title: 4015C_LAN_0month

value: LAN


title: Genomic DNA from breast tumor 14 (Breast_T14)

status: Public on Jun 01 2011

type: genomic

city: College Park

first: Hector

last: Corrada Bravo

state: MD - Maryland

address: 3114F Biomolecular Sciences Building

department: Center for Bioinformatics and Computational Biology

country: USA

institute: University of Maryland

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized using standard Illumina protocols.

scan_protocol: Arrays were imaged using BeadArray Reader using the standard recommended Illumina scanner settings.

data_processing: We quantile normalized separately the raw intensity data from the Cy5 and Cy3 channels representing methylated and unmethylated DNA (R/Bioconductor, preprocessCore package). The methylation level (beta) was calculated as the ratio of the Cy5 intensity over the sum of the intensities from both channels.

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tumor

label_protocol: Standard Illumina protocol.

extract_protocol: DNA purification was done using the DNeasy Blood and Tissue Kit (Qiagen) following standard instructions.

tag: tissue

value: breast

tag: batch

tag: tissue type

value: tumor

tag: age


title: 4014B_RBN_0month

type: RNA

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Experimental bias (hybridization batch) was removed by fitting linear models & taking residuals. Statistical packages marray and limma in the R environment was used.

molecule: total RNA

source_name: human prostate collected at 0month

label_protocol: One microgram of total target RNA from randomized samples, side by side with 1 µg of universal human reference RNA (Stratagene #740000), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

extract_protocol: Core needle biopsies were collected at baseline and 3 months. Total RNA for micro-array analyses were extracted from areas of normal prostate peripheral-zone tissue containing both stroma and epithelial cells. A #10 scalpel blade was used to scrape tissue from the pathologic area of interest. Tissue was homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

treatment_protocol: Eighty-four men with low risk prostate cancer were stratified based on self-reported dietary consumption of fish and tomatoes and then randomly assigned to a 3-month intervention of lycopene (n = 29) or fish oil (n = 27) supplementation or placebo (n = 28). Gene expression in morphologically normal prostate tissue was studied at baseline and at 3 months via cDNA microarray analysis. Differential gene expression and pathway analyses were performed to identify genes and pathways modulated by dietary intake of fish or tomato or by lycopene or fish oil supplementation. All men were also given a standard multivitamin (1 tablet/day, Dixon/Akyma) and instructed to refrain from any other types of vitamin or mineral supplements during the three months of intervention. Baseline dietary data on fish and tomato consumption was used for stratification with patients randomized from within each stratum to allow for a balanced comparison of the intervention arms.

value: Prostate

tag: biopsy location

value: RBN

tag: ID

tag: intervention

value: B

tag: biopsy time

source_name: Stratagene Reference RNA

tag: reference

value: Stratagene Reference Pooled RNA


title: 4014B_RBN_3month

source_name: human prostate collected at 3month


title: Genomic DNA from breast tumor 13 (Breast_T13)


title: dab1 homozygous sample 1 (BALB/c)

city: Syracuse

first: Tohru

last: Matsuki

state: NY

address: 766 Irving Avenue

department: Depertment of Neuroscience and Physiology

institute: SUNY Upstate Medical University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina Beadstation

data_processing: mRNA expression data were analyzed using the Gene Expression Module 3.2.7 within BeadStudio.

label: biotin

organism: Mus musculus

source_name: mouse hippocampus

label_protocol: Amplified cRNA was hybridized and labeled on Mouse-6 v1.0 Expression BeadChips (Illumina, Inc., San Diego, CA).

extract_protocol: All mice were anesthetized and sacrificed at postnatal day 19. Hippocampi were excised from wild type or dab1 mutant mice of C57BL/6 and BALB/c strains. The hippocampus was homogenized and subjected to total RNA purification using RNeasy mini kit (Qiagen, Valencia, CA). cRNA probes were synthesized and amplified using Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).

tag: strain

value: BALB/c

value: postnatal day 19

value: hippocampus

tag: genotype/variation

value: dab1 mutant


title: patient 26

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

hyb_protocol: Followed manufacturer's instructions

scan_protocol: Followed manufacturer's instructions

data_processing: Probe cell intensity data from the Affymetrix GeneChips were analyzed using Affymetrix Expression Console software. The application uses the RMA-Sketch workflow analysis as the default to create CHP files. The CHP log2 expression files were then merged in Expression Console with the annotation file and the annotated log2 results were exported as a text file. The previous identification of approximately 3500 unique mRNAs in the ejaculate of fertile males prompted us to limit our mRNA content analysis to ensure that the multiple comparisons of many null genes would not dilute out any potentially important signals. Therefore, we selected a total of 276 genes, including 177 imprinted genes as well as 99 candidate autosomal genes with biallelic expression where an a priori hypothesis for association with subfertility or epigenetic regulation exists. The LIMMA procedure (available through the R package limma) used motility values to fit a simple linear regression model to test, univariately, for each gene, whether changes in motility are associated with mRNA content extent. Resulting p-values were adjusted for multiple comparisons via the R package qvalue, which produced q-values representing false-discovery rate in the same way that p-values represent family-wise error rate. The final result of this analysis was a list of differentially mRNA candidates sorted by q-value, and an estimate of the strength and direction of the association represented by the slope.

source_name: sperm

label_protocol: Followed manufacturer's instructions

extract_protocol:
sperm isolation protcol: Preparing Semen Samples for Separation  1. Determine the number of tubes needed for isolations based on the volume used for DNA/RNA. You will use ¼ of the total semen volume for DNA isolation and the remaining ¾ for RNA isolations.  a. Up to 1 ml of semen can be used per conical tube  b. Example: 4 mls semen  i. 1 ml is for DNA → therefore 1 conical tube is required for  DNA analysis prep  ii. 3 mls for RNA → therefore 3 conical tubes are required for RNA analysis prep  2. Label tubes with sample number and either “RNA” or “DNA”    Sperm Separation: Percolling:  1. When preparing Percoll and 2x PBS, do under sterile conditions to keep the Percoll sterile.  a. Add up to 1 ml 2x PBS and 1 ml Percoll to a 15 ml conical tube.  2. Gently pipette up to 1 ml semen sample on top.  3. Spin samples at 1200 rpm for 40 min → will see visible pellet at the bottom  4. Remove supernatant until the interface layer right before the pellet in bleach.    Sperm Separation: Washing:  1. Combine sperm pellets and remaining supernatant from DNA and RNA tubes, respectively, to reduce the number of tubes you are working with.  2. Add 1x PBS to a total volume of 10 ml.  3. Spin samples at 2000 rpm for 7 minutes and remove as much supernatant as you can without disrupting sperm.  4. Repeat washes 2x.  5. Resuspend pellet in 1 ml 1x PBS.  6. Add suspensions to properly labeled tubes for DNA and RNA.  7. Spin DNA tube at max speed to pellet the cells.  8. Remove supernatant, flash freeze pellets in liquid nitrogen, and store in -80 freezer.  9. Continue with RNA isolation protocol.
Sperm mRNA was extracted from 18 of the 21 men using a modified Stat 60 (IsoTex Diagnostics, Inc., Friendswood TX, USA) protocol in addition to components of Qiagen’s RNeasy kit (Qiagen Sciences, Germantown, MD, USA).

tag: count

tag: motility

tag: morphology


title: 4013A_LAN_0month

value: A


title: wild type sample 2 (BALB/c)

value: wild-type


title: wild type sample 1 (BALB/c)


title: dab1 homozygous sample 2 (BALB/c)


title: patient 23


title: 4013A_LAN_3month


title: Genomic DNA from breast tumor 12 (Breast_T12)


title: patient 22


title: dab1 homozygous sample 3 (C57BL/6)


title: 4012B_RAN_3month

value: RAN


title: 4012B_RBNC_0month

value: RBNC


title: wild type sample 3 (BALB/c)


title: Genomic DNA from breast tumor 10 (Breast_T10)


title: Genomic DNA from breast tumor 1 (Breast_T1)


title: Pulmonary Fibrosis patient 116

city: Toronto

first: Marco

last: Mura

state: Ontario

address: 585 University Avenue

department: Medicine/Surgery

country: Canada

institute: Toronto Lung Transplant Program

description: Gene expression data from PF patient, validation set

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarray was performed with Genechip Human Gene 1.0 ST on an Affymetrix Genechip Scanner 3000 and Genechip Fluidics Station 450

data_processing: Affymetrix CEL files were imported into Partek software (Partek) and probe-level data were pre-processed. This included robust multi-array average (Rma) background correction and data normalization, which was performed across all arrays using quantile normalization. Background-adjusted, normalized values were then compiled, or summarized, using the median polish technique, to generate a single measure of expression. As an exploratory data analysis, Principal Component Analysis (PCA) mapping and F Ratio analysis (signal-to-noise ratio) were also performed.

source_name: Lung sample from recipient organ

label_protocol: cDNA was synthesized from 4 ug of RNA with high capacity cDNA Reverse Transcription kits (Applied Byosystems). cDNA-synthesis was carried out on a PTC-100 Programmable Thermal controller (MJ Research). RNA was qualified by RNA nano chips on an Agilent 2100 Bilanalyzer (Agilent Technologies).

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

treatment_protocol: Fresh frozen lung tissue specimens were obtained from the recipient organs of Pulmonary Fibrosis patients undergoing lung transplantation. Specimens were obtained as soon as the first recipient lung was taken out, snap frozen in liquid nitrogen, and stored at -80ºC

value: Lung

tag: disease state

value: validation set for PH


title: dab1 homozygous sample 2 (C57BL/6)


title: Pulmonary Fibrosis patient 115


title: Genomic DNA from breast tumor 11 (Breast_T11)


title: Genomic DNA from breast normal tissue 9 (Breast_N9)

source_name: breast normal tissue

value: normal


title: 4010C_LMN_0month

value: LMN

value: C


title: 4010C_LMN_3month

value: Prostate


title: dab1 homozygous sample 1 (C57BL/6)


title: 4009A_LBN_3month

value: LBN


title: Pulmonary Fibrosis patient 113


title: Pulmonary Fibrosis patient 112


title: Pulmonary Fibrosis patient 111


title: Pulmonary Fibrosis patient 114


title: 4009A_LBNC_0month

value: LBNC


title: Pulmonary Fibrosis patient 110


title: 4008C_LBN_3month

value: Stratagene Reference Pooled RNA


title: wild type sample 3 (C57BL/6)


title: Genomic DNA from breast normal tissue 8 (Breast_N8)

value: breast


title: Pulmonary Fibrosis patient 109


title: Genomic DNA from breast normal tissue 7 (Breast_N7)


title: wild type sample 1 (C57BL/6)

value: postnatal day 19


title: Genomic DNA from breast normal tissue 6 (Breast_N6)


title: 4008C_LBN_0month


title: Genomic DNA from breast tumor 4 (Breast_T4)

value: tumor


title: 4007C_RMN_0month

value: RMN


title: 4006C_LMN_3month


title: Pulmonary Fibrosis patient 105


title: w4_4

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
NHNP_w4.5
4256290020_G

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio version 3.1.3, quantile normalization

label: Biotin

source_name: NHNP, 4 week

label_protocol: Biotin

growth_protocol: Neurobasal A with 10% BIT, 1% Glutamax, 2.5 micromolar heparin, and 2% penicillin and streptomycin; 10ng/ml EGF and bFGF

extract_protocol: Qiagen Rneasy kit

treatment_protocol: 10ng/ml retinoic acid, NT-3, and BDNF; 10mM KCl

tag: cell type

value: Primary normal human neuronal progenitor cells

tag: time

value: 4 week


title: w2_4

description:
NHNP_w2.5
4256290020_F

source_name: NHNP, 2 week

value: 2 week


title: 4007C_RMN_3month

tag: tissue


title: Genomic DNA from breast tumor 3 (Breast_T3)

tag: batch


title: Pulmonary Fibrosis patient 108


title: Pulmonary Fibrosis patient 106


title: w8_4

description:
NHNP_w8.4
4256290020_H

source_name: NHNP, 8 week

value: 8 week


title: Genomic DNA from breast tumor 6 (Breast_T6)

