title: 400488_C

source_name: Patient 400488; Tissue mucosa


title: 400464_C

status: Public on Sep 13 2017

type: genomic

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Hybridisation was performed according to the standard Illumina Infinium HD Methylation protocol for Infinium® HumanMethylation450 BeadChip assays

scan_protocol: Arrays were imaged using iScan Reader with default Illumina scanner settings

data_processing: Microarray data was pre-processed using the Illumina Genome Studio software before analysis using the R minfi package.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient 400464; Tissue mucosa

label_protocol: Labelling was performed according to the standard Illumina Infinium HD Methylation protocol for Infinium® HumanMethylation450 BeadChip assays

extract_protocol: Tumour tissue and adjacent mucosa were collected from patients undergoing surgery. All tissues samples were reviewed by a pathologist to ensure their quality and high content of malignant cells. Genomic DNA was extracted from the tissues using the Qiagen QIAamp AllPrep DNA/RNA mini kit, according to the manufacturer's  protocol.

tag: patientid

tag: gender

value: M

tag: age

tag: tissue

value: mucosa

tag: disease state

value: Colorectal cancer


title: 400728_C

source_name: Patient 400728; Tissue mucosa


title: 400480_C

source_name: Patient 400480; Tissue mucosa

value: F


title: 401144_C

source_name: Patient 401144; Tissue mucosa


title: 401264_C

source_name: Patient 401264; Tissue mucosa


title: 400464_A

source_name: Patient 400464; Tissue tumor

value: tumor


title: 400712_A

source_name: Patient 400712; Tissue tumor


title: 400600_A

source_name: Patient 400600; Tissue tumor


title: 400728_A

source_name: Patient 400728; Tissue tumor


title: 400864_A

source_name: Patient 400864; Tissue tumor


title: 401144_A

source_name: Patient 401144; Tissue tumor


title: 401312_C1

source_name: Patient 401312; Tissue mucosa


title: 400864_C1

source_name: Patient 400864; Tissue mucosa


title: 401264_A

source_name: Patient 401264; Tissue tumor


title: 401344_C

source_name: Patient 401344; Tissue mucosa


title: 401352_A

source_name: Patient 401352; Tissue tumor


title: 400520_C

source_name: Patient 400520; Tissue mucosa


title: 401344_A

source_name: Patient 401344; Tissue tumor


title: 401312_A

source_name: Patient 401312; Tissue tumor


title: 401368_A1

source_name: Patient 401368; Tissue tumor


title: 400520_A

source_name: Patient 400520; Tissue tumor


title: 400360_C

source_name: Patient 400360; Tissue mucosa


title: 400360_A

source_name: Patient 400360; Tissue tumor


title: 401120C

source_name: Patient 401120; Tissue mucosa


title: 401648C1

source_name: Patient 401648; Tissue mucosa


title: 401464C1

source_name: Patient 401464; Tissue mucosa


title: 401352_C

source_name: Patient 401352; Tissue mucosa


title: 400896C1

source_name: Patient 400896; Tissue mucosa


title: 400392_C

source_name: Patient 400392; Tissue mucosa


title: 400352_A

source_name: Patient 400352; Tissue tumor


title: 400720_C

source_name: Patient 400720; Tissue mucosa


title: 401464A

source_name: Patient 401464; Tissue tumor


title: 401864C1

source_name: Patient 401864; Tissue mucosa


title: 401864A

source_name: Patient 401864; Tissue tumor


title: 404280_C

source_name: Patient 404280; Tissue mucosa


title: 400720_A

source_name: Patient 400720; Tissue tumor


title: 400896A

source_name: Patient 400896; Tissue tumor


title: 401664C1

source_name: Patient 401664; Tissue mucosa


title: 401648A

source_name: Patient 401648; Tissue tumor


title: 401664A

source_name: Patient 401664; Tissue tumor


title: 400392_A

source_name: Patient 400392; Tissue tumor


title: 401088A

source_name: Patient 401088; Tissue tumor


title: 404200_C2

source_name: Patient 404200; Tissue mucosa


title: 404848_C1

source_name: Patient 404848; Tissue mucosa


title: 404264_A

source_name: Patient 404264; Tissue tumor


title: 404848_A

source_name: Patient 404848; Tissue tumor


title: 404280_A

source_name: Patient 404280; Tissue tumor


title: 404200_A

source_name: Patient 404200; Tissue tumor


title: 404208_A

source_name: Patient 404208; Tissue tumor


title: 403944_C1

source_name: Patient 403944; Tissue mucosa


title: 404264_C1

source_name: Patient 404264; Tissue mucosa


title: 401368_C

source_name: Patient 401368; Tissue mucosa


title: 404768_C1

source_name: Patient 404768; Tissue mucosa


title: 400296_C

source_name: Patient 400296; Tissue mucosa


title: 404344_C1

source_name: Patient 404344; Tissue mucosa


title: 402872_C1

source_name: Patient 402872; Tissue mucosa


title: 403064_C1

source_name: Patient 403064; Tissue mucosa


title: 403728_C1

source_name: Patient 403728; Tissue mucosa


title: 402800_C1

source_name: Patient 402800; Tissue mucosa


title: 400280_C

source_name: Patient 400280; Tissue mucosa


title: 404656_A

source_name: Patient 404656; Tissue tumor


title: 403432_C1

source_name: Patient 403432; Tissue mucosa


title: 404656_C2

source_name: Patient 404656; Tissue mucosa


title: 404344_A

source_name: Patient 404344; Tissue tumor


title: 400352_C

source_name: Patient 400352; Tissue mucosa


title: 404208_C1

source_name: Patient 404208; Tissue mucosa


title: 400200_C

source_name: Patient 400200; Tissue mucosa


title: 403672_C1

source_name: Patient 403672; Tissue mucosa


title: 404480_C1

source_name: Patient 404480; Tissue mucosa


title: 404368_C1

source_name: Patient 404368; Tissue mucosa


title: 400256_C

source_name: Patient 400256; Tissue mucosa


title: 401288_C

source_name: Patient 401288; Tissue mucosa


title: 403704_C1

source_name: Patient 403704; Tissue mucosa


title: 401200_C

source_name: Patient 401200; Tissue mucosa


title: 400456_C1

source_name: Patient 400456; Tissue mucosa


title: 402768_C1

source_name: Patient 402768; Tissue mucosa


title: 404456_A

source_name: Patient 404456; Tissue tumor


title: 401400_C2

source_name: Patient 401400; Tissue mucosa


title: 404096_C1

source_name: Patient 404096; Tissue mucosa


title: 404456_C2

source_name: Patient 404456; Tissue mucosa


title: 404088_C1

source_name: Patient 404088; Tissue mucosa


title: 404088_A

source_name: Patient 404088; Tissue tumor


title: 404056_A

source_name: Patient 404056; Tissue tumor


title: 403664_C1

source_name: Patient 403664; Tissue mucosa


title: 401848_C

source_name: Patient 401848; Tissue mucosa


title: 403968_A

source_name: Patient 403968; Tissue tumor


title: 403968_C

source_name: Patient 403968; Tissue mucosa


title: 404304_C1

source_name: Patient 404304; Tissue mucosa


title: 403976_C

source_name: Patient 403976; Tissue mucosa


title: 404056_C2

source_name: Patient 404056; Tissue mucosa


title: 403928_C1

source_name: Patient 403928; Tissue mucosa


title: 403928_A

source_name: Patient 403928; Tissue tumor


title: 404312_C1

source_name: Patient 404312; Tissue mucosa


title: 404296_C1

source_name: Patient 404296; Tissue mucosa


title: 404096_A

source_name: Patient 404096; Tissue tumor


title: 404296_A

source_name: Patient 404296; Tissue tumor


title: 404304_A

source_name: Patient 404304; Tissue tumor


title: 403736_C1

source_name: Patient 403736; Tissue mucosa


title: 403840_A

source_name: Patient 403840; Tissue tumor


title: 404312_A

source_name: Patient 404312; Tissue tumor


title: 402968_C2

source_name: Patient 402968; Tissue mucosa


title: 401368_A

source_name: Patient 401368; Tissue tumor


title: 403416_C

source_name: Patient 403416; Tissue mucosa


title: 402152_C1

source_name: Patient 402152; Tissue mucosa


title: 402536_A

source_name: Patient 402536; Tissue tumor


title: 402232_A

source_name: Patient 402232; Tissue tumor


title: 401976_A

source_name: Patient 401976; Tissue tumor


title: 404328_C1

source_name: Patient 404328; Tissue mucosa


title: 403976_A

source_name: Patient 403976; Tissue tumor


title: 403456_C2

source_name: Patient 403456; Tissue mucosa


title: 402296_C2

source_name: Patient 402296; Tissue mucosa


title: 403320_C1

source_name: Patient 403320; Tissue mucosa


title: 401624_C

source_name: Patient 401624; Tissue mucosa


title: 401424_A

source_name: Patient 401424; Tissue tumor


title: 404328_A

source_name: Patient 404328; Tissue tumor


title: 402608_C

source_name: Patient 402608; Tissue mucosa


title: 403320_A

source_name: Patient 403320; Tissue tumor


title: 402392_C2

source_name: Patient 402392; Tissue mucosa


title: 402872_A

source_name: Patient 402872; Tissue tumor


title: 403800_C1

source_name: Patient 403800; Tissue mucosa


title: 402576_C1

source_name: Patient 402576; Tissue mucosa


title: 402400_C1

source_name: Patient 402400; Tissue mucosa


title: 404360_A

source_name: Patient 404360; Tissue tumor


title: 401624_A

source_name: Patient 401624; Tissue tumor


title: 403752_C1

source_name: Patient 403752; Tissue mucosa


title: 3KD d22

type: RNA

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Mouse Genome 430 2.0 microarrays in the GeneChip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the GeneChip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions.

data_processing: The quality control (QC) matrices were confirmed with Expression Console software (Affymetrix, USA) and Partek Genomics Suite version 6.6 (Partek Inc., St. Louis, USA). QC passed CEL files were further analyzed using Partek Genomics Suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: third chip KD day 22

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer.

extract_protocol: Total RNA from the cells was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen.

