title: kidney_tumor_poolN1 (expression set)

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
R1T Cy5 (14)
251368010014_rim2_1TCy5_2NCy3

Pooled samples are from 14 clear cell RCC patients, 2 papillary RCC patients, and 1 chromophobe RCC patient.

hyb_protocol: A total of four array slides were hybridized with 750 ng of Cy3- or Cy5-labeled cRNAs. Hybridization was performed with an Agilent in situ Hybridization Kit Plus, as recommended by the manufacturer.

scan_protocol: Slides were washed and processed according to the Agilent Oligo Microarray Processing protocol and scanned on a GenePix 4000B scanner (Molecular Devices).

data_processing: To extract intensity data from the scanned images we used ArrayVision Software (Imaging Research Inc.). The raw data employed in our analyses is the Median-based Trimmed Mean density value (MTM) for each spot. The MTM density for each spot was subtracted by the individual background surrounding the spot. The resulting subtracted intensity raw data (sMTM) is available in suplemmentary tables. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, expression data were normalized between experiments by quantile (Bolstad et al., 2003. Bioinformatics, 19(2): p. 185-93). Genes were considered expressed if intensity spot was above the mean plus 2 SD intensity of negative controls spots in 3 out 4 microarrays. Only spots considered valid and expressed have the normalized data value at matrix template. All the others are assigned as "Null". For the present study, we analyzed only valid and expressed spots (4303 spots) corresponding to unique antisense lncRNAs (see GPL4051 description).

source_name: kidney, tumor tissue

label_protocol: 17 tumor patient samples were combined into four pools by mixing equal amounts of total RNA. The total RNA pool (300 ng) was used as template for amplification of poly(A) RNA by T7-RNA polymerase with the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies), which generated Cy5- or Cy3-labeled cRNAs.

extract_protocol: Total RNA was purified from tissue extracts by the Trizol protocol (Technologies, Rockville, MD). Total RNA was treated with RNase-free DNase (RNeasy - Qiagen) for 15min to minimize genomic DNA contaminants. Purity of the isolated RNA was estimated by measuring the ratio A 260/A 280. Integrity of the total RNA was checked by electrophoresis using the total RNA Nano assay in the 2100 Bioanalyzer (Agilent Technologies).

tag: disease

value: renal cell carcinoma (RCC)

tag: tissue

value: kidney tumor

tag: sample type

value: pool


title: SKBR3_reamplified single-cell WGA_PCR-T2_10probes

status: Public on Jan 21 2014

type: genomic

city: Regensburg

first: Zbigniew

middle: Tadeusz

last: Czyz

address: Josef-Engert-Strasse 9

department: Project Group Personalized Tumor Therapy, Regensburg

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

description:
SKBR3 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
US94700331_252206026397_S01_CGH_107_Sep09_1_3.txt
SKBR3_reamplified single-cell WGA_PCR-T2
samples used to assess the accuracy of the single-cell aCGH protocol in terms of quantitative assessment of CNAs. Profile of this samples is depicted in the Fig. 4 of the manuscript.

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011). Slight modifications were introduced WGA products processed with the PCR-based labeling approaches. Here, the hybridization mix consisted of 5.0 µg of Cot1-DNA (Roche Diagnostics), 12 µl of 10x Blocking Reagent (Agilent Technologies), 60 µl of 2x Hi RPM Hybridization Buffer, 1% (v/v) of both Tween20 and Igepal and 19 µl of both test and reference DNA. For each hybridization 100 µl of the hybridization mix was applied on the array and hybridized at 65◦C for 24 h. Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature, twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing: Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 6.5.0.18 Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 6.5. Centralization algorithm was set to a threshold of 6.0 and bin size of 10. To avoid false positive calls, aberration filters were applied to define the minimum log2 ratio (minimum absolute average log ratio for region = 0.3) and the minimum number of probes in an aberrant interval (minimum number of probes in region = 10 for unamplified DNA and freshly picked cells or minimum number of probes in region = 25 for WGA products generated with immunostained cells and FFPE samples).  The log2 ratios were obtained using the Agilent Genomic Workbench 6.5.0.18.