tag: tissue type


title: w4_3

description:
NHNP_w4.3
4256290020_C


title: w0_4

description:
NHNP_w0.4
4256290020_E

source_name: NHNP, 0 week

value: 0 week


title: Genomic DNA from breast normal tissue 26 (Breast_N26)


title: Genomic DNA from breast normal tissue 25 (Breast_N25)

tag: age


title: Genomic DNA from breast normal tissue 24 (Breast_N24)


title: Pulmonary Fibrosis patient 107

value: Lung

value: validation set for PH


title: Pulmonary Fibrosis patient 104


title: 4006C_RA-AH_0month

tag: biopsy location

value: RA-AH


title: Pulmonary Fibrosis patient 103


title: Pulmonary Fibrosis patient 102


title: 4005A_LAN_3month

value: LAN

tag: ID

value: A


title: w2_3

description:
NHNP_w2.4
4256290020_B


title: w8_3

description:
NHNP_w8.3
4256290020_D


title: w0_3

description:
NHNP_w0.3
4256290020_A


title: w8_2

description:
NHNP_w8.2
4256290015_H


title: 4005A_LAN_0month

value: Prostate

tag: intervention


title: 4004A_LBN_3month

value: LBN

tag: biopsy time


title: Genomic DNA from breast normal tissue 23 (Breast_N23)

value: normal


title: Genomic DNA from breast normal tissue 20 (Breast_N20)

value: breast


title: Genomic DNA from breast normal tissue 22 (Breast_N22)


title: Genomic DNA from breast normal tissue 21 (Breast_N21)


title: Pulmonary Fibrosis patient 101


title: Genomic DNA from breast normal tissue 2 (Breast_N2)


title: 4003B_LMN_3month

value: LMN

value: B

tag: reference

value: Stratagene Reference Pooled RNA


title: w4_2

description:
NHNP_w4.2
4256290015_G

value: Primary normal human neuronal progenitor cells


title: Pulmonary Fibrosis patient 100


title: Genomic DNA from breast normal tissue 19 (Breast_N19)


title: w0_2

description:
NHNP_w0.2
4256290015_E


title: Pulmonary Fibrosis patient 99


title: 4003B_LMN_0month


title: w2_2

description:
NHNP_w2.3
4256290015_F


title: w8_1

description:
NHNP_w8.1
4256290015_D


title: Genomic DNA from breast normal tissue 18 (Breast_N18)


title: Pulmonary Fibrosis patient 98


title: 4004A_RBN_0month

value: RBN


title: 4001B_LBN_3month


title: Pulmonary Fibrosis patient 96


title: Genomic DNA from breast normal tissue 17 (Breast_N17)


title: w2_1

description:
NHNP_w2.2
4256290015_B

value: 2 week


title: 4001B_RBN_0month


title: Pulmonary Fibrosis patient 95


title: Genomic DNA from breast normal tissue 16 (Breast_N16)


title: Pulmonary Fibrosis patient 97


title: w0_1

description:
NHNP_w0.1
4256290015_A


title: w4_1

description:
NHNP_w4.1
4256290015_C

value: 4 week


title: 4002B_RBN_3month


title: Genomic DNA from breast normal tissue 15 (Breast_N15)


title: Genomic DNA from breast normal tissue 14 (Breast_N14)


title: 4002B_RMN_0month

value: RMN


title: Pulmonary Fibrosis patient 94

value: Lung


title: Genomic DNA from breast normal tissue 13 (Breast_N13)


title: Pulmonary Fibrosis patient 93

value: validation set for PH


title: Genomic DNA from breast normal tissue 12 (Breast_N12)


title: 3036A_LBN_0month


title: Pulmonary Fibrosis patient 92


title: 3035A_RANatr_3month

value: RANatr


title: 3035A_RAN_0month

value: RAN


title: A. fumigatus_response_to_16HBE_cells_rep4

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

institute: UBC - iCAPTURE Centre

description: Samples of conidiospores incubated with 16HBE cells contained a mixture of human and A. fumigatus RNA.

hyb_protocol: Samples representing conidiospores incubated alone and conidiospores incubated with 16HBE cells were paired using a dye-swap design, and 2μg of RNA from each sample was added to each microarray slide and hybridized overnight at 50°C in 2X formamide buffer (Genisphere, Hatfield, PA).

scan_protocol: Slides were washed and scanned on an Axon GenePix 4200AL microarray scanner (Molecular Devices, Sunnyvale, CA), and images were analyzed using ImaGene 8.0 software (BioDiscovery, El Segundo, CA).

data_processing: The intensity for each probe in each channel was obtained by first subtracting the “background median” from the “signal median” for each spot, then averaging these values across the two replicate spots per probe. “Infected” and “Control” intensities were then normalized using Lowess transformation. Probes with normalized intensity values in the “Infected” channel greater than 300 in at least four of the eight arrays were retained for further analysis. Gene expression ratios were obtained by dividing the “Infected” intensity by the “Control” intensity in each array, then averaging dye-swapped arrays for each replicate.

organism: Aspergillus fumigatus

source_name: A. fumigatus conidiospores incubated with 16HBE cells for 6 hours

label_protocol: RNA from each sample was amplified via in vitro transcription with aminoallyl-UTP, amplified RNA was coupled to both Cy3 and Cy5, and fragmented prior to hybridization.

growth_protocol: Aspergillus fumigatus was grown on MYPD agar plates at 37°C for 3 days to obtain mature conidiospores.

extract_protocol: Cells were lysed in 450μl buffer RLT (Qiagen, Hilden, Germany), and RNA was extracted using the RNeasy Mini Kit with QIAshredder (Qiagen), following the manufacturer’s recommendations. To ensure that conidiospore walls would be adequately broken down, samples were immersed in liquid nitrogen for 5 minutes and thoroughly ground using plastic mini-pestles (DiaMed, Mississauga, ON) as they thawed  RNA yield from each sample was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: A. fumigatus conidiospores were incubated with 16HBE cell monolayers (Infected), or alone (Control), for 6 hours at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate.

tag: developmental stage

value: mature conidiospores

tag: protocol

value: infected (incubated with 16HBE cells)

source_name: A. fumigatus conidiospores incubated alone for 6 hours

value: control


title: Pulmonary Fibrosis patient 91


title: wild type sample 2 (C57BL/6)

tag: strain

value: postnatal day 19

value: hippocampus

tag: genotype/variation

value: wild-type


title: Genomic DNA from breast normal tissue 11 (Breast_N11)

value: breast

value: normal


title: Genomic DNA from breast normal tissue 10 (Breast_N10)


title: Genomic DNA from breast normal tissue 5 (Breast_N5)


title: 3033C_RMN_3month

value: Prostate

value: C

value: Stratagene Reference Pooled RNA


title: Genomic DNA from breast normal tissue 1 (Breast_N1)


title: Genomic DNA from thyroid normal tissue 4 (ThyPTC_N4)

source_name: thyroid normal tissue

value: ThyPTC


title: Genomic DNA from thyroid normal tissue 5 (ThyFA_N5)

value: ThyFA


title: Genomic DNA from breast normal tissue 5 (DCIS_N5)

value: DCIS


title: 3030B_LAN_3month

value: LAN

value: B


title: 3036A_LBNP_3month

value: LBNP

value: A


title: Pulmonary Fibrosis patient 90

value: Lung

value: validation set for PH


title: 3031B_LMN_3month

value: LMN


title: 3031B_RMN_0month

value: RMN


title: TGFb-stimulated slide 1, replicate 2

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description: TGFb-stimulated biological replicate 2 of 2, slide 1

hyb_protocol: Labeled amplified DNA (Cy5 and Cy3) was combined and hybridized to Agilent 44K two-array whole genome promoter sets for 40 h at 65°C

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing:
Agilent Feature Extraction Software (v 9.5.1.1) was used
Data was thresholded to 1, Cy5/Cy3 ratio computed, log transformed followed by baseline transformation in Genespring GX11

source_name: TGFb1-stimulated A549 cell line, SMAD3 IP

label_protocol: Purified PCR products of SMAD3 IP and Mock IP were labeled with cyanine-5 (Cy5) and cyanine-3 (Cy3) florescent dyes (PerkinElmer Life and Analytical Sciences, Boston, MA), respectively, using the BioPrime® Array CGH Genomic Labeling kit (Invitrogen, Carlsbad, CA)

growth_protocol: Lung alveolar epithelial carcinoma cell line A549 (CCL-185, ATCC, Manassas, VA) was grown in F12-K culture medium supplemented with 10% fetal bovine serum and subcultured at 80-90% confluency

extract_protocol: Cells were cross-linked with formaldehyde, quenched with glycine. Following washes, the samples were sonicated, lysates incubated with 25 µg of anti-Smad3 antibody or control IgG (both from Millipore, Billerica, MA) for 1 h at 4°C. Immunoprecipitation (IP) was carried out using Protein A/G PLUS-Agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA) at 4°C overnight. The immune complexes were washed and eluted at 65°C for 15 min. Immunoprecipitated DNA-protein complexes were then reverse cross-linked at 65°C overnight and purified by phenol-chloroform extraction and ethanol precipitation. Purified nucleic acid of ChIP reactions was blunt-ended using T4 DNA polymerase, ligated to linkers and amplified

treatment_protocol: 1 x 107 A549 cells were treated with TGFβ1 (2 ng/ml) for up to 2 h. Control cells were untreated

value: lung alveolar epithelial cell line

tag: cell line

source_name: TGFb1-stimulated A549 cell line, anti-FLAG IP


title: 3032C_RMN_0month


title: A. fumigatus_response_to_16HBE_cells_rep3

value: mature conidiospores

value: infected (incubated with 16HBE cells)

value: control


title: 3033C_RBNC_0month

value: Prostate

value: RBNC

value: C


title: Pulmonary Fibrosis patient 87

tag: disease state


title: Pulmonary Fibrosis patient 89


title: Pulmonary Fibrosis patient 86


title: cell line patient 8 (LN metastasis)

city: Vienna

first: Norbert

last: Schweifer

address: Dr. Boehringer Gasse 5-11

country: Austria

institute: Boehringer Ingelheim Austria

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HuGeneFL GeneChip® arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned according to manufacture’s instructions

data_processing: GeneChip® expression data were normalized with the robust multi-array analysis (RMA) described by Irizarry et al and implemented within Bioconductor (version 1.8.1). The RMA-algorithm of the “affy” package (version 1.3.27) was used with default parameter settings such as convolution background correction, quantile normalization and multi-chip summarization. Genes with a coefficient of variation (CV) larger than a cut-off of 0.1 were selected for hierarchical clustering with the Spotfire Decision Site 7.3 (version 11, Spotfire®), thereby using complete linkage as clustering method and the cosine correlation algorithm for similarity measure.

source_name: patient 8

label_protocol: Labeled cRNA was synthesized according to manufacture’s instructions (GeneChip® Expression Analysis Technical Manual, Affymetrix, 1999; Santa Clara, CA) or with minor modifications for LCM samples by using two rounds of T7 amplification17 in one quarter of the reaction mixture during synthesis of sscDNA. The first in vitro transcription (IVT)-reaction was performed with unlabeled rNTPs (18.75 mM each, Promega, Mannheim, Germany). Subsequently, 1 µg random hexamers (Promega) was used for re-conversion into cDNA at 70° C for 10 min.

extract_protocol: Tissue sections were stained either with Harris hematoxylin and eosin or with Mayers hematoxylin (all from Sigma, Vienna, Austria). For histological classification morphological criteria such as solid or tubular were examined independently of the grading (well, moderately, poorly). Laser capture micro-dissection (LCM) was performed using either the Robot-Micro Beam from PALM (Bernried, Germany) or the Pix Cell II laser-system (Arcturus, Molecular Devices, Mountain View, CA, USA). Cells of selected areas were lysed in 50 µl TRIzol (Invitrogen, Lofer, Austria) and isolation of total RNA was performed as recommended by the manufacturer.

