title: 201 Area3 9 04 13


title: 202 Area1 17 05 13

status: Public on May 05 2015

type: RNA

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

country: Canada

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal.

molecule: total RNA

organism: Bos taurus

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Oocytes were collected from slaughterhouse-derived ovaries and grouped according to the chromatin configuration as described by Lodde et al. 2007.

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 11 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cumulus-oocyte complexes (COC’s) were collected byaspiration with a 16G needle mount on an aspiration pump. The COC’s were denuded by vortexing, washed and stained with Hoechst 33342. Chromatin organization was evaluated under a inverted fluorescence microscope and classified according to the degree of chromatin condensation within the nuclear enveloppe. Oocytes were then washed, collected in small volumes of PBS, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: tissue

value: oocyte

tag: chromatin condensation stage


title: Clonal B-Cells from Smoldering Waldenström's Macroglobulinemia 71-97861

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

country: Spain

institute: Clinica Universidad de Navarra

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label: biotin

organism: Homo sapiens

source_name: Bone marrow

label_protocol: The integrity of extracted RNA was assessed using Agilent 2100 Bioanalyzer. Afterwards, RNA was amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix), and then hybridized to Human Gene 1.0 ST Array (Affymetrix)

extract_protocol: RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions

tag: cell type


title: Clonal B-Cells from Waldenström's Macroglobulinemia 85-97220


title: Normal bone marrow CD25- B-cells from healthy donor 125

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

tag: subject status

value: healthy donor

tag: donor id

value: donor 125

value: Bone marrow

value: CD25- B-cells


title: 200 Area4 9 04 13


title: 200 Area3 9 04 13


title: Clonal B-Cells from Waldenström's Macroglobulinemia 86-103874


title: Clonal B-Cells from Smoldering Waldenström's Macroglobulinemia 59-97940


title: Clonal B-Cells from Waldenström's Macroglobulinemia 58-103420


title: 201 Area1 9 04 13


title: 200 Area1 9 04 13


title: 199 Area4 5 04 13


title: 200 Area2 9 04 13


title: Clonal B-Cells from Smoldering Waldenström's Macroglobulinemia 45-97150


title: 199 Area3 5 04 13


title: 199 Area1 5 04 13


title: 199 Area2 5 04 13


title: Clonal B-Cells from Smoldering Waldenström's Macroglobulinemia 63-100663


title: Clonal B-Cells from Waldenström's Macroglobulinemia 44-105403


title: Normal bone marrow CD25- B-cells from healthy donor 122

value: donor 122


title: MDA-MB-231 cells stimulated with LPA, Rep3

city: Lyon

first: Olivier

last: Peyruchaud

state: Rhone Alpes

address: UFR de medicine Lyon Est (Domaine Laennec), 7-11 Rue Guillaume Paradin

country: France

institute: INSERM U1033

hyb_protocol: Array hybridized for 20h using miRNA complete labeling and hybridization kit (Agilent).

scan_protocol: The arrays were washed with gene expression wash buffer kit (Agilent) and read with High-resolution microarray scanner (Agilent).

data_processing:
The data was extracted using Agilent feature extraction software (Agilent v11.5.1.1). The data was internally normalized by spike labelling. 3 samples from platform GPL13264 and 3 samples from platform GPL19263 were averaged together. So in total we have 6 samples.
The mean fluorescent intensities were obtained after subtracting background.
The mean of different probesets for each miRNA was calculated
All the samples with negative values (Negative values -  the miRNA's expression value after subtracting the background was negative) were eliminated as a quality check.
The remaining 182 miRNAs were overall median normalized.

source_name: MDA-MB-231 cells stimulated with LPA

label_protocol: Total RNA including miRNA (100 ng) was directly labeled with Cyanine-3-labeled

growth_protocol: The MDA-MB-231 cells were cultured in DMEM Medium, suplemented with 10% FBS and 1% Penicillin/streptomycin at 37°C in a 5% CO2 incubator

extract_protocol: Total RNA including miRNA was extracted using the miRNeasy kit (QIAGEN) as per manufacturer's protocol

treatment_protocol: The cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min.

tag: cell line

value: human breast cancer cell line

tag: stimulated with

value: LPA (1µM) for 45min


title: MDA-MB-231 cells stimulated with LPA, Rep2


title: 201 Area2 9 04 13


title: Normal bone marrow CD25+ B-cells from healthy donor 76

value: Normal bone marrow CD25+ B-cells


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 48-98644


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 39-97713


title: Serum starved MDA-MB-231 cells, Rep3

source_name: Serum starved MDA-MB-231 cells

value: none (control)


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 122-106533


title: Clonal B-Cells from Waldenström's Macroglobulinemia 47-103284


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 40-99624


title: Normal bone marrow CD25- B-cells from healthy donor 38

value: Normal bone marrow CD25- B-cells


title: Normal bone marrow CD25- B-cells from healthy donor 57


title: Normal bone marrow CD25- B-cells from healthy donor 36


title: Normal bone marrow CD25- B-cells from healthy donor 121


title: Normal bone marrow CD25+ B-cells from healthy donor 54


title: Normal bone marrow CD25- B-cells from healthy donor 79


title: Normal bone marrow CD25+ B-cells from healthy donor 120


title: granulocyte, rep. 2

city: Aurora

first: Eric

middle: M

last: Pietras

state: CO

address: 12700 E. 19th Avenue, Research Complex 2 Room 10014

department: Medicine

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
Gene expression data from mouse bone marrow hematopoietic populations
Gr-2

hyb_protocol: Labeled cRNA were hybridized following the GeneChip Expression Analysis Technical Manual 702232 Rev. 3.

scan_protocol: Microarray chips were scanned using an Affymetrix GCS 3000 Scanner.

data_processing: Gene expression microarray data were normalized using RMA followed by quantile normalization as implemented in the 2.15.1 R package.

organism: Mus musculus

source_name: granulocyte

label_protocol: Sense-strand RNA was transcribed from amplified RNA with the NuGen WT-Ovation Exon Module, purified using Qiagen QIAquick columns and subsequently fragmented and biotinylated using the NuGen Encore Biotin module according to manufacturers' instructions. All samples were  checked for proper amplification and fragmentation on an Agilent 2100 Bioanalyzer using RNA pico chips according to manufacturer's instructions. Amplified products were quantified using a NanoDrop spectrophotometer.

extract_protocol: Total RNA was isolated using the Arcturus PicoPure kit according to manufacturer's instructions, and included an in-column Dnase I digest using Qiagen DNase I. Resulting RNA was amplified using the NuGen Pico WTA kit. Amplified products were purified using Qiagen QIAquick columns according to the NuGen protocol.

treatment_protocol: HSC, MPP, CMP and GMP populations were isolated from bone marrow by flow cytometry. cKit-enriched cells were stained on ice in Hanks Buffered Salt Solution (HBSS) containing 2% heat-inactivated FBS, with unconjugated lineage antibodies (Gr1, Mac1, B220, CD3, CD4, CD5, CD8, Ter119) followed by goat anti-rad PE-Cy5 secondary antibody and cKit-APC-eFluor780, Sca-1-Pacific Blue, Flk2-biotin, CD48-APC, CD150-PE, CD34-FITC, FcγR-PerCP-eFluor710 and streptavidin-PE-Cy7. Mature myeloid BM cells were stained with Mac-1-PE-Cy7 and Gr1-Pacific Blue. Dead cells were excluded using 1 μg/ml propidium iodide. Cells were double-sorted on a BD FACSAria II cell sorter to ensure maximum purity, and 20,000 cells from each population were sorted directly into Trizol LS for RNA extraction.