molecule: genomic DNA

organism: Homo sapiens

source_name: SKBR3 breast cancer cell line

label_protocol:
Random-primed DNA labeling approach (RP labeling):
Test and reference DNA samples were labeled using SureTag DNA Labeling Kit (Agilent Technologies) according to the instruction provided by the supplier (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011). Briefly, 1.5 - 2.0 µg of the purified input DNA (WGA product or unamplified genomic DNA) was supplemented with 5 µl of Random Primer Mix and filled up with H2O to 31 µl. Unamplified DNA and WGA products samples were denatured at 95◦C for 10 or 3 minutes, respectively. Sample tubes were transferred on ice and incubated for 5 min. The labeling reaction with exo-Klenow fragment consisted of the following ingredients: 31 µl of denatured DNA, 10 µl of 5x Reaction Buffer, 5.0 µl of 10x dNTP Mix, 3.0 µl of Cy5-dUTP (test) or Cy3-dUTP (reference) and 1.0 µl of Exo(-) Klenow fragment. Labeling reaction was run at 37◦C for two hours, followed by an inactivation step at 65◦C for 10 minutes. Labeled DNA was purified using Ultra 0.5 purification system with a size cut-off of 30 kDa. DNA yields and dye incorporation rates were quantified using the NanoDrop ND-1000 instrument.
PCR-based labeling using dye-conjugated universal primer (PCR-T1):
Placement of the dye on the universal primer provides the advantage that all restriction digestion fragments present in the WGA product irrespectively of their size will be labeled with the same amount of dye. To avoid cross-hybridization of adapter sequences flanking amplicons in the WGA products, test and reference samples were labeled using different PCR-adapters. Test samples were labeled with the PCR-adapter incorporated in the Ampli1™ WGA kit, while all the reference DNA samples were amplified using the following adapters: MIB5 (5’-TGAGCTGGTCATTGCGCATGGT-3’) and ddMse XI (5’-TAACCATGCGC-3’). Universal primers used in the labeling reaction were directly conjugated with either Cy5 in the case of Ampli1™ universal primer [5’-TAGTGGGATTCCTGCTGTCAGT-3’] or Cy3 in the cases of MIB5 primer [5’-TGAGCTGGTCATTGCGCATGGT-3’] (underscores indicate the placement of the dye). The labeling PCR was run in a total volume of 50 µl reaction composed of 5 µl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 µM of dye-conjugated LIB1 or MIB5 primer (for test and reference sample, respectively), 350 µM of dNTPs, 0.5 µl BSA (Roche), 3.75 U of Expand-Long-Template DNA Polymerase (Roche Diagnostics) and 1.0 µl of the template DNA. The PCR was programmed as follows: 10 cycle of 94◦C for 15 sec, 51◦C for 30 sec and 65◦C for 3:30 min, 2 cycles of 94◦C for 15 sec, 51◦C for 30 sec and 65◦C for 3:30 min (extended by 10 sec every cycle), followed by a final elongation step of 7 min at 65◦C. Products were purified using the Amicon Ultra 0.5 System (cut-off size 100 kDa) and quantified with the NanoDrop ND-1000 instrument.
PCR-based labeling using incorporation of dye-conjugated dNTPs (PCR-T2):
WGA products were labeled by PCR in the presence of Cy5 or Cy3 conjugated dCTP and dUTP. Incorporation of the fluorescent dyes using the dNTPs provided the advantage that adapters flanking each amplicon in the WGA product could be removed prior to aCGH hybridization, thereby avoiding unspecific cross-hybridization of test sample with reference DNA and oligonucleotide probes on the array. For each sample two 50µl PCR reactions were run in parallel each comprising 5 µl of 10x Expanded Long Template Buffer 1 (Roche Diagnostics), 2.4 µM of the universal primer (LIB1 or MseLig-21, depending on the adapter sequence incorporated in the WGA product), 350 µM of dATP and dGTP, 315 µM of dCTP and dTTP, 35 µM of Cy5/Cy3-dCTP and Cy5/Cy3-dUTP (GE Healthcare), 0.5 µl of BSA (Roche Diagnostics), 7.5 U of Expand-Long-Template DNA Polymerase (Roche) and 0.5 µl of the template DNA. Labeling products were pooled and purified using the Amicon Ultra 0.5 System (100 kDa cut-off). DNA yields and dye incorporation rates were quantified using the NanoDrop ND-1000 Instrument.

growth_protocol: Esophageal cancer cell lines (PT-1590 and OE-19) were grown in RPMI 1640 medium (PAN-Biotech) supplemented with 10% fetal calf serum (FCS)(PAN-Biotech), 2mM L-Glutamic acid (PAN-Biotech) and 1% of Penicillin/Streptomycin solution (PEN STREP) (PAN-Biotech). Breast cancer cell lines SKBR3, MDA-MB-453 and MDA-MB-361 were cultured in DMEM (PAN-Biotech) medium supplemented with 10% FCS (PAN-Biotech), 2mM L-Glutamic acid (PAN-Biotech) and  1% PEN STREP (PAN-Biotech). BT-474 was grwon in RPMI 1640 medium supplemented with 10% FCS, 2mM L-Glutamic acid, 1% P/S and 1mM sodium pyruvate.

extract_protocol: Total genomic DNA (bulk DNA) was extracted using the Dbeasy Blood & Tissue Kit (QIAgen) following manufacture's instructions. All single cells, cell pools (few hundred cells) and microdissected specimens from formalin fixed paraffin embedded (FFPE) tumor tissue were amplified using the Ampli1™ WGA Kit (Silicon Biosystems).

tag: cell line/clinical sample

value: cell line (DSMZ)

tag: tumor sample/healthy donor

value: tumor sample

tag: amplified/unamplified dna

value: amplified - Ampli1 WGA

tag: primary/reamplified wga

value: reamplified WGA

tag: labeling protocol

tag: gender

value: female

tag: bulk dna/cell pool wga/single-cell wga

value: single-cell WGA

source_name: Healthy donor: cord blood; a pool of 4 single-cell WGA products from the same donor

value: Clinical sample

value: healthy donor


title: ABC_lymph node metastasis_FFPE_PCR-2_10probes

description:
Advanced breast cancer patient; Lymph Node Metastasis; FFPE tissue sample (10 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_1.txt
ABC_lymph node metastasis_FFPE_PCR-2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

source_name: Lymph node metastasis, microdissected FFPE sample

value: clinical sample

value: WGA FFPE


title: ABC_DCC_time point 2_single cell 1_10probes

description:
Advanced breast cancer patient; DCC; time point #2; single cell #1 (10 probes)
Raw data file:
252206033107_201303131422_S01_CGH_107_Sep09_1_2.txt
ABC_DCC_time point 2_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