treatment_protocol: no pre-treatment of patient before surgery

tag: grading and morphology

value: colon cancer cell line

tag: cell type


title: A. fumigatus_response_to_16HBE_cells_rep2


title: A. fumigatus_response_to_16HBE_cells_rep1


title: Pulmonary Fibrosis patient 84

description: Gene expression data from PF patient without PH

tag: tissue

value: no PH


title: cell line patient 8 (primary tumor)


title: Pulmonary Fibrosis patient 88


title: Genomic DNA from thyroid tumor 4 (ThyHC_T4)

source_name: thyroid tumor

value: ThyHC

tag: batch

value: tumor


title: Genomic DNA from thyroid tumor 4 (ThyPTC_T4)

value: ThyPTC

tag: tissue type


title: Genomic DNA from breast normal tissue 4 (DCIS_N4)

value: DCIS

value: normal

tag: age


title: Pulmonary Fibrosis patient 83

value: Lung


title: 3032C_RAN_3month

tag: biopsy location

value: RAN

source_name: Stratagene Reference RNA

value: Stratagene Reference Pooled RNA


title: Pulmonary Fibrosis patient 82


title: cell line patient 2 (primary tumor)

source_name: patient 2


title: liver metastasis patient 10

source_name: patient 10

value: moderatly diff. (tubular)

value: liver metastasis


title: unstimulated slide 1, replicate1

description: Control biological replicate 1 of 2, slide 1

source_name: control A549 cell line, SMAD3 IP

value: lung alveolar epithelial cell line

source_name: control A549 cell line, anti-FLAG IP


title: cell line patient 13 (primary tumor)

source_name: patient 13


title: Pulmonary Fibrosis patient 81

source_name: Lung sample from recipient organ


title: 3029B_RMNC_0month

source_name: human prostate collected at 0month

value: RMNC

tag: ID

value: B


title: TGFb-stimulated slide 1, replicate 1

description: TGFb-stimulated biological replicate 1 of 2, slide 1


title: 3029B_LANC_3month

source_name: human prostate collected at 3month

value: Prostate

value: LANC

tag: intervention


title: unstimulated slide 1, replicate2

description: Control biological replicate 2 of 2, slide 1


title: Pulmonary Fibrosis patient 79


title: liver metastasis patient 9

source_name: patient 9

value: poorly diff. (tubular)


title: Pulmonary Fibrosis patient 85

value: validation set for PH


title: 3030B_LAN_0month

value: LAN

tag: biopsy time


title: lymph node metastasis patient 8

value: lymph node metastasis


title: Genomic DNA from colon adenoma 4 (Adenoma_T4)

source_name: colon adenoma

value: adenoma


title: Genomic DNA from thyroid tumor 3 (ThyPTC_T3)

value: ThyPTC

value: tumor


title: 3028C_RAN_0month

value: C

tag: reference


title: 3028C_LMN_3month

value: LMN


title: lymph node metastasis patient 6-1

source_name: patient 6


title: lymph node metastasis patient 7

source_name: patient 7


title: Genomic DNA from thyroid tumor 3 (ThyHC_T3)

value: ThyHC


title: Pulmonary Fibrosis patient 77

value: Lung

value: no PH


title: Pulmonary Fibrosis patient 78


title: 3026A_RBNC_3month

value: RBNC

value: A

value: Stratagene Reference Pooled RNA


title: Genomic DNA from colon adenoma 3 (Adenoma_T3)


title: Pulmonary Fibrosis patient 80


title: Pulmonary Fibrosis patient 76


title: lymph node metastasis patient 6-2

value: moderatly diff. (tubular)


title: Genomic DNA from thyroid normal tissue 2 (ThyFVPTC_N2)

source_name: thyroid normal tissue

value: ThyFVPTC

value: normal


title: Genomic DNA from thyroid normal tissue 3 (ThyFVPTC_N3)


title: 3026A_LMN_0month

value: Prostate


title: 3024C_RAN_3month

value: RAN


title: 3025C_LMN_0month


title: lymph node metastasis patient 4

source_name: patient 4

value: poorly diff. (solid)

value: lymph node metastasis


title: 3025C_LMN_3month


title: Pulmonary Fibrosis patient 75


title: Genomic DNA from thyroid tumor 2 (ThyHC_T2)


title: lymph node metastasis patient 1-1

source_name: patient 1


title: Pulmonary Fibrosis patient 74


title: 3024C_RAN_0month


title: Pulmonary Fibrosis patient 73


title: lymph node metastasis patient 3

source_name: patient 3


title: lymph node metastasis patient 1-2


title: Pulmonary Fibrosis patient 72


title: lymph node metastasis patient 5

source_name: patient 5

value: poorly diff. (tubular)


title: 3023B_RBN_3month

value: RBN

value: B

source_name: Stratagene Reference RNA


title: Genomic DNA from thyroid tumor 1 (ThyHC_T1)

source_name: thyroid tumor

value: tumor


title: Genomic DNA from thyroid normal tissue 1 (ThyFVPTC_N1)


title: Genomic DNA from thyroid tumor 6 (ThyHC_T6)

value: ThyHC


title: primary tumor patient 10

source_name: patient 10

value: primary tumor


title: Pulmonary Fibrosis patient 70

value: Lung

value: no PH


title: Pulmonary Fibrosis patient 71


title: primary tumor patient 11

source_name: patient 11


title: primary tumor patient 12

source_name: patient 12


title: 3021B_LAN_3month

value: LAN


title: Genomic DNA from thyroid tumor 1 (ThyPTC_T1)

value: ThyPTC


title: 3023B_RBN_0month

value: Stratagene Reference Pooled RNA


title: Genomic DNA from breast tumor 30 (Breast_T30)

source_name: breast tumor

value: breast


title: Genomic DNA from breast normal tissue 29 (Breast_N29)

source_name: breast normal tissue

value: normal


title: Genomic DNA from breast normal tissue 28 (Breast_N28)


title: primary tumor patient 9


title: Pulmonary Fibrosis patient 68

source_name: Lung sample from recipient organ


title: Pulmonary Fibrosis patient 69


title: primary tumor patient 8

source_name: patient 8


title: 3020C_RBN_3month

source_name: human prostate collected at 3month

value: Prostate

value: C


title: 3020C_RBN_0month

source_name: human prostate collected at 0month


title: Genomic DNA from colon adenoma 12 (Adenoma_T12)

source_name: colon adenoma

value: adenoma


title: Pulmonary Fibrosis patient 67


title: Genomic DNA from colon adenoma 11 (Adenoma_T11)


title: Pulmonary Fibrosis patient 65


title: 3021B_RAN_0month

value: RAN


title: Pulmonary Fibrosis patient 66


title: 3018A_LantN_3month

value: LantN

value: A


title: Genomic DNA from colon adenoma 13 (Adenoma_T13)


title: Genomic DNA from colon adenoma 10 (Adenoma_T10)


title: primary tumor patient 7

source_name: patient 7

value: moderatly diff. (tubular)


title: Pulmonary Fibrosis patient 64


title: Genomic DNA from thyroid normal tissue 10 (ThyPTC_N10)

source_name: thyroid normal tissue


title: primary tumor patient 6

source_name: patient 6

value: well differenciated


title: 3018A_Rant_0month

value: Rant


title: Genomic DNA from thyroid normal tissue 9 (ThyPTC_N9)


title: Genomic DNA from thyroid normal tissue 8 (ThyPTC_N8)


title: 3017C_LMN_0month

value: LMN


title: Pulmonary Fibrosis patient 62

description: Gene expression data from PF patient with intermediate PH

value: Lung

value: intermediate PH


title: Pulmonary Fibrosis patient 63

value: no PH


title: Genomic DNA from thyroid tumor 9 (ThyPTC_T9)

value: ThyPTC

value: tumor


title: 3016A_LMN_3month

value: Stratagene Reference Pooled RNA


title: Genomic DNA from thyroid tumor 8 (ThyPTC_T8)


title: 3017C_LMN_3month


title: normal colon patient 8

source_name: patient 9

value: normal colon epithelium


title: 3016A_RMN_0month

value: Prostate

value: RMN


title: Genomic DNA from thyroid tumor 8 (ThyHC_T8)

value: ThyHC


title: Genomic DNA from thyroid tumor 7 (ThyPTC_T7)


title: Genomic DNA from thyroid tumor 7 (ThyHC_T7)


title: 3014B_RAN_3month

value: RAN

value: B


title: Genomic DNA from thyroid normal tissue 7 (ThyFVPTC_N7)

value: ThyFVPTC

value: normal


title: Genomic DNA from colon adenoma 6 (Adenoma_T6)

value: adenoma


title: primary tumor patient 1-2

source_name: patient 1

value: well differenciated

value: primary tumor


title: Pulmonary Fibrosis patient 61

value: Lung


title: primary tumor patient 4

source_name: patient 4

value: poorly diff. (solid)


title: 3011C_LBN_3month

value: LBN

value: C

source_name: Stratagene Reference RNA


title: primary tumor patient 2

source_name: patient 2


title: Pulmonary Fibrosis patient 59

value: intermediate PH


title: primary tumor patient 3

source_name: patient 3

value: moderatly diff. (tubular)


title: 3011C_LBN_0month

value: Stratagene Reference Pooled RNA


title: normal colon patient 2

value: normal colon epithelium


title: 3013A_LMN_0month

value: Prostate

value: LMN

value: A


title: Pulmonary Fibrosis patient 54


title: 3013A_LMN_3month


title: normal colon patient 9


title: 3015B_LMN_3month

value: B


title: Pulmonary Fibrosis patient 55


title: 3015B_RAN_0month

value: RAN


title: normal colon patient 4


title: normal colon patient 5

source_name: patient 5


title: Pulmonary Fibrosis patient 60


title: 3014B_RBN_0month

value: RBN


title: Genomic DNA from thyroid tumor 5 (ThyFC_T5)

source_name: thyroid tumor

value: ThyFC

value: tumor


title: Genomic DNA from colon adenoma 5 (Adenoma_T5)

value: adenoma


title: Genomic DNA from thyroid normal tissue 5 (ThyFVPTC_N5)

value: ThyFVPTC

value: normal


title: Genomic DNA from thyroid tumor 5 (ThyFVPTC_T5)


title: etiolated cop1BBX22-GFPox, biological rep3

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description:
4-days-old, dark grown.
cop1BBX22-GFPox_D_3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Arabidopsis thaliana

source_name: cop1-4BBX22-GFPox, etiolated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seeds were surface sterilized and plated on 1/2 MS plates supplemented with 1% sucrose and grown 4 days at 21oC under the dark.

extract_protocol: Pine Tree Method as described in Chang et al, Plant J 54, 205 (2008) (PMID 18182030).