tag: strain

tag: genotype

value: wild-type

value: bone marrow

tag: immunophenotypic definition

value: granulocyte


title: granulocyte, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
Gr-1


title: pre-granulocyte, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
PreGr-3

source_name: pre-granulocyte

value: pre-granulocyte


title: granulocyte, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
Gr-3


title: Normal bone marrow CD25+ B-cells from healthy donor 74


title: hESC-Shef6

type: genomic

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description: Genomic DNA extracted from hES cells was genotyped using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays

hyb_protocol: Labelled fragments were hybridized to Multi BeadChips as per the Infinium HD Assay Ultra Protocol Guide

scan_protocol: Hybridized beads were scanned with the iScan system and the BeadArray Reader

data_processing: Illumina GenomeStudio (v1.94)

label: C/G-biotin and A/T-DNP

molecule: genomic DNA

source_name: Human embryonic stem cells

label_protocol: 200ng of genomic DNA (quantified by the PicoGreen assay) was labelled as per the Infinium HD Assay Ultra Protocol Guide

growth_protocol: Various self-renewing media and matrices. Media included Essential 8, StemPro, or NutriStem, and matrices included CellStart or Laminin-521.

extract_protocol: Genomic DNA was isolated from cell pellets using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). Briefly, hES cell pellets were lysed with Tissue and Cell Lysis Solution, followed by Proteinase K and RNase A treatment. Proteins were precipitated with MPC Protein Precipitation Reagent and removed by centrifugation. Genomic DNA was precipitated with isopropanol, pelleted by centrifugation and then resuspended in TE buffer to a final concentration of 50 ng/μl. Purity was checked by spectrophotometry using the NanoDrop 1000 spectrophotometer (Thermo Fisher).

treatment_protocol: Self-renewing conditions.

value: embryonic stem cells

tag: gender

value: Female

tag: passage

value: passage 45


title: granulocyte-macrophage progenitor, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
GMP-3

source_name: granulocyte-macrophage progenitor

value: granulocyte-macrophage progenitor


title: granulocyte-macrophage progenitor, rep. 4

description:
Gene expression data from mouse bone marrow hematopoietic populations
GMP-4


title: Clonal B-Cells from Waldenström's Macroglobulinemia 55-97559


title: pre-granulocyte, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
PreGr-2


title: granulocyte-macrophage progenitor, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
GMP-1


title: granulocyte-macrophage progenitor, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
GMP-2


title: pre-granulocyte, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
PreGr-1


title: Normal bone marrow CD25- B-cells from healthy donor 124

value: healthy donor

value: donor 124


title: common myeloid progenitor, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
CMP-3

source_name: common myeloid progenitor

value: common myeloid progenitor


title: multipotent progenitor (MPP) 4, rep. 5

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP4-5

source_name: multipotent progenitor (MPP) 4

value: multipotent progenitor (MPP) 4


title: hESC-MasterShef14

value: passage 13


title: multipotent progenitor (MPP) 4, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP4-3


title: common myeloid progenitor, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
CMP-2


title: multipotent progenitor (MPP) 4, rep. 4

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP4-4


title: common myeloid progenitor, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
CMP-1


title: hESC-MasterShef12

value: passage 16


title: Non-persisting clone M3

city: Bethesda

first: Udai

last: Kammula

state: MD

address: 10 Center Drive

department: Surgery Branch

institute: NCI

description: Gene expression data from non-persisting CD8+ T cell clone

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 Array (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Washing, staining, and scanning of the microarray were carried out under strictly controlled conditions with the Affymetrix Fluidics Station and Scanner.

data_processing: Raw data from the generated cell-intensity files (.cel' extension) were imported into Partek Genomics Suite with normalization performed by robust multichip analysis (RMA) algorithm.

label: Biotin

source_name: Nonpersisting clone

label_protocol: About 100 ng of total RNA samples were reverse transcribed and labeled by biotin according to the standard Affymetrix protocol.

growth_protocol: Human PBMCs were sensitized in vitro with antigen and IL-2 and then underwent limiting dilution cloning and expansion to derive the final infusion product for adoptive therapy into metastatic melanoma patients.

extract_protocol: Total RNA was isolated from pre-infusion samples of persisting or nonpersisting CD8+ T cell clones (Qiagen RNeasy kit) and quality was validated with Agilent Bioanalyzer.

value: CD8+ T cell


title: Non-persisting clone gp6


title: multipotent progenitor (MPP) 3, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP3-3

source_name: multipotent progenitor (MPP) 3

value: multipotent progenitor (MPP) 3


title: hESC-MasterShef11

value: Male

value: passage 17


title: Non-persisting clone M1


title: multipotent progenitor (MPP) 4, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP4-2

value: wild-type

value: bone marrow


title: multipotent progenitor (MPP) 4, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP4-1


title: multipotent progenitor (MPP) 2, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP2-3

source_name: multipotent progenitor (MPP) 2

value: multipotent progenitor (MPP) 2


title: multipotent progenitor (MPP) 3, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP3-2


title: hESC-MasterShef13

description: Genomic DNA extracted from hES cells was genotyped using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays

value: embryonic stem cells

value: passage 11


title: multipotent progenitor (MPP) 2, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP2-2


title: multipotent progenitor (MPP) 3, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP3-1


title: hESC-MasterShef5

value: passage 37


title: Non-persisting clone gp5


title: hESC-MasterShef4

value: passage 35


title: short-term HSC, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCST-2

source_name: short-term HSC

value: short-term HSC


title: hESC-MasterShef3

value: Female

value: passage 22


title: Persisting clone M2b

description: Gene expression data from persisting CD8+ T cell clone

source_name: Persisting clone


title: multipotent progenitor (MPP) 2, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
MPP2-1


title: short-term HSC, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCST-3


title: long-term HSC, rep. 4

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCLT-4

source_name: long-term HSC

value: long-term HSC


title: Persisting clone M4


title: hESC-RC17


title: hESC-MasterShef7


title: hESC-MasterShef8

value: passage 19


title: hESC-MasterShef2

value: passage 18


title: hESC-RC11


title: long-term HSC, rep. 3

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCLT-3


title: long-term HSC, rep. 2

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCLT-2


title: hESC-Man12

value: passage 20


title: long-term HSC, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCLT-1


title: Persisting clone gp1

value: CD8+ T cell


title: Persisting clone M2a


title: S47-CDKN2A-/- Stat5ca-d15

status: Public on May 04 2015

city: MARSEILLE

first: Nathalie

last: AUPHAN-ANEZIN

address: Parc Scientifique de Luminy

institute: CIML

hyb_protocol: Affy-169 : 125.0 ng at 45 degree_C during 17 hours

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

data_processing:
AMBION WT Expression kit-Affy
Expression console data processing

source_name: S47-CDKN2A-/- Stat5ca-d15

extract_protocol: none provided

value: Spleen and lymph nodes

tag: amount in (g)

tag: origin

value: purified CD8 T lymphocytes

tag: developmental stage

value: activated CD8 T lymphocytes transduced to express Stat5ca and transferred in congenic hosts (d15)

tag: rin number


title: Persisting clone gp10


title: hESC-RC9

value: Male

value: passage 17


title: short-term HSC, rep. 1

description:
Gene expression data from mouse bone marrow hematopoietic populations
HSCST-1

value: wild-type

value: bone marrow


title: Bos taurus_neck muscle_DE27_D14

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

country: Italy

institute: university of padua

description: Sample of bovine neck muscle stored under vacuum at 4°C and collected at D14

