title: 72h-3

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Canine Genome 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

organism: Canis lupus familiaris

source_name: mast cell tumor cellline C2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 2ug total RNA

extract_protocol: C2 cells were cultured in RPMI-1640 with stable glutamine medium (Biowest) supplemented with 10% FCS (Biowest), sodium pyruvate (Biochrome), MEM non-essential Amino Acids (Biowest) and penicilline/streptomycine (Gibco) and kept at 5% CO2 and 37°C [44]. Cells were passaged every 6 to 7 days and rethawed from an original stock every 10 to 12 weeks. In all experiments, cells from passages 3 through 10 were used. On time point 0 cell culture flasks were incubated with 100 nM Masitinib Mesylate (AB Science) and kept at 5% CO2 and 37°C. RNA and protein were obtained at time point 0 before and after 12, 24, 48 and 72 hours of masitinib incubation. The supernatant of each flask was centrifuged at 500 g for 5 minutes and washed twice with un-supplemented RPMI-1640 medium (Biowest) with centrifugation steps at 1,000 g for 1 minute. Finally the cell pellet of each flask was equally divided and used for protein or mRNA isolation, respectively. Cell pellets were resolved in 250 µl protein lysis buffer (GE Healthcare) or 500 µl RA1 lysis buffer (NucleoSpin RNA; Macherey&Nagel), respectively. Samples were stored at -80 °C until further use. Cell numbers were determined at each time point using Trypan Blue exclusion (Biochrome) and viable cells were counted in a Neubauer microscope counting chamber. For mRNA isolation pellets were transferred into 500 µl of RA1 lysis buffer (NucleoSpin RNA; Macherey&Nagel) containing 5 µl β-mercaptoethanol and homogenized by pipetting. mRNA was extracted and purified using a commercial system (NucleoSpin RNA; Macherey&Nagel). RNA quality was controlled using the BioAnalyzer (Agilent Technologies, USA) and only high quality RNA (RIN>9) was used for microarray analyses.

tag: cell line

value: mast cell tumor cell line C2

value: masitinib


title: cerebellum_Atxn2 Knock-In_replicate2

status: Public on Jul 25 2012

type: RNA

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Bioconductor package 'affy' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: cerebellum_Atxn2 Knock-In

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

tag: tissue

value: cerebellum

tag: genotype/variation

value: Atxn2 Knock-In


title: 72h-2

tag: agent

tag: time


title: Asian sample no.43

type: genomic

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Asian lung cancer sample 15

hyb_protocol: Labeled tumor and reference DNA were combined together with 100 μg human Cot-1 DNA (Invitrogen). Hybridization was performed using MAUI hybridization system (BioMcro Systems, Salt Lake City, UT), agitating the hybridization solution for 50 hours at 50℃.

scan_protocol: The arrays were scanned using scanner GenePix4000B (Axon Instruments, Foster City, CA) and the images were segmented and transformed to Cy3-Cy5 log ratio using GenePix software by Axon Instruments, Inc. (http://www.axon.com).

data_processing: Further data processing, a normalization method called “block-wise normalization”, which normalized the array-CGH data by the log ratio of the self-self hybridization of reference DNA according to the mean and the standard deviations of each array block, was established.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor sample

label_protocol: 500 ng of tumor genomic DNA and reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: commercial human genomic DNA, Invitrogen) were labeled by random priming using BioPrime DNA Labeling System (Invitrogen) with Cy3-dCTP (tumor) or Cy5-dCTP (reference).

extract_protocol: The genomic DNA was prepared using proteinase K digestion and phenol-chloroform extraction.

value: lung

tag: disease status

value: non-small cell lung cancer (NSLCL)

tag: race

value: Asian

source_name: Reference sample

tag: reference source

value: 28 matched-normal genomic DNA pool from Aaian lung cancer


title: brainstem_Atxn2 Knock-In_replicate3

source_name: brainstem_Atxn2 Knock-In

value: brainstem


title: cerebellum_Atxn2 Knock-In_replicate4


title: brainstem_Atxn2 Knock-In_replicate1


title: 72h-1


title: isw1  FLAG-H3 IP Replicate 2

city: Kansas City

first: Michaela

last: Smolle

state: Missouri

address: 1000 E 50th Street

country: USA

institute: Stowers Institute for Medical Research

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG IP over Input in the isw1 YMS131 strain.

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc), and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US45102919 Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data processed in R (version 2.13.0) using Bioconductor MEDIAN normalization.

organism: Saccharomyces cerevisiae

source_name: IP DNA FLAG antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 0.4. a-factor was added to a final concentration of 2 uM and the cells were grown for an additional 5 hrs. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate FLAG (15 ul per IP) or Myc (2 ul per IP) antibodies.

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate FLAG- and Myc-tagged histone H3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65°C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

tag: strain

tag: antibody

value: Flag M2

tag: vendor

value: Sigma #F1804

source_name: Input DNA


title: 24h-3


title: cerebellum_Atxn2 Knock-In_replicate1


title: 24h-2


title: 24h-1


title: WT Myc-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the WT MDY510 strain.

source_name: IP DNA Myc antibody

value: -c-myc

value: Sigma #4439


title: Asian sample no.42

description: Asian lung cancer sample 14


title: WT FLAG-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG IP over Input in the WT MDY510 strain.


title: 12h-3


title: liver_Atxn2 Knock-In_replicate4

source_name: liver_Atxn2 Knock-In

value: liver


title: WT Myc-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the WT MDY510 strain.


title: WT Myc-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the WT MDY510 strain.


title: Asian sample no.39

description: Asian lung cancer sample 12


title: Asian sample no.41

description: Asian lung cancer sample 13


title: isw1 FLAG-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG IP over Input in the isw1 YMS131 strain.


title: WT FLAG-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG IP over Input in the WT MDY510 strain.


title: WT FLAG-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG IP over Input in the WT MDY510 strain.


title: 12h-2


title: liver_Atxn2 Knock-In_replicate1


title: Asian sample no.26

description: Asian lung cancer sample 9


title: 0h-3

value: control


title: Asian sample no.32

description: Asian lung cancer sample 10


title: WT_mNKcellsStageF_rep3

city: Ann Arbor

first: Yasmina

last: Laouar

state: Michigan

address: 1150 West Medical Center Drive

department: Microbiology and Immunology

institute: University of Michigan

description: Control

data_processing:
Data was analyzed with Global Pattern Recognition (GPR) software. This software determine the best normalizer genes (up to 10) based on the experimental results, i.e., it looks for the genes that do not change under the experiment conditions being tested. GPR then normalizes the data, calculates the fold change, and determines which changes are significant. The normalized Ct values are not an output of the GPR software, and therefore, are not provided.
Fold change data (TG mNK cells/ WT mNK cells) ratios for each stage (D, E, and F) are available in the 'GSE39511_fold_change.txt' file, which is linked to the GSE39511 record as a supplementary file.

label: SYBR Green

source_name: bone marrow NK cells, WT, stage F

label_protocol: PCR assays were performed using a customized cell cycle pathway PCR assay panel (StellARay; Lonza) following the manufacturer's instructions.

extract_protocol: mNK cells at stages D, E, and F were obtained by cell sorting. Total RNA was extracted with the RNeasy Micro kit (Qiagen), followed by DNase I treatment.

tag: strain/background

tag: genotype

value: WT

tag: cell type

value: natural killer cells from bone marrow

tag: developmental stage

value: F


title: TG_mNKcellsStageF_rep2

description: Test

source_name: bone marrow NK cells, TG, stage F


title: TG_mNKcellsStageF_rep1

description: Test


title: WT_mNKcellsStageF_rep2

description: Control


title: TG_mNKcellsStageF_rep3

description: Test


title: Asian sample no.25

description: Asian lung cancer sample 8


title: WT_mNKcellsStageF_rep1

description: Control


title: brainstem_wild type_replicate3

source_name: brainstem_wild type

value: wild type


title: 12h-1

value: mast cell tumor cell line C2

value: masitinib


title: Asian sample no.34

description: Asian lung cancer sample 11

value: lung


title: Asian sample no.20

description: Asian lung cancer sample 7

value: non-small cell lung cancer (NSLCL)


title: brainstem_wild type_replicate4


title: liver_Atxn2 Knock-In_replicate3

value: Atxn2 Knock-In


title: brainstem_wild type_replicate2


title: 0h-2


title: Asian sample no.19

description: Asian lung cancer sample 6

value: Asian

value: 28 matched-normal genomic DNA pool from Aaian lung cancer


title: TG_mNKcellsStageE_rep3

description: Test

source_name: bone marrow NK cells, TG, stage E

value: E


title: liver_Atxn2 Knock-In_replicate2


title: TG_mNKcellsStageE_rep1

description: Test


title: TG_mNKcellsStageE_rep2

description: Test


title: MBC of OLA, biological rep2

city: WuHan

first: li

last: bei

address: Shizishan Street

country: China

institute: Huazhong Agricultural University

description: Gene expression data from Escherichia coli treated with MBC of olaquindox.

hyb_protocol: Following fragmentation, 6 ug of cdNA were hybridized for 16 hr at 45C on GeneChip E.coli Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

organism: Escherichia coli

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in  anaerobic incubator for 1h at 37℃ and drugs were added according to the different concentrations. The cultures were incubated for 30min.

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

treatment_protocol: The cells were centrifuged at 8000 rpm for 5min at 4°C. The cell pellets were snap-frozen in liquid nitrogen and kept at -80°C


title: brainstem_wild type_replicate1

value: brainstem


title: MBC of OLA, biological rep3

source_name: Escherichia coli treated with MBC of olaquindox


title: Asian sample no.17

description: Asian lung cancer sample 5


title: MBC of OLA, biological rep1


title: Asian sample no.10

description: Asian lung cancer sample 3


title: MIC of OLA, biological rep3

description: Gene expression data from Escherichia coli treated with MIC of olaquindox.


title: cerebellum_wild type_replicate4

source_name: cerebellum_wild type

value: cerebellum


title: WT_mNKcellsStageE_rep2

description: Control

source_name: bone marrow NK cells, WT, stage E


title: Asian sample no.E

description: Asian lung cancer sample 2


title: WT_mNKcellsStageE_rep3

description: Control


title: WT_mNKcellsStageE_rep1

description: Control


title: MBC of CYA, biological rep3

description: Gene expression data from Escherichia coli treated with MBC of cyadox.


title: 0h-1


title: cerebellum_wild type_replicate1


title: MIC of OLA, biological rep1

source_name: Escherichia coli treated with MIC of olaquindox


title: Asian sample no.14

description: Asian lung cancer sample 4


title: TG_mNKcellsStageD_rep3

description: Test

source_name: bone marrow NK cells, TG, stage D

value: D


title: Asian sample no.D

description: Asian lung cancer sample 1


title: MIC of OLA, biological rep2


title: MBC of CYA, biological rep2

source_name: Escherichia coli treated with MBC of cyadox


title: TG_mNKcellsStageD_rep2

description: Test


title: MBC of CYA, biological rep1


title: cerebellum_wild type_replicate2


title: liver_wild type_replicate4

source_name: liver_wild type

value: liver


title: cerebellum_wild type_replicate3


title: liver_wild type_replicate3


title: 0.5MIC of CYA, biological rep3

description: Gene expression data from Escherichia coli treated with 0.5MIC of cyadox.