tag: genotype

value: whole seedlings

value: 4 days

tag: growth condition

value: dark

tag: ecotype

value: Columbia (Col-0)


title: 3010B_LMN_3month

value: Stratagene Reference Pooled RNA


title: Pulmonary Fibrosis patient 58

source_name: Lung sample from recipient organ

value: Lung

value: intermediate PH


title: primary tumor patient 1-1

value: well differenciated

value: primary tumor


title: Genomic DNA from thyroid normal tissue 4 (ThyFVPTC_N4)


title: Pulmonary Fibrosis patient 52


title: Genomic DNA from thyroid tumor 10 (ThyFC_T10)


title: Genomic DNA from thyroid tumor 4 (ThyFVPTC_T4)


title: 3009A_RAN_0month

value: Prostate

value: A


title: Pulmonary Fibrosis patient 56


title: etiolated cop1BBX22-GFPox, biological rep2

description:
4-days-old, dark grown.
cop1BBX22-GFPox_D_2


title: 3007A_Lant_3month

value: Lant


title: Genomic DNA from thyroid tumor 3 (ThyFVPTC_T3)


title: Pulmonary Fibrosis patient 57


title: Pulmonary Fibrosis patient 53


title: 3008A_RMN_0month

value: RMN


title: Pulmonary Fibrosis patient 51


title: etiolated cop1, biological rep2

description:
4-days-old, dark grown.
cop1_D_2

source_name: cop1-4, etiolated


title: 3008A_LAN_3month

source_name: human prostate collected at 3month

value: LAN


title: Pulmonary Fibrosis patient 46


title: 3007A_LMN_0month

source_name: human prostate collected at 0month

value: LMN


title: Pulmonary Fibrosis patient 47


title: etiolated cop1, biological rep3

description:
4-days-old, dark grown.
cop1_D_3


title: Pulmonary Fibrosis patient 48


title: Pulmonary Fibrosis patient 49


title: Pulmonary Fibrosis patient 45


title: Genomic DNA from thyroid tumor 2 (ThyFVPTC_T2)

value: ThyFVPTC

value: tumor


title: Genomic DNA from thyroid tumor 3 (ThyFC_T3)

value: ThyFC


title: 3005C_LMN_3month

value: C


title: etiolated cop1BBX22-GFPox, biological rep1

description:
4-days-old, dark grown.
cop1BBX22-GFPox_D_1

value: whole seedlings

value: 4 days

value: dark


title: Pulmonary Fibrosis patient 50

value: Lung


title: Genomic DNA from thyroid tumor 2 (ThyFC_T2)


title: CRP mutant strain AAM167, rep 3

city: SA

first: David

last: Kolodrubetz

address: 7703 Floyd Curl Dr

department: Microbiology and Immunology

institute: UTHSCSA

description: This sample is of A. actinomycetemcomitans strain  AAM167, an isogenic deletion mutant  in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette.  It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Roche NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Robust Multi-Array Analysis (RMA; Irizarry et al. Biostatistics 4:249) in the NimbleScan Software Package (v2.5, Roche NimbleGen, Madison, WI) was first used to do background corrections of raw expression data (.pair files) from individual sample sets.  Then RMA was used to do quantile normalization (Bolstad et al. Bioinformatics 19:185) across the six sample sets being compared and to do median polishing  to reduce the contribution of outlier probes to the single expression value derived from multiple probes for a given gene in a sample set.

organism: Aggregatibacter actinomycetemcomitans

source_name: CRP mutant strain AAM167

label_protocol: Labeling was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: A. actinomycetemcomitans strains JP2 and AAM167 were grown anaerobically (5% CO2, 10% H2, 85% N2) to mid-log phase (OD600nm = 0.35 ) in a Coy chamber (Coy Laboratory Products, Ann Arbor, MI) at 37°C with shaking in TSBYE (3% tryptic soy broth plus 0.6% yeast extract).

extract_protocol: RNA was isolated from mid-log phase A. actinomycetemcomitans cells using RNAprotect® Bacterial Reagent (Qiagen, Inc., Valencia, CA) and the RNeasy® Mini Kit (Qiagen).  The manufacturer’s instructions were followed with the following notes:  2.5 ml of cells were lysed with 10 mg/ml lysozyme (Sigma, St. Louis, MO) for 15 min.  The RNase-free DNase Set (Qiagen) was used for DNase treatment.  RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at Roche-Nimblegen.

tag: strain

tag: phenotype

value: Expresses Low Levels of Leukotoxin


title: etiolated cop1, biological rep1

description:
4-days-old, dark grown.
cop1_D_1

value: Columbia (Col-0)


title: 3006C_RAN_0month

value: RAN

value: Stratagene Reference Pooled RNA


title: 3006C_RAN_3month

value: Prostate


title: 3009A_LBN_3month

value: LBN

value: A


title: 3004B_LBN_0month

value: B


title: Pulmonary Fibrosis patient 40

tag: disease state

value: intermediate PH


title: 3005C_RBN_0month

value: RBN


title: Pulmonary Fibrosis patient 43


title: 3010B_LMN_0month

value: LMN


title: Pulmonary Fibrosis patient 44


title: etiolated Col-0, biological rep2

description:
4-days-old, dark grown.
Col-0_D_2

source_name: Col-0, etiolated

value: wild type


title: 3004B_LAN_3month

value: LAN


title: etiolated Col-0, biological rep3

description:
4-days-old, dark grown.
Col-0_D_3

value: whole seedlings


title: CRP mutant strain AAM167, rep 2

description: This sample is of A. actinomycetemcomitans strain  AAM167, an isogenic deletion mutant  in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette.  It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Pulmonary Fibrosis patient 39


title: etiolated Col-0, biological rep1

description:
4-days-old, dark grown.
Col-0_D_1

value: 4 days


title: Pulmonary Fibrosis patient 42


title: Pulmonary Fibrosis patient 41


title: 3003B_RAN_3month


title: Pulmonary Fibrosis patient 38


title: Pulmonary Fibrosis patient 37


title: CRP mutant strain AAM167, rep 1

description: This sample is of A. actinomycetemcomitans strain  AAM167, an isogenic deletion mutant  in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette.  It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: wild type strain JP2, rep 1

description: This sample is of wild-type A. actinomycetemcomitans strain JP2. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: wild type strain JP2

value: Expresses High Levels of Leukotoxin


title: wild type strain JP2, rep 2

description: This sample is of wild-type A. actinomycetemcomitans strain JP2. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: wild type strain JP2, rep 3

description: This sample is of wild-type A. actinomycetemcomitans strain JP2. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Pulmonary Fibrosis patient 35

value: Lung


title: 2011A_LAN_3month


title: Pulmonary Fibrosis patient 36


title: Pulmonary Fibrosis patient 33


title: 3002B_RMN_3month

value: RMN


title: Pulmonary Fibrosis patient 32


title: 3001C_LAN_3month

value: C


title: Pulmonary Fibrosis patient 34


title: Total RNA Wildtype-2

city: Boston

first: Tatsuya

last: Kobayashi

state: MA

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: Microarray suite 5

source_name: Primary chondrocytes; Wt; total RNA

label_protocol: Ovation Pico +  Affymetrix starndard

growth_protocol: Primary rib chondroyctes overnight culture in 10 cm dish in 10%FCD-containing DMEM

extract_protocol: Total RNA was extracted by SurePrep (Fisher).  Ago2 immunoprecipitation was performed using WAKO's microRNA isolation Kit, mouse Ago2

value: Primary chondrocytes

value: Wt

tag: genetic background

value: 129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant


title: Ago2-IP RNA Mir140 KO-2

source_name: Primary chondroyctes; Mir140 KO; Ago2-IP

tag: cell type

value: Mir140 KO

tag: antibody

value: Ago2 antibody

tag: antibody manufacturer

value: Wako biochemicals

tag: antibody catalog #

tag: antibody lot #


title: Ago2-IP RNA Wildtype-2

source_name: Primary chondroyctes; Wt; Ago2-IP


title: 3002B_AN_0month

tag: tissue

value: Prostate

tag: biopsy location

value: AN

value: B

value: Stratagene Reference Pooled RNA


title: 3003B_RMN_0month

tag: ID

tag: intervention


title: 3001C_LAN_0month

value: LAN

tag: biopsy time

tag: reference


title: 2011A_LMN_0month

value: LMN

value: A


title: 32B7

first: Guanggan

last: Hu

email: hug@msl.ubc.ca, kronstad@msl.ubc.ca

address: 2185 East Mall

department: Michael Smith Laboratories

institute: The University of British Columbia

description: CGH 32B7  vs H99

hyb_protocol: The hybridization was performed in NimbleGen as described in www.nimblegen.com

scan_protocol: The signal scan was performed in NimbleGen as described in www.nimblegen.com

data_processing: Arrays were processed using Nimblegen's standard protocol (NimbleScan 2.0 software) for data extraction.

organism: Cryptococcus neoformans

label_protocol: DNA labeling was performed in Nimblegen. Briefly, genomic DNA was randomly fragmented by sonication to a size of 500-2000 bp. Each DNA sample was denatured at 98oC in the presence of 1OD of 50-Cy3- or 50-Cy5- labeled random nonamer. The denatured sample was incubated with 100 units of Klenow fragment and 1.5mM dNTP mix for 2 hours at 37oC. The Cy3- and Cy5- labeled samples (15 µg each) were combined and dried by vacuum centrifugation.

growth_protocol: YPD

extract_protocol: The lyophilized cells (2X109 cells) were breaking down in a bead breaker and the genomic DNA was isolated in a CTAB (hexadecyltrimethylammonium bromide) extraction buffer. DNA was precipated with ethanol, and treated with 10 mg/µl RNase

value: environmental strain

source_name: H99 [reference]

value: standard strain H99


title: 33W1

description: CGH 33W1  vs H99


title: RCT55-D4-1

description: CGH RCT55-D4-1  vs H99

value: clinical strain


title: RCT17-D1C

description: CGH RCT17-D1C  vs H99


title: CBS7779 W3MB13

description: CGH CBS7779 W3MB13  vs H99

value: modified clinical strain


title: CBS7779 W2MB5

description: CGH CBS7779 W2MB5  vs H99

source_name: CBS7779 W2MB5


title: RCT60-D1-3

description: CGH RCT60-D1-3  vs H99


title: CBS7779 W2MB4

description: CGH CBS7779 W2MB4  vs H99

source_name: CBS7779 W2MB4


title: 2010B_RAN_3month

value: RAN

source_name: Stratagene Reference RNA


title: Pulmonary Fibrosis patient 31

value: Lung

value: intermediate PH


title: 2010B_RBN_0month

value: RBN


title: 2008A_RAN_3month


title: Total RNA Mir140 KO-2

source_name: Primary chondrocytes;Mir140 KO; total RNA

value: Primary chondrocytes

tag: genotype

value: Mir140 KO

value: 129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant


title: Pulmonary Fibrosis patient 28


title: Pulmonary Fibrosis patient 29


title: Pulmonary Fibrosis patient 27


title: Pulmonary Fibrosis patient 30


title: 2007B_RAN_3month

value: Prostate


title: CBS7779 W2MB8

description: CGH CBS7779 W2MB8  vs H99

source_name: CBS7779 W2MB8


title: Pulmonary Fibrosis patient 26


title: Total RNA Wildtype-1

value: Wt


title: 2008A_RMN_0month

value: RMN

value: Stratagene Reference Pooled RNA


title: 2007B_LBN_0month

value: LBN

value: B


title: Pulmonary Fibrosis patient 24


title: Pulmonary Fibrosis patient 25


title: 2006B_LBN_3month


title: RCT52-D1-3

description: CGH RCT52-D1-3  vs H99


title: 2006B_LBN_0month


title: Ago2-IP RNA Wildtype-1

value: Ago2 antibody

value: Wako biochemicals


title: RCT55-D1-1

description: CGH RCT55-D1-1  vs H99

value: clinical strain

value: standard strain H99


title: 2005B_RBN_3month


title: Pulmonary Fibrosis patient 23


title: H99 34W2

description: CGH H99 34W2  vs H99

value: environmental strain


title: J0278-1

description: CGH J0278-1  vs H99


title: CBS7779 W2MB3

description: CGH CBS7779 W2MB3  vs H99

source_name: CBS7779 W2MB3

value: modified clinical strain


title: H99 32B8

description: CGH H99 32B8  vs H99


title: RCT50-D1-2

description: CGH RCT50-D1-2  vs H99


title: VSa16cell_min, E

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Sparus aurata

source_name: ECM mineralization-induced VSa16 cell culture

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: VSa16 cell culture collected after induction of ECM mineralization by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2 for 4 weeks

extract_protocol: Total RNA was extracted from cell culture using denaturation solution (4M guanidinium isothiocyanate, 0.75 M sodium citrate, 10% (w/v) n-Lauryl-sarcosine and β-mercaptoethanol; pH 7.0) and phenol/chloroform/isoamyl alcohol extraction as described by Chomczynski and Sacchi (1987)

value: VSa16 osteoblast-like cell culture


title: Pulmonary Fibrosis patient 20

source_name: Lung sample from recipient organ

value: Lung

value: intermediate PH


title: Ago2-IP RNA Mir140 KO-1

value: Primary chondrocytes

value: Mir140 KO


title: 2003C_RAN_3month

source_name: human prostate collected at 3month

value: Prostate

value: RAN

value: C


title: RCT17-D1B

description: CGH RCT17-D1B  vs H99


title: 2003C_RAN_0month

source_name: human prostate collected at 0month

value: Stratagene Reference Pooled RNA


title: VSa16cell_min, F


title: Pulmonary Fibrosis patient 19


title: 2005B_RMN_0month

value: RMN


title: Total RNA Mir140 KO-1

value: 129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant


title: Pulmonary Fibrosis patient 18


title: Pulmonary Fibrosis patient 21


title: VSa16cell_controls, B

source_name: Control VSa16 cell culture

growth_protocol: Cells cultured in D-MEM supplemented with  10% FBS, 1% penicillin-streptomycin, 1% fungizone, and 3 mM L-glutamine, and incubated at 33°C in a 10% CO2 humidified atmosphere.