treatment_protocol: WT ESCs, SCR ESCs and KD ESCs (d0) were differentiated applying the hanging drop protocol for 2-, 4-, 12-, 15- and 22-days (Gaspar, J. A. et al. Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells. Stem Cells Dev 21, 2471-2484, doi:10.1089/scd.2011.0637 (2012)). Total RNA from the undifferentiated (d0) and 2-, 4-, 12-, 15- and 22-days EBs was isolated and gene expression was analyzed by the Affymetrix Mouse430 2.0 chip.

tag: strain/background

value: Male

tag: genotype/variation

value: Mageb16 knockdown (KD)

tag: cell type

value: embryoid bodies (EBs)

tag: time of differentiation

value: day 22


title: 402240_C

source_name: Patient 402240; Tissue mucosa


title: 401896_C1

source_name: Patient 401896; Tissue mucosa


title: 3KD d15

source_name: third chip KD day 15

value: day 15


title: 402216_C1

source_name: Patient 402216; Tissue mucosa


title: 3KD d4

source_name: third chip KD day 4

value: day 4


title: 3KD d2

source_name: third chip KD day 2

value: day 2


title: 3KD d0

source_name: third chip KD day 0

value: embryonic stem cells (ESCs)

value: day 0


title: 403064_A

source_name: Patient 403064; Tissue tumor


title: 402240_A

source_name: Patient 402240; Tissue tumor


title: 403456_A

source_name: Patient 403456; Tissue tumor


title: 402128_C1

source_name: Patient 402128; Tissue mucosa


title: 402880_C1

source_name: Patient 402880; Tissue mucosa


title: 2KD d22

source_name: second chip KD day 22


title: 402400_A

source_name: Patient 402400; Tissue tumor


title: 404336_C2

source_name: Patient 404336; Tissue mucosa


title: 3KD d12

source_name: third chip KD day 12

value: day 12


title: 403848_C1

source_name: Patient 403848; Tissue mucosa


title: 401896_A

source_name: Patient 401896; Tissue tumor


title: 2KD d15

source_name: second chip KD day 15


title: 2KD d12

source_name: second chip KD day 12


title: 403392_C1

source_name: Patient 403392; Tissue mucosa


title: 2KD d4

source_name: second chip KD day 4


title: 2KD d2

source_name: second chip KD day 2


title: 402672_A

source_name: Patient 402672; Tissue tumor


title: 402200_C

source_name: Patient 402200; Tissue mucosa


title: 402672_C1

source_name: Patient 402672; Tissue mucosa


title: 402128_A

source_name: Patient 402128; Tissue tumor


title: 401000_A

source_name: Patient 401000; Tissue tumor


title: 2KD d0

source_name: second chip KD day 0


title: 1KD d22

source_name: First chip KD day 22


title: 402264_C1

source_name: Patient 402264; Tissue mucosa


title: 1KD d15

source_name: First chip KD day 15


title: 403752_A

source_name: Patient 403752; Tissue tumor


title: 402760_C1

source_name: Patient 402760; Tissue mucosa


title: 402376_C1

source_name: Patient 402376; Tissue mucosa


title: 404352_C1

source_name: Patient 404352; Tissue mucosa


title: 1KD d4

source_name: First chip KD day 4


title: 402384_C

source_name: Patient 402384; Tissue mucosa


title: 1KD d2

source_name: First chip KD day 2


title: 3SCR d22

source_name: third chip SCR day 22

value: scrambled control (SCR)


