control 1

status: Public on Sep 30 2010

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Mid-log phase cells were grown in the presence of DMSO for 3 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: Saccharomyces cerevisiae strain SEY6210 treated with the corresponding amount of DMSO (used to dissolve OGT2468) in the treatment experiments


title: wild type 1 microMolar OGT2468 3

growth_protocol: Mid-log phase cells were grown in the presence of 1 microMolar OGT2468 for 3 hours

tag: Saccharomyces cerevisiae strain SEY6210 treated with 1 microMolar OGT2468 (treatment experiments)


title: pmt1 pmt4 (2)

growth_protocol: Saccharomyces cerevisiae strain pmt1 pmt4  was grown overnight and dilluted to 0.1 OD, allowed to grow until 0.45 and then was grown for 3 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy Midi kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: Saccharomyces cerevisiae strain pmt1 pmt4 from SEY6210 background


title: wild type 1 microMolar OGT2468 2


title: CP-CymR03-cy5

status: Public on Oct 01 2010

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Biological replicate 3 of 4

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed in Agilent washing buffers.

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridium perfringens

source_name: strain 13 grown with cystine

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), and each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. perfringens strains were grown in minimal medium in the presence of 0.5 mM cystine until late exponential growth phase.

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

tag: strain

tag: genome/variation

value: wild type

source_name: strain 13∆cpe1786 erm grown with cystine

value: ∆cpe1786 erm


title: wild type DMSO control 3


title: wild type 0.1 microMolar OGT2468 2

growth_protocol: Mid-log phase cells were grown in the presence of 0.1 microMolar OGT2468 for 3 hours

tag: Saccharomyces cerevisiae strain SEY6210 treated with 0.1 microMolar OGT2468 (treatment experiments)


title: pmt1 pmt2 (2)

growth_protocol: Saccharomyces cerevisiae strain pmt1 pmt2  was grown overnight and dilluted to 0.1 OD, allowed to grow until 0.45 and then was grown for 3 hours

tag: Saccharomyces cerevisiae strain pmt1 pmt2 from SEY6210 background


title: CP-CymR01-cy3

description: Biological replicate 1 of 4


title: CP-CymR04-cy3

description: Biological replicate 4 of 4


title: CP-CymR04-cy5

description: Biological replicate 4 of 4


title: wild type 0.1 microMolar OGT2468 3


title: wild type DMSO control 2


title: wild type 1 microMolar OGT2468 1


title: pmt1 pmt4 (1)


title: wild type 0.1 microMolar OGT2468 1


title: CP-CymR02-cy3

description: Biological replicate 2 of 4


title: Roots-WildType-Untreated-REP3

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from untreated root cells (wild type)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: Roots, Wild Type, Untreated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the oas-a1.1 mutant (SALK_072213) seeds were grown on Petri dishes on MS medium containing 2.5 g L-1 Phytagel (Sigma-Aldrich) and 1% (w/v) Suc for two weeks and then seedlings were transferred to hydroponic culture. The nutrient solution contained 2 mM Ca(NO3)2, 0.5 mM KH2PO4, 0.75 mM MgSO4, 10 mM KNO3, 1.5 µM CuSO4, 2 µM ZnSO4, 10 µM MnSO4, 50 µM H3BO3, 0.1 µM MoO3, 50 µM KCl, and 50 µM Fe-Na-EDTA, and was replaced once a week. The Cd treatment of hydroponically-grown plants was performed by adding 50 mM of CdCl2 to the above-described nutrient solution after a two-week period of acclimation to the hydroponic conditions. Plants were grown under a photoperiod of 16 h of white light (120 mE m-2 s-1) at 20ºC / 8 h dark at 18ºC.

extract_protocol: Hydroponically-grown plants were cultured in the absence and presence of 50 mM CdCl2 for 18 and 24 h. The untreated-roots, 18 h treated-roots, untreated-shoots and 24h treated-shoots were collected and RNA extracted from each sample. Total RNA was isolated with Trizol reagent (Invitrogen) followed by cleaning with the RNeasy Plant Mini Kit (Qiagen).