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

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

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software

label: Cyanine 3

source_name: Bovine neck muscle collected at the slaughterhouse

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

extract_protocol: Extracted using the QiAgen RNeasy Mini Kit protocol for tissue samples

treatment_protocol: DE: Dexamethazone 0.4 mg/animal day per os for 31 days plus estradiol 5 mg/animal/week im for 6 times

value: neck muscle

tag: treatment

value: DEXAMETHAZONE+ESTRADIOL

tag: collection day


title: hESC-Man11

value: embryonic stem cells

value: passage 21


title: S46-CDKN2A-/- Stat5ca-d15

source_name: S46-CDKN2A-/- Stat5ca-d15

tag: tissue


title: Bos taurus_neck muscle_DE31_D14


title: hESC-KCL039

tag: cell type

value: passage 8


title: Bos taurus_neck muscle_D31_D0


title: Bos taurus_neck muscle_DE29_D14


title: hESC-KCL040

value: Female


title: Bos taurus_neck muscle_DE32_D0


title: Bos taurus_neck muscle_DE32_D14


title: Bos taurus_neck muscle_K10_D14

description: Sample of bovine neck muscle stored under vacuum at 4°C and collected at D0

value: control


title: Bos taurus_neck muscle_K9_D14


title: Bos taurus_neck muscle_DE29_D0


title: hESC-KCL033


title: Bos taurus_neck muscle_K10_D0


title: hESC-KCL037


title: Bos taurus_neck muscle_DE30_D0


title: Bos taurus_neck muscle_DE27_D0


title: Bos taurus_neck muscle_K8_D0


title: hESC-KCL034

value: passage 19


title: hESC-KCL032

value: passage 7


title: Bos taurus_neck muscle_K6_D14


title: Bos taurus_biceps brachii_RN39

description: Sample of bovine biceps brachii

source_name: Bovine biceps brachii samples collected at the slaughterhouse

treatment_protocol: P: Prednisolone 15 mg/animal/day per os for 31 days; Brotizolam 0.02 mg/Kg per os for 31 days plus estradiol im 5 mg/animal/week for 6 times; Dexamethazone 0.4 mg/animal day per os for 31 days plus estradiol 5 mg/animal/week im for 6 times; Ractopamina 80 mg/animal/day per os for 31 days plus nandrosol 150 mg/animal every 2 weeks for 4 times

value: biceps brachii

value: RACTOPAMINE+NANDROSOL


title: Bos taurus_neck muscle_K3_D14


title: Bos taurus_neck muscle_K9_D0


title: Bos taurus_neck muscle_K6_D0


title: hESC-KCL031


title: Bos taurus_biceps brachii_RN38

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_DE31

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RN33

description: Sample of bovine biceps brachii


title: Persisting clone M5

value: CD8+ T cell


title: Bos taurus_biceps brachii_RN37

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_DE29

description: Sample of bovine biceps brachii


title: Bos taurus_neck muscle_K3_D0


title: Bos taurus_biceps brachii_DE30

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE26

description: Sample of bovine biceps brachii

value: BROTIZOLAM+ESTRADIOL


title: Bos taurus_biceps brachii_BE23

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RN36

description: Sample of bovine biceps brachii


title: hESC-KCL038

value: Male

value: passage 9


title: Bos taurus_biceps brachii_DE27

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE20

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE21

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RN34

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE25

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_DE28

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RN35

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE24

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE19

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_P16

description: Sample of bovine biceps brachii

value: PREDNISOLONE


title: Bos taurus_biceps brachii_P14

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_P13

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_BE22

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_P18

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_P12

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K10

description: Sample of bovine biceps brachii

value: CONTROL


title: Bos taurus_biceps brachii_P11

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K9

description: Sample of bovine biceps brachii


title: U251 tumor_2nd metroCPA (pool JD9 and JD10) versus U251 tumor_control (pool JD5 and JD6)_Human microarray

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Total RNA was prepared and pooled from each set of U251 tumor xenografts, either metronomic cyclophosphamide-treated or untreated controls, as indicated.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software.

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1). The Rosetta error model provides a gene-specific estimate of error by incorporating two elements: a technology-specific estimate of error and an error estimate derived from replicate arrays. The technology-specific component utilizes an intensity-dependent model of error derived from numerous self-self hybridizations. By including the technology-specific estimate, the Rosetta error model avoids false positives that occur from under-estimation of error when a small number of replicate arrays are available, thus resulting in an increase in statistical power equivalent to that which would be obtained with at least one additional replicate. Furthermore, a log-ratio error estimate was derived in the Rosetta error model from the individual error estimates of each sample (color) used in the co-hybridization. Then, for each feature an average log ratio and associated p-value was obtained from replicate measurements (arrays) using the Rosetta error model error-weighted averaging method, which weighs the ratio of each sample inversely proportional to the variance of that sample. This gives an averaged ratio with the smallest possible error.

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 (channel 1 label) or Alexa 647  (channel 2 label) by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: Male ICR/Fox Chase immune deficient scid mice 5-6 weeks old (24-26 g) (Taconic Farms, Germantown, NY) were housed in the Boston University Laboratory of Animal Care Facility and treated in accordance with approved protocols and federal guidelines. U251 cells (6.0 E06) were injected s.c. on each posterior flank in 0.2 ml serum-free DMEM using a 0.5-inch 29-gauge needle and a 1 ml insulin syringe. Tumor areas (length x width) were measured twice weekly using Vernier calipers (VWR, Cat. #62379-531) and tumor volumes were calculated based on Vol = (π/6)*(L*W)3/2. Tumors were monitored and treatment groups were normalized (each tumor volume set to 100%) once average tumor volumes reached ~500 mm3.

extract_protocol: Trizol extraction of total RNA. Total RNA was prepared from individual tumors, and then pooled (n=8 independent tumor RNA samples for each of two independent pools of untreated tumors, and n=6-7 independent tumor RNA samples for each of two independent pools of metronomic cyclophosphamide-treated tumors for each of the time points), with each set of tumor RNA pools corresponding to an independent biological replicate). RNA pools were prepared by combining equal amounts of RNA from each tumor included in the pool to minimize the effects of inter-tumor variability

treatment_protocol: Mice were treated with cyclophosphamide monohydrate on an intermittent metronomic schedule (140 mg cyclophosphamide/kg body weight, every 6 days), with the dose reported here based on the non-hydrate molecular weight of 261. Tumor sizes and mouse body weights were measured at least twice weekly. Tumor growth rates prior to drug treatment were similar among all normalized groups. Cyclophosphamide-treated tumors were collected 6 days after the 2nd or after the 3rd cyclophosphamide treatment cycle, i.e., treatment day 12 and day 18, respectively. Drug-free control tumors were collected on days 6, 12, and 18, where day 0 is the first day of drug treatment.

tag: tumor

value: Human glioma U251 tumor xenograft

tag: drug treatment

value: Metronomic cyclophosphamide, 6 days after 2 cycles

source_name: U251 tumor_control (pool JD5 and JD6)

value: Untreated control


title: Bos taurus_biceps brachii_K8

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_RN40

description: Sample of bovine biceps brachii


title: Bos taurus_neck muscle_K8_D14

value: neck muscle


title: Bos taurus_biceps brachii_P15

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K5

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_P17

description: Sample of bovine biceps brachii


title: Bos taurus_biceps brachii_K4

description: Sample of bovine biceps brachii


title: Bos taurus_neck muscle_DE30_D14

value: DEXAMETHAZONE+ESTRADIOL


title: Bos taurus_biceps brachii_K7

description: Sample of bovine biceps brachii


title: U251 tumor_3rd metroCPA (pool JD7 and JD8) versus U251 tumor_control (pool JD5 and JD6)_Human microarray

value: Metronomic cyclophosphamide, 6 days after 3 cycles


title: miR-27a-F, miR-27a over-expressing cell, biological replicate 3 (miR-27a-F)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description: Gene expression profiling of RH36 cells transfected with pre-miR-27a (miR-27a-F)