source_name: Disseminated cancer cell obtained from bone marrow

tag: time

value: time point 2


title: OE-19_reamplified single-cell WGA_RP-labeling_10probes

description:
OE-19 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
252206026310_201205101421_S01_CGH_107_Sep09_1_4.txt
OE-19_reamplified single-cell WGA_RP-labeling
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. S3 of the manuscript

source_name: OE-19 esophageal cancer cell line

value: cell line (European Collection of Cell Cultures)

value: RP-labeling

value: male

value: single-cell WGA (2.0µg)


title: OE-19_primary single-cell WGA_RP-labeling_10probes

description:
OE-19 genomic DNA; single-cell WGA; primary WGA (10 probes)
Raw data file:
252206026310_201205101421_S01_CGH_107_Sep09_1_3.txt
OE-19_primary single-cell WGA_RP-labeling
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. 2 of the manuscript

value: primary WGA


title: kidney_tumor_poolN2 (expression set)

type: RNA

country: USA

description:
R2T Cy3 (13)
251368010013_rim1_1NCy5_2TCy3

Pooled samples are from 14 clear cell RCC patients, 2 papillary RCC patients, and 1 chromophobe RCC patient.

molecule: total RNA

value: renal cell carcinoma (RCC)

value: kidney tumor

value: pool


title: OE-19_reamplified single-cell WGA_PCR-T2_10probes

description:
OE-19 genomic DNA; single-cell WGA; reamplified WGA (10 probes)
Raw data file:
252206025381_201203291502_S01_CGH_107_Sep09_1_2.txt
OE-19_reamplified single-cell WGA_PCR-T2
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. S3 of the manuscript

value: tumor sample

value: amplified - Ampli1 WGA


title: ABC_DCC_time point 1_single cell 1_10probes

description:
Advanced breast cancer patient; DCC; time point #1; single cell #1 (10 probes)
Raw data file:
252206033109_201303131509_S01_CGH_107_Sep09_1_3.txt
ABC_DCC_time point 1_single cell 1
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

value: time point 1

value: reamplified WGA

value: female


title: ABC_primary tumor_FFPE_PCR-2_10probes

description:
Advanced breast cancer patient; Primary Tumor; FFPE tissue (10 probes)
Raw data file:
252206026513_201304171359_S01_CGH_107_Sep09_1_4.txt
ABC_primary tumor_FFPE_PCR-2
sample used to identify minimal regions among DCCs and corresponding tumor tissues of advanced breast cancer patient. Data depicted in the Fig. 5 and S5 of the manuscript

source_name: Primary breast tumor, microdissected FFPE sample

value: Clinical sample

value: healthy donor

value: single-cell WGA


title: OE-19_primary single-cell WGA_PCR-T2_10probes

description:
OE-19 genomic DNA; single-cell WGA; primary WGA (10 probes)
Raw data file:
252206025381_201203291502_S01_CGH_107_Sep09_1_1.txt
OE-19_primary single-cell WGA_PCR-T2
sample used to compare the performance of the primary and secondary WGA and simultaniously assess the performance of two labeling approaches (RP-labeling vs. PCR-T2 labeling). aCGH profiles depicted in the Fig. 2 of the manuscript


title: Mouse fetal intestinal spheroid/organoid pair _E16_2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

data_processing: A non-linear Lowess (locally weighted scatter plot) normalization method was carried out.

organism: Mus musculus

source_name: Mouse E16 intestinal spheroid _Biological Replica2

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment

growth_protocol: Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee. Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum. Small intestine were cultured ex vivo from a given embryo/mouse (at E16, E18 or P0) in matrigel in a culture medium composed of  Advanced-DMEM/F12 medium supplemented with 2 mM L-Glutamine, penicillin-streptomycin cocktail and 2% fetal bovine serum containing the following growth factors at a final concentration: 50 ng/ml EGF (Peprotech), 100 ng/ml Noggin (Peprotech), and 500 ng/ml R-spondin1 (R&D System).

extract_protocol: total RNA from ex vivo cultures was extracted using the Mirvana kit (Ambion, Texas, USA)

treatment_protocol: For each cultured sample, after the first seeding, spheroids and organoids were selectively picked up and replated for 3 passages to reach sample homogeneity.

tag: strain background

tag: genotype

value: Wild-type

value: cultured small intestine epithelial cells

tag: culture

value: spheroid cells

tag: Stage

source_name: Mouse E16 intestinal organoid _Biological Replica2

value: organoid cells


title: kidney_tumor_patient29T_replica2 (survival set)

description:
29T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

hyb_protocol: Labeled targets were resuspended in 200 µl of 1 x hybridization buffer (50% formamide, 25% of proprietary Microarray Hybridization Buffer Version 2 from Amersham Biosciences cat. RPK0325), denatured for 2 min at 92 ºC and centrifuged at 13,000 rpm for 5 min. All slide processing steps (blocking, hybridization, washing) were carried out on an automated slide processor (ASP) from Amersham Biosciences. The slides were incubated for 16h at 42ºC and subsequently washed at room temperature in 1xSSC/0.2%SDS for 5min, 0.1xSSC/0.2%SDS for 5 min and in 0.1XSSC for 3 min. After the washing steps, slides were flushed with isopropanol and dried with an air flush at 42ºC.

scan_protocol: Images were obtained by laser scanning using the GenIII Array Scanner (Amersham Biosciences). Slides were scanned with 600 volts of PMT voltage.