title: liver_wild type_replicate1


title: liver_wild type_replicate2


title: testis-wt-7

city: Rotterdam

first: frank

last: sleutels

address: Dr Molewaterplein 50

department: cell biology and genetics

country: Netherlands

institute: ErasmusMC

description: Gene expression data from wildtype testis

hyb_protocol: cRNA was hybridized to the GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station Fluidics 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm

source_name: testis day P23

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

value: testis


title: TG_mNKcellsStageD_rep1

description: Test


title: WT_mNKcellsStageD_rep3

description: Control

source_name: bone marrow NK cells, WT, stage D

value: WT


title: testis-ko-8

description: Gene expression data from CTCFL mutant testis


title: WT_mNKcellsStageD_rep2

description: Control

value: natural killer cells from bone marrow


title: WT_mNKcellsStageD_rep1

description: Control


title: 0.5MIC of CYA, biological rep2

source_name: Escherichia coli treated with 0.5MIC of cyadox


title: C106 Tg

city: Richmond

first: Devanand

last: Sarkar

state: VA

address: 1220 E Broad St, Room 7044

department: Department of Human and Molecular Genetics

institute: Virginia Commonwealth University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Liver Tumor from Transgenic mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: To generate Alb/AEG-1 transgenic mice, a 5.3-kb XhoI fragment was excised from the Alb/AEG-1 construct and microinjected at a concentration of 2 ng/ul into the male pronucleus of single-cell mouse embryos obtained from mating B6CBAF1/J (C57BL/6 × CBA) males and females. The injected embryos were then reimplanted into the oviducts of pseudopregnant CD-1 female mice.

treatment_protocol: For induction of chemical carcinogenesis, a single i.p. injection of 10 ug/gm body weight of N-nitrosodiethylamine (DEN) was given at 14 days of age to male WT and Alb/AEG-1 mice. The animals were sacrificed at 28 weeks of age and liver tumors were collected.

value: Alb/AEG-1 Transgenic

tag: background strain


title: C80 Tg


title: testis-wt-6


title: testis-ko-5


title: Solvent control, biological rep3

description: Gene expression data from Escherichia coli treated with 1%DMSO.

source_name: Escherichia coli treated with 1%DMSO


title: Solvent control, biological rep1


title: 0.5MIC of CYA, biological rep1


title: Solvent control, biological rep2


title: testis-ko-3


title: testis-wt-2


title: C66 WT

source_name: Liver Tumor from WT mouse


title: C107 WT


title: testis-wt-4


title: testis-wt-1


title: C108 WT


title: C76 Tg


title: hgDNA176 [child vs. mother hybridization]

status: Public on Jul 24 2012

city: vancouver

first: Farah

middle: R

last: Zahir

state: BC

address: Box 153, 4500 Oak Street

country: Canada

institute: UBc

description: 176_CNV Summary.txt

hyb_protocol: Roche NimbleGen CHG Analysis User’s Guide V5.1 Mar 16, 2009

scan_protocol: Scanned with Molecular Devices GenePix 4000B at 5µm. Sample Tracking Control was used in all 12-plex reactions. Data was extracted using NimbleScan v2.5. Only those arrays passing all QC measures outlined in NimbleScan v2.5 Software User Guide were analysed for CNVs.

data_processing:
SegMNT files were generated using the following settings: Min segment difference = 0.1, Min Segment length = 5, Acceptance percentiles = 0.999, Averaging window – 1X, Including non-uniques probes, spatial correction, normalized. SegMNT files were imported in Nexus v4.0.
CNVs were identified with the following settings: log2 ratio >0.2 (duplications) or <0.2 (deletions) with a minimum of 5 probes affected, maximum probe distance was <10 Kb (>10Kn these were treated as separate CNVs)

source_name: peripheral blood

extract_protocol: Genomic DNA was extracted from blood samples with the use of the Puregene DNA kit (Gentra Systems).

tag: group

value: child

value: mother


title: hgDNA150 [child vs. mother hybridization]

description: 150_CNV Summary.txt

label_protocol: Roche NimbleGen CHG Analysis User’s Guide V5.1 Mar 16, 2009


title: hgDNA148 [child vs. father hybridization]

description: 148_CNV Summary.txt

value: father


title: hgDNA176 [child vs. father hybridization]

description: 176_CNV Summary.txt


title: hgDNA148 [child vs. mother hybridization]

description: 148_CNV Summary.txt


title: hgDNA141 [child vs. mother hybridization]

description: 141_CNV Summary.txt


title: hgDNA135 [child vs. mother hybridization]

description: 135_CNV Summary.txt


title: hgDNA166 [child vs. mother hybridization]

description: 166_CNV Summary.txt


title: hgDNA164 [child vs. mother hybridization]

description: 164_CNV Summary.txt


title: hgDNA190 [child vs. mother hybridization]

description: 190_CNV Summary.txt


title: hgDNA190 [child vs. father hybridization]

description: 190_CNV Summary.txt


title: hgDNA150 [child vs. father hybridization]

description: 150_CNV Summary.txt


title: hgDNA136 [child vs. father hybridization]

description: 136_CNV Summary.txt


title: hgDNA125 [child vs. mother hybridization]

description: 125_CNV Summary.txt


title: hgDNA164 [child vs. father hybridization]

description: 164_CNV Summary.txt


title: hgDNA135 [child vs. father hybridization]

description: 135_CNV Summary.txt


title: hgDNA118 [child vs. mother hybridization]

description: 118_CNV Summary.txt


title: hgDNA166 [child vs. father hybridization]

description: 166_CNV Summary.txt


title: hgDNA141 [child vs. father hybridization]

description: 141_CNV Summary.txt


title: hgDNA125 [child vs. father hybridization]

description: 125_CNV Summary.txt


title: hgDNA118 [child vs. father hybridization]

description: 118_CNV Summary.txt


title: hgDNA112 [child vs. mother hybridization]

description: 112_CNV Summary.txt


title: hgDNA116 [child vs. mother hybridization]

description: 116_CNV Summary.txt


title: hgDNA7484 [child vs. father hybridization]

description: 7484_CNV Summary.txt


title: hgDNA112 [child vs. father hybridization]

description: 112_CNV Summary.txt


title: hgDNA136 [child vs. mother hybridization]

description: 136_CNV Summary.txt


title: hgDNA7484 [child vs. mother hybridization]

description: 7484_CNV Summary.txt


title: hgDNA6942 [child vs. mother hybridization]

description: 6942_CNV Summary.txt


title: hgDNA8135 [child vs. mother hybridization]

description: 8135_CNV Summary.txt


title: hgDNA116 [child vs. father hybridization]

description: 116_CNV Summary.txt


title: hgDNA8612 [child vs. father hybridization]

description: 8612_CNV Summary.txt


title: hgDNA8612 [child vs. mother hybridization]

description: 8612_CNV Summary.txt


title: hgDNA8135 [child vs. father hybridization]

description: 8135_CNV Summary.txt


title: hgDNA7581 [child vs. mother hybridization]

description: 7581_CNV Summary.txt


title: hgDNA9313 [child vs. father hybridization]

description: 9313_CNV Summary.txt


title: hgDNA6932 [child vs. father hybridization]

description: 6932_CNV Summary.txt


title: hgDNA7581 [child vs. father hybridization]

description: 7581_CNV Summary.txt


title: hgDNA7093 [child vs. mother hybridization]

description: 7093_CNV Summary.txt


title: hgDNA9390 [child vs. father hybridization]

description: 9390_CNV Summary.txt


title: hgDNA6942 [child vs. father hybridization]

description: 6942_CNV Summary.txt


title: hgDNA6932 [child vs. mother hybridization]

description: 6932_CNV Summary.txt


title: hgDNA7093 [child vs. father hybridization]

description: 7093_CNV Summary.txt


title: hgDNA9390 [child vs. mother hybridization]

description: 9390_CNV Summary.txt


title: hgDNA5993 [child vs. father hybridization]

description: 5993_CNV Summary.txt


title: hgDNA8327 [child vs. father hybridization]

description: 8327_CNV Summary.txt


title: hgDNA9313 [child vs. mother hybridization]

description: 9313_CNV Summary.txt


title: hgDNA3519 [child vs. mother hybridization]

description: 3519_CNV Summary.txt


title: hgDNA2569 [child vs. father hybridization]

description: 2569_CNV Summary.txt


title: hgDNA2332 [child vs. father hybridization]

description: 2332_CNV Summary.txt


title: hgDNA2569 [child vs. mother hybridization]

description: 2569_CNV Summary.txt


title: hgDNA3519 [child vs. father hybridization]

description: 3519_CNV Summary.txt


title: hgDNA2377 [child vs. father hybridization]

description: 2377_CNV Summary.txt


title: hgDNA987 [child vs. mother hybridization]

description: 987_CNV Summary.txt


title: hgDNA970 [child vs. father hybridization]

description: 970_CNV Summary.txt


title: hgDNA998 [child vs. mother hybridization]

description: 998_CNV Summary.txt


title: hgDNA1780 [child vs. mother hybridization]

description: 1780_CNV Summary.txt


title: hgDNA2332 [child vs. mother hybridization]

description: 2332_CNV Summary.txt


title: hgDNA977 [child vs. father hybridization]

description: 977_CNV Summary.txt


title: hgDNA987 [child vs. father hybridization]

description: 987_CNV Summary.txt


title: hgDNA1780 [child vs. father hybridization]

description: 1780_CNV Summary.txt


title: hgDNA977 [child vs. mother hybridization]

description: 977_CNV Summary.txt


title: hgDNA998 [child vs. father hybridization]

description: 998_CNV Summary.txt


title: hgDNA969 [child vs. father hybridization]

description: 969_CNV Summary.txt


title: hgDNA2377 [child vs. mother hybridization]

description: 2377_CNV Summary.txt


title: hgDNA970 [child vs. mother hybridization]

description: 970_CNV Summary.txt


title: hgDNA960 [child vs. father hybridization]

description: 960_CNV Summary.txt


title: hgDNA964 [child vs. father hybridization]

description: 964_CNV Summary.txt


title: hgDNA969 [child vs. mother hybridization]

description: 969_CNV Summary.txt


title: hgDNA964 [child vs. mother hybridization]

description: 964_CNV Summary.txt


title: hgDNA960 [child vs. mother hybridization]

description: 960_CNV Summary.txt


title: hgDNA953 [child vs. father hybridization]

description: no CNVs called


title: hgDNA8327 [child vs. mother hybridization]

description: 8327_CNV Summary.txt


title: hgDNA953 [child vs. mother hybridization]

description: no CNVs called


title: hgDNA923 [child vs. mother hybridization]

description: 923_CNV Summary.txt


title: hgDNA936 [child vs. father hybridization]

description: 936_CNV Summary.txt


title: hgDNA5993 [child vs. mother hybridization]

description: 5993_CNV Summary.txt


title: hgDNA931 [child vs. father hybridization]

description: 931_CNV Summary.txt


title: hgDNA944 [child vs. mother hybridization]

description: no CNVs called


title: hgDNA946 [child vs. father hybridization]

description: 946_CNV Summary.txt


title: hgDNA947 [child vs. mother hybridization]

description: 947_CNV Summary.txt


title: hgDNA944 [child vs. father hybridization]

description: no CNVs called


title: hgDNA931 [child vs. mother hybridization]

description: 931_CNV Summary.txt


title: hgDNA948 [child vs. mother hybridization]

description: 948_CNV Summary.txt


title: hgDNA918 [child vs. father hybridization]

description: 918_CNV Summary.txt


title: hgDNA942 [child vs. mother hybridization]

description: 942_CNV Summary.txt


title: hgDNA947 [child vs. father hybridization]

description: 947_CNV Summary.txt


title: hgDNA936 [child vs. mother hybridization]

description: 936_CNV Summary.txt


title: hgDNA912 [child vs. mother hybridization]

description: 912_CNV Summary.txt


title: hgDNA923 [child vs. father hybridization]

description: 923_CNV Summary.txt


title: hgDNA912 [child vs. father hybridization]