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GE Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 83% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.  Cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology 2006;411:134-93). Identification of differentially expressed genes was performed with SAM two class paired program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

source_name: RH36 cells transfected with precursor of miR-27a were analyzed 48h after transfection

label_protocol: Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent Technologies) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop).

growth_protocol: RH36 embryonal RMS cell line, negative for PAX3/FOXO1 translocation, was maintained in modified Eagle's medium (DMEM) containing 10% fetal calf serum, penicillin (100 U/ml), and streptomycin (100 μg/ml) (Life Technologies) at 37°C, 5% CO2 in a humidified incubator. RH36 was obtained from Dr. M. Tsokos (NCI, Bethesda, MD).

extract_protocol: Total RNA was isolated from 10 6 cells by using Trizol® Reagent (Life Technologies) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 7, or higher, were used for microarray analysis.

treatment_protocol: To obtain transient pre-miR-27a (MC10939, Ambion, Life Technologies) expression, cells were plated in 6-well plates at 50-60% confluency and transfected 24h later using SiPORT transfection reagent (Ambion) according to the manufacturer’s instructions, with 10 nM pre-miR-27a or with pre-control pre-miR. Cells were tested for miR overexpression 24h later.

tag: cell line

value: RH36 (embryonal RMS cell line, negative for PAX3/FOXO1 translocation)


title: Bos taurus_biceps brachii_K3

description: Sample of bovine biceps brachii


title: miR-27a-D, miR-27a over-expressing cell, biological replicate 1 (miR-27a-D)

description: Gene expression profiling of RH36 cells transfected with pre-miR-27a (miR-27a-D)

value: transfected with precursor of miR-27a were analyzed 48h after transfection


title: Bos taurus_biceps brachii_K6

description: Sample of bovine biceps brachii


title: CTR-2, control, biological replicate 2 (CTR-B)

description: Gene expression profiling of RH36 cells transfected with negative control (CTR-B)

value: transfected with negative control


title: miR-27a-E, miR-27a over-expressing cell, biological replicate 2 (miR-27a-E)

description: Gene expression profiling of RH36 cells transfected with pre-miR-27a (miR-27a-E)


title: CTR-3, control, biological replicate 3 (CTR-C)

description: Gene expression profiling of RH36 cells transfected with negative control (CTR-C)


title: Bos taurus_biceps brachii_K2

description: Sample of bovine biceps brachii

value: biceps brachii


title: Hepatocellular carcinoma tissue_12t

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

description: Expression analysis of hepatocellular carcinoma tissue

hyb_protocol: Samples were hybridized on the Human Gene Expression 12x135K Arrays (Nimblegen-Roche, Madison, WI, USA) following manufacturer instructions

scan_protocol: Microarrays were scanned with Axon GenePix 4400A microarray scanner setting laser power to 100%. PMT gain was set in order to obtain about 1e-5 normalized counts at 65.000 intensity level for both channels.

data_processing: Feature data were extracted, summarized using RMA algorithm and quantile normalized using NimbleScan 2.5 software.

source_name: Expression of hepatocellular carcinoma tissue

label_protocol: 10 ug of total RNA were utilized to synthesize double-stranded cDNA by Superscript® Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA, USA); 1ug of cDNA was labeled by One-Color DNA Labeling Kit (NimbleGen-Roche, Madison, WI, USA) and 4 ug of Cy3-labeled cDNA were hybridized on the array.

extract_protocol: After surgical excision, tissue samples for nucleic acids extraction were immediately sliced into aliquots of about 100 mg, snap-frozen in liquid nitrogen and stored at -80°C until use. For RNA extraction, each liver tissue aliquot (100 mg) was kept on ice, immediately homogenized in 2 ml of TriReagent® (Sigma-Aldrich, St. Louis, MO, USA) and the homogenate stored at -80°C until use. RNA was extracted by guanidinium thiocyanate-phenol-chloroform-based method using TRIReagent® (Sigma-Aldrich, St. Louis, MO, USA)

value: Hepatocellular carcinoma


title: Bos taurus_biceps brachii_K1

description: Sample of bovine biceps brachii


title: Hepatocellular carcinoma tissue_50t


title: Hepatocellular carcinoma tissue_55t


title: CTR-1, control, biological replicate 1 (CTR-A)

description: Gene expression profiling of RH36 cells transfected with negative control (CTR-A)


title: Hepatocellular carcinoma tissue_28t


title: Hepatocellular carcinoma tissue_4t


title: Liver-non_neoplastic_control_50s

description: Expression analysis of non neoplastic liver tissue

source_name: Expression of non neoplatic control from liver

value: Liver


title: Hepatocellular carcinoma tissue_52t


title: Liver-non_neoplastic_control_55s


title: Hepatocellular carcinoma tissue_17t


title: RH28_biol. rep. 2

description: miRNA expression profiling of the R28 rhabdomyosarcoma cell line (RH28-B)

hyb_protocol: Microarray hybridization was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 μL of 3×SSC. Labeled RNA was dissolved in 6 μL of 3X miRNA Hybridization Buffer (Ambion), denatured at 95°C for 3 min and applied directly to the slides. Microarrays were covered with a 24×24 mm cover slip and hybridized for 21 hours at 42°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Hybridized slides were successively washed in: Low and High Stringency Buffer (Ambion) for 30 sec. and dried by centrifugation (500 x g).

scan_protocol: Array scanning was carried out using a GSI Lumonics LITE dual confocal laser scanner with a ScanArray Microarray Analysis System (Perkin Elmer), and raw images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Inter-array normalization of expression levels was performed with VSN (Variance Stabilizing Normalization) [Rocke & Durbin, 2003 - Bioinformatics, 19(8):966-72]. Cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite [Saeed et al., 2006 - Methods in Enzymology, 411:134-93]. In particular, hierarchical cluster analysis was performed with Pearson correlation as distance measure with complete linkage. Identification of differentially expressed miRNAs was performed with SAM two class analysis (FDR<8%) [Tusher et al., 2001 - PNAS USA, 98:5116-121].

source_name: pool of the 8 RMS cell lines, control

label_protocol: Small RNA molecules (< 200 nt) were labelled with the mirVana Labeling Kit and amine-reactive dyes as recommended by the manufacturer (Ambion, Austin, TX). Poly(A) polymerase and a mixture of unmodified and amine-modified nucleotides were used first to append a poly-nucleotide tail to the 3’ end of each miRNA. The amine-modified miRNAs were then cleaned up and coupled to NHS-ester modified Cy5 or Cy3 dyes (GE Healthcare, Little Chalfont, UK). Unincorpored dyes were removed with a second glass fibre-based clean-up procedure as described by Shingara et al. (2005).

growth_protocol: Human alveolar RMS (ARMS) cell lines, positive for PAX3/FOXO1 translocation (RH4, RH30, RH28), negative for PAX3/FOXO1 translocation (RH18) and human embryonal RMS (ERMS) cells (RD, RH36, CCA, SMS-CTR), negative for PAX3/FOXO1 translocation, were maintained in modified Eagle's medium (DMEM) containing 10% fetal calf serum, penicillin (100 U/ml), and streptomycin (100 μg/ml) (Invitrogen) at 37°C, 5% CO2 in a humidified incubator. The human RMS cell lines RH30, RH28 and RD were purchased from ATCC (Manassas, VA); RH4 and RH18 were a gift of Dr P.J. Houghton (St Jude Children's Hospital Memphis, TN); SMS-CTR, RH36, CCA were obtained  from Dr M. Tsokos (NCI, Bethesda, MD).