title: CBS7779 W2MW2

description: CGH CBS7779 W2MW2  vs H99

source_name: CBS7779 W2MW2


title: RCT50-D1-3

description: CGH RCT50-D1-3  vs H99


title: VSa16cell_min, D


title: RCT50-D1-1

description: CGH RCT50-D1-1  vs H99


title: CBS7779 W2MB7

description: CGH CBS7779 W2MB7  vs H99

source_name: CBS7779 W2MB7


title: Pulmonary Fibrosis patient 22


title: 2001A_LMN_3month

value: LMN

value: A


title: Pulmonary Fibrosis patient 17

description: Gene expression data from PF patient with severe PH

value: severe PH


title: VSa16cell_controls, C


title: 1029A_LMN_0month


title: 1027C_LAN_3month

value: LAN


title: 1028A_LBNC_0month

value: LBNC


title: 1029A_LMNatr_3month

value: LMNatr


title: Pulmonary Fibrosis patient 12


title: 1028A_LMN_3month


title: 2001A_RLMN_0month

value: RLMN


title: RCT55-D1-3

description: CGH RCT55-D1-3  vs H99

value: clinical strain

value: standard strain H99


title: Pulmonary Fibrosis patient 11

value: Lung


title: Pulmonary Fibrosis patient 13


title: Pulmonary Fibrosis patient 15


title: VSa13cell_controls, H

description: Cells cultured in D-MEM supplemented with 10% FBS, 1% penicillin-streptomycin, 1% fungizone, and 3 mM L-glutamine, and incubated at 33°C in a 10% CO2 humidified atmosphere.

source_name: Control VSa13 cell culture

extract_protocol: Total RNA was extracted from cell culture using denaturation solution (4M guanidinium isothiocyanate, 0.75 M sodium citrate, 10% (w/v) n-Lauryl-sarcosine and b?mercaptoethanol; pH 7.0) and phenol/chloroform/isoamyl alcohol extraction as described by Chomczynski and Sacchi (1987)  Total RNA was extracted from cell culture using denaturation solution (4M guanidinium isothiocyanate, 0.75 M sodium citrate, 10% (w/v) n-Lauryl-sarcosine and β-mercaptoethanol; pH 7.0) and phenol/chloroform/isoamyl alcohol extraction as described by Chomczynski and Sacchi (1987)

value: VSa13 chondrocyte-like cell culture


title: VSa13cell_min, L

description: VSa13 cell culture collected after induction of ECM mineralization by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2 for 4 weeks

source_name: ECM mineralization-induced VSa13 cell culture


title: Pulmonary Fibrosis patient 14


title: VSa16cell_controls, A

value: VSa16 osteoblast-like cell culture


title: VSa13cell_min, K


title: CBS7779 B6MB20

description: CGH CBS7779 B6MB20  vs H99

value: modified clinical strain


title: CBS7779 W3MW6

description: CGH CBS7779 W3MW6  vs H99

source_name: CBS7779 W3MW6


title: D16-11

description: CGH D16-11  vs H99

value: environmental strain

source_name: H99 [reference]


title: VSa13cell_controls, I


title: CBS7779 W2MW1

description: CGH CBS7779 W2MW1  vs H99

source_name: CBS7779 W2MW1


title: RCT17-D1A

description: CGH RCT17-D1A  vs H99


title: Pulmonary Fibrosis patient 16


title: RSA730

description: CGH RSA730  vs H99


title: RCT52-D1-2

description: CGH RCT52-D1-2  vs H99


title: VSa13cell_min, J


title: VSa13cell_controls, G


title: RCT55-D4-3

description: CGH RCT55-D4-3  vs H99


title: HS vs LS in Kromelite-LW2 (Dye Swap)

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

description: Either HS or LS can be the experimental sample while the other as control sample.

hyb_protocol: Labelled cDNA was hybridised using the radiata pine 18K cDNA microarrays developed in CSIRO Plant Industry. Slides were placed in water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS) at 42 °C, 0.1x SSC (+0.1 % SDS), 0.1x SSC and 0.01x SSC at room temperature, each for 5 min prior to drying and scanning.

scan_protocol: Hybridized microarray slides were scanned using GenePix Personal 4100A microarray scanner (Axon Instruments, CA). Image pre-processing was performed using GenePix® Pro 4.0 and Acuity software (Axon Instruments, CA).

data_processing: Data analysis was carried out using GEPAS v3.1. The mean values from each channel were log2 transformed and normalized using print-tip lowess and slide scale normalization.

label: Alexa Fluor 555

organism: Pinus radiata

label_protocol: Equal amounts of total RNA (20 or 30 µg) of the two bulked samples to be compared were reversely transcribed using Superscript reverse transcriptase, and generated fluorescently labelled cDNA using Alexa Fluor® 555-aha-dUTP and Alexa Fluor® 647-aha-dUTP, following the protocol of the SuperScriptTM Plus Direst cDNA Labelling System (Invitrogen, CA).

growth_protocol: Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn, Victoria (38º 14' S, 146º 45' E) and Kromelite, South Australia (37º 50' S, 140º 55' E). The two field trials included 249 and 110 half- or full-sib families, respectively, and only 16 full-sib families are common to both trials. At time of sampling the cambial ages (ring numbers at breast height) of sampled trees in Flynn and Kromelite trials were 7 and 6 yr, respectively, representing a developing stage at juvenile wood (JW) formation in radiata pine.

extract_protocol: Developing xylem tissues were ground and total RNA was extracted using the method of Chang et al (1993) with a slight modification

treatment_protocol: Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn and Kromelite, Australia. Based on the IML-based MOE measurement, five families with highest and lowest MOE each were selected from each trial, which represented two segregant populations with contrasting wood stiffness. Two individuals from each selected family were further sampled. Developing xylem tissues of selected trees in Flynn trial were sampled in spring (October) and autumn (April), representing earlywood (EW) and latewood (LW) of juvenile aged trees, respectively. Collection of xylem tissues from Kromelite trial was arranged in summer (late November) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. In Flynn trial EW and LW tissues were collected from the same sampled trees on opposite sides of the trunk. Transcript accumulation was compared in trees with highest (HS) and lowest stiffness (LS) using xylem samples from Flynn collected in spring (EW) and autumn (LW), as well as Kromelite in summer (LW), respectively. Bulked segregant analysis (BSA) was used for the experiment design.

tag: replicate

value: 2 dye swap

tag: developmental stage

value: LW

label: Alexa Fluor 647


title: 1026C_RAN_3month

value: Prostate

value: RAN

value: C

value: Stratagene Reference Pooled RNA


title: 1027C_LAN_0month

value: LAN


title: Pulmonary Fibrosis patient 10

value: severe PH


title: HS vs LS in Kromelite-LW1


title: 1025A_RMN_3month

value: RMN

value: A


title: CBS7779 W3MB16

description: CGH CBS7779 W3MB16  vs H99

tag: strain


title: Pulmonary Fibrosis patient 7

tag: disease state


title: Pulmonary Fibrosis patient 8


title: HS vs LS in Flynn-LW1 (Dye Swap)

value: 1 dye swap


title: 1024C_RAN_3month


title: HS vs LS in Kromelite-LW1 (Dye Swap)


title: RCT55-D1-2

description: CGH RCT55-D1-2  vs H99

value: clinical strain

value: standard strain H99


title: RCT52-D1-1

description: CGH RCT52-D1-1  vs H99


title: Pulmonary Fibrosis patient 5

value: Lung


title: 1026C_RBN_0month

value: RBN


title: RCT60-D1-1

description: CGH RCT60-D1-1  vs H99


title: HS vs LS in Flynn-LW2


title: 1025A_RMN_0month


title: 1024C_RMN_0month


title: HS vs LS in Flynn-LW1


title: Pulmonary Fibrosis patient 3


title: Pulmonary Fibrosis patient 4


title: HS vs LS in Flynn-EW2 (Dye Swap)

value: EW


title: HS vs LS in Kromelite-LW2


title: HS vs LS in Flynn-LW2 (Dye Swap)


title: Pulmonary Fibrosis patient 6


title: Pulmonary Fibrosis patient 9


title: HS vs LS in Flynn-EW2


title: Pulmonary Fibrosis patient 2


title: 1023A_LMN_0month

value: LMN


title: CBS7779 B6MW10

description: CGH CBS7779 B6MW10  vs H99

value: modified clinical strain


title: RCT60-D1-2

description: CGH RCT60-D1-2  vs H99


title: 1022A_LMNP_0month

value: LMNP


title: Pulmonary Fibrosis patient 1


title: 1023A_RAN_3month

value: Prostate


title: HS vs LS in Flynn-EW1


title: HS vs LS in Flynn-EW1 (Dye Swap)


title: rep1_Ch1:clonogenic_Ch2:nonclonogenic

first: Christine

last: Ichim

state: ON

address: 2075 Bayview Avenue

department: Molecular and Cell Biology

institute: Sunnybrook Research Institute

description: pooled clonogenic single cells (Cy3) versus pooled non-clonogenic single cells (Cy5)

hyb_protocol: Hybridization was carried out as follows: hybridization buffer (DIG Easy Hyb, Roche Diagnostics Canada) containing 50 ug each of yeast tRNA (Invitrogen) and calf thymus DNA (Sigma-Aldrich) per 100 ul was added to concentrated Cy3 and Cy5 labeled cDNA to a total volume of 50 ul, heated to 65°C for 2 min, and pipetted onto a 24 x 30 mm coverslip. A microarray slide was lowered onto the coverslip, inverted, placed in a closed, water-containing plastic hybridization chamber, and incubated on a level surface for 16 h at 42°C in a covered water bath. The coverslip was removed by immersion of the array in 1 x SSC. The array was washed five times for 5 min at room temperature in 0.1 x SSC/0.1% (vol/vol) SDS with agitation, rinsed 3 times in 0.1x SSC, dried by centrifugation, and scanned with minimum delay.

scan_protocol: Hybridized arrays were scanned on a ScanArray 4000XL (Packard BioChip Technologies, Billerica, MA). The Cy3 and Cy5 channels were balanced by eye with the ScanArray Software to ensure a similar dynamic range for the two channels. Final scans were taken at 10 m resolution, and images for each channel were saved as separate 16-bit TIFF files. These were imported into GenePix (Axon Instruments, Union City, CA) for quantitation.

data_processing: Arrays were normalized and processed using Genepix, flagged spots were  removed from dataset

source_name: pooled clonogenic single cells

label_protocol: Diluted amplified stock cDNA (1:100, 1 l) was added to 98 l polymerase buffer containing 0.5 absorbance units/ml; A260, 0.7 M SR-T24 primer, 0.1 mM dTTP, and 0.2 mM each of dCTP, dGTP, dATP and aminoallyl-dUTP (Sigma-Aldrich, St. Louis, MO). Taq polymerase (2 units) was added at 94°C, and the mixture was amplified through 25 cycles (15 s at 94°C; 30 s at 60°C; 1 min at 72°C). This step entails a further 104-fold amplification. Aminoallyl cDNA (typically 5 g) was purified on a Microcon-30 column (Millipore) according to directions, and concentrated to 2–3 l by centrifugation under vacuum, and 1 l was added to 5 l of 0.1 M NaHCO3, pH 9.0. The contents of one vial of Cy3 or Cy5 monofunctional reactive dye (Amersham/Pharmacia) was dissolved in 45 l dimethyl sulfoxide. Aminoallyl cDNA (5 l) was mixed with 5 l of dye and the tube was wrapped in foil to exclude light and incubated 30 min at room temperature. Labeled cDNA was isolated using a High Pure PCR purification kit (Boehringer Mannheim) according to directions, and the eluate was concentrated to 5–7 l by vacuum centrifugation. Labeling efficiency was measured in some samples by absorbance at 260 nm and 550 nm for Cy3 or 650 nm for Cy5.