description: 912_CNV Summary.txt


title: hgDNA922 [child vs. mother hybridization]

description: 922_CNV Summary.txt


title: hgDNA948 [child vs. father hybridization]

description: 948_CNV Summary.txt


title: hgDNA946 [child vs. mother hybridization]

description: 946_CNV Summary.txt


title: hgDNA905 [child vs. mother hybridization]

description: 905_CNV Summary.txt


title: hgDNA918 [child vs. mother hybridization]

description: 918_CNV Summary.txt


title: hgDNA922 [child vs. father hybridization]

description: 922_CNV Summary.txt


title: hgDNA904 [child vs. father hybridization]

description: 904_CNV Summary.txt


title: hgDNA901 [child vs. father hybridization]

description: 901_CNV Summary.txt


title: hgDNA894 [child vs. mother hybridization]

description: 894_CNV Summary.txt


title: hgDNA881 [child vs. father hybridization]

description: 881_CNV Summary.txt


title: hgDNA881 [child vs. mother hybridization]

description: 881_CNV Summary.txt


title: hgDNA901 [child vs. mother hybridization]

description: 901_CNV Summary.txt


title: hgDNA894 [child vs. father hybridization]

description: 894_CNV Summary.txt


title: hgDNA905 [child vs. father hybridization]

description: 905_CNV Summary.txt


title: hgDNA871 [child vs. father hybridization]

description: 871_CNV Summary.txt


title: hgDNA862 [child vs. father hybridization]

description: 862_CNV Summary.txt


title: hgDNA877 [child vs. father hybridization]

description: 877_CNV Summary.txt


title: hgDNA856 [child vs. father hybridization]

description: 856_CNV Summary.txt


title: hgDNA904 [child vs. mother hybridization]

description: 904_CNV Summary.txt


title: hgDNA862 [child vs. mother hybridization]

description: 862_CNV Summary.txt


title: hgDNA877 [child vs. mother hybridization]

description: 877_CNV Summary.txt


title: hgDNA869 [child vs. mother hybridization]

description: 869_CNV Summary.txt


title: hgDNA869 [child vs. father hybridization]

description: 869_CNV Summary.txt


title: hgDNA886 [child vs. father hybridization]

description: 886_CNV Summary.txt


title: hgDNA856 [child vs. mother hybridization]

description: 856_CNV Summary.txt


title: hgDNA871 [child vs. mother hybridization]

description: 871_CNV Summary.txt


title: hgDNA852 [child vs. mother hybridization]

description: 852_CNV Summary.txt


title: hgDNA852 [child vs. father hybridization]

description: 852_CNV Summary.txt


title: hgDNA942 [child vs. father hybridization]

description: 942_CNV Summary.txt


title: hgDNA848 [child vs. father hybridization]

description: 848_CNV Summary.txt


title: hgDNA846 [child vs. mother hybridization]

description: no CNVs called


title: hgDNA847 [child vs. mother hybridization]

description: 847_CNV Summary.txt


title: hgDNA837 [child vs. father hybridization]

description: 837_CNV Summary.txt


title: hgDNA828 [child vs. father hybridization]

description: 828_CNV Summary.txt


title: hgDNA837 [child vs. mother hybridization]

description: 837_CNV Summary.txt


title: hgDNA848 [child vs. mother hybridization]

description: 848_CNV Summary.txt


title: hgDNA820 [child vs. father hybridization]

description: 820_CNV Summary.txt


title: hgDNA793 [child vs. mother hybridization]

description: 793_CNV Summary.txt


title: hgDNA846 [child vs. father hybridization]

description: no CNVs called


title: hgDNA828 [child vs. mother hybridization]

description: 828_CNV Summary.txt


title: hgDNA809 [child vs. mother hybridization]

description: 809_CNV Summary.txt


title: hgDNA836 [child vs. mother hybridization]

description: 836_CNV Summary.txt


title: hgDNA820 [child vs. mother hybridization]

description: 820_CNV Summary.txt


title: hgDNA808 [child vs. father hybridization]

description: 808_CNV Summary.txt


title: hgDNA791 [child vs. father hybridization]

description: 791_CNV Summary.txt


title: hgDNA781 [child vs. father hybridization]

description: 781_CNV Summary.txt


title: hgDNA847 [child vs. father hybridization]

description: 847_CNV Summary.txt


title: hgDNA791 [child vs. mother hybridization]

description: 791_CNV Summary.txt


title: hgDNA808 [child vs. mother hybridization]

description: 808_CNV Summary.txt


title: hgDNA836 [child vs. father hybridization]

description: 836_CNV Summary.txt


title: hgDNA809 [child vs. father hybridization]

description: 809_CNV Summary.txt


title: hgDNA839 [child vs. mother hybridization]

description: 839_CNV Summary.txt


title: hgDNA832 [child vs. mother hybridization]

description: 832_CNV Summary.txt


title: hgDNA747 [child vs. mother hybridization]

description: 747_CNV Summary.txt


title: hgDNA781 [child vs. mother hybridization]

description: 781_CNV Summary.txt


title: hgDNA839 [child vs. father hybridization]

description: 839_CNV Summary.txt


title: hgDNA793 [child vs. father hybridization]

description: 793_CNV Summary.txt


title: hgDNA832 [child vs. father hybridization]

description: 832_CNV Summary.txt


title: hgDNA747 [child vs. father hybridization]

description: 747_CNV Summary.txt


title: hgDNA742 [child vs. father hybridization]

description: 742_CNV Summary.txt


title: hgDNA886 [child vs. mother hybridization]

description: 886_CNV Summary.txt


title: hgDNA741 [child vs. father hybridization]

description: 741_CNV Summary.txt


title: hgDNA731 [child vs. father hybridization]

description: 731_CNV Summary.txt


title: hgDNA717 [child vs. father hybridization]

description: 717_CNV Summary.txt


title: hgDNA733 [child vs. mother hybridization]

description: 733_CNV Summary.txt


title: hgDNA735 [child vs. father hybridization]

description: 735_CNV Summary.txt


title: hgDNA739 [child vs. father hybridization]

description: 739_CNV Summary.txt


title: hgDNA717 [child vs. mother hybridization]

description: 717_CNV Summary.txt


title: hgDNA739 [child vs. mother hybridization]

description: 739_CNV Summary.txt


title: hgDNA742 [child vs. mother hybridization]

description: 742_CNV Summary.txt


title: hgDNA706 [child vs. father hybridization]

description: 706_CNV Summary.txt


title: hgDNA647 [child vs. father hybridization]

description: 647_CNV Summary.txt


title: hgDNA649 [child vs. father hybridization]

description: 649_CNV Summary.txt


title: hgDNA691 [child vs. mother hybridization]

description: 691_CNV Summary.txt


title: hgDNA735 [child vs. mother hybridization]

description: 735_CNV Summary.txt


title: hgDNA647 [child vs. mother hybridization]

description: 647_CNV Summary.txt


title: hgDNA698 [child vs. mother hybridization]

description: 698_CNV Summary.txt


title: hgDNA741 [child vs. mother hybridization]

description: 741_CNV Summary.txt


title: hgDNA733 [child vs. father hybridization]

description: 733_CNV Summary.txt


title: hgDNA665 [child vs. mother hybridization]

description: 665_CNV Summary.txt


title: hgDNA644 [child vs. father hybridization]

description: 644_CNV Summary.txt


title: hgDNA691 [child vs. father hybridization]

description: 691_CNV Summary.txt


title: hgDNA665 [child vs. father hybridization]

description: 665_CNV Summary.txt


title: hgDNA698 [child vs. father hybridization]

description: 698_CNV Summary.txt


title: hgDNA699 [child vs. father hybridization]

description: no CNVs called


title: hgDNA649 [child vs. mother hybridization]

description: 649_CNV Summary.txt


title: hgDNA731 [child vs. mother hybridization]

description: 731_CNV Summary.txt


title: hgDNA706 [child vs. mother hybridization]

description: 706_CNV Summary.txt


title: hgDNA699 [child vs. mother hybridization]

description: no CNVs called


title: hgDNA631 [child vs. father hybridization]

description: 631_CNV Summary.txt


title: hgDNA626 [child vs. mother hybridization]

description: 626_CNV Summary.txt


title: hgDNA623 [child vs. father hybridization]

description: 623_CNV Summary.txt


title: hgDNA600 [child vs. mother hybridization]

description: 600_CNV Summary.txt


title: hgDNA594 [child vs. father hybridization]

description: 594_CNV Summary.txt


title: UZHRCC217_renal_tissue_reference_genomic

city: Zurich

last: Baudis

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

description: Per case segmentation files (... segments.csv) and raw copy number files after aroma.affymetrix normalization (... ,CN,raw.csv) are provided as tab-delimited text files. Probes are mapped by their position in genome build 36 / HG18. Probes are ordered according to their linear position on the Golden Path.

hyb_protocol: Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).

data_processing: CEL files were processed with R using the aroma.affymetrix package. Background correction was done using the CRMAv2 method (Bengtstroem et al.). Segmentation was done using the circular binary segmentation (CBS) method. Post-segmentation thresholding & visualization were done using tools implemented through the Progenetix project (www.progenetix.net). For detection of small regional CNAs, adaptive thresholding was used, with a 100-300kb size filter and +/-0.13-0.15 thresholds on the segmentation data.

source_name: normal renal tissue

extract_protocol: standard genomic DNA extraction methods

treatment_protocol: untreated tissue biopsies and cell lines

tag: sample type

value: reference

tag: gender

value: male

tag: grade

tag: stage

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

tag: organ site

value: kidney

tag: tissue type

value: normal renal tissue

tag: study cluster id


title: UZHRCC219_renal_tissue_reference_genomic

scan_protocol: Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).


title: UZHRCC218_renal_tissue_reference_genomic

label_protocol: Labeling, hybridization and array scanning were performed at the Broad institute, as per manufacturer's instructions (Affymetrix).