extract_protocol: Total RNA was prepared from eight cell lines of human rhabdomyosarcoma using a modified TRIzol (Life Technologies Corporation, Carlsbad, CA, USA) protocol for small RNA enrichment. A pellet of about 6 × 106 - 9 × 106 cells was dissolved in 1 ml of TRIzol and the supernatant, containing total RNA, was purified by PureLink™ miRNA Isolation Kit (Life Technologies Corporation) that was specifically designed to enrich total RNA preparation for < 200-nt RNA molecules. RNA quantity and quality were assessed by Nanodrop (NanoDrop Technologies, Wilmington, DE, USA) spectrophotometry and microelectrophoresis using Small RNA Nano LabChip by Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) respectively.

value: Pool of eight RMS cell lines (RH30, RH4, RH28, RH18, SMS-CTR, CCA, RH36, RD)

source_name: RH28, ARMS cell line

value: RH28, ARMS cell line

value: PAX3/FOXO1 translocation positive RMS cell line


title: Hepatocellular carcinoma tissue_10t


title: RH28_biol. rep. 1

description: miRNA expression profiling of the R28 rhabdomyosarcoma cell line (RH28-A)


title: Liver-non_neoplastic_control_28s


title: Liver-non_neoplastic_control_12s


title: RH30_biol. rep. 2

description: miRNA expression profiling of the R30 rhabdomyosarcoma cell line (RH30-B)

source_name: RH30, ARMS cell line

value: RH30, ARMS cell line


title: Liver-non_neoplastic_control_17s


title: Liver-non_neoplastic_control_52s


title: RH30_biol. rep. 1

description: miRNA expression profiling of the R30 rhabdomyosarcoma cell line (RH30-A)


title: RH4_biol. rep. 1

description: miRNA expression profiling of the RH4 rhabdomyosarcoma cell line (RH4-A)

source_name: RH4, ARMS cell line

value: RH4, ARMS cell line


title: CCA_biol. rep. 2

description: miRNA expression profiling of the CCA rhabdomyosarcoma cell line (CCA-B)

source_name: CCA, ERMS cell line

value: CCA, ERMS cell line

value: PAX3/FOXO1 translocation negative RMS cell line


title: Liver-non_neoplastic_control_4s


title: Liver-non_neoplastic_control_10s


title: CCA_biol. rep. 1

description: miRNA expression profiling of the CCA rhabdomyosarcoma cell line (CCA-A)


title: RH36_biol. rep. 2

description: miRNA expression profiling of the RH36 rhabdomyosarcoma cell line (RH36-B)

source_name: RH36, ERMS cell line

value: RH36, ERMS cell line


title: RH36_biol. rep. 1

description: miRNA expression profiling of the RH36 rhabdomyosarcoma cell line (RH36-A)


title: MCF7 4

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Hybridization cocktails containing fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization performed according to standard Affymetrix protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
CHP files representing RMA expression values were generated as follows:
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HJAY
program-name = Expression Console
Raw data were processed with the Exon Array Computational Tool (Affymetrix). Data analysis and statistical evaluations were performed by Genosplice. https://www.easana.com. We used the cluster transcripts with high and medium confidence in genes with a not significant fold-change. For each gene, a Student?s t-test that compares mean values between the two experimental conditions was performed. This test provides the fold-change and p-value. All the data processing was perforned by Genosplice (www..easana.con)
probe group file: HJAY_r2.pgf
meta-probeset file: HJAY_r2.full.mps
We used the "ProbeSelect" software (Xing et al., 2006) that selects the probesets (only exon probesets, not junction) that have a highly correlated intensity across all samples. We used these probesets to have a global gene value in each sample. The final results include the p-value and the fold-change for each gene Up or Down regulated in MCF7 compared to MCF10. For the exon level analysis, the intensities, up or down regulation in MCF7 with respect to MCF10, and the fold change value for each of the junctions and exon probes, are given for each cassette exon. High and Medium confidence transcript clusters were selected. The final processed data generated by Genosplice is available in the matrix_processed_data.xls (linked as a supplementary file on the Series record). In http://archimedes.imim.es:9007/biomart/martview/  processed ChIP-Seq samples (GSE56826) and alternative splicing events used in this study are available.

source_name: MCF7 breast cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labelin

growth_protocol: Cells were growth in DMEM-Glutamax(10% SFB)

extract_protocol: RNA was extracted from MCF-7 cells and  MCF-10A cells and then purified using (Rneasy kit QIAGEN).


title: RH18_biol. rep. 2

description: miRNA expression profiling of the RH18 rhabdomyosarcoma cell line (RH18-B)

source_name: RH18, ARMS cell line

value: RH18, ARMS cell line


title: RH4_biol. rep. 2

description: miRNA expression profiling of the RH4 rhabdomyosarcoma cell line (RH4-B)


title: Bos taurus_biceps brachii_DE32

description: Sample of bovine biceps brachii

value: DEXAMETHAZONE+ESTRADIOL


title: The nox Complemented Strain Replicate 3

city: Richmond

first: Xiuchun

last: Ge

state: VA

address: 521 North 11th Street

institute: Virginia Commonwealth University

description:
Biological replicate 3 of 3.
nox-compl-3

hyb_protocol: After prehybridization, spotted microarray was hybridized with Cy3- and Cy5-labeled cDNA for 16 h at 42 °C according to the protocol for hybridization of labeled DNA and cDNA probes at The J. Craig Venter Institute

scan_protocol: Hybridized microarray was scanned using GenePix 4200A Scanner (Axon Instruments).

data_processing: Images were quantified using TIGR Spotfinder Software (version 3.2.1). Data were filtered and LOWESS normalized by TIGR Midas Software (version 2.22).

organism: Streptococcus sanguinis

source_name: Total RNA from the nox complemented strain at exponential growth phase

label_protocol: Aminoallyl-labeled cDNA was labeled by Cy5 for test or Cy3 for reference as described in the manual for microbial RNA aminoallyl labeling for microarrays at The J. Craig Venter Institute.

growth_protocol: The nox mutant was grown in BM medium at 37 °C ovenight under anaerobic conditions. The overnight cultures were diluted 1:100 in BM medium and incubated under the same conditions as above.

extract_protocol: Total RNA extracted using Qiagen RNeasy mini kit following manufacturer's instructions

treatment_protocol: The cultures at exponential phase were haversted and used for RNA isolation.

value: nox complemented strain

source_name: Total RNA from the wild-type strain SK36 at exponential growth phase


title: MCF7 2


title: RH18_biol. rep. 1

description: miRNA expression profiling of the RH18 rhabdomyosarcoma cell line (RH18-A)


title: SMS-CTR_biol. rep. 2

description: miRNA expression profiling of the SMS-CTR rhabdomyosarcoma cell line (SMS-CTR-B)

source_name: SMS-CTR, ERMS cell line

value: SMS-CTR, ERMS cell line


title: SMS-CTR_biol. rep. 1

description: miRNA expression profiling of the SMS-CTR rhabdomyosarcoma cell line (SMS-CTR-A)


title: MCF7 1


title: The nox Complemented Strain Replicate 1

description:
Biological replicate 1 of 3.
nox-compl-1


title: 9L tumor_4th metroCPA (pool JD3 and pool JD4) versus 9L tumor_control (pool JD1 and pool JD2)_Mouse microarray

description: Total RNA was prepared and pooled from each set of U251 tumor xenografts, either metronomic cyclophosphamide-treated or untreated controls, as indicated.