title: 401984_A

source_name: Patient 401984; Tissue tumor


title: 404352_A

source_name: Patient 404352; Tissue tumor


title: 402368_C1

source_name: Patient 402368; Tissue mucosa


title: 403568_C1

source_name: Patient 403568; Tissue mucosa


title: 401440_B

source_name: Patient 401440; Tissue mucosa


title: 1KD d0

source_name: First chip KD day 0


title: 402800_A

source_name: Patient 402800; Tissue tumor


title: 403840_C1

source_name: Patient 403840; Tissue mucosa


title: 3SCR d15

source_name: third chip SCR day 15


title: 402264_A

source_name: Patient 402264; Tissue tumor


title: 401984_C

source_name: Patient 401984; Tissue mucosa


title: 403848_A

source_name: Patient 403848; Tissue tumor


title: 403568_A

source_name: Patient 403568; Tissue tumor


title: 402760_A

source_name: Patient 402760; Tissue tumor


title: 402536_C1

source_name: Patient 402536; Tissue mucosa


title: 403032_C1

source_name: Patient 403032; Tissue mucosa


title: 3SCR d4

source_name: third chip SCR day 4


title: 2SCR d22

source_name: second chip SCR day 22


title: 3SCR d2

source_name: third chip SCR day 2


title: 2SCR d15

source_name: second chip SCR day 15


title: 403736_A

source_name: Patient 403736; Tissue tumor


title: 1KD d12

source_name: First chip KD day 12


title: 402016_C1

source_name: Patient 402016; Tissue mucosa


title: 402232_C1

source_name: Patient 402232; Tissue mucosa


title: 404360_C

source_name: Patient 404360; Tissue mucosa


title: 2SCR d12

source_name: second chip SCR day 12


title: 401976_C1

source_name: Patient 401976; Tissue mucosa


title: 403744_C1

source_name: Patient 403744; Tissue mucosa


title: 402432_A

source_name: Patient 402432; Tissue tumor


title: 2SCR d4

source_name: second chip SCR day 4


title: 3SCR d12

source_name: third chip SCR day 12


title: 402744_C1

source_name: Patient 402744; Tissue mucosa


title: 2SCR d0

source_name: second chip SCR day 0


title: 3SCR d0

source_name: third chip SCR day 0


title: 401424_C1

source_name: Patient 401424; Tissue mucosa


title: 2SCR d2

source_name: second chip SCR day 2


title: 1SCR d2

source_name: First chip SCR day 2


title: 1SCR d15

source_name: First chip SCR day 15


title: 402640_C

source_name: Patient 402640; Tissue mucosa


title: 402200_A

source_name: Patient 402200; Tissue tumor


title: 1SCR d12

source_name: First chip SCR day 12


title: 1SCR d4

source_name: First chip SCR day 4


title: 1SCR d22

source_name: First chip SCR day 22


title: 1SCR d0

source_name: First chip SCR day 0


title: 402208_A

source_name: Patient 402208; Tissue tumor


title: 402432_C1

source_name: Patient 402432; Tissue mucosa


title: 3ESC d22

source_name: third chip ESC day 22

value: WT


title: 402640_A

source_name: Patient 402640; Tissue tumor


title: 402208_C1

source_name: Patient 402208; Tissue mucosa


title: 3ESC d15

source_name: third chip ESC day 15


title: 3ESC d12

source_name: third chip ESC day 12


title: 3ESC d4

source_name: third chip ESC day 4


title: 402424_C

source_name: Patient 402424; Tissue mucosa

value: M


title: 402048_C

source_name: Patient 402048; Tissue mucosa

value: mucosa


title: 3ESC d2

source_name: third chip ESC day 2


title: 3ESC d0

source_name: third chip ESC day 0


title: 2ESC d22

source_name: second chip ESC day 22


title: 403368_C

source_name: Patient 403368; Tissue mucosa

value: Colorectal cancer


title: 2ESC d15

source_name: second chip ESC day 15


title: 2ESC d12

source_name: second chip ESC day 12


title: 2ESC d4

source_name: second chip ESC day 4


title: 2ESC d0

source_name: second chip ESC day 0


title: 403056_C1

source_name: Patient 403056; Tissue mucosa


title: 402440_A

source_name: Patient 402440; Tissue tumor


title: 1ESC d15

source_name: First chip ESC day 15


title: 2ESC d2

source_name: second chip ESC day 2


title: 402048_A

source_name: Patient 402048; Tissue tumor


title: 402992_A

source_name: Patient 402992; Tissue tumor


title: 402096_A

source_name: Patient 402096; Tissue tumor


title: 1ESC d12

source_name: First chip ESC day 12


title: 402992_C

source_name: Patient 402992; Tissue mucosa


title: 402512_A

source_name: Patient 402512; Tissue tumor


title: 1ESC d22

source_name: First chip ESC day 22


title: 402096_C1

source_name: Patient 402096; Tissue mucosa


title: 402440_C2

source_name: Patient 402440; Tissue mucosa


title: 1ESC d4

source_name: First chip ESC day 4


title: 404048_C

source_name: Patient 404048; Tissue mucosa


title: 402512_C1

source_name: Patient 402512; Tissue mucosa


title: 402648_C1

source_name: Patient 402648; Tissue mucosa


title: 404048_A

source_name: Patient 404048; Tissue tumor


title: 403056_A

source_name: Patient 403056; Tissue tumor


title: 403304_A

source_name: Patient 403304; Tissue tumor

value: F


title: 403304_C

source_name: Patient 403304; Tissue mucosa


title: 1ESC d2

source_name: First chip ESC day 2


title: 1ESC d0

source_name: First chip ESC day 0


title: 402648_A

source_name: Patient 402648; Tissue tumor

value: tumor


title: 403888_A

source_name: Patient 403888; Tissue tumor


title: 403368_A

source_name: Patient 403368; Tissue tumor


title: 403080_A

source_name: Patient 403080; Tissue tumor


title: 403080_C1

source_name: Patient 403080; Tissue mucosa


title: 402408_C1

source_name: Patient 402408; Tissue mucosa


title: 403624_C1

source_name: Patient 403624; Tissue mucosa


title: 403888_C1

source_name: Patient 403888; Tissue mucosa


title: 403176_A

source_name: Patient 403176; Tissue tumor


title: 400152_C

source_name: Patient 400152; Tissue mucosa


title: 403176_C1

source_name: Patient 403176; Tissue mucosa


title: 400152_A

source_name: Patient 400152; Tissue tumor


title: 402408_A

source_name: Patient 402408; Tissue tumor


title: 403616_A

source_name: Patient 403616; Tissue tumor


title: 403624_A

source_name: Patient 403624; Tissue tumor


title: 400216_A

source_name: Patient 400216; Tissue tumor


title: 400072_C

source_name: Patient 400072; Tissue mucosa


title: 400288_A

source_name: Patient 400288; Tissue tumor


title: 400240_A

source_name: Patient 400240; Tissue tumor


title: 400240_C

source_name: Patient 400240; Tissue mucosa


title: 400408_A

source_name: Patient 400408; Tissue tumor


title: 400072_A

source_name: Patient 400072; Tissue tumor


title: 403616_C1

source_name: Patient 403616; Tissue mucosa


title: 400264_C

source_name: Patient 400264; Tissue mucosa


title: 402168_A

source_name: Patient 402168; Tissue tumor


title: 400704_A

source_name: Patient 400704; Tissue tumor


title: 400888_C1

source_name: Patient 400888; Tissue mucosa


title: 402168_C

source_name: Patient 402168; Tissue mucosa


title: 400704_C

source_name: Patient 400704; Tissue mucosa


title: 400992_C

source_name: Patient 400992; Tissue mucosa


title: 400688_C

source_name: Patient 400688; Tissue mucosa


title: Adult LG, biological rep3

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

description: manually dissected out LG, epithelial and mesenchymal compartments

hyb_protocol: GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 3, Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data-analysis consisted of data pre-processing, quality analysis and detection of statistically differentially expressed genes between the sample groups.  The .CEL files [2] of each of the six arrays were loaded into the Affymetrix Expression Console software [3]. They were processed with two different analysis methods [4]:  * Gene level SST-RMA (Signal Space Transformation - Robust Multichip Analysis), includes background reduction and SST intensity normalization to produce the gene expression difference results  * Exon level SST-Alt Splicing - includes additionally the extraction of all exon, exon-exon splice junction and transcript isoform expression changes  These results can be found from the .CHP files [5] included in the project folder. The file names indicate which method has been used. These files in turn are used with the Affymetrix Transcriptome Analysis Console (TAC) Software [6] to produce the differential expression tables and charts. [7]  REFERENCES  [1] MTA 1.0 - http://www.affymetrix.com/catalog/prod870009/AFFY/Mouse+Transcriptome+Assay+1.0  [2] CEL file format -  http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html  [3] Affymetrix Expression Console Software -  http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131414  [4] Affymetrix Expression Console Software Manual -  http://media.affymetrix.com/support/downloads/manuals/expression_console_userguide.pdf  [5] CHP file format -  http://dept.stat.lsa.umich.edu/~kshedden/Courses/Stat545/Notes/AffxFileFormats/chp.html  [6] Affymetrix Transcriptome Analysis Console (TAC) Software -  http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=prod760001&navAction=jump  [7] Affymetrix Transcriptome Analysis Console (TAC) Software Manual -  http://media.affymetrix.com/support/downloads/manuals/tac_user_manual.pdf

source_name: adult murine LG

label_protocol: Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays P/N 703262 Rev. 1

growth_protocol: Mice were kept in a pathogen-free animal facility until sample collection

extract_protocol: Extraction of total RNA was performed with RNeasy microkit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Not applicable

tag: strain

value: ICR

value: lacrimal gland, epithelial and mesenchymal compartments

tag: developmental stage

value: 34 wks old adult

value: female


title: 400448_C

source_name: Patient 400448; Tissue mucosa


title: 401816A

source_name: Patient 401816; Tissue tumor


title: Adult LG, biological rep1


title: embryonic LG, biological rep3

source_name: minimum 10 embryonic E18 murine LGs pooled together

value: E18 embryos


title: 400264_A

source_name: Patient 400264; Tissue tumor


title: 400872_C

source_name: Patient 400872; Tissue mucosa


title: 400408_C

source_name: Patient 400408; Tissue mucosa


title: Adult LG, biological rep2


title: embryonic LG, biological rep2


title: 400688_A

source_name: Patient 400688; Tissue tumor


title: 400992_A

source_name: Patient 400992; Tissue tumor


title: PC-9 cells_control vs 20 nM gefitinib_24h

city: Helsinki

first: Liang

last: Wang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

description: Gene expression level after treatment with 20 nM gefitinib in PC-9 cells

hyb_protocol: samples were applied to microarrays enclosed in  hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on ancapitalbio luxscan scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: NSCLC PC-9 cells, 20 nM gefitinib treatment, 24h

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: All cells were cultured in the RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 units/mL penicillin-streptomycin

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

treatment_protocol: After seed cells on the plate for 24 hours, diluent the stocking gefitinib solution with RPMI 1640 medium and then add the medium into the cells for additional 24 culture

value: Lung

tag: genotype

value: EGFR delE746-A750

tag: cell line

value: NSCLC

source_name: NSCLC PC-9 cells, control, 24h


title: A549 cells_control vs 20 µM gefitinib_24h

description: Gene expression level after treatment with 20 µM gefitinib in A549 cells

source_name: NSCLC A549 cells, 20 µM gefitinib treatment, 24h

value: EGFR wild type

source_name: NSCLC A549 cells, control, 24h


title: 401696C1

source_name: Patient 401696; Tissue mucosa


title: embryonic LG, biological rep1


title: 400904_A

source_name: Patient 400904; Tissue tumor


title: control3

status: Public on Sep 12 2017

city: Tianjin

first: Ding

last: Yahui

state: Tianjin

address: weijin Road 94

country: China

institute: nankai university

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: blood

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: KG1a cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. 7l induced gene expression in KG1a cell was measured at 24 hours after exposure to doses of 2µM. Each sample was performed in triplicate.

value: KG1a cell line


title: 401696A

source_name: Patient 401696; Tissue tumor


title: 7l2

description: replicate 2


title: 402256A

source_name: Patient 402256; Tissue tumor


title: PCH1-O

city: Shanghai

first: Chen

last: Su

state: Please select...

address: Fengyang Road

institute: Changzheng Hospital

description: BSD treated stable cell line

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: PCH1-Brachyury overexpression

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Establishment of PCH cell line: The chordoma samples were obtained intraoperatively with no history of adjuvant therapies before surgery. All patients gave informed consent for the use of tumor samples for investigational and analytical studies under Changzheng Institutional Review Board guidelines. All samples were placed on ice immediately following surgical resection and transported to the laboratory. Tumor tissue was finely minced and, after extensively washing with PBS, transferred into a 100mm culture dish, culturing in Dulbecco's Modified Eagle Medium (DMEM) at 37°C, with 5% CO2. The cells were routinely passed every five days in the first 3-6 passages. Other cell lines like H460 and U2OS were bought from ATCC and cultured in Dulbecco's Modified Eagle Medium (DMEM) at 37°C, with 5% CO2.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Virus infection and RNAi: Lentivirus constructs of RNAi against Brachyury, overexpression of Brachyury and control RNAi were purchased from Shanghai Research &Science Company. The RNAi sequences are from Sigma Aldrich: shT sequence: CCGGCGAGGAGATCACAGCTCTTAACTCGAGTTAAGAGCTGTGATCTCCTCGTTTTT. DNA was synthesized from Invitrogen company. Virus infection and the establishment of stable cell lines was done according to a protocol provided by Shanghai Research &Science Company.

value: primary chordoma

tag: lentivirus

value: constructs of RNAi  overexpression of Brachyury


title: PCH1-I

description: BSD treated stable cell line

source_name: PCH1-Brachyury silencing

value: constructs of RNAi against Brachyury


title: 7l3

description: replicate 2


title: U2OS-NC

description: BSD treated stable cell line

value: osteosarcoma

value: constructs of control RNAi


title: U2OS-O

description: BSD treated stable cell line

source_name: U2OS-Brachyury overexpression


title: control2

description: replicate 1


title: PCH1-NC

description: BSD treated stable cell line


title: control1

description: replicate 1


title: 401728A

source_name: Patient 401728; Tissue tumor

value: M

value: Colorectal cancer


title: H460-I

description: BSD treated stable cell line

source_name: H460-Brachyury silencing

value: lung


title: Case 6A

city: Lund

first: Elsa

last: Arbajian

address: klinikgatan 28, BMC C13

department: Clinical genetics

country: Sweden

institute: Lund University

description: Project p1501

hyb_protocol: performed by SCIBLU, Lund University

scan_protocol: performed by SCIBLU, Lund University

data_processing: data were analyzed in Expression console and processed by standard RMA

source_name: SEF tumor

label_protocol: Biotinylated cRNA were prepared from 2ug of RNA according to the standard Affymetrix protocol

growth_protocol: tumor pieces are kept in -80 degrees celsius prior to RNA extraction

extract_protocol: Qiagen Kit

treatment_protocol: not applicable

tag: tumor type

tag: outcome*

tag: fusion gene

value: Female


title: Case 8

description: Project p1307

value: M 0, DoD 4

value: Male


title: Case 5

description: Project p1501

value: M 0, DoD 15


title: 401816C

source_name: Patient 401816; Tissue mucosa

tag: patientid

value: mucosa


title: Case 15B

description: Project p1501

value: hybrid SEF/LGFMS_metastasis with SEF morphology

value: DoD 53

tag: gender


title: H460-NC

description: BSD treated stable cell line


title: Case 15A

description: Project p1501

value: hybrid SEF/LGFMS_reccurence with SEF morphology

tag: age


title: 401728C

source_name: Patient 401728; Tissue mucosa

tag: tissue


title: 402272A

source_name: Patient 402272; Tissue tumor

value: tumor

tag: disease state


title: Case 7

description: Project p1307

value: DoD 39


title: 7l1

description: replicate 2

value: KG1a cell line


title: OVCAR3cell

city: Tokyo

first: Akira

last: Yokoi

state: Tokyo-to

address: 5-1-1 Tsukiji, Chuo-ku

department: Group for Research of Molecular Functions and Targets

country: Japan

institute: National Cancer Center　Research Institute

description:
Total RNA extracted form cells, and 100 ng of RNA for analysis
miRNA

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Agilent DNA microarray scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cellular RNA of NIH-OVCAR3

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

growth_protocol: Human OvCa cell lines were purchased from the American Type Culture Collection (ATCC), the European Collection of Cell Cultures (ECACC) and the Japanese Collection of Research Bioresources (JCRB) cell bank. The SKOV3, OVCAR3, CAOV3, ES-2, and OC-90 lines were from the ATCC, the A2780, OAW42, and COV362 were from the ECACC, and the MCAS, RMG-1, RMUG-S, and KURAMOCHI lines were from JRCB. HOSE1-3 were kindly gifted from Dr. Tohru Kiyono (National Cancer Center, Tokyo, Japan). All cell lines were cultured in optimal medium according to the suppliers’ recommendations.