data_processing: We employed in our analyses the background subtracted Median-based Trimmed Mean (sMTM) density value calculated for each spot by ArrayVision software. The MTM value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median. The MTM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels). Genes were considered expressed if its probe intensity was higher than the local background intensity and above the threshold defined by the average intensity plus three standard deviations of a set of plant-derived negative control cDNA probes (GE Healthcare). Probes were excluded from further analyses when they were detected in less than 90% of the arrays in any of the two groups, alive without disease or dead after 5-years of follow-up, for the statistical analysis. We normalized expression data (3205 valid spots) between experiments by quantile (Bolstad et al., 2003. Bioinformatics, 19(2): p. 185-93).

source_name: tumor kidney tissue, cancer-specific death

label_protocol: Complementary RNA (cRNA) was obtained by amplification following the Wang protocol method (Wang et al. Nat Biotechnol 2000, 18:457-459). Briefly, using a poly-dT primer incorporating a T7 promoter, cDNA was synthesized from 3 ug total RNA using Superscript III enzyme (Invitrogen, Carlsbad, CA). Double-stranded cDNA was obtained using a template switch oligo primer and the Advantage cDNA Polymerase mix kit (Clontech Laboratories, Mountain View, CA). Double-stranded cDNA was purified by phenol/chloroform extraction. The aqueous phase was isolated using Phase-Lock Gel Heavy (Brinkmann Instruments, Westbury, NY) and cDNA was precipitated with ethanol. Subsequently, cRNA was generated from the double-stranded cDNA template through in vitro transcription with RNA Polymerase T7 MegaScript (Ambion, Austin, TX). The amplified cRNA was purified using TRIzol reagent (Life Technologies). A second round of amplification was performed with 1 ug of cRNA obtained in the previous step, in the presence of amino-allyl-UTP (Ambion). Amino-allyl-cRNA was treated with RNase-free DNase (RNeasy Mini kit; Qiagen) to remove potential DNA contamination, quantified by spectrophotometry (Nanodrop), and checked for quality with a Bioanalyzer 2100 system (Agilent). A coupling and quenching reaction of amino-allyl-cRNA with Cy5 monoreactive dye was performed (Amersham Pharmacia Biotech, Piscataway, NJ,). Labeled cRNAs were purified from free dye using the RNeasy Mini kit (Qiagen), concentrated with microcon YM-30 columns (Millipore Corporation, Billerica, MA) and resuspended in 50uL of water.

tag: patient identifier

value: clear cell renal cell carcinoma (RCC)

value: male

tag: age at surgery (yrs)

tag: fuhrman grade

value: IV

tag: tumor size (cm)

tag: necrosis

value: yes

tag: capsule infiltration

tag: tnm classification (t)

tag: tnm classification (n)

value: no data available

tag: tnm classification (m)

tag: organ metastasis at surgery

value: lung

tag: organ metastasis after surgery

value: bones

tag: patient status

value: cancer-specific death

tag: follow-up (months)


title: kidney_tumor_patient30T_replica1 (survival set)

description:
30T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: disease

tag: tissue

value: kidney tumor

tag: gender

value: II

value: brain, lung, bones


title: kidney_tumor_patient28T_replica1 (survival set)

description:
28T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

source_name: tumor kidney tissue, alive without cancer

value: III

value: no

value: alive without cancer


title: kidney_tumor_patient29T_replica1 (survival set)

description:
29T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient33T_replica1 (survival set)

description:
33T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient28T_replica2 (survival set)

description:
28T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient30T_replica2 (survival set)

description:
30T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: female


title: kidney_tumor_patient33T_replica2 (survival set)

description:
33T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient32T_replica2 (survival set)

description:
32T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: peritoneum


title: kidney_tumor_patient32T_replica1 (survival set)

description:
32T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: Mouse fetal intestinal spheroid/organoid pair _E18

scan_protocol: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes

source_name: Mouse E18 intestinal spheroid

tag: strain background

tag: genotype

value: Wild-type

value: cultured small intestine epithelial cells

tag: culture

value: spheroid cells

tag: Stage

source_name: Mouse E18 intestinal organoid

value: organoid cells


title: kidney_tumor_poolN3 (expression set)

description:
R3T Cy5 (16)
251368010016_rim4_3TCy5_4NCy3

Pooled samples are from 14 clear cell RCC patients, 2 papillary RCC patients, and 1 chromophobe RCC patient.

value: renal cell carcinoma (RCC)

tag: sample type

value: pool


title: OE-19_ bulk gDNA_10probes

description:
OE-19 genomic DNA; bulk DNA (10 probes)
Raw data file:
US94700331_252206026494_S01_CGH_107_Sep09_1_1.txt
OE-19_ bulk gDNA
sample used as benchmark for comparison with the corresponding single-cell WGA samples: profiles of the sampels included in the Fig.2 and Fig.S3 of the manuscript

tag: cell line/clinical sample

value: cell line (European Collection of Cell Cultures)

tag: tumor sample/healthy donor

value: tumor sample

tag: amplified/unamplified dna

value: unamplified

tag: primary/reamplified wga

tag: labeling protocol

value: RP-labeling

value: male

tag: bulk dna/cell pool wga/single-cell wga

value: bulk DNA (1.5µg)