organism: Rattus norvegicus

extract_protocol: Trizol extraction of total RNA. Total RNA was prepared from individual tumors, and then pooled (n=7-8 independent tumor RNA samples for each of two independent pools of untreated tumors, and n=4 independent tumor RNA samples for each of two independent pools of metronomic cyclophosphamide-treated tumors for each of the time points), with each set of tumor RNA pools corresponding to an independent biological replicate). RNA pools were prepared by combining equal amounts of RNA from each tumor included in the pool to minimize the effects of inter-tumor variability

treatment_protocol: Mice were treated with cyclophosphamide monohydrate on an intermittent metronomic schedule (140 mg cyclophosphamide/kg body weight, every 6 days), with the dose reported here based on the non-hydrate molecular weight of 261. Tumor sizes and mouse body weights were measured at least twice weekly. Tumor growth rates prior to drug treatment were similar among all normalized groups. Cyclophosphamide-treated tumors were collected 6 days after the 4th cyclophosphamide treatment cycle, i.e., treatment day 24. Drug-free control tumors were collected on days 0 and 10, where day 0 is the first day of drug treatment.

value: Rat glioma 9L tumor xenograft

value: Metronomic cyclophosphamide, 6 days after 4 cycles

value: Untreated control


title: U251 tumor_2nd metroCPA (pool JD9 and JD10) versus U251 tumor_control (pool JD5 and JD6)_Mouse microarray

value: Human glioma U251 tumor xenograft

value: Metronomic cyclophosphamide, 6 days after 2 cycles


title: MCF10 3

source_name: MCF10 breast cells


title: The nox Mutant Replicate 3

description:
Biological replicate 3 of 3.
nox-3

source_name: Total RNA from the nox mutant at exponential growth phase

value: nox mutant


title: RD_biol. rep. 2

description: miRNA expression profiling of the RD rhabdomyosarcoma cell line (RD-B)

value: Pool of eight RMS cell lines (RH30, RH4, RH28, RH18, SMS-CTR, CCA, RH36, RD)

source_name: RD, ERMS cell line

value: RD, ERMS cell line


title: The nox Mutant Replicate 1

description:
Biological replicate 1 of 3.
nox-1


title: MCF10 1


title: The nox Mutant Replicate 2

description:
Biological replicate 2 of 3.
nox-2


title: RD_biol. rep. 1

description: miRNA expression profiling of the RD rhabdomyosarcoma cell line (RD-A)


title: U251 tumor_3rd metroCPA (pool JD7 and JD8) versus U251 tumor_control (pool JD5 and JD6)_Mouse microarray

value: Metronomic cyclophosphamide, 6 days after 3 cycles

source_name: U251 tumor_control (pool JD5 and JD6)


title: The nox Complemented Strain Replicate 2

description:
Biological replicate 2 of 3.
nox-compl-2


title: MCF10 2


title: Hepatocellular carcinoma tissue_55t

description: MeDIP-chip hepatocellular carcinoma tissue

hyb_protocol: Samples were hybridized on the Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array (NimbleGen-Roche, Madison, WI, USA) following manufacturer instructions

data_processing: Data were quantile normalized and logged fold change of immunoprecipitated sample (IP) over control (INPUT) sample was calculated

source_name: MeDIP of hepatocellular carcinoma tissue

label_protocol: One and a half μg of IP and 1.5 μg INPUT samples were labelled with Cy5 and Cy3 respectively by Dual-Color DNA Labeling Kit (NimbleGen-Roche, Madison, WI, USA).

extract_protocol: After surgical excision, tissue samples for nucleic acids extraction were immediately sliced into aliquots of about 100 mg, snap-frozen in liquid nitrogen and stored at -80°C until use. Aliquots for DNA extraction were homogenized in 2ml of chilled NaCl 0.9% w/v; cell lysis was achieved by using Nonidet P40 (Sigma-Aldrich, St. Louis, MO, USA) 0.1% and lysis solution (NaCl 100 mM, EDTA 25 mM, SDS 1.6 %, pH 8). Samples were treated with proteinase K/RNase and DNA extracted with a standard phenol/chloroform procedure. The methylated DNA immunoprecipitation (MeDIP) was performed with MeDIP kit™ by Diagenode (Liège, Belgium). IP and INPUT samples were amplified by GenomePlex Complete Genome Amplification (WGA) kit (Sigma-Aldrich, St. Louis, MO, USA) following the producer’s protocol.

value: Hepatocellular carcinoma

source_name: INPUT DNA from hepatocellular carcinoma tissue


title: keratinocytes 100 nM IM treatment replicate 2

status: Public on May 03 2015

city: Zurich

first: Sandra

middle: Nicole

last: Freiberger

state: Zurich

address: Gloriastrasse 31

department: Department of Dermatology

country: Switzerland

institute: University Hospital Zurich

description: gene expression after 100 nM IM treatment

hyb_protocol: 600 ng of the obtained Cy3-labeled cRNA was was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Sure Print GE 8x60 K v2 Microarrays (Agilent Technologies)  (G4112A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent  G2565CA Microarray Scanner System (Scan Control Software 8.5, Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Data was imported into R by maarray, background corrected and quantile normalized

source_name: keratinocytes treated with 100 nM IM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).Quantification and and quality assessment  were done using Nanodrop spectrophotometer  (Witec)  and Agilent 2100 Bioanalyzer (Agilent Technologies)    respectively.

growth_protocol: primary keratinocytes and SCC cells were grown in CnT07 medium (CELLnTEC)

extract_protocol: RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol

treatment_protocol: cells were treated for 24h with either DMSO or IM (1 nM, 100 nM, 10 uM)

value: primary keratinocytes


title: keratinocytes DMSO treatment replicate 3

description: gene expresison after 24h DMSO

source_name: keratinocytes treated with DMSO


title: keratinocytes 100 nM IM treatment replicate 3


title: keratinocytes DMSO treatment replicate 1

description: gene expresison after 24h DMSO


title: keratinocytes 10 uM IM treatment replicate 1

description: gene expression after 10 uM IM treatment

source_name: keratinocytes treated with 10 uM IM


title: keratinocytes 10 uM IM treatment replicate 2


title: keratinocytes 100 nM IM treatment replicate 1


title: SCC cells 10 uM IM treatment replicate 2

source_name: SCC cells treated with 10 uM IM

value: primary squamous cell carcinoma (SCC) cells


title: Hepatocellular carcinoma tissue_17t


title: keratinocytes 10 uM IM treatment replicate 3


title: SCC cells 10 uM IM treatment replicate 1


title: SCC cells 10 uM IM treatment replicate 3


title: Hepatocellular carcinoma tissue_10t


title: Hepatocellular carcinoma tissue_52t


title: keratinocytes DMSO treatment replicate 2

description: gene expresison after 24h DMSO


title: SCC cells 1 nM IM treatment replicate 3

description: gene expression after 1 nM IM treatment

source_name: SCC cells treated with 1 nM IM


title: SCC cells 100 nM IM treatment replicate 1

source_name: SCC cells treated with 100 nM IM


title: SCC cells 1 nM IM treatment replicate 2

description: gene expression after 1 nM IM treatment


title: S16 [NanoString]

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: S16 [NanoString]

hyb_protocol: Buffer, CodeSet and samples are added to a tube and hybridized overnight, according to nCounter miRNA expression assay instructions

scan_protocol: Automated digital anaylzer performs direct digital counting of barcoded reporter probes

data_processing:
Data output files include the target identifier and count number along with a comprehensive set of internal controls as RCC files, loaded into nSolver software for normalization to the top 100 miRNAs
The 'Processed_normalised_data_+_threshold_of_2SD_S7-S16.xlsx' file contains the normalised tabulated counts of individual miRNAs for each sample (S7-S16) with a high stringency threshold applied, calculated by adding 2SD to the mean of the negative controls  included internally (threshold=mean+2SD) so only miRNAs above this calculated threshold are portrayed in this file.