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: Cellular RNA of A2780cisThe cells were washed with phosphate-buffered saline (PBS), and the culture medium was replaced with advanced Dulbecco’s modified Eagle’s medium for ES-2, SKOV3, CAOV3, OV-90, OAW42, COV362 and MCAS cells, advanced DMEM/Ham's F-12 medium for RMG-1, RUG-S and HOSE1-3 cells, or advanced RPMI medium for A2780, OVCAR3 and KURAMOCHI cells. In all cases, the cell culture medium contained antibiotic and antifungal drugs as well as 2 mM L-glutamine (but not FBS). After incubation for 48 h, the conditioned medium (CM) was collected and centrifuged at 2,000 x g for 10 min at 4°C. To thoroughly remove cellular debris, the supernatant was filtered through a 0.22-m filter (Millipore). The CM was then used for EV isolation. To prepare EVs, CM was ultracentrifuged at 35,000 rpm using a SW41Ti rotor for 70 min at 4°C. The pellets were washed with PBS, ultracentrifuged at 35,000 rpm using the SW41Ti rotor for 70 min at 4°C and resuspended in PBS.

tag: rna amount (nanograms)

tag: cellular compartment

value: cellular RNA


title: Case 4

description: Project p1501


title: KURA-cell

source_name: Cellular RNA of KURAMOCHI

value: KURAMOCHI


title: A2780ccell

source_name: Cellular RNA of A2780cis


title: Case 11

description: Project p1501

value: FUS/CREM


title: Case 12

description: Project p1501

value: not known


title: Case 3

description: Project p1501

value: M 9_DoD 36


title: MCAScell

source_name: Cellular RNA of MCAS

value: MCAS


title: ES-2cell

source_name: Cellular RNA of ES-2


title: RMG-Icell

source_name: Cellular RNA of RMG-1


title: KURA-exo

description:
Total RNA extracted form exosomes, and 50 ng of RNA for analysis
miRNA

source_name: Exosomes collected from KURAMOCHI cells

value: exosomes


title: OVCAR3exo

source_name: Exosomes collected from NIH-OVCAR3 cells


title: RMG-Iexo

source_name: Exosomes collected from RMG-1 cells


title: 401504C

source_name: Patient 401504; Tissue mucosa

value: M

value: Colorectal cancer


title: OAW42cell

source_name: Cellular RNA of OAW42


title: MCASexo

source_name: Exosomes collected from MCAS cells


title: OV-90exo

source_name: Exosomes collected from OV-90 cells


title: AIPG_EXE vs AIPG_NoEXE

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: Sample 1

hyb_protocol: For pre-hybridization the slides were re-hydrated with water vapor at 60°C, and fixed with two cycles of UV light (1200J). After boiling for two minutes at 92°C, slides were washed with 95% ethanol for one minute and prehybridzed in 5X SSC, 0.1% SDS and 1% BSA for one hour at 42°C. The slides were washed and dried for further hybridization. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the 22 thousand oligos mouse arrays for 14 h at 42°C.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Alexa555 and Alexa647 density mean value (Dty), background mean value (Bck) and Signal (Sig) cross channel loees normalization value (by subgrids) were calculated with software ArrayPro Analyzer from Media Cibernetics.

data_processing: Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM. GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean. zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 1.5 standard deviations would be the significantly differentially expressed genes.

source_name: reference AIPG mice

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

extract_protocol: Total RNA was purified using the RNeasy® Lipid Tissue Mini Kit (QIAGEN) extraction kit, following the manufacturer's protocol. The amount and integrity of the purified RNA was verified using the RNA 6000 Nano kit and the 2100 Bionalyzer (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: PGIA mice of test group were exercised for ten weeks with a frequency of 3 sessions/week and duration of 25 min of exercise/session. The speed was gradually increased from 20 % to 75 % in increments of 13 % every 6 sessions. Each session included the phases: 1) acclimatization: mice were placed for 5 min on the treadmill switched off; 2) warm-up: mice walked for 5 min at lowest speed; 3) PE: mice run for 25 min at the corresponding speed; and 4) cool down: mice walked for 5 min at lowest speed. PGIA mice of control group were kept without exercise.

value: BALB/c

value: female

value: 8 - 11 months

value: Tarsal bone and joint

tag: sample group

value: reference

source_name: test AIPG mice

value: Treadmill exercise


title: HOSE2cell

source_name: Cellular RNA of HOSE2


title: A2780cexo

source_name: Exosomes collected from A2780cis cells


title: HOSE1cell

source_name: Cellular RNA of HOSE1


title: SKOV3cell

source_name: Cellular RNA of SKOV3


title: A2780cell

source_name: Cellular RNA of A2780


title: ES-2exo

source_name: Exosomes collected from ES-2 cells


title: RMUG-Sexo

source_name: Exosomes collected from RMUG-S cells

value: RMUG-S


title: HOSE3exo

source_name: Exosomes collected from HOSE3 cells


title: HOSE3cell

source_name: Cellular RNA of HOSE3


title: COV362exo

source_name: Exosomes collected from COV362 cells


title: COV362cell

source_name: Cellular RNA of COV362


title: CAOV3exo

source_name: Exosomes collected from CAOV3 cells


title: SKOV3exo

source_name: Exosomes collected from SKOV3 cells


title: 402272C1

source_name: Patient 402272; Tissue mucosa

value: mucosa


title: 402256C1

source_name: Patient 402256; Tissue mucosa


title: OAW42exo

source_name: Exosomes collected from OAW42 cells


title: HOSE2exo

source_name: Exosomes collected from HOSE2 cells


title: HOSE1exo

source_name: Exosomes collected from HOSE1 cells


title: A2780exo

source_name: Exosomes collected from A2780 cells


title: Control, mouse P0 forebrain, biological rep3

status: Public on Sep 11 2017

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

state: Hamburg

address: Martinistr. 52

department: Institute of Neuropathology

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression data from Control forebrains

hyb_protocol: Samples were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) at the Gene Center Munich (Ludwig-Maximilians-University, 81377 Munich, Germany)

scan_protocol: Samples were scanned at the Gene Center Munich (Ludwig-Maximilians-University, 81377 Munich, Germany)

data_processing: Robust Multi-array Average (RMA)-summarized gene-level expression values computed using Affymetrix Expression Console

label: Biotin

source_name: Control, mouse P0 forebrain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: hGFAP-cre mice were bred with Ctnnb1(ex3)Fl/+SmoM2Fl/+ mice, pups were euthanized at postnatal day 0

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

treatment_protocol: no treatment

value: postnatal day 0

value: Control forebrain


title: GBS, mouse P0 forebrain, biological rep3

description: Gene expression data from GBS tumors

source_name: GBS, mouse P0 forebrain

value: GBS tumor


title: Liver_Irradiated_6 Gy

status: Public on Sep 09 2017

city: Busan

first: Sungmin

last: Lee

address: 2, Busandaehak-ro 63 beon-gil

department: Integrated Biological Science

country: South Korea

institute: Pusan National University

description: Gene expression data from liver of 6 Gy gamma-ray irradiated 9 weeks old C57BL/6 mouse

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: C57BL/6 Mouse Irradiated

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: The mice were maintained in animal care facilities in a temperature-regulated room (23±1°C) with a 12 h light/dark cycle. All animals were fed water and standard mouse chow ad libitum.

extract_protocol: Qiagen Rneasy RNA extraction kit was used for total RNA isolation

treatment_protocol: The mice received whole body irradiation using Gamma Cell 40 Extractor (Nordion International Inc., Kanata, Ontario, Canada) at a dose rate of 0.81 Gy/min. The anesthetized mice were placed in the irradiation chamber

value: Male

value: 9 weeks

tag: treated with

value: 6 Gy of single gamma-ray

value: Liver


title: GB, mouse P0 forebrain, biological rep2

description: Gene expression data from GB forebrains

source_name: GB, mouse P0 forebrain

value: GB forebrain


title: GS, mouse P0 forebrain, biological rep3

description: Gene expression data from GS forebrains

source_name: GS, mouse P0 forebrain

value: GS forebrain


title: DKO-II+III [PJI-16]

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E. Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing:
The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the SST-RMA procedure.  The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters. The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Mouse
program-name = Expression Console
program-version = 1.4.1.46

source_name: DKO-II+III

label_protocol: Microarray was performed at the Genomics Core Facility at the University of Chicago. The RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 700 pg of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

growth_protocol: The bone marrow lineage negative/progenitor cells were purified according to the manufacturer’s instructions using the biotin mouse lineage panel (BD Pharmingen,Cat#559971). These cells were cultured with IMDM containing 15% fetal bovine serum, 1% bovine serum albumin, 10μg/ml recombinant human insulin, 200μg/ml recombinant human holo-transferrin, 0.1 mM β-mercapto-ethanol, 1% penicillin-streptomycin, 2 mM L-glutamine, 2U/µL erythropoietin for different time points.

extract_protocol: Total RNA was isolated by Trizol, according to the manufacturer’s instructions.

treatment_protocol: 100ng/mL recombinant mouse IL-6 were added into the EPO-containing medium at the beginning of the in vitro culture.