tag: genotype

value: Wild Type

tag: tissue

value: Root


title: CP-CymR03-cy3

description: Biological replicate 3 of 4


title: Roots-oas-a1.1-Untreated-REP3

description: Gene expression data from untreated root cells (oas-a1.1 mutant)

source_name: Roots, oas-a1.1, Untreated

value: oas-a1.1 mutant


title: Roots-WildType-18h-REP2

description: Gene expression data from 18h-treated root cells (wild type)

source_name: Roots, Wild Type, 18h


title: Roots-WildType-18h-REP3


title: CP-CymR01-cy5

description: Biological replicate 1 of 4


title: CP-CymR02-cy5

description: Biological replicate 2 of 4


title: pmt1 pmt2 (1)


title: Roots-oas-a1.1-Untreated-REP2


title: wild type control 1

growth_protocol: Saccharomyces cerevisiae strain SEY6210 was grown overnight and dilluted to 0.1 OD, allowed to grow until 0.45 and then was grown for 3 hours

tag: Saccharomyces cerevisiae strain SEY6210


title: wild type control 2


title: HSIL_patient #16

status: Public on Aug 01 2010

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: PREHYBRIDIZATION:  1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS.   2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar.   3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible.   4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water.  5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.     HYBRIDIZATION:   Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (moDC 0h- and 16h-post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature.     Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions:   1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber.   2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber.   3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place.   4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

scan_protocol: Scanning of slides using the Agilent G2565AA DNA microarray scanner:  Resolution: 10 um   Red laser PMT= 100%, Green laser PMT= 100%

data_processing: Pre-processing of the data was performed using BRB-ArrayTools v3.4.0 software. Manually flagged bad spots were eliminated and the local background was subtracted, followed by the averaging of replicate features on the array. Data points were removed when intensities values for both dyes were below 200% of background.  Feature extraction was performed with QuantArray v3.0 software, using the adaptative circle method for measuring the Median signal intensity and Median background intensity.For background calculations were considered the 5-20 percentile of least intense pixels and for signal calculations the 80-95 percentile of most intense pixels. The feature extraction grid was adjusted manually and visually bad spots were flagged using the software flag tool.  A global median normalization of microarray data was applied and log2 intensity ratios (M values) were obtained.

source_name: Commercial normal cervix RNA pool

label_protocol: Total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 µg of total RNA from test and reference (pool of 4 First Choice Human Cervix RNAs, Ambion) samples were incubated with Cy5- and Cy3-ULS, respectively for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS. Dye incorporation was monitored by UV-visible spectroscopy.

extract_protocol: Total RNA was extracted using the miRVanaTM miRNA isolation kit (Ambion). Briefly, tissues were disrupted in lysis solution using a homogeneizer and miRNA homogenate additive added. An acid phenol:chloroform extraction was then performed followed by a filter cartridge purification.RNA quantity and quality was assessed using the Nanodrop and Agilent 2100 bioanalyzer systems, respectively. Samples with a RIN number above 7 were used in the study.

tag: hpv status

value: no specified

tag: cin and tumour stage

value: Normal cervix

source_name: High-grade intraepithelial lesion RNA from patient #16

value: positive

value: CINIII


title: HSIL_patient #14

source_name: High-grade intraepithelial lesion RNA from patient #14


title: HSIL_patient #18

source_name: High-grade intraepithelial lesion RNA from patient #18

value: negative


title: HSIL_patient #15

source_name: High-grade intraepithelial lesion RNA from patient #15


title: LSIL_patient #10

source_name: Low-grade intraepithelial lesion RNA from patient #10

value: CINI


title: LSIL_patient #4

source_name: Low-grade intraepithelial lesion RNA from patient #4


title: HSIL_patient #12

source_name: High-grade intraepithelial lesion RNA from patient #12


title: HSIL_patient #2

source_name: High-grade intraepithelial lesion RNA from patient #2

value: CINII


title: LSIL_patient #21

source_name: Low-grade intraepithelial lesion RNA from patient #21


title: LSIL_patient #20

source_name: Low-grade intraepithelial lesion RNA from patient #20


title: LSIL_patient #17

source_name: Low-grade intraepithelial lesion RNA from patient #17


title: HSIL_patient #7

source_name: High-grade intraepithelial lesion RNA from patient #7