source_name: Liver tumour tissue

label_protocol: Sample preparation involves a multiplexed annealing of the specific tags to their target miRNA, a ligation reaction, and an enzymatic purification to remove the unligated tags, using the nCounter® miRNA Sample Preparation Kit

extract_protocol: Total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion)  according to manufacturer's instructions

tag: patient

value: hepatoblastoma


title: SCC cells 100 nM IM treatment replicate 3


title: SCC cells 100 nM IM treatment replicate 2


title: S15 [NanoString]

description: S15 [NanoString]


title: S13 [NanoString]

description: S13 [NanoString]


title: Hepatocellular carcinoma tissue_12t


title: SCC cells 1 nM IM treatment replicate 1

description: gene expression after 1 nM IM treatment


title: SCC cells DMSO treatment replicate 3

description: gene expresison after 24h DMSO

source_name: SCC cells treated with DMSO


title: Hepatocellular carcinoma tissue_50t


title: S14 [NanoString]

description: S14 [NanoString]


title: Liver-non_neoplastic_control_12s

description: MeDIP-chip non neoplastic liver tissue

source_name: MeDIP of non neoplatic control from liver

value: Liver

source_name: INPUT DNA from non neoplatic control from liver


title: Hepatocellular carcinoma tissue_28t


title: S5B [microarray]

description: Technical replicate 2 of 2.

hyb_protocol: Biotin-labeled sample and hybridization master mix were combined and hybridized for 16-18 hours at 48°C in a rotating oven. Microarrays were washed and stained on the Fluidics Station 450.

scan_protocol: GeneChips were scanned using a 3000 7G scanner.

data_processing: The CEL files were loaded into the statistical computing environment, R, and the oligo package from Bioconductor was used to perform normalization of the raw probe intensities using the RMA approach.

label_protocol: 400 ng of RNA per sample was labelled with the Affymetrix FlashTag Biotin HSR Labeling kit according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion) according to manufacturer's instructions.


title: Hepatocellular carcinoma tissue_4t


title: S5A [microarray]

description: Technical replicate 1 of 2.


title: Liver-non_neoplastic_control_10s

description: MeDIP-chip non neoplastic liver tissue


title: Liver-non_neoplastic_control_28s

description: MeDIP-chip non neoplastic liver tissue


title: S4B [microarray]

description: Technical replicate 2 of 2.


title: S7 [NanoString]

description: S7 [NanoString]


title: S8 [NanoString]

description: S8 [NanoString]


title: S10 [NanoString]

description: S10 [NanoString]


title: S9 [NanoString]

description: S9 [NanoString]


title: S12 [NanoString]

description: S12 [NanoString]


title: S11 [NanoString]

description: S11 [NanoString]


title: S4A [microarray]

description: Technical replicate 1 of 2.


title: SCC cells DMSO treatment replicate 2

description: gene expresison after 24h DMSO


title: Liver-non_neoplastic_control_52s

description: MeDIP-chip non neoplastic liver tissue


title: Liver-non_neoplastic_control_17s

description: MeDIP-chip non neoplastic liver tissue


title: Liver-non_neoplastic_control_55s

description: MeDIP-chip non neoplastic liver tissue


title: S6B [microarray]

description: Technical replicate 2 of 2.


title: Liver-non_neoplastic_control_4s

description: MeDIP-chip non neoplastic liver tissue


title: S6A [microarray]

description: Technical replicate 1 of 2.


title: SCC cells DMSO treatment replicate 1

description: gene expresison after 24h DMSO


title: Inguinal WAT_21D_29degC_biorep7

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description: Sample name: 21D_29C_2907

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent Fragmentation Buffer and 2x Agilent Gene Expression Blocking Agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37Â°C Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for G3 Microarray Formats.

data_processing: The scanned images were analyzed with Feature Extraction Software v. 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized among the samples by quantile method. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring GX 12 Software (Agilent).

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer.

extract_protocol: Total RNA from the inguinal WAT of 8 10- and 8 21 day-old mice maintained at 17 °C and 8 10- and 8 21 day-old mice maintained at 29°C was isolated using TRI Reagent and BCP phase separation reagent (Molecular Research Center Inc. Cincinnati, OH, United States). RNA was further purified using the RNAeasy minikit (QIAGEN, Valencia, CA, United States) and stored at -80°C in RNase-free H2O with addition of SUPERase-In (Ambion, Austin, TX, United States) for RNA protection. Quality and quantity of RNA was determined using UV spectrophotometry (Nanodrop). RNA samples with RNA Integrity number range from 8.6 to 9.4 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) were used for microarray analysis of each individual mouse.

treatment_protocol: From birth C57BL/6J mice were maintained at either 17oC or 29oC in environmentally controlled chambers (EHRET GmbH, Emmendingen, Germany) together with their parents and littermates (8 pups/ litter). Male mice were used for the analysis at 10 or 21 days of post-natal development.

value: inguinal white adipose tissue (WAT)

tag: strain

tag: temperature

value: male

tag: age

value: 21 day-old


title: Liver-non_neoplastic_control_50s

description: MeDIP-chip non neoplastic liver tissue


title: Inguinal WAT_10D_29degC_biorep7

description: Sample name: 10D_29C_4264

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 7

tag: gender

value: 10 day-old


title: Inguinal WAT_10D_29degC_biorep5

description: Sample name: 10D_29C_4669

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 5


title: Inguinal WAT_21D_29degC_biorep1

description: Sample name: 21D_29C_2913

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 1


title: Inguinal WAT_21D_29degC_biorep6

description: Sample name: 21D_29C_3113

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 6


title: Inguinal WAT_21D_29degC_biorep5

description: Sample name: 21D_29C_3108

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 5


title: Inguinal WAT_10D_29degC_biorep3

description: Sample name: 10D_29C_4263

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 3


title: Inguinal WAT_21D_29degC_biorep8

description: Sample name: 21D_29C_2912

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 8


title: S5 [NanoString]

hyb_protocol: Buffer, CodeSet and samples are added to a tube and hybridized overnight, according to nCounter miRNA expression assay instructions.

scan_protocol: Automated digital analyzer performs direct digital counting of barcoded reporter probes.

data_processing: Data output files include the target identifier and count number along with a comprehensive set of internal controls as RCC files, loaded into nSolver software for normalization to the top 100 miRNAs.

label_protocol: Sample preparation involves a multiplexed annealing of the specific tags to their target miRNA, a ligation reaction, and an enzymatic purification to remove the unligated tags, using the nCounter® miRNA Sample Preparation Kit.