tag: strain background

tag: Sex

tag: genotype/variation

value: mDia1-miR-146a double KO

value: 1 year

tag: mouse status

value: Healthy

tag: tissue/cell type

value: Basophilic(II) and polychromatic(III) erythroblasts


title: GS, mouse P0 forebrain, biological rep2

description: Gene expression data from GS forebrains

tag: genotype


title: DKO-IV [PJI-20]

source_name: DKO-IV

value: female

value: Orthochromatic(IV) erythroblasts


title: Control, mouse P0 forebrain, biological rep1


title: GS, mouse P0 forebrain, biological rep1

description: Gene expression data from GS forebrains


title: GB, mouse P0 forebrain, biological rep3

description: Gene expression data from GB forebrains


title: GB, mouse P0 forebrain, biological rep1

description: Gene expression data from GB forebrains


title: DKO-II+III [PJI-19]


title: GBS, mouse P0 forebrain, biological rep2

description: Gene expression data from GBS tumors


title: Control, mouse P0 forebrain, biological rep2


title: GBS, mouse P0 forebrain, biological rep1

description: Gene expression data from GBS tumors


title: DKO-IV [PJI-17]


title: CAOV3cell

source_name: Cellular RNA of CAOV3

tag: cell line

value: cellular RNA


title: DWT-II+III [PJI-13]

source_name: DWT-II+III

value: double WT


title: MCAO + Vehicle treated, biological rep 3

city: Riverside

first: Byron

last: Ford

state: CA

address: 0207 School of Medicine Research Building

institute: University of California,Riverside

description: Gene expression data from animals treated with 1% bovine serum albumin(BSA) in phosphate buffered saline (PBS) following MCAO

hyb_protocol: Per manufacturing guidelines, following fragmentation and Labeling Single-Stranded cDNA and 3.5 ug of cRNA was added to Affymetrix Hybridization Master Mix and hybridized for 16 hr at 45C on Affymetrix Rat Genome 2.0st GeneChip. 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 in R Bioconductor using the oligo package.
RMA

organism: Rattus norvegicus

source_name: MCAO_3 hours + Vehicle treated

label_protocol: Fragmented DNA is labeled using an Affymetrix proprietary DNA Labeling Reagent which is covalently linked to biotin by terminal deoxynucleotidyl transferase (TdT), which is added to 5.5 ug total RNA. This and all steps were completed via manufacturing guidelines. (GeneChip® WT PLUS Reagent Kit Manual, 2013, Affymetrix).

treatment_protocol: MCAO was induced by the intraluminal suture method.  A 4 cm length 4-0 surgical monofilament nylon suture coated with silicon (Doccol Corp., Sharon, MA, diameter 0.37 mm, length 2.3-2.5 mm) was inserted from the external carotid artery (ECA) into the internal carotid artery. (ICA) and then into the Circle of Willis, to occlude the origin of the left middle cerebral artery (MCA). Rats in the sham control group underwent the same procedure as those in the injury group, but a filament was not inserted into the ICA. Rats in the sham control group underwent the same procedure as those in the injury group, but a filament was not inserted into the ICA. NRG-1 was administered immediately before MCA occlusion.

value: brain (cortex)

value: adult

value: male


title: Liver_Control

description: Gene expression data from liver of control 9 weeks old C57BL/6 mouse

source_name: C57BL/6 Mouse Control

tag: strain

value: Male

value: none (control)


title: MCAO + Vehicle treated, biological rep 2


title: DWT-IV [PJI-11]

source_name: DWT-IV


title: DWT-I [PJI-12]

source_name: DWT-I

value: Proerythroblasts(I)


title: sham control, biological repl 3

description: Gene expression data from sham control


title: DKO-I [PJI-15]

source_name: DKO-I


title: DWT-IV [PJI-14]


title: OV-90cell

source_name: Cellular RNA of OV-90


title: RMUG-Scell

source_name: Cellular RNA of RMUG-S

value: RMUG-S


title: DKO-I [PJI-18]


title: D2-Control [PJI-5]

value: WT

value: Erythroblasts


title: D2-Control [PJI-6]


title: D1-IL6 [PJI-4]

value: 100ng/mL recombinant mouse IL-6


title: D1-IL6 [PJI-3]


title: sham control, biological repl 2

description: Gene expression data from sham control


title: MCAO + NRG treated , biological rep2

description: Gene expression data from animals treated with NRG-1 following pMCAO

source_name: MCAO_3 hours + NRG treated


title: MCAO + NRG treated , biological rep1


title: MCAO + Vehicle treated, biological rep 1


title: H2_treated_liver_CDAA_rep3

status: Public on Sep 08 2017

city: Kasugai

first: Masatoshi

last: Ichihara

state: Aichi

address: 1200 Matsumoto-cho

institute: Chubu University

description: SAMPLE 15

hyb_protocol: The biotin-labeled aRNAs were hybridized with the array strips at 45°C for 16 h. After hybridization, the strips were washed and stained in the GeneAtlas Fluidics Station using the GeneAtlas Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The intensity of each hybridized probe was measured using the GeneAtlas Imaging Station.

data_processing: The obtained CEL files were normalized and summarized using the robust multiarray average (RMA) method with Expression Console software (Affymetrix).

label_protocol: Comparative analysis of gene expression profiles was performed using the RG-230 PM Array Strips and the Affymetrix GeneAtlas microarray system (Affymetrix, Santa Clara, CA, USA), according to the manufacturer's instructions. For RNA samples from the rat livers, the corresponding amplified and biotin-labeled antisense RNA (aRNA) was synthesized using a GeneChip 3'IVT Express kit (Affymetrix). The resulting aRNA was fragmented as described by the manufacturer.

extract_protocol: Livers from rats of four groups were immersed in RNAlater solution (Ambion, Austin, TX) for several days at 4°C and then total RNA was isolated using RNeasy mini kit (Qiagen, Hilden, Germany) from the rats.

treatment_protocol: For control/normal diet group, F344 rats were fed with basal rodent chow (CE-2; CLEA Japan Inc., Tokyo, Japan) and control dehydrogenized water (CDW) in air for 3 weeks. For hydrogen-treated/normal diet group, F344 rats were fed with basal rodent chow and hydrogen-rich water (HRW) in hydrogen-containing air (HCA; 2% hydrogen/98% air) for 3 weeks. For control/CDAA diet group, F344 rats were fed with a choline-deficient L-amino acid-defined diet (CDAA diet; A06083101, Research Diets, Inc., New Brunswick, NJ) and CDW in air for 3 weeks. For hydrogen-treated/CDAA diet group, F344 rats were fed with CDAA diet and HRW in HCA for 3 weeks. HRW (0.7mM dissolved hydrogen) was generated from distilled water with 0.44 mM Na2SO4 using Aquela Blue, a water-electrolyzing device to produce electrolyzed hydrogen-saturated water near neutral pH (MiZ Co., Ltd, Fujisawa, Japan). The CDW was prepared by gently stirring hydrogen-rich water in open air for 24 hours.

value: 4 weeks

tag: treatment group

value: H2 and CDAA diet

value: Liver


title: DWT-I [PJI-9]

value: 1 year

value: Healthy


title: Control_lung_rep1

description: SAMPLE 1

label_protocol: Comparative analysis of gene expression profiles was performed using the MG-430 PM Array Strips and the Affymetrix GeneAtlas microarray system (Affymetrix, Santa Clara, CA, USA), according to the manufacturer's instructions. For RNA samples from the mouse lungs, the corresponding amplified and biotin-labeled antisense RNA (aRNA) was synthesized using a GeneChip 3'IVT Express kit (Affymetrix). The resulting aRNA was fragmented as described by the manufacturer.

extract_protocol: Lungs from control and hydrogen-treated mice were immersed in RNAlater solution (Ambion, Austin, TX) for several days at 4°C and then total RNA was isolated using RNeasy mini kit (Qiagen, Hilden, Germany) from the lungs.

treatment_protocol: For a hydrogen-treated group, BALB/c mice were administrated with H2-containing air (2% H2 gas/98% air) for 3 weeks. For a control group, BALB/c mice were reared in normal air.

value: BALB/c

tag: gender

value: 10 weeks

value: control

value: lung


title: H2_treated_lung_rep3

description: SAMPLE 6

value: male

tag: age


title: D2-IL6 [PJI-8]

value: female


title: sham control, biological repl 4

description: Gene expression data from sham control

tag: tissue

value: brain (cortex)

value: adult


title: MCAO + NRG treated , biological rep3


title: H2_treated_liver_CDAA_rep1

description: SAMPLE 13


title: Control_liver_CDAA_rep4

description: SAMPLE 12

value: CDAA diet


title: DWT-II+III [PJI-10]

value: double WT

value: Basophilic(II) and polychromatic(III) erythroblasts


title: D1-Control [PJI-2]

value: WT

value: Erythroblasts


title: sham control, biological rep 1

description: Gene expression data from sham control


title: Control_lung_rep3

description: SAMPLE 3


title: H2_treated_liver_CDAA_rep2

description: SAMPLE 14

value: 4 weeks

value: H2 and CDAA diet


title: H2_treated_lung_rep2

description: SAMPLE 5


title: D2-IL6 [PJI-7]

value: 100ng/mL recombinant mouse IL-6


title: H2_treated_liver_CDAA_rep4

description: SAMPLE 16

value: Liver


title: Control_liver_CDAA_rep2

description: SAMPLE 10


title: Human ES cell line-H9-KSR/bFGF on feeder

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

institute: Osaka University

hyb_protocol: GeneChip hybridization oven 645 as per manufacturer (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G System

data_processing:
CNV, LOH and Loss or Gain Mosaic was anlyzed by Single Sample Anlysis NA33 in Affimetrix Chromosome Analysis Suite 3.1 with smoothing window of 0 Mb
CNV, LOH and Mosaic segements detected with filter of 0 marker count and 0kb size

source_name: Human ES cell line H9

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: AKIT or Essential 8 medium on 0.5µg/cm2 Laminin-E8 fragment-coated dishes, or standard KSR/bFGF medium on MEF feeder layer

extract_protocol: Proteinase K and Rnase I treatment followed by phenol-chloroform extraction and isopropanol precipitation

tag: cell type

value: embryonic stem cell

tag: culture medium

value: KSR/bFGF

tag: culture condition

value: on feeder


title: Human ES cell line-KhES-1-AKIT feeder-free

source_name: Human ES cell line KhES-1

value: AKIT

value: feeder-free


title: Human ES cell line-H9-E8 feeder-free


title: H2_treated_liver_rep2

description: SAMPLE 6

value: male


title: H2_treated_lung_rep1

description: SAMPLE 4

value: BALB/c

value: 10 weeks

value: lung


title: Human ES cell line-H9-AKIT feeder-free


title: Human ES cell line-KhES-1-E8 feeder-free


title: Control_liver_CDAA_rep1

description: SAMPLE 9

value: CDAA diet


title: Control_liver_rep4

description: SAMPLE 4

value: control


title: Control_lung_rep2

description: SAMPLE 2


title: D1-Control [PJI-1]

value: female

value: WT

value: Healthy


title: Human ES cell line-KhES-1-KSR/bFGF on feeder


title: Control_liver_rep1

description: SAMPLE 1

value: 4 weeks


title: Control_liver_CDAA_rep3

description: SAMPLE 11


title: H2_treated_liver_rep3

description: SAMPLE 7


title: H2_treated_liver_rep1

description: SAMPLE 5


title: H2_treated_liver_rep4

description: SAMPLE 8


title: LF3 RGCs

city: Taipei

first: Aliaksandr

middle: A

last: Yarmishyn

address: No. 201, Section 2, Shipai Road, Beitou District

country: Taiwan

institute: Taipei Veterans General Hospital

hyb_protocol: According to standard Affymetrix protocol.