source_name: Healthy donor: cord blood bulk gDNA

value: Clinical sample

value: healthy donor


title: Mouse fetal intestinal spheroid/organoid pair _E16_1

source_name: Mouse E16 intestinal spheroid_Biological Replica1

source_name: Mouse E16 intestinal organoid_Biological Replica1


title: Mouse Newborn intestinal spheroid/organoid pair _P0

source_name: Mouse P0 intestinal spheroid

source_name: Mouse P0 intestinal organoid


title: kidney_tumor_patient26T_replica2 (survival set)

description:
26T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: patient identifier

value: clear cell renal cell carcinoma (RCC)

value: kidney tumor

tag: age at surgery (yrs)

tag: fuhrman grade

value: II

tag: tumor size (cm)

tag: necrosis

value: no

tag: capsule infiltration

value: yes

tag: tnm classification (t)

tag: tnm classification (n)

value: no data available

tag: tnm classification (m)

tag: organ metastasis at surgery

tag: organ metastasis after surgery

value: alive without cancer


title: kidney_tumor_patient24T_replica1 (survival set)

description:
24T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: disease

tag: tissue

tag: gender

value: IV

value: liver, spleen

tag: patient status

value: cancer-specific death

tag: follow-up (months)


title: kidney_tumor_patient11T_replica2 (survival set)

description:
11T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: III


title: kidney_tumor_patient24T_replica2 (survival set)

description:
24T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient9T_replica1 (survival set)

description:
9T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient26T_replica1 (survival set)

description:
26T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: female


title: kidney_tumor_patient13T_replica1 (survival set)

description:
13T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient15T_replica2 (survival set)

description:
15T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient13T_replica2 (survival set)

description:
13T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient15T_replica1 (survival set)

description:
15T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient9T_replica2 (survival set)

description:
9T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient10T_replica2 (survival set)

description:
10T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient11T_replica1 (survival set)

description:
11T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient31T_replica2 (malignancy set)

description:
31T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

data_processing: We employed in our analyses the background subtracted Median-based Trimmed Mean (sMTM) density value calculated for each spot by ArrayVision software. The MTM value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median. The MTM density for each spot was subtracted by the median background surrounding the spot (distance of 2 pixels with 3 widths of pixels). Genes were considered expressed if its probe intensity was higher than the local background intensity and above the threshold defined by the average intensity plus three standard deviations of a set of plant-derived negative control cDNA probes (GE Healthcare). Probes were excluded from further analyses when they were detected in less than 90% of the arrays in any of the two groups, nontumor or tumor for the statistical analysis. We normalized expression data (3055 valid spots) between experiments by quantile (Bolstad et al., 2003. Bioinformatics, 19(2): p. 185-93).

source_name: kidney, tumor tissue

value: primary kidney tumor

value: lung, adjacent tissues

value: alive with cancer


title: kidney_tumor_patient30T_replica1 (malignancy set)

description:
30T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: brain, lung, bones


title: kidney_tumor_patient7T_replica2 (survival set)

description:
7T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: male


title: kidney_tumor_patient10T_replica1 (survival set)

description:
10T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: clear cell renal cell carcinoma (RCC)


title: kidney_tumor_patient30T_replica2 (malignancy set)

description:
30T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient28T_replica1 (malignancy set)

description:
28T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient31T_replica1 (malignancy set)

description:
31T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient3T_replica1 (survival set)

description:
3T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: kidney tumor

value: endocava, bones


title: kidney_tumor_patient1T_replica2 (survival set)

description:
1T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient7T_replica1 (survival set)

description:
7T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: II


title: kidney_tumor_patient5T_replica1 (survival set)

description:
5T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: yes

value: liver


title: kidney_tumor_patient5T_replica2 (survival set)

description:
5T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: no data available


title: kidney_tumor_patient3T_replica2 (survival set)

description:
3T_rep_R

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: IV


title: kidney_tumor_patient26T_replica2 (malignancy set)

description:
26T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: no

value: alive without cancer


title: kidney_tumor_patient24T_replica2 (malignancy set)

description:
24T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: liver, spleen

value: cancer-specific death


title: kidney_tumor_patient26T_replica1 (malignancy set)

description:
26T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: primary kidney tumor

value: female


title: kidney_tumor_patient1T_replica1 (survival set)

description:
1T_rep_L

A total of 3205 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3205 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 150 spots detected in less than 90% of the arrays in one of the two groups (alive without disease or dead after 5-years of follow-up) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: III


title: kidney_tumor_patient11T_replica2 (malignancy set)

description:
11T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient11T_replica1 (malignancy set)

description:
11T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_poolN4 (expression set)

description:
R4T Cy3 (15)
251368010015_rim3_3NCy5_4TCy3

Pooled samples are from 14 clear cell RCC patients, 2 papillary RCC patients, and 1 chromophobe RCC patient.

value: renal cell carcinoma (RCC)

tag: sample type

value: pool


title: kidney_tumor_patient10T_replica2 (malignancy set)

description:
10T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: patient identifier

value: clear cell renal cell carcinoma (RCC)


title: kidney_tumor_patient10T_replica1 (malignancy set)

description:
10T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: age at surgery (yrs)


title: kidney_tumor_patient9T_replica2 (malignancy set)

description:
9T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: male

tag: fuhrman grade


title: kidney_tumor_patient28T_replica2 (malignancy set)

description:
28T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: tumor size (cm)


title: kidney_tumor_patient8T_replica2 (malignancy set)

description:
8T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: necrosis

value: dead from other causes


title: kidney_tumor_patient8T_replica1 (malignancy set)

description:
8T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: II

tag: capsule infiltration


title: kidney_tumor_patient5T_replica1 (malignancy set)