title: hgDNA576 [child vs. mother hybridization]

description: 576_CNV Summary.txt


title: hgDNA644 [child vs. mother hybridization]

description: 644_CNV Summary.txt


title: hgDNA625 [child vs. mother hybridization]

description: 625_CNV Summary.txt


title: hgDNA600 [child vs. father hybridization]

description: 600_CNV Summary.txt


title: hgDNA576 [child vs. father hybridization]

description: 576_CNV Summary.txt


title: hgDNA570 [child vs. father hybridization]

description: 570_CNV Summary.txt


title: hgDNA575 [child vs. father hybridization]

description: 575_CNV Summary.txt


title: hgDNA622 [child vs. mother hybridization]

description: 622_CNV Summary.txt


title: hgDNA603 [child vs. father hybridization]

description: 603_CNV Summary.txt


title: hgDNA631 [child vs. mother hybridization]

description: 631_CNV Summary.txt


title: hgDNA601 [child vs. mother hybridization]

description: 601_CNV Summary.txt


title: hgDNA622 [child vs. father hybridization]

description: 622_CNV Summary.txt


title: hgDNA601 [child vs. father hybridization]

description: 601_CNV Summary.txt


title: hgDNA615 [child vs. father hybridization]

description: 615_CNV Summary.txt


title: UZHRCC216_renal_tissue_reference_genomic


title: hgDNA603 [child vs. mother hybridization]

description: 603_CNV Summary.txt


title: hgDNA575 [child vs. mother hybridization]

description: 575_CNV Summary.txt


title: hgDNA623 [child vs. mother hybridization]

description: 623_CNV Summary.txt


title: hgDNA615 [child vs. mother hybridization]

description: 615_CNV Summary.txt


title: hgDNA594 [child vs. mother hybridization]

description: 594_CNV Summary.txt


title: UZHRCC215_renal_tissue_reference_genomic


title: UZHRCC214_renal_tissue_reference_genomic


title: UZHRCC213_renal_tissue_reference_genomic

value: female


title: hgDNA625 [child vs. father hybridization]

description: 625_CNV Summary.txt


title: UZHRCC212_renal_tissue_reference_genomic


title: UZHRCC211_renal_tissue_reference_genomic


title: UZHRCC210_renal_tissue_reference_genomic


title: UZHRCC208_renal_tissue_reference_genomic


title: UZHRCC209_renal_tissue_reference_genomic


title: UZHRCC207_renal_tissue_reference_genomic


title: UZHRCC205_renal_tissue_reference_genomic


title: UZHRCC206_renal_tissue_reference_genomic


title: UZHRCC202_renal_tissue_reference_genomic


title: UZHRCC204_renal_tissue_reference_genomic


title: UZHRCC203_renal_tissue_reference_genomic


title: UZHRCC200_renal_tissue_reference_genomic


title: hgDNA561 [child vs. father hybridization]

description: no CNVs called


title: hgDNA561 [child vs. mother hybridization]

description: no CNVs called


title: UZHRCC199_renal_tissue_reference_genomic


title: UZHRCC198_renal_tissue_reference_genomic


title: hgDNA570 [child vs. mother hybridization]

description: 570_CNV Summary.txt


title: hgDNA546 [child vs. father hybridization]

description: 546_CNV Summary.txt


title: UZHRCC197_renal_tissue_reference_genomic


title: hgDNA528 [child vs. father hybridization]

description: 528_CNV Summary.txt


title: UZHRCC201_renal_tissue_reference_genomic


title: UZHRCC196_renal_tissue_reference_genomic


title: hgDNA556 [child vs. father hybridization]

description: 556_CNV Summary.txt


title: hgDNA549 [child vs. father hybridization]

description: 549_CNV Summary.txt


title: hgDNA546 [child vs. mother hybridization]

description: 546_CNV Summary.txt


title: hgDNA543 [child vs. mother hybridization]

description: 543_CNV Summary.txt


title: hgDNA528 [child vs. mother hybridization]

description: 528_CNV Summary.txt


title: hgDNA513 [child vs. mother hybridization]

description: 513_CNV Summary.txt


title: hgDNA493 [child vs. father hybridization]

description: 493_CNV Summary.txt


title: hgDNA543 [child vs. father hybridization]

description: 543_CNV Summary.txt


title: hgDNA513 [child vs. father hybridization]

description: 513_CNV Summary.txt


title: hgDNA504 [child vs. mother hybridization]

description: 504_CNV Summary.txt


title: hgDNA498 [child vs. father hybridization]

description: 498_CNV Summary.txt


title: UZHRCC195_renal_tissue_reference_genomic


title: hgDNA504 [child vs. father hybridization]

description: 504_CNV Summary.txt


title: hgDNA490 [child vs. father hybridization]

description: 490_CNV Summary.txt


title: hgDNA493 [child vs. mother hybridization]

description: 493_CNV Summary.txt


title: hgDNA498 [child vs. mother hybridization]

description: 498_CNV Summary.txt


title: UZHRCC193_renal_tissue_reference_genomic


title: UZHRCC194_renal_tissue_reference_genomic


title: hgDNA626 [child vs. father hybridization]

description: 626_CNV Summary.txt


title: hgDNA556 [child vs. mother hybridization]

description: 556_CNV Summary.txt


title: UZHRCC190_renal_tissue_reference_genomic


title: UZHRCC192_renal_tissue_reference_genomic


title: UZHRCC189_renal_tissue_reference_genomic


title: UZHRCC188_renal_tissue_reference_genomic


title: UZHRCC187_renal_tissue_reference_genomic


title: UZHRCC191_renal_tissue_reference_genomic


title: UZHRCC185_renal_tissue_reference_genomic


title: UZHRCC186_renal_tissue_reference_genomic


title: UZHRCC184_renal_tissue_reference_genomic


title: UZHRCC183_renal_tissue_reference_genomic


title: UZHRCC181_renal_tissue_reference_genomic


title: UZHRCC180_renal_tissue_reference_genomic


title: UZHRCC182_renal_tissue_reference_genomic


title: hgDNA484 [child vs. father hybridization]

description: 484_CNV Summary.txt


title: UZHRCC179_renal_tissue_reference_genomic


title: hgDNA484 [child vs. mother hybridization]

description: 484_CNV Summary.txt


title: hgDNA489 [child vs. father hybridization]

description: 489_CNV Summary.txt


title: hgDNA489 [child vs. mother hybridization]

description: 489_CNV Summary.txt


title: hgDNA468 [child vs. father hybridization]

description: 468_CNV Summary.txt


title: hgDNA486 [child vs. father hybridization]

description: 486_CNV Summary.txt


title: hgDNA477 [child vs. father hybridization]

description: 477_CNV Summary.txt


title: hgDNA481 [child vs. father hybridization]

description: 481_CNV Summary.txt


title: hgDNA486 [child vs. mother hybridization]

description: 486_CNV Summary.txt


title: hgDNA481 [child vs. mother hybridization]

description: 481_CNV Summary.txt


title: UZHRCC177_renal_tissue_reference_genomic


title: UZHRCC178_renal_tissue_reference_genomic


title: UZHRCC176_renal_tissue_reference_genomic


title: hgDNA490 [child vs. mother hybridization]

description: 490_CNV Summary.txt


title: hgDNA463 [child vs. father hybridization]

description: no CNVs called


title: hgDNA477 [child vs. mother hybridization]

description: 477_CNV Summary.txt


title: hgDNA461 [child vs. father hybridization]

description: 461_CNV Summary.txt


title: UZHRCC175_renal_tissue_reference_genomic


title: hgDNA549 [child vs. mother hybridization]

description: 549_CNV Summary.txt


title: UZHRCC174_renal_tissue_reference_genomic


title: hgDNA468 [child vs. mother hybridization]

description: 468_CNV Summary.txt


title: UZHRCC173_renal_tissue_reference_genomic


title: hgDNA457 [child vs. father hybridization]

description: 457_CNV Summary.txt


title: UZHRCC172_renal_tissue_reference_genomic


title: UZHRCC171_renal_tissue_reference_genomic


title: UZHRCC170_renal_tissue_reference_genomic


title: UZHRCC169_renal_tissue_reference_genomic


title: UZHRCC168_renal_tissue_reference_genomic


title: hgDNA457 [child vs. mother hybridization]

description: 457_CNV Summary.txt


title: hgDNA461 [child vs. mother hybridization]

description: 461_CNV Summary.txt


title: hgDNA452 [child vs. father hybridization]

description: 452_CNV Summary.txt


title: hgDNA450 [child vs. father hybridization]

description: 450_CNV Summary.txt


title: UZHRCC165_renal_tissue_reference_genomic


title: UZHRCC167_renal_tissue_reference_genomic


title: UZHRCC164_renal_tissue_reference_genomic


title: UZHRCC166_renal_tissue_reference_genomic


title: UZHRCC163_renal_tissue_reference_genomic


title: UZHRCC162_renal_tissue_reference_genomic


title: UZHRCC161_renal_tissue_reference_genomic


title: hgDNA463 [child vs. mother hybridization]

description: no CNVs called


title: hgDNA450 [child vs. mother hybridization]

description: 450_CNV Summary.txt


title: hgDNA447 [child vs. mother hybridization]

description: 447_CNV Summary.txt


title: UZHRCC160_renal_tissue_reference_genomic


title: UZHRCC159_renal_tissue_reference_genomic


title: hgDNA452 [child vs. mother hybridization]

description: 452_CNV Summary.txt


title: UZHRCC158_renal_tissue_reference_genomic


title: hgDNA441 [child vs. father hybridization]

description: 441_CNV Summary.txt


title: hgDNA442 [child vs. father hybridization]

description: 442_CNV Summary.txt


title: UZHRCC005_renal_tissue_reference_genomic


title: UZHRCC156_renal_tissue_reference_genomic


title: hgDNA432 [child vs. mother hybridization]

description: 432_CNV Summary.txt


title: hgDNA419 [child vs. mother hybridization]

description: 419_CNV Summary.txt


title: hgDNA447 [child vs. father hybridization]

description: 447_CNV Summary.txt


title: hgDNA433 [child vs. mother hybridization]

description: 433_CNV Summary.txt


title: hgDNA433 [child vs. father hybridization]

description: 433_CNV Summary.txt


title: hgDNA441 [child vs. mother hybridization]

description: 441_CNV Summary.txt


title: hgDNA419 [child vs. father hybridization]

description: 419_CNV Summary.txt


title: hgDNA442 [child vs. mother hybridization]

description: 442_CNV Summary.txt


title: hgDNA432 [child vs. father hybridization]

description: 432_CNV Summary.txt


title: UZHRCC004_renal_tissue_reference_genomic


title: UZHRCC003_renal_tissue_reference_genomic


title: UZHRCC002_renal_tissue_reference_genomic


title: hgDNA413 [child vs. father hybridization]

description: 413_CNV Summary.txt


title: UZHRCC157_renal_tissue_reference_genomic


title: hgDNA414 [child vs. father hybridization]

description: 414_CNV Summary.txt


title: hgDNA413 [child vs. mother hybridization]

description: 413_CNV Summary.txt


title: hgDNA414 [child vs. mother hybridization]

description: 414_CNV Summary.txt


title: UZHRCC154_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [clear cell RCC]

value: neoplasia

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]


title: UZHRCC155_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [papillary RCC]

value: papillary renal cell carcinoma

value: renal cell carcinoma [papillary RCC]


title: hgDNA412 [child vs. mother hybridization]

description: 412_CNV Summary.txt


title: UZHRCC153_renal_tissue_neoplasia_genomic


title: UZHRCC104_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [mixed papillary and clear cell RCC]

value: renal cell carcinoma

value: C


title: UZHRCC001_renal_tissue_reference_genomic


title: UZHRCC100_renal_tissue_neoplasia_genomic


title: hgDNA412 [child vs. father hybridization]

description: 412_CNV Summary.txt


title: UZHRCC101_renal_tissue_neoplasia_genomic


title: hgDNA391 [child vs. mother hybridization]

description: 391_CNV Summary.txt


title: hgDNA391 [child vs. father hybridization]

description: 391_CNV Summary.txt


title: hgDNA384 [child vs. mother hybridization]

description: 384_CNV Summary.txt


title: UZHRCC098_renal_tissue_neoplasia_genomic


title: UZHRCC096_renal_tissue_neoplasia_genomic


title: UZHRCC095_renal_tissue_neoplasia_genomic


title: UZHRCC092_renal_tissue_neoplasia_genomic


title: UZHRCC087_renal_tissue_neoplasia_genomic


title: UZHRCC099_renal_tissue_neoplasia_genomic


title: UZHRCC075_renal_tissue_neoplasia_genomic

value: A


title: hgDNA354 [child vs. father hybridization]

description: 354_CNV Summary.txt


title: hgDNA341 [child vs. mother hybridization]

description: 341_CNV Summary.txt


title: hgDNA341 [child vs. father hybridization]

description: 341_CNV Summary.txt


title: hgDNA321 [child vs. mother hybridization]

description: 321_CNV Summary.txt


title: UZHRCC073_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [chromophobe RCC]

value: renal cell carcinoma, chromophobe

value: renal cell carcinoma [chromophobe RCC]

value: B


title: hgDNA331 [child vs. father hybridization]

description: 331_CNV Summary.txt

value: child

value: father


title: UZHRCC079_renal_tissue_neoplasia_genomic


title: UZHRCC072_renal_tissue_neoplasia_genomic


title: hgDNA369 [child vs. mother hybridization]