data_processing: The raw intensity data were background corrected, log2 transformed and quantile normalized using RMA algorithm implemented by Bioconductor affy package.

source_name: RGC, LF3

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

value: iPSC-derived retinal ganglion cells

value: MT-ND4 mutation

tag: disease status

value: Leber's hereditary optic neuropathy (LHON)


title: 0707 RGCs

scan_protocol: According to standard Affymetrix protocol.

value: unaffected


title: NTA RGCs

source_name: RGC, NTA

label_protocol: According to standard Affymetrix protocol.


title: Control_liver_rep2

description: SAMPLE 2

value: Liver


title: Control_liver_rep3

description: SAMPLE 3


title: Superior cervical ganglion, biological rep4

city: Seville

first: Lin

last: Gao

address: Avda Manuel Siurot, Hospital Virgen del Rocío

country: Spain

institute: Instituto de Biomedicina de Sevilla

hyb_protocol: 5.2 µg of cRNA was hybridized for 16 hr at 45oC on GeneChip Mouse Transcriptome 1.0 Array (Affymetrix). GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix) following protocols outlined in the user manual for cartridge arrays.

data_processing: Data were processed for gene-level background subtraction, normalization and signal summarization (SST-RMA) using Affymetrix Expression Console.

source_name: Superior cervical ganglion

label_protocol: Amplification was performed with 50 ng of total RNA input following procedures described in the WT PLUS Reagent Kit user manual (Affymetrix). 5.5 μg of single-stranded cDNA product was fragmented and labeled following protocols outlined in the user manual.

extract_protocol: Total RNA was isolated using RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.

value: Superior cervical ganglion

value: male and female

value: 2 months old


title: Superior cervical ganglion, biological rep3


title: Carotid body, biological rep3

source_name: Carotid body

value: Carotid body


title: Adrenal medulla, biological rep4

source_name: Adrenal medulla

value: Adrenal medulla


title: Superior cervical ganglion, biological rep1


title: Adrenal medulla, biological rep3


title: Adrenal medulla, biological rep2


title: Superior cervical ganglion, biological rep2


title: Carotid body, biological rep1


title: Carotid body, biological rep2


title: healthy control3 peripheral blood CD4+ T cell

city: Fujian

first: Li-Li

last: Liu

address: No.201 Hubin South Road

institute: Zhongshan Hospital, Medical College of Xiamen University

description: lncRNA and mRNA expression in  peripheral blood CD4+ T cell

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: peripheral blood CD4+ T cell

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole-blood cells using density centrifugation with Ficoll (Axis-Shield, Oslo, Norge). Then, CD4+ T cells were isolated from PBMCs by negative selection using a human CD4+ T Cell Isolation Kit（Miltenyi Biotec, Bergisch Gladbach, Germany) under the guidance of the manufacturer’s instructions.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer .

tag: disease

value: healthy

value: male


title: healthy control2 peripheral blood CD4+ T cell


title: healthy control1 peripheral blood CD4+ T cell


title: Adrenal medulla, biological rep1


title: neurosyphilis patient2 peripheral blood CD4+ T cell

value: neurosyphilis


title: PC_coex_path_010_normal

status: Public on Sep 07 2017

city: New York

first: Wei-Yi

last: Cheng

state: New York

address: Roche Translational and Clinical Research Center, 430 East 29th Street

department: Pharma Research and Early Development

institute: Roche Innovation Center New York

hyb_protocol: 3 ug (15 ul) labeled cDNA + 105ul  Master Mix. Hybridization was done using GeneTitan Hybridization, Wash and Stain Kit

scan_protocol: Scanning was done using GeneTitan Instrument

data_processing: The CEL files were normalized and summarized into probe-set values using RMA normalization.

source_name: Total RNA Seq profiling of sample

label_protocol: Biotin-Labeling and enzymatic fragmentation

growth_protocol: Samples were extracted from tumor or adjacent normal tissue, and then formalin-fixed and paraffin embedded

extract_protocol: Extraction was done using High Pure FFPET RNA Isolation Kits /Cat. No. 06650775001

treatment_protocol: Tumor samples were formalin-fixed and paraffin embedded. RNA amplification: 100ng total RNA

tag: cancer type

value: PCA

tag: normal

value: yes

tag: batch i/ii

value: II

tag: histology

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: tumorlocalization

tag: Stage

tag: radicality

tag: grading

tag: dignity


title: neurosyphilis patient1 peripheral blood CD4+ T cell

description: lncRNA and mRNA expression in peripheral blood CD4+ T cell

tag: disease

tag: gender

tag: age


title: PC_coex_path_004_normal

tag: cancer type

tag: normal

tag: batch i/ii

tag: histology

tag: weight

tag: bodyheight


title: PC_coex_path_009_normal

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: ischemiatime


title: PC_coex_path_003_normal

tag: tumorcontent

tag: organ

tag: tumorlocalization

tag: Stage

tag: radicality

tag: grading


title: neurosyphilis patient3 peripheral blood CD4+ T cell

tag: disease

tag: gender

tag: age


title: PC_coex_path_002_normal

tag: cancer type

tag: normal

tag: batch i/ii

tag: histology

tag: weight

tag: dignity


title: PC_coex_path_009

value: no

tag: bodyheight

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize


title: PC_coex_path_005_normal

tag: ischemiatime

tag: tumorcontent

tag: organ

tag: tumorlocalization

tag: Stage

tag: radicality


title: PC_coex_path_008_normal

tag: cancer type

tag: normal

tag: age

tag: gender

tag: grading


title: PC_coex_path_010

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: PC_coex_path_008

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: PC_coex_path_002

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: PC_coex_path_005

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: PC_coex_path_006

tag: normal

tag: age

tag: gender

tag: grading


title: PC_coex_path_003

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: PC_coex_path_001

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: PC_coex_path_004

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M976-TS13

tag: cancer type

value: adenocarcinoma

value: m

value: malignant neoplasm of prostate

value: primary tumor

value: prostate

tag: tumorlocalization

value: prostate base

tag: Stage

tag: radicality

value: malign


title: PC_coex_path_007

tag: normal

tag: age

tag: gender

tag: grading


title: M960-TS12

tag: histology

tag: weight

tag: bodyheight

value: prostate several partitions overlapping

value: IV

tag: dignity


title: M969-TSn17

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: III


title: M957-TSn19

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M970-TS12

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M958-TS13

tag: normal

tag: age

tag: gender

tag: grading


title: M831-TS12

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M900-TS11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: M822-TS14

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M877-TS11

tag: cancer type

tag: tumorlocalization

value: prostate left

tag: Stage

tag: radicality


title: M968-TS14

tag: normal

tag: age

tag: gender

tag: grading


title: M810-TS11

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M888-TSn18

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: M950-TS13

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M820-TS13

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M846-TS12

tag: normal

tag: age

tag: gender

tag: grading


title: M938-TS13

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M947-TS12

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: prostate right


title: M807-TS12

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M783-TS12

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M940-TS11

tag: normal

tag: age

tag: gender

tag: grading


title: M945-TSn18

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M834-TS11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: M746-TS11

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M701-TS13

tag: cancer type

value: adenocarcinoma with acinar type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M778-TS11

value: PCA

tag: normal

tag: age

tag: gender

tag: grading


title: M711-TS14

tag: histology

tag: weight

tag: bodyheight

value: prostate apex

tag: dignity


title: M678-TS11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: II


title: M676-TS14

value: no

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M671-TS11

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M801-TS12

tag: normal

value: adenocarcinoma

tag: age

tag: gender

tag: grading


title: M643-TS12

tag: histology

value: m

tag: weight

tag: bodyheight

tag: dignity


title: M777-TS14

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of prostate

tag: primary / relapse tumor


title: M666-TS12

value: primary tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M617-TS12

tag: cancer type

value: prostate

tag: tumorlocalization

tag: Stage

tag: radicality


title: M627-TS13

tag: normal

tag: age

tag: gender

tag: grading


title: M626-TS12

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M561-TS12

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: M550-TS12

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: M502-TS11

tag: cancer type

tag: tumorlocalization

tag: Stage

tag: radicality


title: M603-TS12

tag: normal

tag: age

tag: gender

tag: grading


title: M531-TS11

tag: histology

tag: weight

tag: bodyheight

tag: dignity


title: M613-TS11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor


title: M510-TS12

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: NSCLC_coex_path_010_normal

tag: cancer type

value: NSCLC

value: yes

tag: batch i/ii

tag: tumorlocalization

tag: Stage

tag: radicality


title: M563-TS11

tag: normal

tag: histology

tag: age

tag: gender

value: prostate several partitions overlapping

tag: grading

value: malign


title: M527-TS12

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

value: IV

tag: dignity


title: M628-TS13

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: III


title: M564-TS12

tag: cancer type

tag: organ

tag: tumorlocalization

tag: Stage


title: M562-TS12

tag: normal

tag: histology

tag: age

tag: radicality


title: P1415-Tp13_normal

tag: batch i/ii

value: adenocarcinoma with mixed subtypes

tag: gender

value: f

tag: weight

tag: bodyheight

value: malignant neoplasm of upper lobe of lung

value: lung

value: superior pulmonary lobe right S I

value: IB

tag: grading


title: NSCLC_coex_path_005_normal

value: I

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: dignity


title: NSCLC_coex_path_007_normal

tag: cancer type

value: II

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: organ


title: P1432-Tp11_normal

tag: normal

tag: histology

value: squamous cell carcinoma

tag: age

value: m

tag: tumorlocalization

value: upper pulmonary lobe left

tag: Stage

value: III B


title: R67-Tp13

value: NSCLC

value: no

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of lower lobe of lung

value: primary tumor

value: lower pulmonary lobe left

tag: radicality


title: M493-TS11

value: PCA

value: adenocarcinoma with acinar type

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of prostate

tag: primary / relapse tumor

value: prostate

value: prostate several partitions overlapping

tag: grading

value: malign


title: P968-Tc15

tag: cancer type

value: I

value: malignant neoplasm of upper lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lung