description:
5T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: yes

tag: tnm classification (t)


title: kidney_tumor_patient5T_replica2 (malignancy set)

description:
5T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: tnm classification (n)

value: liver


title: kidney_tumor_patient3T_replica2 (malignancy set)

description:
3T_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: no data available

tag: tnm classification (m)

value: endocava, bones


title: kidney_tumor_patient24T_replica1 (malignancy set)

description:
24T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: IV

tag: organ metastasis at surgery


title: kidney_nontumor_patient28N_replica1 (malignancy set)

description:
28N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

source_name: kidney, adjacent nontumor tissue

value: adjacent nontumor kidney tissue

value: alive without cancer


title: kidney_nontumor_patient26N_replica1 (malignancy set)

description:
26N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient26N_replica2 (malignancy set)

description:
26N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient24N_replica1 (malignancy set)

description:
24N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: cancer-specific death


title: kidney_tumor_patient9T_replica1 (malignancy set)

description:
9T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: primary kidney tumor

tag: organ metastasis after surgery


title: kidney_nontumor_patient11N_replica2 (malignancy set)

description:
11N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: disease


title: kidney_nontumor_patient10N_replica1 (malignancy set)

description:
10N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: tissue

value: female


title: kidney_nontumor_patient11N_replica1 (malignancy set)

description:
11N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: gender


title: kidney_nontumor_patient10N_replica2 (malignancy set)

description:
10N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

tag: patient status


title: kidney_nontumor_patient30N_replica1 (malignancy set)

description:
30N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient30N_replica2 (malignancy set)

description:
30N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient28N_replica2 (malignancy set)

description:
28N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_tumor_patient3T_replica1 (malignancy set)

description:
3T_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient31N_replica1 (malignancy set)

description:
31N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.

value: alive with cancer


title: kidney_nontumor_patient5N_replica1 (malignancy set)

description:
5N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient9N_replica2 (malignancy set)

description:
9N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient9N_replica1 (malignancy set)

description:
9N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient5N_replica2 (malignancy set)

description:
5N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient8N_replica2 (malignancy set)

description:
8N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient24N_replica2 (malignancy set)

description:
24N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient3N_replica2 (malignancy set)

description:
3N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient31N_replica2 (malignancy set)

description:
31N_rep_R

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient3N_replica1 (malignancy set)

description:
3N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: kidney_nontumor_patient8N_replica1 (malignancy set)

description:
8N_rep_L

A total of 3055 spots were considered valid and expressed for analysis from the total of 4608 contained in the platform GPL3985. The Sample data table contains only these 3055 valid spots. Therefore, a total of 1253 spots corresponding to positive controls, negative controls, empty spots or contaminants were eliminated (see platform GPL3985 for a more detailed description). Additionally, 300 spots detected in less than 90% of the arrays in one of the two groups (nontumor or tumor) were filtered. Each array contains one technical replica, named replica left (L) and replica right (R) for each sample.


title: Surg-CTL2, BIOLOGICAL REPLICATE 2

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Human Genome Gene v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (EukGE-Ws2v4).

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

data_processing: The digital data retrieved from the CEL files were processed by Partek Genomic Suite version 6.5 using modified RMA-algorithm.

label: BIOTIN

source_name: normal bowel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Two-Cycle cDNA Synthesis Kit and IVT labeling kit).

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy micro kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

tag: developmental stage

value: neonatal

value: bowel tissue

tag: diagnosis

value: normal bowel


title: Surg-CTL3, BIOLOGICAL REPLICATE 3


title: Pulmonary arterial smooth muscle cells_24 hours in 10%FBS DMEM/F-12_3 mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: PASMC-KO vs. PASMC-WT

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. The normalized data were globally normalized, such that Cy3/Cy5 ratio median=1. The data was generated by Microsoft Excel.

source_name: PASMC-WT

label_protocol: cDNA and Amino Allyl aRNA was synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed according to the protocol supplied by TORAY Industries, Inc.

growth_protocol: Pulmonary arterial smooth muscle cells were incubated in DMEM/F-12 medium containing 10% FBS.

extract_protocol: RNA samples were extracted using the RNeasy kit following the manufacturer's instructions (Qiagen).

treatment_protocol: Pulmonary arterial smooth muscle cells (passages 3) were seeded at 1.5×10^5 cells per well in 12-well plates and incubated in DMEM/F-12 containing 10% FBS for 24 hours.

tag: strain/background

tag: genotype/variation

value: wild-type

value: male

tag: cell type

value: pulmonary arterial smooth muscle cells

source_name: PASMC-KO

value: NOX1 deficient


title: Surg-CTL1, BIOLOGICAL REPLICATE 1


title: SIP5, BIOLOGICAL REPLICATE 5

source_name: spontaneous intestinal perforation (SIP)


title: SIP1, BIOLOGICAL REPLICATE 1

value: spontaneous intestinal perforation (SIP)


title: SIP2, BIOLOGICAL REPLICATE 2


title: NEC5, BIOLOGICAL REPLICATE 5

source_name: necrotising enterocolitis (NEC)

value: necrotising enterocolitis (NEC)


title: PDL-L2_siCont_rhBMP2_12h

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

institute: Osaka Prefecture University

hyb_protocol: Done according to the manufacturer's protocol

data_processing: For individual probe sets, signal intensities from mismatch probes were subtracted from those from perfect match probes to generate net signal intensities. Normalized signal intensities for the individual probe sets were calculated as weighted means from the net signal intensities by the method of Tukey's Biweight Estimate using Affymetrix GCOS ver 1.4.