growth_protocol: Early passages of the OCI/AML-4 cell lines (obtained from Dr. M.D. Minden, University Health Network, Toronto, Canada) were cultured on an irradiated OP9 feeder layer in IMDM  with α-thioglycerol, 5% v/v fetal bovine serum (FBS) and supplemented with recombinant human (rh)G-CSF (50ng/mL), rhIL-11 (30ng/mL), rhFlt3 ligand (30ng/mL), rhGM-CSF (30ng/mL),  rhIL-6 (1ng/mL), 3% v/v conditioned medium of Chinese hamster ovary (CHO) cells transfected with a vector expressing murine c-kit ligand (KL-CM) (D. Donaldson, Genetics Institute, Cambridge, MA), insulin (10μg/mL), transferrin (5μg/mL), and 0.5% v/v bovine serum albumin (BSA). Cultures were passaged twice weekly to maintain a density of 2 x 105 cells/mL.  To limit selection for highly proliferative subclones through continuous passaging, cultures were discarded after approximately three months of passage.

extract_protocol: Global cDNA from each individual single cell was amplified through 65 cycles of PCR, followed by an additional 25 cycles for incorporation of aminoallyl-dUTP. In detail, RNA in 0.5 ul H2O was added to 4 ul first strand buffer (50 mM Tris-HCl, pH 8.3, 75 mM KCl, 3mM MgCl2, 0.5% (vol/vol) NP-40, 1 mM DTT, 100 ug/ml acetylated BSA, 2.9 ul/100 ul RNAguard (Amersham Biosciences), 0.1 ul/100ul Prime RNase Inhibitor (Eppendorf - 5 Prime, Boulder, CO), 10 uM fresh dNTPs) in a 200 ul PCR tube. After heating to 65°C for 90 s, the tube was cooled to 50°C and reverse transcription was initiated by addition of 0.5 ul (100 units) SuperScript II (Invitrogen) and 0.2 ul SR-T24 primer (5'-GTTAACTCGAGAATTCT24) to a reaction concentration of 0.00245 absorbance units/ml (A260, 3.5 nM). After 15 min, the reaction was terminated by heating to 70°C for 10 min. RNAse H (1.0 ul; Amersham/Pharmacia) and 0.7 ul MgCl2 (75 mM, combined final concentration, 9.4 mM Mg2+) were added and RNA was digested at 37°C for 15 min. The cDNA strands were tailed by addition of 6.5 ul 2x tailing buffer (Roche/Boehringer Mannheim, Mannheim, Germany; final reaction concentrations 25 mM Tris-HCl, 200 mM potassium cacodylate, pH 6.6, 1.5 mM CoCl2) containing dATP to a final reaction concentration of 750 uM and 0.5 ul (25 units) terminal deoxynucleotidyl transferase (Roche/Boehringer Mannheim), and incubated at 37°C for 15 min. Tailing was stopped by heating to 65°C for 10 min. Reaction product (4 ul) was added to each of three tubes containing 15 ul polymerase buffer (10 mM Tris-HCl, pH 8.3, 50 mM KCl, 1.5 mM MgCl2, 100 ug/ml BSA, and 0.05% (vol/vol) Triton X-100), 0.875 mM dNTPs (7.5 absorbance units/ml; A260), and 11 uM SR-T24 primer. The resulting mixture contained totals of 13 mM Tris-HCl, pH 8.3, 2.5 mM MgCl2, and residual 0.3 mM CoCl2. To generate the second cDNA strands, the mixture was overlaid with mineral oil and 2 units Taq and 0.05 units Pfu (Stratagene) polymerases were added at 94°C. Primer was annealed at 50°C for 2 min followed by 2 min of extension at 72°C. After amplification through 30 additional cycles (15 s at 94°C; 30 s at 60°C; 2 min at 72°C), 1 ul from each of the three tubes was pooled and 0.2 ul added to 18 ul of polymerase buffer containing 0.2 mM dNTPs and 2.5 uM primer at 1.8 absorbance units/ml; A260. The mixture was overlaid with mineral oil, Taq and Pfu polymerases were added at 94°C, and an additional 35 cycles of amplification were carried out. Amplified stock cDNA was stored at -20°C.

treatment_protocol: We were interested in determining genes differentially expressed between clonogenic and non-clonogenic early passage OCI/AML4 cells. We previously shown that OCI/AML-4 clonal siblings display coordinated growth patterns, so that the behaviour of a single cell that is destroyed in the generation of global single cell cDNA may be predicted by the growth patterns of its clonal siblings.  Cells were plated in 96 well plates at limiting dilutions. Localized clusters of four cells were identified and micromanipulated such that three of the constituent cells were placed separately into individual microtitre wells containing growth medium and a feeder layer of OP9 cells, while the fourth cell was lysed and processed for global RT-PCR.  The cells in each culture well were counted at 2 -3 day intervals until growth stopped. In this manner cDNA was generated from individual clonogenic OCI/AML-4 cells (sibling cells able to generate between 9-100 cells) or from individual non-clonogenic OCI/AML-4 cells (sibling cells were not able to generate more than 8 cells). Respective single cell cDNA was then pooled and compared by hybridization to cDNA microarrays.

tag: cell line

value: early passage OCI/AML-4

source_name: pooled non-clonogenic single cells


title: 1021B_LMN_0month

value: B

source_name: Stratagene Reference RNA


title: H99 35W1

description: CGH H99 35W1  vs H99

value: environmental strain


title: ML vs JL rep3 (Dye Swap)

description: Either JW or MW can be the experimental sample while the other as control sample.

label_protocol: Equal amounts of total RNA (20 or 30 µg) of the two samples to be compared were reversely transcribed using Superscript reverse transcriptase, and generated fluorescently labelled cDNA using Alexa Fluor® 555-aha-dUTP and Alexa Fluor® 647-aha-dUTP, following the protocol of the SuperScriptTM Plus Direst cDNA Labelling System (Invitrogen, CA).

growth_protocol: Nine radiata pine trees (different genotypes) at juvenile (5 yrs) and mature (13 yrs) ages (based on wood ring number at breast height, 1.3m) each were sampled in commercial plantations at Bondo, NSW (35º 16' 44.04 S, 148º 26' 54.66 E). The 18 sampled trees were growing within 100 m of each other with similar field environment.

treatment_protocol: Developing xylem tissues from trees at juvneile (5 yrs) and mature (13 yrs) ages were collected on the same dates in spring (October) and autumn (March) to represent earlywood (EW) and latewood (LW) samples, respectively. To avoid the presence of compression wood in the samples, EW and LW tissues were collected from the same tree at breast height (1.3m) on opposite sides of the trunk perpendicular to the prevailing wind direction. The xylem tissues were scraped from the exposed xylem surface with a sharp chisel after removing the bark of the sampling area. Each time of sample collection was finished within two hours in the morning to minimize the fluctuated gene expression. The sampled tissues were immediately placed into liquid nitrogen in the field until stored in the lab at -80oC.

tag: development

value: juvenile

tag: wood type

value: late

value: mature


title: 1022A_LBNC_3month

value: LBNC

value: A

value: Stratagene Reference Pooled RNA


title: rep3_Ch1:nonclonogenic_Ch2:clonogenic

description: pooled non-clonogenic single cells (Cy3) versus pooled clonogenic single cells (Cy5)


title: RCT55-D4-2

description: CGH RCT55-D4-2  vs H99

value: clinical strain

value: standard strain H99


title: ML vs JL rep2 (Dye Swap)


title: RSA731

description: CGH RSA731  vs H99


title: H99 32W1

description: CGH H99 32W1  vs H99


title: 1021B_LMN_3month


title: HC-2c

description: CGH HC-2c  vs H99


title: ML vs JL rep2


title: rep2_Ch1:clonogenic_Ch2:nonclonogenic


title: ML vs JL rep3


title: Wild Type Replicate Four

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

department: Medicine

institute: McGill University

description:
raw data file Hy3: 1_Exiqon_13978197_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978197_S01_Cropped.txt
Biological Replicate 4 of 7 for BALB WT mice

hyb_protocol: The Hy3TM and Hy5TM labelled samples were mixed pairwise and hybridization was performed according to the miRCURYTM LNA array manual (Exiqon) using a Tecan HS4800 hybridization station

scan_protocol: Microarray slides were scanned using the Agilent G2565BA Microarray Scanner System.  Image Analysis used ImaGene 8.0 software.

data_processing: LOWESS normalized and background corrected (Normexp with offset value 10)

source_name: BALB WT Control

label_protocol: 1 μg of total RNA from sample and reference was labelled with Hy3TM and Hy5TM respectively using miRCURYTM LNA Array power labelling kit from Exiqon according to the manufacturer's protocol.

growth_protocol: All mice were maintained on Colyte from 3 weeks to age of euthanasia, at 12 weeks

extract_protocol: Total RNA from mouse ileum was extracted using miRNeasy Mini kits from Qiagen according to manufacturer's protocol.

value: Balbc/J Cftrtm1UNC +/+

tag: gender

value: male

tag: tissue type

value: Ileum

source_name: Control RNA from Exiqon

value: Control RNA from Exiqon


title: Wild Type Replicate Five

description:
raw data file Hy3: 1_Exiqon_13978198_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978198_S01_Cropped.txt
Biological Replicate 5 of 7 for BALB WT mice

value: female


title: Wild Type Replicate Six

description:
raw data file Hy3: 1_Exiqon_13978199_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978199_S01_Cropped.txt
Biological Replicate 6 of 7 for BALB WT mice


title: Wild Type Replicate Seven

description:
raw data file Hy3: 1_Exiqon_13978144_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978144_S01_Cropped.txt
Biological Replicate 7 of 7 for BALB WT mice


title: HC-3a

description: CGH HC-3a  vs H99


title: 1018C_RMN_3month

label_protocol: One microgram of total target RNA from randomized samples, side by side with 1 µg of universal human reference RNA (Stratagene #740000), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

extract_protocol: Core needle biopsies were collected at baseline and 3 months. Total RNA for micro-array analyses were extracted from areas of normal prostate peripheral-zone tissue containing both stroma and epithelial cells. A #10 scalpel blade was used to scrape tissue from the pathologic area of interest. Tissue was homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

value: Prostate

value: RMN

value: C


title: ML vs JL rep1 (Dye Swap)


title: Wild Type Replicate Three

description:
raw data file Hy3: 1_Exiqon_13978196_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978196_S01_Cropped.txt
Biological Replicate 3 of 7 for BALB WT mice


title: 1019B_LBN_0month

value: LBN

value: B


title: 1019B_RMN_3month


title: Bt9

description: CGH Bt9  vs H99

value: environmental strain


title: Wild Type Replicate Two

description:
raw data file Hy3: 1_Exiqon_13978194_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978194_S01_Cropped.txt
Biological Replicate 2 of 7 for BALB WT mice


title: 1018C_LMN_0month

value: LMN


title: Arg1373

description: CGH Arg1373  vs H99


title: 1020B_LBN_3month


title: ME vs JE rep3 (Dye Swap)

value: juvenile

value: early

value: mature


title: 1017B_LAN_3month

value: LAN

value: Stratagene Reference Pooled RNA


title: HC-3b

description: CGH HC-3b  vs H99

value: clinical strain

value: standard strain H99


title: HC-4a

description: CGH HC-4a  vs H99


title: ME vs JE rep3


title: 1020B_RBN_0month

value: RBN


title: RTC31-mix

description: CGH RTC31-mix  vs H99


title: ML vs JL rep1

value: late


title: Wild Type Replicate One

description:
raw data file Hy3: 1_Exiqon_13978193_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978193_S01_Cropped.txt
Biological Replicate 1 of 7 for BALB WT mice