value: superior pulmonary lobe right S III

value: IB

tag: dignity


title: P1607-Tp12_normal

tag: normal

value: yes

tag: histology

value: adenocarcinoma with mixed subtypes

tag: age

value: f

value: malignant neoplasm of middle lobe of lung

tag: organ

tag: tumorlocalization

value: middle pulmonary lobe right

value: IA


title: P1111-Tp11_normal

value: NSCLC

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of lower lobe of lung

value: primary tumor

value: inferior pulmonary lobe right S X

tag: Stage


title: P897-Tc16

value: no

value: squamous cell carcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: lower pulmonary lobe left

value: IIB

tag: radicality


title: K30-Tp11_normal

tag: cancer type

value: II

value: m

value: malignant neoplasm of upper lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lung

value: superior pulmonary lobe left S I + II

value: III A

tag: grading

value: malign


title: NSCLC_coex_path_008_normal

tag: normal

value: yes

value: I

tag: histology

tag: age

tag: organ

tag: dignity


title: P959-Tc15

value: NSCLC

tag: batch i/ii

value: adenocarcinoma with mixed subtypes

tag: gender

tag: weight

tag: bodyheight

tag: tumorlocalization

value: superior pulmonary lobe right S I

value: IB


title: P658-Tp12

value: no

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of lower lobe of lung

tag: primary / relapse tumor

value: primary tumor

tag: Stage

value: III B


title: P1633-Tp12

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: IIB

tag: radicality


title: P705-Tp13

tag: normal

tag: histology

tag: age

value: f

tag: organ

value: upper pulmonary lobe left

tag: grading


title: P662-Tp12

tag: batch i/ii

value: squamous cell carcinoma

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of upper lobe of lung

value: lung

tag: dignity


title: P682-Tp11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization

value: III A

value: malign


title: P393-Tc15

tag: cancer type

value: I

value: m

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: inferior pulmonary lobe left S VIII

tag: Stage


title: P1456-Tp12

value: NSCLC

tag: normal

tag: histology

tag: age

tag: organ

value: superior pulmonary lobe right S I

tag: radicality


title: P1432-Tp11

value: no

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: grading


title: P1537-Tp11

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: dignity


title: P775-Tp14

tag: cancer type

value: malignant neoplasm of lower lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization

value: lower pulmonary lobe right


title: P634-Tp11

tag: normal

tag: histology

value: adenocarcinoma with mixed subtypes

tag: age

value: primary tumor

tag: organ

tag: Stage

value: III B


title: P450-Tp14

tag: batch i/ii

tag: gender

value: f

tag: weight

tag: bodyheight

value: lower pulmonary lobe left

value: IB

tag: radicality


title: P200-Tc15

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper lobe of lung

tag: primary / relapse tumor

value: lung

value: upper pulmonary lobe left

tag: grading


title: P1415-Tp13

tag: cancer type

value: I

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: dignity

value: malign


title: P1607-Tp12

tag: normal

tag: histology

tag: age

value: malignant neoplasm of middle lobe of lung

tag: organ

tag: tumorlocalization

value: middle pulmonary lobe right

value: IA


title: P1438-Tp14

value: NSCLC

value: no

tag: batch i/ii

value: squamous cell carcinoma

tag: gender

value: m

tag: weight

tag: bodyheight

tag: Stage


title: P416-Tc15

value: adenocarcinoma with mixed subtypes

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: primary tumor

tag: radicality


title: P149-Tp13

tag: cancer type

value: f

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: upper pulmonary lobe right

tag: grading


title: P1455-Tp12

tag: normal

tag: histology

tag: age

value: malignant neoplasm of lower lobe of lung

tag: organ

value: inferior pulmonary lobe left S X

value: IB

tag: dignity


title: P1394-Tp11

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: lung

tag: tumorlocalization

value: lower pulmonary lobe left


title: P1361-Tp13

value: I

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper lobe of lung

tag: primary / relapse tumor

value: superior pulmonary lobe right S III

tag: Stage

value: malign


title: P1337-Tp13

tag: cancer type

value: NSCLC

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: superior pulmonary lobe right S I

tag: radicality


title: P1246-Tp13

tag: normal

value: no

tag: histology

tag: age

tag: organ

value: III B

tag: grading


title: P138-Tc16

tag: batch i/ii

value: adenocarcinoma with mixed subtypes

tag: gender

tag: weight

tag: bodyheight

value: upper pulmonary lobe left

tag: dignity


title: P1353-Tp14

value: squamous cell carcinoma

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: primary tumor

tag: tumorlocalization


title: P1292-Tp12

tag: cancer type

value: malignant neoplasm of lower lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lower pulmonary lobe right

tag: Stage


title: P1236-Tc16

tag: normal

tag: histology

tag: age

value: f

tag: organ

value: lung

value: inferior pulmonary lobe left S X

tag: radicality


title: P1606-Tp12

tag: batch i/ii

value: I

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of upper lobe of lung

value: IA

tag: grading


title: P1428-Tp14

value: NSCLC

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: inferior pulmonary lobe left S VI

value: IB

tag: dignity

value: malign


title: P1135-Tp12

tag: cancer type

value: no

value: adenocarcinoma with mixed subtypes

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization

value: superior pulmonary lobe right S II


title: P1110-Tc15

tag: normal

tag: histology

tag: age

value: m

tag: organ

tag: Stage

value: IIB


title: P1160-Tp11

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of middle lobe of lung

value: primary tumor

value: middle pulmonary lobe right

tag: radicality


title: NSCLC_coex_path_010

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: grading


title: P1111-Tp11

tag: cancer type

value: f

value: malignant neoplasm of lower lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lung

value: inferior pulmonary lobe right S X

tag: dignity


title: NSCLC_coex_path_009

tag: normal

value: I

tag: histology

tag: age

tag: organ

tag: tumorlocalization


title: NSCLC_coex_path_004

value: NSCLC

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: Stage


title: P1103-Tp11

value: squamous cell carcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper lobe of lung

tag: primary / relapse tumor

value: superior pulmonary lobe left S III

value: III A

tag: radicality


title: P1100-Tp12

tag: cancer type

value: no

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: inferior pulmonary lobe left S VI

value: IB

tag: grading

value: malign


title: NSCLC_coex_path_008

tag: normal

tag: histology

tag: age

tag: organ

tag: dignity


title: NSCLC_coex_path_003

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: tumorlocalization


title: P1043-Tc15

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: lower pulmonary lobe left

tag: Stage


title: CRC_coex_path_006_normal

tag: cancer type

value: CRC

value: yes

value: II

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: radicality


title: K30-Tp11

tag: normal

tag: histology

tag: age

value: primary tumor

tag: organ

value: lung

value: superior pulmonary lobe left S I + II

tag: grading


title: CRC_coex_path_004_normal

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: dignity


title: K5-Tc15

value: NSCLC

value: I

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization

value: superior pulmonary lobe right S I


title: NSCLC_coex_path_006

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: Stage


title: NSCLC_coex_path_001

tag: normal

tag: histology

tag: age

tag: organ

tag: radicality


title: P1109-Tc15

tag: batch i/ii

value: squamous cell carcinoma

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of lower lobe of lung

value: IIB

tag: grading


title: K79-Tp11

value: no

value: adenocarcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper lobe of lung

tag: primary / relapse tumor

value: upper pulmonary lobe left

tag: dignity


title: K22-Tp11

tag: cancer type

value: m

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization

value: inferior pulmonary lobe left S VI

value: IB

value: malign


title: NSCLC_coex_path_005

tag: normal

tag: histology

tag: age

tag: organ

tag: Stage


title: NSCLC_coex_path_002

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: radicality


title: K20-Tc15

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of overlapping lesion of lung

tag: primary / relapse tumor

value: primary tumor

value: several partitions overlapping

value: III A

tag: grading


title: P1083-Tp13

tag: cancer type

value: NSCLC

value: I

value: adenocarcinoma with mixed subtypes

value: f

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lung

value: upper pulmonary lobe right

tag: dignity


title: NSCLC_coex_path_007

tag: normal

value: no

tag: histology

tag: age

tag: organ

tag: tumorlocalization


title: B760-Tp5_normal

value: CRC

value: yes

tag: batch i/ii

value: adenocarcinoma

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of ascending colon

value: colon

value: ascending colon

tag: Stage

value: IV


title: K59-Tp14

value: squamous cell carcinoma

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper lobe of lung

tag: primary / relapse tumor

value: primary tumor

value: superior pulmonary lobe left S III

value: III B

tag: radicality

value: malign


title: K28-Tp11

tag: cancer type

value: NSCLC

value: I

value: malignant neoplasm of lower lobe of lung

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: lung

value: inferior pulmonary lobe right S VIII

value: IB

tag: grading


title: P261-Tp13

tag: normal

value: no

tag: histology

value: adenocarcinoma with mixed subtypes

tag: age

tag: organ

value: upper pulmonary lobe left

tag: dignity


title: A1751-Tp5_normal

value: CRC

value: yes

tag: batch i/ii

value: adenocarcinoma

tag: gender

value: f

tag: weight

tag: bodyheight

value: malignant neoplasm of caecum

value: colon

tag: tumorlocalization

value: ileocaecal

value: IV


title: CRC_coex_path_003_normal

value: II

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: Stage


title: A2234-Tc15_normal

tag: cancer type

value: I

value: m

value: malignant neoplasm of ascending colon

value: primary tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: ascending colon