description: no CNVs called

value: mother


title: hgDNA369 [child vs. father hybridization]

description: no CNVs called


title: hgDNA320 [child vs. father hybridization]

description: 320_CNV Summary.txt


title: hgDNA320 [child vs. mother hybridization]

description: 320_CNV Summary.txt


title: hgDNA331 [child vs. mother hybridization]

description: 331_CNV Summary.txt


title: hgDNA328 [child vs. father hybridization]

description: 328_CNV Summary.txt


title: hgDNA328 [child vs. mother hybridization]

description: 328_CNV Summary.txt


title: hgDNA321 [child vs. father hybridization]

description: 321_CNV Summary.txt


title: UZHRCC069_renal_tissue_neoplasia_genomic

value: kidney


title: hgDNA384 [child vs. father hybridization]

description: 384_CNV Summary.txt


title: hgDNA316 [child vs. father hybridization]

description: 316_CNV Summary.txt


title: UZHRCC070_renal_tissue_neoplasia_genomic

value: male


title: UZHRCC066_renal_tissue_neoplasia_genomic


title: hgDNA316 [child vs. mother hybridization]

description: 316_CNV Summary.txt


title: hgDNA354 [child vs. mother hybridization]

description: 354_CNV Summary.txt


title: hgDNA310 [child vs. father hybridization]

description: no CNVs called


title: hgDNA310 [child vs. mother hybridization]

description: no CNVs called


title: UZHRCC063_renal_tissue_neoplasia_genomic


title: UZHRCC061_renal_tissue_neoplasia_genomic


title: UZHRCC064_renal_tissue_neoplasia_genomic


title: hgDNA308 [child vs. father hybridization]

description: 308_CNV Summary.txt


title: hgDNA305 [child vs. mother hybridization]

description: 305_CNV Summary.txt


title: UZHRCC071_renal_tissue_neoplasia_genomic


title: hgDNA305 [child vs. father hybridization]

description: 305_CNV Summary.txt


title: hgDNA298 [child vs. father hybridization]

description: 298_CNV Summary.txt


title: hgDNA298 [child vs. mother hybridization]

description: 298_CNV Summary.txt


title: UZHRCC151_prost_can_cell_line_BI_mRNA_rep4

hyb_protocol: standard Affymetrix protocol; Broad institute

data_processing: Affymetrix GeneChip data was normalized using MAS5 from Bioconductor

label: Biotin

source_name: prostate adenocarcinoma ,cell line PC3vec3, cDNA

growth_protocol: untreated tissue and cell line samples

extract_protocol: All tumor tissues were selected according to the histologically verified presence of at least 80% tumor cells.  RNA was extracted using the RNeasy minikit (Qiagen).

treatment_protocol: untreated tissue and cell line samples

tag: cell line

value: adenocarcinoma, NOS

value: prostate [cell line]

value: prostate adenocarcinoma [cell line PC3vec3]

tag: cluster id


title: UZHRCC060_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [RCC metastasis]

value: neoplasia

value: kidney [metastasis of RCC to other site]

value: renal cell carcinoma [RCC metastasis]


title: UZHRCC152_RCC_kidney_cell_line_BI_mRNA_rep1

scan_protocol: standard Affymetrix protocol; Broad institute

source_name: renal cell carcinoma ,cell line HK-2, cDNA

value: renal cell carcinoma

value: kidney [cell line]

value: renal cell carcinoma [cell line HK-2]


title: UZHRCC150_prost_can_cell_line_BI_mRNA_rep3

source_name: prostate adenocarcinoma ,cell line PC3vec1, cDNA

label_protocol: standard Affymetrix protocol; Broad institute

value: prostate adenocarcinoma [cell line PC3vec1]


title: hgDNA308 [child vs. mother hybridization]

description: 308_CNV Summary.txt


title: UZHRCC054_renal_tissue_neoplasia_genomic

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: UZHRCC148_prost_can_cell_line_BI_mRNA_rep1

source_name: prostate adenocarcinoma ,cell line PC3hep27, cDNA

value: prostate adenocarcinoma [cell line PC3hep27]


title: UZHRCC050_renal_tissue_neoplasia_genomic

value: renal cell carcinoma [mixed papillary and clear cell RCC]

value: C


title: UZHRCC149_prost_can_cell_line_BI_mRNA_rep2

source_name: prostate adenocarcinoma ,cell line PC3hep30, cDNA

value: male

value: prostate adenocarcinoma [cell line PC3hep30]


title: hgDNA295 [child vs. father hybridization]

description: 295_CNV Summary.txt

value: child

value: father


title: UZHRCC147_RCC_cell_line_meta_BI_mRNA_rep6

source_name: renal cell carcinoma ,cell line SLR23, cDNA

value: neoplasia

value: renal cell carcinoma [cell line SLR23]


title: UZHRCC145_RCC_cell_line_meta_BI_mRNA_rep4

source_name: renal cell carcinoma ,cell line SLR21, cDNA

value: renal cell carcinoma [cell line SLR21]


title: hgDNA295 [child vs. mother hybridization]

description: 295_CNV Summary.txt

value: mother


title: UZHRCC047_renal_tissue_neoplasia_genomic

value: kidney


title: UZHRCC046_renal_tissue_neoplasia_genomic

value: female


title: hgDNA284 [child vs. father hybridization]

description: 284_CNV Summary.txt


title: UZHRCC045_renal_tissue_neoplasia_genomic


title: UZHRCC144_RCC_cell_line_meta_BI_mRNA_rep3

source_name: renal cell carcinoma ,cell line Caki-2, cDNA

value: renal cell carcinoma

value: kidney [cell line]

value: renal cell carcinoma [cell line Caki-2]


title: hgDNA284 [child vs. mother hybridization]

description: 284_CNV Summary.txt


title: UZHRCC143_RCC_cell_line_meta_BI_mRNA_rep2

source_name: renal cell carcinoma ,cell line SLR20, cDNA

value: renal cell carcinoma [cell line SLR20]


title: UZHRCC141_RCC_cell_line_BI_mRNA_rep23

source_name: renal cell carcinoma ,cell line 786O, cDNA

value: renal cell carcinoma [cell line 786O]


title: UZHRCC142_RCC_cell_line_meta_BI_mRNA_rep1

source_name: renal cell carcinoma ,cell line SLR25, cDNA

value: renal cell carcinoma [cell line SLR25]


title: hgDNA282 [child vs. father hybridization]

description: 282_CNV Summary.txt

source_name: peripheral blood


title: UZHRCC042_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [clear cell RCC]

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: UZHRCC139_RCC_cell_line_BI_mRNA_rep21

source_name: renal cell carcinoma ,cell line 786-O, cDNA

value: renal cell carcinoma [cell line 786-O]


title: UZHRCC041_renal_tissue_neoplasia_genomic

value: male


title: UZHRCC138_RCC_cell_line_BI_mRNA_rep20

source_name: renal cell carcinoma ,cell line SK-RC38, cDNA

value: neoplasia

value: renal cell carcinoma [cell line SK-RC38]


title: UZHRCC137_RCC_cell_line_BI_mRNA_rep19

source_name: renal cell carcinoma ,cell line SLR22, cDNA

value: renal cell carcinoma [cell line SLR22]


title: UZHRCC136_RCC_cell_line_BI_mRNA_rep18

source_name: renal cell carcinoma ,cell line SK-RC31, cDNA

value: renal cell carcinoma [cell line SK-RC31]


title: hgDNA268 [child vs. father hybridization]

description: 268_CNV Summary.txt

value: child

value: father


title: UZHRCC040_renal_tissue_neoplasia_genomic

value: kidney


title: UZHRCC135_RCC_cell_line_BI_mRNA_rep17

source_name: renal cell carcinoma ,cell line SW156, cDNA

value: renal cell carcinoma

value: kidney [cell line]

value: renal cell carcinoma [cell line SW156]


title: Day 4 dense

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

description: Tiling array day 4 dense

hyb_protocol: 34 ug of the labelled cDNA was hybridized to each array, and hybridization was performed on 3 separate arrays (3 technical replicates).

scan_protocol: The arrays were scanned on a Molecular Devices GenePix Axon 4400A at 5 uM resolution.

data_processing: The scanned array data was converted into pair and gff files using the NimbleScan software package. Probe intensities across technical replicates were quantile normalised and a three-probe sliding window together with the Hodges-Lehmann estimator of location were used to smooth the data and collapse the replicates into one set per sample  Background subtraction was performed using the top 2% of random probes.  Possible single probe introns were recovered by performing bacground subtraction on pre-smoothened data and setting final probe intensities to zero if their pre-smoothened median across replicates is zero.

organism: Oikopleura dioica

source_name: cDNA from day 4 stage whole animals under dense conditions

label_protocol: For each developmental stage (or stressor), cDNA was labeled and amplified using the Roche NimbleGen gene expression protocol (http://www.nimblegen.com/products/lit/05434505001_NG_Expression_UGuide_v6p0.pdf).

extract_protocol: Animals were allowed to develop to the relevant development stages, anesthetized in cold ethyl 3-aminobenzoate methanesulfonate salt (MS-222) and collected by centrifigation. Total RNA was extracted from whole animals or isolated animal tissues using the Qiagen RNeasy kit. RNA quality control was performed using an Agilent 2100 Bio-analyzer.Double stranded cDNA was generated according to the Roche NimbleGen gene expression protocol (http://www.nimblegen.com/products/lit/05434505001_NG_Expression_UGuide_v6p0.pdf), using the Life technologies/Invitrogen Superscript double stranded cDNA synthesis kit.

value: Day 4

value: Mixed


title: hgDNA268 [child vs. mother hybridization]

description: 268_CNV Summary.txt

value: mother


title: Ovary

description: Tiling array ovary

source_name: cDNA from ovaries of mature female animals

value: Day 6

value: Female


title: UZHRCC134_RCC_cell_line_BI_mRNA_rep16

source_name: renal cell carcinoma ,cell line SK-RC29, cDNA

value: renal cell carcinoma [cell line SK-RC29]


title: Day 4

description: Tiling array day 4

source_name: cDNA from day 4 stage whole animals


title: UZHRCC036_renal_tissue_neoplasia_genomic

value: male

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: UZHRCC140_RCC_cell_line_BI_mRNA_rep22

source_name: renal cell carcinoma ,cell line SK-RC42, cDNA

value: neoplasia

value: renal cell carcinoma [cell line SK-RC42]


title: Testis

description: Tiling array testis

source_name: cDNA from testes of mature male animals

value: Male


title: UZHRCC132_RCC_cell_line_BI_mRNA_rep14

source_name: renal cell carcinoma ,cell line KC12, cDNA

value: renal cell carcinoma [cell line KC12]


title: UZHRCC133_RCC_cell_line_BI_mRNA_rep15

source_name: renal cell carcinoma ,cell line RCC4 (neo), cDNA

value: RCC4 (neo)

value: renal cell carcinoma

value: renal cell carcinoma [cell line RCC4 (neo)]


title: UZHRCC035_renal_tissue_neoplasia_genomic

value: kidney


title: Trunk

description: Tiling array day 5 trunk

source_name: cDNA from trunk of day 5 stage whole animals

value: Day 5

value: Mixed


title: UZHRCC131_RCC_cell_line_BI_mRNA_rep13

source_name: renal cell carcinoma ,cell line 769-P, cDNA

value: kidney [cell line]

value: renal cell carcinoma [cell line 769-P]


title: hgDNA248 [child vs. father hybridization]

description: 248_CNV Summary.txt

source_name: peripheral blood

value: child

value: father


title: UZHRCC034_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [clear cell RCC]