label: biotin

source_name: periodontal ligament fibroblast

growth_protocol: PDL-L2 cells were mainatined in alpha-MEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol: AGPC method

treatment_protocol: PDL-L2 cells were treated with an siRNA for endoglin (siENG) or a control siRNA (siCont), which were supplied as SMARTpool siRNAs from Dharmacon. After 48hr, PDL-L2 cells were exposed by rhBMP-2 (250 ng/ml) in differentiation medium containing ascrobic acid and beta-glycerophosphate.

tag: cell line

value: a cell line derived from periodontal ligament fibroblasts

tag: treated with

value: control siRNA (siCont)

tag: exposed to

value: recombinant human BMP-2 (250 ng/ml)


title: PDL-L2_siENG_rhBMP2_12h

scan_protocol: Done according to the manufacturer's protocol

value: siRNA for endoglin (siENG)


title: Surg-CTL4, BIOLOGICAL REPLICATE 4


title: NEC1, BIOLOGICAL REPLICATE 1


title: NEC2, BIOLOGICAL REPLICATE 2


title: SIP3, BIOLOGICAL REPLICATE 3


title: AK_9

city: London

first: Sally

middle: R

last: Lambert

address: Blizard Institute, 4 Newark Street

department: Centre for Cutaneous Research

country: United Kingdom

institute: Queen Mary, University of London

hyb_protocol: Samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned according to the standard Affymetrix protocol

data_processing: Data were analysed in R/Bioconductor using GCRMA normalisation and filtered using a variance of >0.1

label: Biotin

source_name: Actinic Keratosis

label_protocol: 10 ng of RNA was amplified using the NuGen WT-ovation Pico RNA Amplification System and labelled with the FL-ovation Biotin Kit (NuGen).

extract_protocol: RNA was extracted from fresh frozen tissue specimens by laser capture microdissection.

treatment_protocol: Biopsies of tissue were snap frozen with liquid nitrogen upon excision during surgery and stored at -80 oC until use.

value: Actinic keratosis

tag: differentiation status

tag: immune status

value: Immunosuppressed

tag: patient number

value: Male


title: Epi_Cast_Testo12_rep2

city: Helsinki

first: Olli

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description:
replicate 2, 12-h testosterone-treatment
9323675033_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio Program from Illumina.

source_name: adult male

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

growth_protocol: Mice were housed in standard 12-h light-dark cycle and were fed ad libitum.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Tissues were harvested from adult castrated male mice 12 or 24 hours after single testosterone- or vehicle-injection.

value: caput epididymis


title: Epi_Cast_Vehicle12_rep3

description:
replicate 3, 12-h vehicle-treatment
9249051010_E


title: Epi_Cast_Testo12_rep3

description:
replicate 3, 12-h testosterone-treatment
9323675033_C


title: Epi_Cast_Vehicle12_rep2

description:
replicate 2, 12-h vehicle-treatment
9323675032_F


title: VC_24h_rep3

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

country: China

institute: LVRI

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven  (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s  instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: J1 mESCs_VC_24h

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

growth_protocol: The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol: Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The J1 mESCs were treated with a final concentration of RA (1μM), DMSO (1μL), VC (50μg), ddH2O (1μL)

value: J1 mouse embryonic stem cells

value: VC (Vitamin C 50μg) for 24hrs


title: PDL-L2_siCont_vehicle_12h

label_protocol: Done according to the manufacturer's protocol

value: vehicle


title: Epi_Cast_Testo24_rep3

description:
replicate 3, 24-h testosterone-treatment
9323675033_F


title: NEC4, BIOLOGICAL REPLICATE 4

value: neonatal

value: bowel tissue


title: Epi_Cast_Testo24_rep2

description:
replicate 2, 24-h testosterone-treatment
9323675033_E


title: SIP4, BIOLOGICAL REPLICATE 4


title: NEC3, BIOLOGICAL REPLICATE 3


title: AK_10

value: Immunocompetent


title: Epi_Cast_Testo24_rep1

description:
replicate 1, 24-h testosterone-treatment
9323675033_D


title: AK_8


title: VC_24h_rep1


title: Epi_Cast_Testo12_rep1

description:
replicate 1, 12-h testosterone-treatment
9323675033_A


title: AK_7


title: AK_6


title: Epi_Cast_Vehicle12_rep1

description:
replicate 1, 12-h vehicle-treatment
9323675032_E


title: Kid_Cast_Testo24_rep3

description:
replicate 3, 24-h testosterone-treatment
9371989022_F

value: kidney


title: Pulmonary arterial smooth muscle cells_24 hours in 10%FBS DMEM/F-12_3 KO mice

description: PASMC-KO

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments. The data was generated by Microsoft Excel.

source_name: Pulmonary arterial smooth muscle cells, NOX1 deficiency

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark).

extract_protocol: RNA samples were extracted from cells using the miRNeasy mini kit (Qiagen).