tag: radicality

value: malign


title: CRC_coex_path_001_normal

tag: normal

tag: histology

tag: age

tag: organ

tag: grading


title: CRC_coex_path_010_normal

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: dignity


title: CRC_coex_path_010

value: no

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization


title: CRC_coex_path_007_normal

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: Stage


title: B521-Tp5_normal

tag: normal

tag: histology

tag: age

value: malignant neoplasm of rectum

tag: organ

value: rectum

tag: radicality


title: A2241-Tp11_normal

value: CRC

value: yes

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: grading


title: CRC_coex_path_002_normal

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: dignity


title: CRC_coex_path_007

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization


title: CRC_coex_path_004

tag: normal

tag: histology

tag: age

tag: organ

tag: Stage


title: B794-Tp6

tag: batch i/ii

value: carcinoma

tag: gender

value: f

tag: weight

tag: bodyheight

value: malignant neoplasm of sigmoid colon

value: sigmoid colon

tag: radicality


title: B1100-Tp13

value: adenocarcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: colon

value: IV

tag: grading


title: CRC_coex_path_001

tag: cancer type

value: I

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: dignity


title: CRC_coex_path_003

tag: normal

tag: histology

tag: age

tag: organ

tag: tumorlocalization


title: B760-Tp5

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of ascending colon

tag: Stage


title: B1141-Tc15

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: primary tumor

tag: radicality


title: B798-Tp6

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: grading

value: malign


title: B720-Tc11

tag: normal

value: no

tag: histology

tag: age

tag: organ

tag: dignity


title: B1108-Tp12

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of rectum

tag: tumorlocalization


title: B521-Tp5

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: rectum

tag: Stage


title: CRC_coex_path_006

tag: cancer type

value: CRC

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: radicality


title: CRC_coex_path_002

tag: normal

tag: histology

tag: age

tag: organ

tag: grading


title: B1168-Tp14

tag: batch i/ii

value: mucinous adenocarcinoma

tag: gender

tag: weight

tag: bodyheight

tag: dignity


title: B843-Tp5

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization


title: B936-Tc15

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: Stage


title: A2527-Tp12

tag: normal

tag: histology

tag: age

value: malignant neoplasm of caecum

tag: organ

value: ileocaecal

tag: radicality


title: A2474-Tp11

tag: batch i/ii

tag: gender

value: f

tag: weight

tag: bodyheight

value: ascending colon

tag: grading


title: A2548-Tp12

value: adenocarcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: dignity


title: A2423-Tp12

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: colon

tag: tumorlocalization


title: A2360-Tp13

tag: normal

tag: histology

tag: age

value: malignant neoplasm of sigmoid colon

tag: organ

value: sigmoid colon

tag: Stage

value: IV


title: A2374-Tc15

tag: batch i/ii

value: I

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of hepatic flexure of colon

value: right flexure

tag: radicality


title: A2234-Tc15

value: no

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of ascending colon

tag: primary / relapse tumor

value: primary tumor

tag: grading

value: malign


title: A2349-Tc16

tag: cancer type

value: CRC

value: mucinous adenocarcinoma

value: malignant neoplasm of splenic flexure of colon

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: left flexure

tag: dignity


title: A2097-Tp11

tag: normal

tag: histology

value: adenocarcinoma

tag: age

value: malignant neoplasm of transverse colon

tag: organ

tag: tumorlocalization

value: transverse colon


title: A2031-Tp13

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of sigmoid colon

value: colon

value: sigmoid colon

tag: Stage


title: A2069-Tp11

value: I

value: f

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of rectum

tag: primary / relapse tumor

value: rectum

value: II

tag: radicality


title: A2079-Tp11

tag: cancer type

value: no

value: m

value: primary tumor

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: IV

tag: grading


title: A2086-Tp12

value: CRC

tag: normal

tag: histology

tag: age

tag: organ

tag: dignity

value: malign


title: A2214-Tp11

tag: batch i/ii

value: adenocarcinoma

tag: gender

tag: weight

tag: bodyheight

tag: tumorlocalization


title: A2321-Tp13

value: mucinous adenocarcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: Stage


title: A1845-Tc12

tag: cancer type

value: partially mucinous adenocarcinoma

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: radicality


title: A1913-Tp12

tag: normal

tag: histology

tag: age

tag: organ

tag: grading


title: A2084-Tp11

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of sigmoid colon

tag: dignity


title: A2013-Tp14

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: colon

tag: tumorlocalization


title: A2359-Tp11

tag: cancer type

value: malignant neoplasm of transverse colon

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: transverse colon

tag: Stage


title: A2241-Tp11

tag: normal

value: I

tag: histology

tag: age

value: f

value: malignant neoplasm of ascending colon

tag: organ

value: ascending colon

tag: radicality


title: A2340-Tp11

value: no

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of caecum

value: ileocaecal

tag: grading


title: A2151-Tp13

value: m

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: primary tumor

value: sigmoid colon

value: IV

tag: dignity


title: A1751-Tp5

tag: cancer type

value: CRC

value: adenocarcinoma

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization

value: malign


title: A1877-Tp6

tag: normal

tag: histology

tag: age

value: malignant neoplasm of rectum

tag: organ

value: colon

value: rectum

tag: Stage


title: A1895-Tp5

tag: batch i/ii

value: I

tag: gender

tag: weight

tag: bodyheight

tag: radicality


title: A2064-Tp12

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: grading


title: A1754-Tp6

tag: cancer type

value: f

value: malignant neoplasm of descending colon

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: descending colon

tag: dignity


title: A1774-Tp6

tag: normal

value: no

tag: histology

tag: age

value: malignant neoplasm of sigmoid colon

tag: organ

tag: tumorlocalization


title: A2153-Tp11

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: Stage


title: A1747-Tp5

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: radicality


title: A1195-Tc12

tag: cancer type

value: mucinous adenocarcinoma

value: malignant neoplasm of ascending colon

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: ascending colon

tag: grading


title: A1102-Tp6

tag: normal

tag: histology

tag: age

value: m

value: primary tumor

tag: organ

tag: dignity


title: A1664-Tp5

value: CRC

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

value: malignant neoplasm of caecum

tag: tumorlocalization

value: ileocaecal

value: IV


title: A1092-Tp5

value: adenocarcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

value: colon

tag: Stage

value: malign


title: A1101-Tp5

tag: cancer type

value: I

value: f

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

value: sigmoid colon

tag: radicality


title: A1046-Tp6

tag: normal

value: no

tag: histology

tag: age

value: malignant neoplasm of rectum

tag: organ

value: rectum

tag: grading


title: A1076-Tp6

tag: batch i/ii

tag: gender

tag: weight

tag: bodyheight

tag: dignity


title: BC_coex_path_008_normal

value: BC

value: yes

tag: bmi

tag: diseasecode

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorlocalization


title: BC_coex_path_002_normal

tag: cancer type

tag: tumorsize

tag: ischemiatime

tag: tumorcontent

tag: Stage


title: BC_coex_path_007_normal

tag: normal

tag: histology

tag: age

tag: organ

tag: radicality


title: BC_coex_path_006_normal

tag: gender

tag: weight

tag: bodyheight

tag: grading


title: X1435-Tp11_normal

value: ductal carcinoma

tag: bmi

tag: diseasecode

tag: diseasedescription

value: malignant neoplasm of upper-outer quadrant of breast

value: breast left

value: upper-outer quadrant

tag: dignity


title: BC_coex_path_004_normal

tag: cancer type

tag: primary / relapse tumor

tag: tumorsize

tag: tumorlocalization


title: X1876-Tp12

tag: normal

tag: batch i/ii

value: primary tumor

tag: ischemiatime

tag: tumorcontent

tag: Stage


title: X1435-Tp11

tag: histology

tag: age

tag: gender

tag: organ

tag: radicality


title: X1840-Tp11

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

value: malignant neoplasm of overlapping lesion of breast

value: breast right

value: several partitions overlapping

value: IIA

tag: grading


title: X1390-Tp11

tag: cancer type

value: I

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: dignity

value: malign


title: X1655-Tp12

tag: normal

tag: batch i/ii

value: f

tag: ischemiatime

tag: tumorcontent

tag: tumorlocalization

value: III A


title: X1659-Tp12

value: no

tag: histology

tag: age

tag: gender

tag: organ

tag: Stage

value: III C


title: BC_coex_path_009_normal

value: BC

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

tag: radicality


title: BC_coex_path_010_normal

tag: cancer type

value: yes

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: grading


title: A1172-Tc11

value: CRC

tag: normal

tag: batch i/ii

value: adenocarcinoma

value: m

value: malignant neoplasm of sigmoid colon

tag: ischemiatime

tag: tumorcontent

value: colon

value: sigmoid colon

value: IV

tag: dignity


title: X1492-Tp13

tag: histology

value: ductal carcinoma

tag: age

tag: gender

value: malignant neoplasm of upper-inner quadrant of breast

value: primary tumor

tag: organ

value: breast right

tag: tumorlocalization

value: upper-inner quadrant


title: X1336-Tp14

value: I

value: f

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

value: malignant neoplasm of upper-outer quadrant of breast

value: upper-outer quadrant

tag: Stage

value: IIA

value: malign


title: X1447-Tp11

tag: cancer type

value: BC

value: no

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

tag: radicality


title: X1318-Tp12

tag: normal

tag: batch i/ii

tag: ischemiatime

tag: tumorcontent

value: III A

tag: grading


title: X1580-Tp13

tag: histology

tag: age

tag: gender

tag: organ

value: IIB

tag: dignity


title: X1613-Tp11

tag: weight

tag: bodyheight

tag: bmi

tag: diseasecode

tag: tumorlocalization


title: S82-Tc15

tag: cancer type

tag: diseasedescription

tag: primary / relapse tumor

tag: tumorsize

value: breast left

tag: Stage

value: III B


title: BC_coex_path_005_normal

tag: normal

value: yes

tag: ischemiatime

tag: tumorcontent

tag: radicality


title: S64-Tp11

tag: batch i/ii

tag: histology

value: lobular carcinoma

tag: age

tag: gender

value: malignant neoplasm of overlapping lesion of breast

value: several partitions overlapping

tag: grading


title: S57-Tc16

value: carcinoma

tag: weight

tag: bodyheight

tag: bmi

value: malignant neoplasm of upper-inner quadrant of breast

value: primary tumor

tag: organ

value: breast right

value: upper-inner quadrant

value: III C

tag: dignity