value: male

value: clear cell renal cell carcinoma


title: UZHRCC130_RCC_cell_line_BI_mRNA_rep12

source_name: renal cell carcinoma ,cell line RCC4 (vhl), cDNA

value: RCC4 (vhl)

value: renal cell carcinoma [cell line RCC4 (vhl)]


title: UZHRCC146_RCC_cell_line_meta_BI_mRNA_rep5

source_name: renal cell carcinoma ,cell line KU19-20, cDNA

value: neoplasia

value: renal cell carcinoma [cell line KU19-20]


title: Day 5

description: Tiling array day 5

source_name: cDNA from day 5 stage whole animals


title: UZHRCC033_renal_tissue_neoplasia_genomic

value: renal cell carcinoma [clear cell RCC]

value: A


title: hgDNA248 [child vs. mother hybridization]

description: 248_CNV Summary.txt

value: mother


title: Hatched

description: Tiling array hatched

source_name: Total RNA from hatched stage whole animals

value: Hatched


title: UZHRCC129_RCC_cell_line_BI_mRNA_rep11

source_name: renal cell carcinoma ,cell line Caki-1, cDNA

value: renal cell carcinoma

value: renal cell carcinoma [cell line Caki-1]


title: Tailshift

description: Tiling array tailshift

source_name: Total RNA from tailshift stage whole animals

value: Tailshift

value: Mixed


title: UZHRCC031_renal_tissue_neoplasia_genomic

value: female

value: kidney


title: hgDNA282 [child vs. mother hybridization]

description: 282_CNV Summary.txt

value: child


title: Day 3

description: Tiling array day 3

source_name: cDNA from day 3 stage whole animals

value: Day 3


title: 2-8 cells

description: Tiling array 2-8 cells

source_name: Total RNA from 2-8 cell stage embryos

value: 2-8 cells


title: Early tadpole

description: Tiling array early tadpole

source_name: Total RNA from early tadpole stage whole animals

value: Early tadpole


title: UZHRCC127_RCC_cell_line_BI_mRNA_rep9

source_name: renal cell carcinoma ,cell line A-704, cDNA

value: kidney [cell line]

value: renal cell carcinoma [cell line A-704]


title: hgDNA243 [child vs. father hybridization]

description: 243_CNV Summary.txt

value: father


title: UZHRCC125_RCC_cell_line_BI_mRNA_rep7

source_name: renal cell carcinoma ,cell line ACHN, cDNA

value: ACHN

value: neoplasia

value: renal cell carcinoma [cell line ACHN]


title: UZHRCC126_RCC_cell_line_BI_mRNA_rep8

source_name: renal cell carcinoma ,cell line 786O (vhl30), cDNA

value: renal cell carcinoma [cell line 786O (vhl30)]


title: UZHRCC030_renal_tissue_neoplasia_genomic

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: Day 2

description: Tiling array day 2

source_name: cDNA from day 2 stage whole animals

value: Day 2

value: Mixed


title: UZHRCC123_RCC_cell_line_BI_mRNA_rep5

source_name: renal cell carcinoma ,cell line 786O (vhl19), cDNA

value: renal cell carcinoma

value: renal cell carcinoma [cell line 786O (vhl19)]


title: UZHRCC124_RCC_cell_line_BI_mRNA_rep6

source_name: renal cell carcinoma ,cell line UMRC6, cDNA

value: renal cell carcinoma [cell line UMRC6]


title: Tailbud

description: Tiling array tailbud

source_name: Total RNA from tailbud stage whole animals

value: Tailbud


title: hgDNA243 [child vs. mother hybridization]

description: 243_CNV Summary.txt

source_name: peripheral blood

value: child

value: mother


title: UZHRCC028_renal_tissue_neoplasia_genomic

source_name: renal cell carcinoma [clear cell RCC]

value: female

value: kidney

value: B


title: UZHRCC121_RCC_cell_line_BI_mRNA_rep3

source_name: renal cell carcinoma ,cell line A-498, cDNA

value: neoplasia

value: kidney [cell line]

value: renal cell carcinoma [cell line A-498]


title: hgDNA241 [child vs. father hybridization]

description: 241_CNV Summary.txt

value: father


title: hgDNA241 [child vs. mother hybridization]

description: 241_CNV Summary.txt


title: UZHRCC020_renal_tissue_neoplasia_genomic

value: male

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: C


title: 1HPF

description: Tiling array 1HPF

source_name: Total RNA from 1HPF stage embryos

value: Mixed


title: UZHRCC128_RCC_cell_line_BI_mRNA_rep10

source_name: renal cell carcinoma ,cell line SLR 26, cDNA

value: SLR 26

value: renal cell carcinoma

value: renal cell carcinoma [cell line SLR 26]


title: Day 1

description: Tiling array day 1

source_name: cDNA from day 1 stage whole animals

value: Day 1


title: Day 3 dense

description: Tiling array day 3 dense

source_name: cDNA from day 3 stage whole animals under dense conditions

value: Day 3


title: UZHRCC019_renal_tissue_neoplasia_genomic

value: A


title: UZHRCC017_renal_tissue_neoplasia_genomic

value: kidney


title: UZHRCC016_renal_tissue_neoplasia_genomic


title: Day 2 dense

description: Tiling array day 2 dense

source_name: cDNA from day 2 stage whole animals under dense conditions

value: Day 2


title: UZHRCC009_renal_tissue_neoplasia_genomic

value: neoplasia


title: UZHRCC006_renal_tissue_neoplasia_genomic

value: B


title: Oocyte

description: Tiling array oocyte

source_name: Total RNA from oocytes

value: Oocyte

value: Female


title: UZHRCC122_RCC_cell_line_BI_mRNA_rep4

source_name: renal cell carcinoma ,cell line SK-RC52, cDNA

value: kidney [cell line]

value: renal cell carcinoma [cell line SK-RC52]


title: UZHRCC117_RCC_meta_BI_mRNA_rep13

source_name: renal cell carcinoma ,RCC metastasis

value: kidney [metastasis of RCC to other site]

value: renal cell carcinoma [RCC metastasis]


title: hgDNA240 [child vs. father hybridization]

description: 240_CNV Summary.txt

value: child

value: father


title: UZHRCC120_RCC_cell_line_BI_mRNA_rep2

source_name: renal cell carcinoma ,cell line SLR24, cDNA

value: renal cell carcinoma

value: renal cell carcinoma [cell line SLR24]


title: UZHRCC118_RCC_meta_BI_mRNA_rep14


title: UZHRCC119_RCC_cell_line_BI_mRNA_rep1

source_name: renal cell carcinoma ,cell line UMRC2, cDNA

value: renal cell carcinoma [cell line UMRC2]


title: hgDNA233 [child vs. mother hybridization]

description: 233_CNV Summary.txt

value: mother


title: UZHRCC116_RCC_meta_BI_mRNA_rep12

value: C


title: hgDNA224 [child vs. father hybridization]

description: 224_CNV Summary.txt


title: UZHRCC107_RCC_meta_BI_mRNA_rep3


title: UZHRCC103_RCC_papillary_BII_mRNA_rep6

source_name: renal cell carcinoma ,papillary RCC

value: papillary renal cell carcinoma

value: kidney

value: renal cell carcinoma [papillary RCC]


title: UZHRCC112_RCC_meta_BI_mRNA_rep8

value: neoplasia


title: hgDNA240 [child vs. mother hybridization]

description: 240_CNV Summary.txt


title: UZHRCC106_RCC_meta_BI_mRNA_rep2

value: A


title: UZHRCC110_RCC_meta_BI_mRNA_rep6


title: wtMtb vs WhiB4KO replicate 3

city: New Delhi

first: Amit

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: Immunology

country: India

institute: International Center for Genetic Engineering and Biotechnology

description:
Biological replicate 3 of 3
Comp3_Mtb-C(cy3) vs WhiB4KO-C(cy5)

hyb_protocol: Prehybridization 1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS 2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides. 3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42C. 4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down. 5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down. 6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization III. Hybridization 1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS 2. Heat to 98C for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min. 3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate). 4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50C water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe. IV. Post Hyb washes (next day) 1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking. 2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking. 3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: The arrays were scanned with a GenePix4200AL scanner (Molecular Devices, Sunnyvale, CA).

data_processing: The chips were normalized by the print-tip Lowess method (Dudoit, 2000). The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if they were not at least 2-fold above the background in one or both channels.  Also, spots were flagged if they were not present in two out of three replicates.  The data is presented in log ratio.

organism: Mycobacterium tuberculosis H37Rv

source_name: wild type

label_protocol: Synthesis and Labeling of cDNA  1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube)with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents). 2. Heat 2 min at 98C, snap cool on ice. 3. (Keep on ice) and add 11.1µl of the following reaction mix: 5.0µl 5X First-Strand buffer 2.5µl 100 mM DTT 2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock) 1.5ul Cy3 or Cy5 Then add 1.2ul Superscript, vortex to mix and spin to collect contents 4. Incubate 10 min at 25C followed by 90 min at 42C in PCR machine. **Can freeze or leave at 4oC overnight if necessary 5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg. Empty flow-through in collection tube and return primed column. Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min). Wash with 200µl TE and spin until almost dry (<5µl). 6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min. 7. Bring sample to 5µl with TE. The detailed labeling and hybridization protocol can be obtained at http://www.cag.icph.org/downloads_page.htm#LabelingProtocols

growth_protocol: Mtb strains were aerobically grown in MB 7H9 medium supplemented with 1XADS supplement till an OD 600 nm of 0.4. 20 ml of these cells were harvested for the total RNA extraction.

extract_protocol: Total RNA was extracted using MP Fastprep blue RNA isolation kit using manufacturer's instructions.

treatment_protocol: 20 ml of culture was aerbocally grown in inkwell bottle (60 ml) till OD 600 nm reaches to 0.4.

tag: genotype/variation

value: wild type

tag: culture

value: grown till an OD600 nm~ 0.4

source_name: WhiB4 mutant

value: WhiB4 mutant


title: UZHRCC115_RCC_meta_BI_mRNA_rep11

value: kidney [metastasis of RCC to other site]


title: wtMtb vs WhiB4KO replicate 2

description:
Biological replicate 2 of 3
Comp2_Mtb-B(cy3) vs WhiB4KO-B(cy5)


title: UZHRCC113_RCC_meta_BI_mRNA_rep9

value: renal cell carcinoma [RCC metastasis]


title: hgDNA229 [child vs. father hybridization]

description: 229_CNV Summary.txt

value: child


title: hgDNA227 [child vs. mother hybridization]

description: 227_CNV Summary.txt


title: hgDNA227 [child vs. father hybridization]

description: 227_CNV Summary.txt

value: father


title: hgDNA224 [child vs. mother hybridization]

description: 224_CNV Summary.txt


title: wtMtb vs WhiB4KO replicate 1

description:
Biological replicate 1 of 3
Comp1_Mtb-A(cy3) vs WhiB4KO-A(cy5)


title: hgDNA233 [child vs. father hybridization]

description: 233_CNV Summary.txt


title: UZHRCC109_RCC_meta_BI_mRNA_rep5

value: renal cell carcinoma


title: UZHRCC105_RCC_meta_BI_mRNA_rep1


title: UZHRCC102_RCC_papillary_BII_mRNA_rep5


title: hgDNA229 [child vs. mother hybridization]

description: 229_CNV Summary.txt


title: UZHRCC108_RCC_meta_BI_mRNA_rep4


title: UZHRCC104_RCC_papillary_BII_mRNA_rep7

source_name: renal cell carcinoma ,mixed papillary and clear cell RCC

value: male

value: renal cell carcinoma [mixed papillary and clear cell RCC]


title: UZHRCC111_RCC_meta_BI_mRNA_rep7


title: UZHRCC114_RCC_meta_BI_mRNA_rep10


title: hgDNA212 [child vs. father hybridization]

description: 212_CNV Summary.txt

source_name: peripheral blood


title: UZHRCC099_RCC_papillary_BII_mRNA_rep2


title: CHO_24h_ctrl, biological rep4

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description: Gene expression in pair-fed high fat control liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

organism: Rattus norvegicus

source_name: Pair-fed high fat control liver

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was purified using RNeasy mini kit (Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100

treatment_protocol: Liver tissue was freeze-clamped in liquid nitrogen at the time of partial hepatectomy (PHx) and 1 h, 6 h, 12 h, and 24 h after PHx.  Tissue was then stored at -80 degrees C.