value: Balbc/J Cftrtm1UNC +/+

value: male

value: Ileum

value: Control RNA from Exiqon


title: Cystic Fibrosis Replicate Eight

description:
raw data file Hy3: 1_Exiqon_13978189_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978189_S01_Cropped.txt
Biological Replicate 8 of 8 for BALB CF mice

source_name: BALB CF knockout

value: Balbc/J Cftrtm1UNC -/-


title: Cystic Fibrosis Replicate Seven

description:
raw data file Hy3: 1_Exiqon_13978188_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978188_S01_Cropped.txt
Biological Replicate 7 of 8 for BALB CF mice


title: A1-35-8

description: CGH A1-35-8  vs H99


title: ME vs JE rep2


title: Cystic Fibrosis Replicate Five

description:
raw data file Hy3: 1_Exiqon_13978186_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978186_S01_Cropped.txt
Biological Replicate 5 of 8 for BALB CF mice

value: female


title: 1017B_LAN_0month

value: Prostate

value: B


title: C45

description: CGH C45  vs H99

value: environmental strain


title: ME vs JE rep2 (Dye Swap)

value: juvenile

value: early


title: HC-2b

description: CGH HC-2b  vs H99


title: Cystic Fibrosis Replicate Three

description:
raw data file Hy3: 1_Exiqon_13978183_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978183_S01_Cropped.txt
Biological Replicate 3 of 8 for BALB CF mice


title: 13weeks, mutant, biol.rep3

city: Krakow

first: Grzegorz

last: Kreiner

address: Smetna 12

department: Dept. Brain Biochemistry

country: Poland

institute: Institute of Pharmacology

hyb_protocol: Microarray experiments were carried out using GeneChip Mouse Genome 430A 2.0 arrays (Affymetrix, Santa Clara, CA, USA) according to manufacturer's instructions.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Analysis of array data was performed using the R/Bioconductor suite. Data was normalized and expression values were computed using the gcrma method.
Expression data was logarithmed (Log2) before statistical analyses.

source_name: mouse at 13 week, mutant

label_protocol: Labeling of the target RNAs (1-2μg total RNA).

extract_protocol: Extraction of total RNA was performed using QIAgen columns according to manufacturer's instructions. RNA quality was validated on Agilent Bioanalyser.

tag: age

value: 13 weeks

value: striatum

tag: cell type

value: medium spiny neurons (MSNs)

tag: genotype/variation

value: TIF-IAD1RCre mutant


title: Cystic Fibrosis Replicate Six

description:
raw data file Hy3: 1_Exiqon_13978187_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978187_S01_Cropped.txt
Biological Replicate 6 of 8 for BALB CF mice


title: ME vs JE rep1

value: mature


title: 13weeks, mutant, biol.rep2

tag: tissue


title: 1016A_RMN_3month

first: Mark

last: Magbanua

address: 1450 3rd Street, PO Box 589001

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Experimental bias (hybridization batch) was removed by fitting linear models & taking residuals. Statistical packages marray and limma in the R environment was used.

source_name: human prostate collected at 3month

tag: biopsy location

value: RMN

tag: ID

tag: intervention

value: A

value: Stratagene Reference Pooled RNA


title: ME vs JE rep1 (Dye Swap)


title: 1016A_LMN_0month

source_name: human prostate collected at 0month

value: LMN

tag: biopsy time

tag: reference


title: 1015C_RMN_3month

value: C


title: HC-6

description: CGH HC-6  vs H99

value: clinical strain

value: standard strain H99


title: Cystic Fibrosis Replicate Two

description:
raw data file Hy3: 1_Exiqon_13978182_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978182_S01_Cropped.txt
Biological Replicate 2 of 8 for BALB CF mice

tag: genotype

value: Balbc/J Cftrtm1UNC -/-

value: female

value: Ileum

value: Control RNA from Exiqon


title: 1015C_LMN_0month

value: Prostate


title: Cystic Fibrosis Replicate Four

description:
raw data file Hy3: 1_Exiqon_13978184_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978184_S01_Cropped.txt
Biological Replicate 4 of 8 for BALB CF mice


title: 1013A_RAN_0month

value: RAN


title: HC-6d

description: CGH HC-6d  vs H99

tag: strain


title: 13weeks, control, biol.rep3

source_name: mouse at 13 week, control

value: 13 weeks

value: striatum

value: control


title: 13weeks, control, biol.rep2

value: medium spiny neurons (MSNs)


title: 1013A_RAN_3month


title: 1012B_LBN_3month

value: LBN

value: B


title: Cystic Fibrosis Replicate One

description:
raw data file Hy3: 1_Exiqon_13978181_S01_Cropped.txt
raw data file Hy5: 0_Exiqon_13978181_S01_Cropped.txt
Biological Replicate 1 of 8 for BALB CF mice

value: male


title: HC-6c

description: CGH HC-6c  vs H99


title: 13weeks, control, biol.rep1


title: Arg1366

description: CGH Arg1366  vs H99

value: environmental strain


title: 13weeks, mutant, biol.rep1

value: TIF-IAD1RCre mutant


title: 1012B_LBN_0month

value: Stratagene Reference Pooled RNA


title: HC-4c

description: CGH HC-4c  vs H99

value: clinical strain

value: standard strain H99


title: 1011B_RMN_3month

value: RMN


title: C8

description: CGH C8  vs H99


title: RTC31-1

description: CGH RTC31-1  vs H99


title: 9weeks, mutant, biol.rep3

source_name: mouse at 9 week, mutant

value: 9 weeks


title: 1010C_LMN_3month

value: LMN

value: C


title: 1011B_LMN_0month

value: Prostate


title: 9weeks, mutant, biol.rep1


title: 9weeks, mutant, biol.rep2


title: C23

description: CGH C23  vs H99


title: 1010C_RAN_0month

value: RAN


title: 9weeks, control, biol.rep2

source_name: mouse at 9 week, control

value: striatum


title: HC-5b

description: CGH HC-5b  vs H99


title: 1008C_RMN_3month


title: 9weeks, control, biol.rep3

value: control


title: 9weeks, control, biol.rep1

value: medium spiny neurons (MSNs)


title: 1007C_RMN_3month


title: normal muscle control muscle 1

city: Durham

first: Jordan

middle: M

last: Blum

state: NC

address: LSRC 450 Research Dr

department: Department of Radiation Oncology

institute: Duke University

description: Gene expression data from normal muscle as control for myogenic tumors

hyb_protocol: Following fragmentation, cRNA is hybridized for 16 hours at 45c on  Mouse genome 430A 2.0 arrays and underwent automated washinging and staining on the fluidics station.

scan_protocol: Genechips were scanned using the GeneChip Scanner 3000 7g

data_processing: All data was analyzed using the RMA algorithm was used to normalize data.

source_name: muscle 1

label_protocol: Labeling was performed with the Ambion Message Amp Premier kit (500ng input)

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions for normal muscle and the RNEasy Fibrous Tissue Mini Kit (Qiagen) for in vitro and in vivo tumors

treatment_protocol: Mice were injected in the hindlimb with 4-hydroxytamoxifen; subsequently, tumors formed and were removed after euthanizing the mice as required by IACUC.  These tumors were then digested to form cell lines for further RNA processing.

value: Muscle

value: littermate control

value: 3-6 weeks

tag: sample type


title: 1007C_LAN_0month

value: LAN


title: HC-3c

description: CGH HC-3c  vs H99


title: In2637

description: CGH In2637  vs H99

value: environmental strain


title: A7-35-23

description: CGH A7-35-23  vs H99


title: A4-34-6

description: CGH A4-34-6  vs H99


title: Ug2467

description: CGH Ug2467  vs H99


title: normal muscle control muscle 2

source_name: muscle 2

value: normal muscle as control for myogenic tumors


title: Bt68

description: CGH Bt68  vs H99


title: 1006C_LAN_3month

value: Stratagene Reference Pooled RNA


title: 1006C_LMN_0month


title: 1005B_LBN_3month

value: LBN

value: B


title: RTC23-2

description: CGH RTC23-2  vs H99

value: clinical strain

value: standard strain H99


title: HC-5c

description: CGH HC-5c  vs H99


title: allograft-derived tumor CSM4B 4

description: Gene expression data from tumors derived from CSM4B cells transformed in vitro

source_name: CSM4B 4

value: Tumor


title: allograft-derived tumor CSM4B 5

source_name: CSM4B 5

value: tumors derived from CSM4B cells transformed in vitro


title: normal muscle control muscle 3

source_name: muscle 3


title: RTC23-3

description: CGH RTC23-3  vs H99

source_name: H99 [reference]


title: 1004A_LBN_3month

value: Prostate

value: A


title: allograft-derived tumor CSM4B 2

source_name: CSM4B 2


title: A5-35-17

description: CGH A5-35-17  vs H99


title: T1 Replica

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

hyb_protocol: Labeled RNA samples (1,500 ng) were hybridized 18h at 58C to HumanHT-12 array

scan_protocol: BeadChip microarray was scanned using an Illumina BeadArray Reader

data_processing: Raw data were processed using Feature Extraction software ver. 10.5. The initial analysis and normalization were performed using GeneSpring GX software (Agilent)

source_name: xenograft of MCF7(-)/MT1-MMP(WT) orthotopic tumors in mouse

label_protocol: The samples of total RNAs (500 ng) were labeled using an Illumina RNA Amplification kit (Ambion)

growth_protocol: Cells were routinely grown in DMEM-10% FBS.

extract_protocol: Total RNA was extracted from cultured cells and xenograft tumors using TRIZOL reagent and purified using RNAeasy columns (Qiagen)

treatment_protocol: The cDNA fragments encoding the full-length wild-type human MT1-MMP (MT1), the L50D and E240A mutants were generated by the PCR mutagenesis. The amplified fragments were cloned into the pLenti6/V5-D-TOPO vector (Invitrogen). MCF7 cells were transfected with the MT1, L50D and E240A constructs. The stable transfectants were selected in DMEM supplemented with 10 ug/ml blasticidin.

value: xenograft in mice


title: T4 Replica

source_name: xenograft of MCF7(-)/MT1-MMP(E240A) orthotopic tumors in mouse (no tumor control)


title: HC-2a

description: CGH HC-2a  vs H99


title: C2 Replica

description: MCF7(-)/MMP14(WT) cells

source_name: MCF7(-)/MMP14(WT) cells

value: cell culture


title: Pax7CreER-derived tumor mouse 343

description: Gene expression data from tumors derived from Pax7-expressing cells in vivo

source_name: mouse 343


title: 1003A_RMN_3month

city: San Francisco

department: HemOnc

value: RMN

source_name: Stratagene Reference RNA


title: 1004A_LBN_0month


title: 1005B_RAN_0month

value: RAN


title: Pax7CreER-derived tumor mouse 331

source_name: mouse 331

value: 3-6 weeks

value: tumors derived from Pax7-expressing cells in vivo


title: HC-5a

description: CGH HC-5a  vs H99


title: C27

description: CGH C27  vs H99

value: environmental strain


title: HC-4b

description: CGH HC-4b  vs H99


title: A1-38-2

description: CGH A1-38-2  vs H99


title: T4

description: MCF7(-)/MT1-MMP(E240A) orthotopic tumors in mouse (no tumor control)


title: 1003A_LAN_0month

source_name: human prostate collected at 0month

value: LAN


title: 1002A_LLBN_0month

value: LLBN

value: Stratagene Reference Pooled RNA


title: 1001B_RAN_3month

source_name: human prostate collected at 3month

value: B


title: Pax7CreER-derived tumor mouse 357

source_name: mouse 357


title: 1001B_LAN_0month


title: Pax7CreER-derived tumor mouse 341

source_name: mouse 341


title: 1002A_RBN_3month

value: RBN


title: C3

description: MCF7(-)/MMP14(L50D) cells

source_name: MCF7(-)/MMP14(L50D) cells


title: C4

description: MCF7(-)/MMP14(E240A) cells

source_name: MCF7(-)/MMP14(E240A) cells


title: C2

description: MCF7(-)/MMP14(WT) cells


title: A2-102-5

description: CGH A2-102-5  vs H99

value: standard strain H99


title: T1

description: MCF7(-)/MT1-MMP(WT) orthotopic tumors in mouse


title: RTC23-1

description: CGH RTC23-1  vs H99

value: clinical strain


title: TGFb-stimulated slide 2, replicate 1

description: TGFb-stimulated biological replicate 1 of 2, slide 2

source_name: TGFb1-stimulated A549 cell line, SMAD3 IP

value: lung alveolar epithelial cell line

tag: cell line

source_name: TGFb1-stimulated A549 cell line, anti-FLAG IP


title: Pax7CreER-derived tumor mouse 332

source_name: mouse 332

value: Tumor


title: Pax7CreER-derived tumor mouse 324

source_name: mouse 324


title: A1-84-14

description: CGH A1-84-14  vs H99

source_name: H99 [reference]