value: NOX1 deficient

value: male

value: pulmonary arterial smooth muscle cells


title: VC_24h_rep2


title: Pulmonary arterial smooth muscle cells_24 hours in 10%FBS DMEM/F-12_3 WT mice

description: PASMC-WT

source_name: Pulmonary arterial smooth muscle cells, wild-type

value: wild-type


title: ddH2O_24h_rep1

source_name: J1 mESCs_ddH2O_24h

value: ddH2O (1μL) for 24hrs


title: ddH2O_24h_rep3


title: AK_5

value: Female


title: AK_4

value: Actinic keratosis


title: Kid_Cast_Testo24_rep1

description:
replicate 1, 24-h testosterone-treatment
9371989022_D


title: AK_3

value: Immunosuppressed


title: ddH2O_24h_rep2


title: Kid_Cast_Testo12_rep2

description:
replicate 2, 12-h testosterone-treatment
9371989022_B


title: AK_2

value: Male


title: Kid_Cast_Testo12_rep3

description:
replicate 3, 12-h testosterone-treatment
9371989022_C


title: Kid_Cast_Testo24_rep2

description:
replicate 2, 24-h testosterone-treatment
9371989022_E


title: Kid_Cast_Testo12_rep1

description:
replicate 1, 12-h testosterone-treatment
9371989022_A


title: Sample 8

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: skin from IL23 mouse treated with IMO-3100

hyb_protocol: RNA was hybridized mouse4302 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: strain

tag: treatment

tag: condition

value: IL23 induced phenotype


title: Kid_Cast_Vehicle12_rep3

description:
replicate 3, 12-h vehicle-treatment
9249051010_C

tag: tissue


title: SCC_29

source_name: Cutaneous squamous cell carcinoma

value: Cutaneous SCC

value: Poorly differentiated

tag: gender


title: Sample 10

source_name: skin from IL23 mouse treated with IMO-3100


title: AK_1


title: PMCA4 knockout replicate 4

city: Toronto

first: Mansoor

last: Husain

state: Ontario

address: Room TMDT-3-910, 101 College St.

department: Toronto Gen. Hosp. Res Institute

country: Canada

institute: University Health Network

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: carotid artery; male mouse

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA Amplification Kit Cat.# IL 1791 for Illumina arrays

growth_protocol: P4KO primary VSMC were serum synchronized. Alternatively, P4KO cells electroporated with PMCA4a cDNA  were serum synchronized.

extract_protocol: Total RNA was extracted with Life Technologies PicoPure RNA extraction kit and quantified by Nanodrop.

treatment_protocol: Cells were stimulated with serum and PDGF-BB and harvested at the late G1/S stage of the cell cycle.

value: primary vascular smooth muscle cells

tag: genotype

value: PMCA4 knockout

tag: genetic background

tag: cell cycle stage

value: late G1/S stage


title: Sample 9


title: Kid_Cast_Vehicle12_rep2

description:
replicate 2, 12-h vehicle-treatment
9323675032_D


title: Sample 7


title: SCC_30

value: Moderately-poorly differentiated


title: PMCA4 knockout replicate 3


title: Kid_Cast_Vehicle12_rep1

description:
replicate 1, 12-h vehicle-treatment
9323675032_C

value: kidney


title: PMCA4 knockout replicate 2


title: Pro_Cast_Testo24_rep3

description:
replicate 3, 24-h testosterone-treatment
9371989027_F

value: prostate


title: PMCA4 knockout replicate 1

value: male


title: Sample 4

description: skin from IL23 mouse treated with IMO-8400


title: P4KO rescued with PMCA4a replicate 4

value: PMCA4 knockout rescued with PMCA4a


title: SCC_27


title: Sample 5

source_name: skin from IL23 mouse treated with IMO-8400


title: Pro_Cast_Testo24_rep2

description:
replicate 2, 24-h testosterone-treatment
9371989027_E


title: Pro_Cast_Testo24_rep1

description:
replicate 1, 24-h testosterone-treatment
9371989027_D


title: SCC_25

value: Immunocompetent


title: SCC_28


title: SCC_26


title: Sample 2


title: SCC_22

value: Moderately differentiated


title: Pro_Cast_Testo12_rep1

description:
replicate 1, 12-h testosterone-treatment
9371989027_A


title: P4KO rescued with PMCA4a replicate 2


title: Sample 3


title: Pro_Cast_Testo12_rep3

description:
replicate 3, 12-h testosterone-treatment
9371989027_C


title: Pro_Cast_Testo12_rep2

description:
replicate 2, 12-h testosterone-treatment
9371989027_B


title: P4KO rescued with PMCA4a replicate 3


title: P4KO rescued with Vector B late G1/S replicate 4

description:
PMCA4 knockout C57bl6 male mouse
replicate 4

growth_protocol: P4WT and P4KO primary VSMC were serum synchronized. Alternatively, P4KO cells electroporated with PMCA4b or Vector DNA  were serum synchronized.

tag: transfection

value: vector control

value: PMC4 KO

value: Late G1/S stage


title: SCC_24

value: Male


title: SCC_23

value: Immunosuppressed


title: P4KO rescued with PMCA4a replicate 1


title: P4KO rescued with Vector B late G1/S replicate 3

description:
PMCA4 knockout C57bl6 male mouse
replicate 3


title: P4KO rescued with Vector B late G1/S replicate 2

description:
PMCA4 knockout C57bl6 male mouse
replicate 2


title: Pro_Cast_Vehicle12_rep3

description:
replicate 3, 12-h vehicle-treatment
9249051010_A


title: Sample 1

value: IL23 induced phenotype


title: Pro_Cast_Vehicle12_rep1

description:
replicate 1, 12-h vehicle-treatment
9323675032_A


title: SCC_18

value: Cutaneous SCC


title: SCC_21