tag: tissue

value: liver

tag: hepatectomy

value: no

tag: animal id

tag: diet

value: Carbohydrate

tag: timepoint

value: 0 (control)

tag: array scan date

tag: outlier


title: UZHRCC096_RCC_papillary_S4_BI_mRNA_rep1

tag: grade

tag: stage

tag: sample type

value: papillary renal cell carcinoma

value: kidney

tag: gender

value: renal cell carcinoma [papillary RCC]

value: C


title: UZHRCC097_RCC_papillary_S4_BI_mRNA_rep2

value: neoplasia

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

tag: organ site

tag: tissue type

value: B


title: UZHRCC101_RCC_papillary_BII_mRNA_rep4

tag: cluster id


title: CHO_24h_phx, biological rep3

description: Gene expression in pair-fed high fat control liver 24h after PHx

source_name: Pair-fed high fat control liver 24h after PHx

value: yes

value: 24 hours


title: hgDNA205 [child vs. mother hybridization]

description: 205_CNV Summary.txt

tag: group

value: child

value: mother


title: UZHRCC100_RCC_papillary_BII_mRNA_rep3


title: UZHRCC098_RCC_papillary_BII_mRNA_rep1

value: female


title: hgDNA203 [child vs. father hybridization]

description: 203_CNV Summary.txt

value: father


title: hgDNA212 [child vs. mother hybridization]

description: 212_CNV Summary.txt


title: hgDNA203 [child vs. mother hybridization]

description: 203_CNV Summary.txt


title: CHO_24h_phx, biological rep4

tag: tissue


title: hgDNA201 [child vs. father hybridization]

description: 201_CNV Summary.txt


title: CHO_24h_ctrl, biological rep2

tag: hepatectomy


title: CHO_24h_phx, biological rep2

tag: animal id


title: UZHRCC095_RCC_papillary_S2_BI_mRNA_rep2


title: hgDNA205 [child vs. father hybridization]

description: 205_CNV Summary.txt


title: CHO_24h_ctrl, biological rep3

tag: diet


title: UZHRCC088_RCC_papillary_BI_mRNA_rep5


title: UZHRCC087_RCC_papillary_BI_mRNA_rep3

value: male


title: UZHRCC093_RCC_papillary_S1_BI_mRNA_rep2


title: UZHRCC090_RCC_papillary_BI_mRNA_rep7


title: UZHRCC091_RCC_papillary_BI_mRNA_rep8


title: UZHRCC094_RCC_papillary_S2_BI_mRNA_rep1


title: UZHRCC092_RCC_papillary_S1_BI_mRNA_rep1


title: UZHRCC089_RCC_papillary_BI_mRNA_rep6


title: hgDNA201 [child vs. mother hybridization]

description: 201_CNV Summary.txt


title: UZHRCC086_RCC_papillary_BI_mRNA_rep2


title: UZHRCC081_RCC_clear_cell_S3_BII_mRNA_rep6

source_name: renal cell carcinoma ,clear cell RCC

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: UZHRCC084_RCC_clear_cell_S4_BII_mRNA_rep2


title: CHO_24h_phx, biological rep1

value: liver

value: Carbohydrate

tag: timepoint

value: no


title: CHO_24h_ctrl, biological rep1

value: 0 (control)

tag: array scan date


title: hgDNA199 [child vs. father hybridization]

description: 199_CNV Summary.txt


title: CHO_6h_phx, biological rep4

description: Gene expression in pair-fed high fat control liver 6h after PHx

source_name: Pair-fed high fat control liver 6h after PHx

value: 6 hours

tag: outlier


title: hgDNA196 [child vs. father hybridization]

description: 196_CNV Summary.txt


title: UZHRCC080_RCC_clear_cell_S3_BII_mRNA_rep5

tag: grade

value: neoplasia

value: kidney


title: UZHRCC083_RCC_clear_cell_S4_BII_mRNA_rep1

tag: stage

value: B


title: UZHRCC078_RCC_clear_cell_S3_BII_mRNA_rep3

tag: sample type


title: hgDNA199 [child vs. mother hybridization]

description: 199_CNV Summary.txt


title: UZHRCC085_RCC_papillary_BI_mRNA_rep1

value: papillary renal cell carcinoma

tag: gender

value: renal cell carcinoma [papillary RCC]


title: CHO_6h_ctrl, biological rep2


title: UZHRCC075_RCC_clear_cell_S2_BII_mRNA_rep3

tag: icd-o 3 code


title: UZHRCC073_RCC_clear_cell_S2_BII_mRNA_rep1

source_name: renal cell carcinoma ,chromophobe RCC

tag: icd-o 3 diagnosis text

value: renal cell carcinoma, chromophobe

value: renal cell carcinoma [chromophobe RCC]


title: UZHRCC074_RCC_clear_cell_S2_BII_mRNA_rep2

tag: organ site


title: UZHRCC077_RCC_clear_cell_S3_BII_mRNA_rep2

tag: tissue type


title: UZHRCC072_RCC_clear_cell_S1_BII_mRNA_rep5

value: female

tag: cluster id


title: CHO_6h_phx, biological rep2

value: yes


title: CHO_6h_phx, biological rep3


title: CHO_6h_ctrl, biological rep3


title: hgDNA196 [child vs. mother hybridization]

description: 196_CNV Summary.txt

tag: group

value: child

value: mother


title: CHO_6h_ctrl, biological rep4

tag: tissue


title: CHO_6h_phx, biological rep1

tag: hepatectomy


title: UZHRCC079_RCC_clear_cell_S3_BII_mRNA_rep4

value: clear cell renal cell carcinoma

value: renal cell carcinoma [clear cell RCC]

value: A


title: UZHRCC076_RCC_clear_cell_S3_BII_mRNA_rep1


title: hgDNA191 [child vs. mother hybridization]

description: 191_CNV Summary.txt


title: hgDNA191 [child vs. father hybridization]

description: 191_CNV Summary.txt

value: father


title: UZHRCC082_RCC_clear_cell_S3_BII_mRNA_rep7


title: UZHRCC068_RCC_clear_cell_S1_BII_mRNA_rep1


title: UZHRCC066_RCC_clear_cell_BII_mRNA_rep41

value: male

value: C


title: UZHRCC069_RCC_clear_cell_S1_BII_mRNA_rep2

value: neoplasia


title: UZHRCC065_RCC_clear_cell_BII_mRNA_rep40

value: kidney


title: UZHRCC070_RCC_clear_cell_S1_BII_mRNA_rep3


title: UZHRCC067_RCC_clear_cell_BII_mRNA_rep42


title: UZHRCC064_RCC_clear_cell_BII_mRNA_rep39


title: UZHRCC071_RCC_clear_cell_S1_BII_mRNA_rep4


title: UZHRCC062_RCC_clear_cell_BII_mRNA_rep37


title: CHO_1h_phx, biological rep4

description: Gene expression in pair-fed high fat control liver 1h after PHx

source_name: Pair-fed high fat control liver 1h after PHx

value: liver

tag: animal id

value: Carbohydrate

value: 1 hour

value: no


title: UZHRCC061_RCC_clear_cell_BII_mRNA_rep36


title: CHO_1h_ctrl, biological rep3

tag: diet

value: 0 (control)


title: UZHRCC059_RCC_clear_cell_BII_mRNA_rep34


title: UZHRCC058_RCC_clear_cell_BII_mRNA_rep33


title: CHO_1h_phx, biological rep3

tag: timepoint


title: CHO_1h_phx, biological rep1

tag: array scan date


title: CHO_1h_ctrl, biological rep4

tag: outlier


title: UZHRCC060_RCC_clear_cell_BII_mRNA_rep35

tag: grade

value: renal cell carcinoma

value: kidney [metastasis of RCC to other site]

value: renal cell carcinoma [RCC metastasis]

value: B


title: UZHRCC057_RCC_clear_cell_BII_mRNA_rep32

tag: stage

value: clear cell renal cell carcinoma


title: CHO_6h_ctrl, biological rep1


title: UZHRCC063_RCC_clear_cell_BII_mRNA_rep38

tag: sample type

value: renal cell carcinoma [clear cell RCC]


title: CHO_1h_ctrl, biological rep2


title: UZHRCC056_RCC_clear_cell_BII_mRNA_rep31

tag: gender

value: A


title: CHO_1h_ctrl, biological rep1


title: CHO_1h_phx, biological rep2

value: yes


title: UZHRCC053_RCC_clear_cell_BII_mRNA_rep28

tag: icd-o 3 code


title: UZHRCC055_RCC_clear_cell_BII_mRNA_rep30

tag: icd-o 3 diagnosis text


title: UZHRCC052_RCC_clear_cell_BII_mRNA_rep27

tag: organ site


title: HF_24h_ctrl, biological rep4

description: Gene expression in pair-fed carbohydrate control liver

source_name: Pair-fed carbohydrate control liver

value: High fat


title: UZHRCC050_RCC_clear_cell_BII_mRNA_rep25

value: male

tag: tissue type

value: renal cell carcinoma [mixed papillary and clear cell RCC]

value: C


title: HF_24h_phx, biological rep4

description: Gene expression in pair-fed carbohydrate control liver 24h after PHx

source_name: Pair-fed carbohydrate control liver 24h after PHx

value: liver

value: 24 hours


title: HF_24h_ctrl, biological rep3


title: UZHRCC049_RCC_clear_cell_BII_mRNA_rep24

value: neoplasia

value: kidney

tag: cluster id


title: MFH 25 mRNA

city: Boston

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: V

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software used for normalization of the mRNA dataset was Genome Studio, Gene Expression Module v1.0, Illumina. For the miRNA data, the normalization and analysis was done in BRB ArrayTools stable release 4.1.0. Sample intensities are scaled by a factor equal to the ratio of average intensity of a virtual reference sample to the average intensity of a given sample. Background is subtracted prior to the scaling.

source_name: MFH

label_protocol: Arrays are washed and stained with strepatavidin-Cy3 then scanned in array reader

extract_protocol: RNA extracted from FFPE blocks using Qiagen Rneasy kit according to company protocol

value: MFH


title: HF_24h_ctrl, biological rep2

value: no

value: 0 (control)


title: HF_24h_phx, biological rep2


title: HF_24h_phx, biological rep1


title: MFH 25.2 mRNA

description: W


title: UZHRCC051_RCC_clear_cell_BII_mRNA_rep26


title: IFN-gR1-KO CD4 T cells, vehicle-treated, biological rep2

city: Kyoto

first: Chengcan

last: Yao

address: Yoshida, Sakyo-ku

department: Pharmacology

country: Japan

institute: Kyoto University

description: Gene expression data from TCR-activated WT CD4 T cells treated with vehicle

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: KO CD4 T cells treated with veh

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: CD4+ T cells were purified from spleens of WT or IFN-gR1-deficient mice by autoMACS, and activated with anti-CD3 plus anti-CD28 for 15 h.