title: TGFb-stimulated slide 2, replicate 2

description: TGFb-stimulated biological replicate 2 of 2, slide 2


title: Tn470

description: CGH Tn470  vs H99


title: 1008C_RMN_0month

value: Prostate

value: C


title: C1

description: MCF7(-) cells

source_name: MCF7(-) cells

value: cell culture


title: unstimulated slide 2, replicate1

description: Control biological replicate 1 of 2, slide 2

source_name: control A549 cell line, SMAD3 IP

source_name: control A549 cell line, anti-FLAG IP


title: T2

source_name: xenograft of MCF7(-)/MT1-MMP(L50D) orthotopic tumors in mouse

value: xenograft in mice


title: CBS7779-B1WB

status: Public on May 31 2011

description: CGH CBS7779-B1Wb vs H99

value: white strain, less melanin production


title: CBS7779 B1WCB4

description: CGH CBS7779-B1WCB4 vs H99

source_name: CBS7779 B1WCB4

value: black strain, more melanin production


title: CBS7779-W3BB

description: CGH CBS7779-W3BB vs H99

value: black strain


title: CBS7779 B1

description: CGH CBS7779-B1 vs H99


title: unstimulated slide 2, replicate2

description: Control biological replicate 2 of 2, slide 2


title: CBS7779-W3

description: CGH CBS7779 W3 vs H99


title: CBS7779 W3BC

description: CGH CBS7779-W3BC vs H99

source_name: CBS7779 W3BC


title: CBS7779 B1WC

description: CGH CBS7779-B1WC vs H99

source_name: CBS7779 B1WC


title: B1WCB1

description: CGH CBS7779 B1WCB1 vs H99


title: CBS7779 W2BB

description: CGH CBS7779-W2BB vs H99

source_name: CBS7779 W2BB


title: JP1086

description: CGH JP1086  vs H99

value: environmental strain


title: OA patient 8 BMMC

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

hyb_protocol: 15 ug of fragmented cRNA were hybridized for 16 hr at 45 on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing:
The data were analyzed with GeneChip Operating Software 1.4 using Affymetrix default signal settings and global scaling as the normalization method. Only data with present or marginal detection calls were selected for further analysis.

The false discovery rate was used to determine statistically significant differences in the mRNA expression levels between the RA and OA groups. The criterion for the statistical significance was q<0.001. Genes were identified as differentially expressed if their mean signal values were at least 50% different between the two groups.

source_name: bone marrow-derived mononuclear cells from OA patient

label_protocol: cDNA were synthesized from 3 ug total RNA according to the One-Cycle Target Labeling protocol, and biotinylated cRNA were prepared followed by fragmentation.

extract_protocol: Patient bone marrow were collected and kept at 4C. All BMMC were isolated by using Ficoll-Paque Plus. Total RNA from BMMC was extracted by using the RNeasy Mini Kit (Qiagen).

value: bone marrow

value: mononuclear cells

value: female

tag: disease

value: osteoarthritis


title: OA patient 9 BMMC


title: CBS7779-W2

description: CGH CBS7779 W2 vs H99


title: OA patient 10 BMMC


title: CBS7779-W2BA

description: CGH CBS7779-W2BA vs H99


title: CBS7779-B6

description: CGH CBS7779 B6 vs H99


title: CBS7779 B4

description: CGH CBS7779 B4 vs H99


title: OA patient 3 BMMC


title: CBS7779-B5

description: CGH CBS7779 B5 vs H99


title: W2WB

description: CGH CBS7779 W2WB vs H99


title: CBS7779-W1

description: CGH CBS7779 W1 vs H99


title: CBS7779 B1WA

description: CGH CBS7779-B1WA vs H99

source_name: CBS7779 B1WA


title: OA patient 7 BMMC


title: OA patient 6 BMMC


title: OA patient 5 BMMC


title: RA patient 5 BMMC

source_name: bone marrow-derived mononuclear cells from RA patient

value: rheumatoid arthritis


title: RA patient 6 BMMC


title: RA patient 4 BMMC


title: RA patient 8 BMMC


title: OA patient 1 BMMC


title: RA patient 2 BMMC


title: RA patient 1 BMMC


title: Clear-cell renal cell carcinoma RO G

status: Public on May 28 2011

city: Rennes

first: Julien

last: Edeline

address: Av prof leon Bernard

country: France

institute: CNRS-Université Rennes1

hyb_protocol: 750 ng of the two cDNA labelled Cyanine 3 and Cyanine 5 were hybridizated using the kit In-Situ Hybridization Kit Plus - PN 5184-3568  - Agilent Technologies

scan_protocol: Agilent Technologies Scanner G2505B US22502565  Agilent Technologies Scanner G2505B US22502565 Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Clear-cell renal cell carcinoma RO G

label_protocol: cRNA were amplified from 350 ng of total RNA were amplified and fluorescent cDNA were synthesis from cRNA using the kit Agilent Low RNA Input Fluorescent Linear Amplification Kit - PN 5184-3523 - Agilent Technologies

extract_protocol: Total RNA was extracted from snap-frozen tumours using the Qiamp total RNA kit - PN 74104 -QIAGEN, Hilden, Germany after histological control.

treatment_protocol: Immediately after nephrectomy, a sample was taken from the tumor and frozen in liquid nitrogen

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: n (tnm stage)

tag: m (tnm stage)

tag: fuhrman grade

tag: renal vein involvement

tag: inferior vena cava involvement

tag: peri-nephric fat involvement

tag: sarcomatoid component

tag: tumor necrosis

tag: microvascular invasion

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

tag: survival time

value: Clear-cell renal cell carcinoma

source_name: Total RNA from pooled tumor RNA samples

value: Total RNA from pooled tumor RNA samples


title: Clear-cell renal cell carcinoma RI P

source_name: Clear-cell renal cell carcinoma RI P

tag: tissue

tag: sample type


title: Clear-cell renal cell carcinoma MA F

source_name: Clear-cell renal cell carcinoma MA F

tag: age at diagnosis (y)

tag: t (tnm stage)


title: Clear-cell renal cell carcinoma PI G

source_name: Clear-cell renal cell carcinoma PI G

tag: n (tnm stage)

tag: m (tnm stage)


title: Clear-cell renal cell carcinoma RO A

source_name: Clear-cell renal cell carcinoma RO A

tag: fuhrman grade

tag: renal vein involvement


title: RA patient 7 BMMC

tag: cell type

tag: gender

tag: age

tag: disease


title: Clear-cell renal cell carcinoma TE M

source_name: Clear-cell renal cell carcinoma TE M

tag: peri-nephric fat involvement

tag: sarcomatoid component

tag: tumor necrosis

tag: microvascular invasion

tag: microvascular density (mvd)


title: Clear-cell renal cell carcinoma PO J

source_name: Clear-cell renal cell carcinoma PO J

tag: inferior vena cava involvement

tag: progression (1=yes, 0=no)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

tag: survival time

tag: tissue


title: Clear-cell renal cell carcinoma TH M

source_name: Clear-cell renal cell carcinoma TH M

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: n (tnm stage)

tag: m (tnm stage)

tag: fuhrman grade

tag: sample type


title: Clear-cell renal cell carcinoma PE R

source_name: Clear-cell renal cell carcinoma PE R

tag: renal vein involvement

tag: peri-nephric fat involvement


title: OA patient 2 BMMC

tag: cell type

tag: gender

tag: age

tag: disease


title: RA patient 9 BMMC


title: Clear-cell renal cell carcinoma PR C

source_name: Clear-cell renal cell carcinoma PR C

tag: inferior vena cava involvement

tag: sarcomatoid component

tag: tumor necrosis

tag: microvascular invasion

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)


title: Clear-cell renal cell carcinoma RI J

source_name: Clear-cell renal cell carcinoma RI J

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

tag: survival time

tag: tissue


title: Clear-cell renal cell carcinoma ST M

source_name: Clear-cell renal cell carcinoma ST M

tag: n (tnm stage)

tag: m (tnm stage)

tag: fuhrman grade

tag: renal vein involvement

tag: peri-nephric fat involvement

tag: sample type


title: Clear-cell renal cell carcinoma LE S

source_name: Clear-cell renal cell carcinoma LE S

tag: inferior vena cava involvement

tag: sarcomatoid component


title: Clear-cell renal cell carcinoma JA E

source_name: Clear-cell renal cell carcinoma JA E

tag: tumor necrosis

tag: microvascular invasion


title: Clear-cell renal cell carcinoma LE G

source_name: Clear-cell renal cell carcinoma LE G

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)


title: Clear-cell renal cell carcinoma LE J

source_name: Clear-cell renal cell carcinoma LE J

tag: age at diagnosis (y)

tag: t (tnm stage)


title: Clear-cell renal cell carcinoma LE A

source_name: Clear-cell renal cell carcinoma LE A

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)


title: Clear-cell renal cell carcinoma LE E

source_name: Clear-cell renal cell carcinoma LE E

tag: survival time

tag: tissue

source_name: Total RNA from pooled tumor RNA samples


title: OA patient 4 BMMC

source_name: bone marrow-derived mononuclear cells from OA patient

tag: cell type

tag: gender

tag: age

tag: disease


title: RA patient 3 BMMC

source_name: bone marrow-derived mononuclear cells from RA patient


title: Clear-cell renal cell carcinoma GU R

source_name: Clear-cell renal cell carcinoma GU R

tag: n (tnm stage)

tag: m (tnm stage)

tag: fuhrman grade

tag: renal vein involvement

tag: peri-nephric fat involvement

tag: sample type


title: Clear-cell renal cell carcinoma GO C

source_name: Clear-cell renal cell carcinoma GO C

tag: inferior vena cava involvement

tag: sarcomatoid component

tag: tumor necrosis

tag: microvascular invasion

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)


title: Clear-cell renal cell carcinoma HE L

source_name: Clear-cell renal cell carcinoma HE L

tag: age at diagnosis (y)

tag: t (tnm stage)

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)

tag: survival time

tag: tissue


title: Clear-cell renal cell carcinoma EM M

source_name: Clear-cell renal cell carcinoma EM M

tag: n (tnm stage)

tag: m (tnm stage)


title: Clear-cell renal cell carcinoma GU N

source_name: Clear-cell renal cell carcinoma GU N

tag: fuhrman grade

tag: renal vein involvement


title: Clear-cell renal cell carcinoma JA J

source_name: Clear-cell renal cell carcinoma JA J

tag: peri-nephric fat involvement

tag: sample type


title: Clear-cell renal cell carcinoma LU M

source_name: Clear-cell renal cell carcinoma LU M

tag: inferior vena cava involvement

tag: sarcomatoid component


title: Clear-cell renal cell carcinoma CH G

source_name: Clear-cell renal cell carcinoma CH G

tag: tumor necrosis

tag: microvascular invasion


title: Clear-cell renal cell carcinoma DE R

source_name: Clear-cell renal cell carcinoma DE R

tag: microvascular density (mvd)

tag: progression (1=yes, 0=no)


title: Clear-cell renal cell carcinoma BO V

source_name: Clear-cell renal cell carcinoma BO V

tag: age at diagnosis (y)

tag: t (tnm stage)


title: Clear-cell renal cell carcinoma DE G

source_name: Clear-cell renal cell carcinoma DE G

tag: death (1=yes, 0=no)

tag: death from cancer (1=yes, 0=no)