extract_protocol: Total RNA was purified by Qiagen Rneasy mini kit.

treatment_protocol: db-cAMP or vehicle control (med) was added into cultures for the last 3 h.

value: spleen

tag: genotype/variation

value: IFN-gR1 KO

tag: age

value: 8 weeks

tag: cell type

value: CD4 T cells


title: IFN-gR1-KO CD4 T cells, cAMP-treated, biological rep1

description: Gene expression data from TCR-activated WT CD4 T cells treated with db-cAMP

source_name: KO CD4 T cells treated with db-cAMP

tag: tissue


title: spindle cell tumor 24 mRNA

description: T

source_name: spindle cell tumor

value: spindle cell tumor


title: WT CD4 T cells, vehicle-treated, biological rep2

source_name: WT CD4 T cells treated with veh

value: wild type


title: IFN-gR1-KO CD4 T cells, cAMP-treated, biological rep2


title: spindle cell tumor 23 mRNA

description: S


title: WT CD4 T cells, cAMP-treated, biological rep2

source_name: WT CD4 T cells treated with db-cAMP


title: IFN-gR1-KO CD4 T cells, vehicle-treated, biological rep1


title: UZHRCC046_RCC_clear_cell_BII_mRNA_rep21

value: clear cell renal cell carcinoma

value: female

value: renal cell carcinoma [clear cell RCC]

value: A


title: HF_24h_ctrl, biological rep1

value: liver

tag: hepatectomy

tag: animal id

tag: diet

value: High fat


title: spindle cell tumor 24.2 mRNA

description: U


title: WT CD4 T cells, cAMP-treated, biological rep1


title: UZHRCC047_RCC_clear_cell_BII_mRNA_rep22

value: neoplasia

value: male


title: HF_24h_phx, biological rep3

value: yes

tag: timepoint

value: 24 hours

tag: array scan date

tag: outlier


title: UZHRCC044_RCC_clear_cell_BII_mRNA_rep19

tag: grade

tag: stage

tag: sample type

value: kidney


title: WT CD4 T cells, vehicle-treated, biological rep1

value: spleen


title: UZHRCC045_RCC_clear_cell_BII_mRNA_rep20

tag: icd-o 3 code

tag: icd-o 3 diagnosis text

tag: gender


title: spindle cell tumor 21.2 mRNA

description: Q


title: UZHRCC048_RCC_clear_cell_BII_mRNA_rep23

tag: organ site

tag: tissue type

tag: cluster id


title: spindle cell tumor 21 mRNA

description: P


title: HF_6h_phx, biological rep4

description: Gene expression in pair-fed carbohydrate control liver 6h after PHx

source_name: Pair-fed carbohydrate control liver 6h after PHx

value: 6 hours

value: no


title: MPNST 12 mRNA

description: O

source_name: MPNST

value: MPNST


title: spindle cell tumor 22 mRNA

description: R

value: spindle cell tumor


title: HF_6h_ctrl, biological rep4

value: 0 (control)


title: MPNST 11 mRNA

description: M


title: MPNST 11.2 mRNA

description: N


title: HF_6h_ctrl, biological rep3


title: UZHRCC040_RCC_clear_cell_BII_mRNA_rep15

value: clear cell renal cell carcinoma


title: UZHRCC041_RCC_clear_cell_BII_mRNA_rep16


title: clonal adipose cell line from inguinal depot [X7]

first: jun

last: wu

address: 450 brookline ave. CLSB11117A

institute: dana-farber cancer institute

description: Gene expression data from clonal adipose cell line of inguinal depot

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: The label, hyb and scan were performed by the Dana-Farber Cancer institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods.

data_processing: The data were normalized using the DNA-chip Analyzer(dChip) software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: clonal adipose cell line fully differentiated

extract_protocol: Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

treatment_protocol: treated with  forskolin (10mM) for 4 hrs.

tag: background strain

value: 129SVE from Taconic

tag: cell line


title: leiomyosarcoma 9 mRNA

description: J

source_name: leiomyosarcoma

tag: tissue

value: leiomyosarcoma


title: clonal adipose cell line from interscapular depot [BAT8]

description: Gene expression data from clonal adipose cell line of interscapular depot


title: HF_6h_phx, biological rep1

tag: hepatectomy

tag: animal id


title: HF_6h_phx, biological rep2

tag: diet

tag: timepoint


title: UZHRCC043_RCC_clear_cell_BII_mRNA_rep18

value: renal cell carcinoma [clear cell RCC]

value: A


title: leiomyosarcoma 10.2 mRNA

description: L


title: UZHRCC039_RCC_clear_cell_BII_mRNA_rep14


title: clonal adipose cell line from interscapular depot [BAT1]


title: clonal adipose cell line from inguinal depot [X9]


title: HF_6h_ctrl, biological rep2

value: liver

value: High fat

tag: array scan date

tag: outlier


title: HF_6h_phx, biological rep3


title: clonal adipose cell line from inguinal depot [X3]


title: clonal adipose cell line from inguinal depot [M4]


title: UZHRCC042_RCC_clear_cell_BII_mRNA_rep17

tag: grade

tag: stage

value: neoplasia

value: male


title: clonal adipose cell line from inguinal depot [N13]


title: clonal adipose cell line from interscapular depot [BAT6]


title: UZHRCC038_RCC_clear_cell_BII_mRNA_rep13

tag: sample type

tag: icd-o 3 code


title: HF_1h_phx, biological rep4

description: Gene expression in pair-fed carbohydrate control liver 1h after PHx

source_name: Pair-fed carbohydrate control liver 1h after PHx

value: yes

value: 1 hour


title: UZHRCC036_RCC_clear_cell_BII_mRNA_rep11

tag: icd-o 3 diagnosis text

value: kidney

tag: gender


title: leiomyosarcoma 8 mRNA

description: I


title: HF_6h_ctrl, biological rep1


title: HF_1h_ctrl, biological rep4


title: leiomyosarcoma 10 mRNA

description: K


title: UZHRCC037_RCC_clear_cell_BII_mRNA_rep12

value: renal cell carcinoma, chromophobe

tag: organ site

tag: tissue type

value: renal cell carcinoma [chromophobe RCC]

value: C


title: synovial sarcoma 7 mRNA

description: H

source_name: synovial sarcoma

value: synovial sarcoma


title: UZHRCC034_RCC_clear_cell_BII_mRNA_rep9

source_name: renal cell carcinoma ,clear cell RCC

tag: cluster id


title: synovial sarcoma 6.2 mRNA

description: G


title: clonal adipose cell line from inguinal depot [M3]

tag: background strain

tag: cell line


title: synovial sarcoma 6 mRNA

description: F

tag: tissue


title: UZHRCC035_RCC_clear_cell_BII_mRNA_rep10


title: clonal adipose cell line from inguinal depot [J6]


title: UZHRCC033_RCC_clear_cell_BII_mRNA_rep8


title: UZHRCC054_RCC_clear_cell_BII_mRNA_rep29


title: clonal adipose cell line from inguinal depot [I2]


title: HF_1h_phx, biological rep3

tag: hepatectomy

tag: animal id

value: no


title: HF_1h_ctrl, biological rep3

tag: diet

tag: timepoint

value: 0 (control)


title: liposarcoma 5.2 mRNA

description: E

source_name: liposarcoma

value: liposarcoma


title: HF_1h_phx, biological rep2

tag: array scan date

tag: outlier


title: UZHRCC032_RCC_clear_cell_BII_mRNA_rep7

tag: grade

tag: stage

value: clear cell renal cell carcinoma


title: clonal adipose cell line from inguinal depot [G23]

value: 129SVE from Taconic


title: UZHRCC031_RCC_clear_cell_BII_mRNA_rep6

tag: sample type

tag: icd-o 3 code

value: female

value: renal cell carcinoma [clear cell RCC]

value: A


title: HF_1h_phx, biological rep1

value: liver

value: High fat


title: HF_1h_ctrl, biological rep2


title: clonal adipose cell line from inguinal depot [G18]


title: liposarcoma 4.2 mRNA

description: C


title: clonal adipose cell line from inguinal depot [G12]


title: liposarcoma 5 mRNA

description: D


title: liposarcoma 2 mRNA

description: A


title: EtOH_24h_phx, biological rep4

description: Gene expression in chronic ethanol-fed liver 24h after PHx

source_name: Chronic ethanol-fed liver 24h after PHx

value: yes

value: 24 hours


title: UZHRCC029_RCC_clear_cell_BII_mRNA_rep4

value: neoplasia

tag: icd-o 3 diagnosis text

value: kidney

tag: gender


title: clonal adipose cell line from inguinal depot [G10]


title: EtOH_24h_phx, biological rep3

value: Ethanol


title: clonal adipose cell line from inguinal depot [F9]


title: UZHRCC028_RCC_clear_cell_BII_mRNA_rep3

tag: organ site

tag: tissue type

value: B


title: clonal adipose cell line from inguinal depot [E3]

tag: background strain


title: HF_1h_ctrl, biological rep1


title: UZHRCC026_RCC_clear_cell_BII_mRNA_rep1

tag: cluster id


title: UZHRCC027_RCC_clear_cell_BII_mRNA_rep2


title: EtOH_24h_ctrl, biological rep4

description: Gene expression in chronic ethanol-fed liver

source_name: Chronic ethanol-fed liver

tag: tissue


title: UZHRCC030_RCC_clear_cell_BII_mRNA_rep5


title: liposarcoma 4 mRNA

description: B


title: UZHRCC024_RCC_clear_cell_S4_BI_mRNA_rep5

value: C


title: UZHRCC025_RCC_clear_cell_S4_BI_mRNA_rep6


title: EtOH_24h_phx, biological rep2

tag: hepatectomy

value: no


title: clonal adipose cell line from inguinal depot [E4]

tag: cell line


title: clonal adipose cell line from inguinal depot [F4]


title: EtOH_24h_ctrl, biological rep3

tag: animal id

tag: diet

value: 0 (control)


title: clonal adipose cell line from inguinal depot [E1]


title: clonal adipose cell line from inguinal depot [D16]


title: siSE1

city: Charlottesville

first: Hui

last: Li

address: 345 Crispell Dr.

institute: University of Virginia

description: Gene expression data from LNCaP cells transfected with siSE1 for 72hrs

hyb_protocol: Hybridize: Incubate arrays in oven 45C, 60rpm, 17hrs. Stain/block: FS450_0007 on Fluidics Station 450

scan_protocol: After hybridization and clean up, the Genechips were scanned in an Affymetrix GeneArray Scanner 3000 7G, following the manufacturer's instruction. (See www.affymetrix.com)

data_processing: The image files produced by the scanning were handled by the software- Affymetrix® GeneChip® Command Console® Software (AGCC, See www.affymetrix.com), to first assembled into a .DAT file which then converted into a digitized .CEL file. The .CEL files were later analyzed by both Affymetrix Expression Console and R/BioConductor (www.bioconductor.org) to generate expression table in excel or text format.

source_name: LNCap cells transfected with siSE1

label_protocol: Ambion WT Expression Kit (p/n 4411974), GeneChip WT Terminal Labeling and Controls Kit (p/n 901524)

growth_protocol: LNCap cells growing in RPMI1640+10%FBS

extract_protocol: trizol

treatment_protocol: siRNAs were trasnfected into LNCaP cells using RNAiMAX

value: LNCaP

tag: transfection


title: UZHRCC023_RCC_clear_cell_S4_BI_mRNA_rep4

value: clear cell renal cell carcinoma


title: EtOH_24h_ctrl, biological rep2

tag: timepoint

tag: array scan date

tag: outlier