title: S6 [NanoString]


title: Inguinal WAT_10D_29degC_biorep4

description: Sample name: 10D_29C_4671

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 4


title: Inguinal WAT_10D_29degC_biorep8

description: Sample name: 10D_29C_4670

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 8


title: Inguinal WAT_21D_29degC_biorep3

description: Sample name: 21D_29C_2911

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 3


title: Inguinal WAT_21D_17degC_biorep8

description: Sample name: 21D_17C_4027

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 8


title: Inguinal WAT_10D_29degC_biorep6

description: Sample name: 10D_29C_3047

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 6


title: Inguinal WAT_21D_17degC_biorep7

description: Sample name: 21D_17C_3320

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 7


title: Inguinal WAT_21D_29degC_biorep2

description: Sample name: 21D_29C_3112

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 2


title: Inguinal WAT_21D_29degC_biorep4

description: Sample name: 21D_29C_2909

source_name: Inguinal WAT, 21 day-old mouse, 29degC, biological replicate 4


title: Inguinal WAT_10D_29degC_biorep1

description: Sample name: 10D_29C_3046

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 1


title: Inguinal WAT_21D_17degC_biorep4

description: Sample name: 21D_17C_3319

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 4


title: Inguinal WAT_10D_17degC_biorep7

description: Sample name: 10D_17C_2844

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 7


title: Inguinal WAT_21D_17degC_biorep5

description: Sample name: 21D_17C_3299

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 5


title: Inguinal WAT_21D_17degC_biorep6

description: Sample name: 21D_17C_4028

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 6


title: Inguinal WAT_21D_17degC_biorep3

description: Sample name: 21D_17C_3322

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 3


title: Inguinal WAT_21D_17degC_biorep2

description: Sample name: 21D_17C_4029

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 2


title: Inguinal WAT_10D_29degC_biorep2

description: Sample name: 10D_29C_4265

source_name: Inguinal WAT, 10 day-old mouse, 29degC, biological replicate 2


title: Inguinal WAT_10D_17degC_biorep6

description: Sample name: 10D_17C_4523

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 6


title: Mouse liver injected with scrambled (non-target) control RNA 3

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

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 Gene-Chip 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 (Affymertix, 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.

source_name: liver

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 mice liver tissues was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

value: C57BL/6 NHsd


title: Inguinal WAT_10D_17degC_biorep5

description: Sample name: 10D_17C_2845

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 5


title: Mouse liver injected with siRNA against Rab5all for silencing Rab5all 3


title: Mouse liver injected with siRNA against Rab5all for silencing Rab5all 4


title: Inguinal WAT_10D_17degC_biorep8

description: Sample name: 10D_17C_2850

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 8


title: Mouse liver injected with scrambled (non-target) control RNA 2


title: Mouse liver injected with siRNA against Rab5all for silencing Rab5all 1


title: Mouse liver injected with scrambled (non-target) control RNA 4


title: Inguinal WAT_10D_17degC_biorep2

description: Sample name: 10D_17C_2848

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 2


title: Inguinal WAT_21D_17degC_biorep1

description: Sample name: 21D_17C_3323

source_name: Inguinal WAT, 21 day-old mouse, 17degC, biological replicate 1


title: Inguinal WAT_10D_17degC_biorep1

description: Sample name: 10D_17C_4783

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 1


title: Mouse liver injected with scrambled (non-target) control RNA 1


title: Mouse liver injected only with PBS 2

value: injected only with PBS


title: Inguinal WAT_10D_17degC_biorep4

description: Sample name: 10D_17C_4186

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 4


title: Mouse liver injected with siRNA against Rab5all for silencing Rab5all 2


title: Inguinal WAT_10D_17degC_biorep3

description: Sample name: 10D_17C_4784

source_name: Inguinal WAT, 10 day-old mouse, 17degC, biological replicate 3


title: Mouse liver injected only with PBS 1


title: Day 14, biological rep2

city: Tianjin

first: Hui

last: Cheng

address: 288 Nanjing road

country: China

institute: Institute of Hematology

description: Gene expression data in normal HSCs (LKS+ cells) from leukemic mice at day 14

hyb_protocol: Following fragmentation, the amplified cRNA was labeled and hybridized to the Affymetrix Mouse Genome Array 430 2.0

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000

data_processing: Raw data were normalized using Microarray Analysis Software v5.0 (Affymetrix).

source_name: CD45.1+LKS+ cells from leukemic mice at day 14

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

growth_protocol: CD45.1+LKS+ cells were flow sorted from leukemia and control groups at different time points

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Mini kit according to the manufacturer's instructions.

treatment_protocol: After sorting, cells were centrifuged and lysis buffer were added into the tube

value: CD45.1+LKS+ cells

tag: time

tag: disease state

value: Leukemic mice

value: bone marrow

value: 8 weeks


title: Day 7, biological rep1

description: Gene expression data in normal HSCs (LKS+ cells) from leukemic mice at day 7

source_name: CD45.1+LKS+ cells from leukemic mice at day 7

value: 7 d


title: Day 14, biological rep1


title: Day 7, biological rep3


title: notte-00422: Sample_350

status: Public on May 02 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

hyb_protocol: See mage-tab files linked to series entry for additional details

value: colon cancer

value: colon

value: Colon

tag: histology


title: notte-00422: Sample_239

scan_protocol: See mage-tab files linked to series entry for additional details

value: colon polyp


title: notte-00422: Sample_238

data_processing: See mage-tab files linked to series entry for additional details


title: notte-00422: Sample_017

label_protocol: See mage-tab files linked to series entry for additional details

value: normal liver


title: notte-00422: Sample_183

extract_protocol: See mage-tab files linked to series entry for additional details


title: notte-00422: Sample_019

value: Liver

value: colon carcinoma metastatic to the liver


title: notte-00422: Sample_126


title: Day 7, biological rep2


title: notte-00422: Sample_341


title: Control, biological rep3

description: Gene expression data in normal HSCs (LKS+ cells) from control mice

source_name: CD45.1+LKS+ cells from control mice

value: control mice


title: notte-00422: Sample_351

value: colon mucosa

value: normal colon mucosa


title: notte-00422: Sample_343


title: notte-00422: Sample_097

value: Lung

value: colon carcinoma metastatic to the lung


title: notte-00422: Sample_185


title: notte-00422: Sample_297


title: notte-00422: Sample_298


title: notte-00422: Sample_042


title: Control, biological rep1

value: CD45.1+LKS+ cells


title: notte-00422: Sample_176


title: Control, biological rep2


title: notte-00422: Sample_041


title: notte-00422: Sample_146


title: notte-00422: Sample_127


title: notte-00422: Sample_038


title: notte-00422: Sample_184


title: notte-00422: Sample_028


title: notte-00422: Sample_029


title: notte-00422: Sample_257


title: notte-00422: Sample_039


title: notte-00422: Sample_200


title: notte-00422: Sample_268


title: notte-00422: Sample_107

value: lung

value: normal lung


title: notte-00422: Sample_357


title: notte-00422: Sample_385

value: colon adenocarcinoma

value: LoVo


title: notte-00422: Sample_204

value: colon cancer


title: notte-00422: Sample_108


title: notte-00422: Sample_111


title: notte-00422: Sample_328


title: notte-00422: Sample_071


title: notte-00422: Sample_022


title: notte-00422: Sample_072


title: notte-00422: Sample_387

value: Normal


title: notte-00422: Sample_138

value: Colon


title: notte-00422: Sample_152


title: notte-00422: Sample_021


title: notte-00422: Sample_279


title: notte-00422: Sample_199


title: notte-00422: Sample_258


title: notte-00422: Sample_278


title: notte-00422: Sample_175


title: notte-00422: Sample_050


title: notte-00422: Sample_259


title: notte-00422: Sample_389


title: notte-00422: Sample_316


title: notte-00422: Sample_277


title: notte-00422: Sample_317


title: notte-00422: Sample_235


title: notte-00422: Sample_275


title: notte-00422: Sample_093


title: Day 14, biological rep3

value: Leukemic mice

value: bone marrow

value: 8 weeks


title: notte-00422: Sample_276

value: Liver

value: normal liver


title: notte-00422: Sample_103

value: colon polyp


title: notte-00422: Sample_342


title: notte-00422: Sample_198


title: notte-00422: Sample_162


title: notte-00422: Sample_009


title: notte-00422: Sample_120


title: notte-00422: Sample_390

value: Colon Carcinoma

value: WiDr


title: notte-00422: Sample_338

value: liver

value: colon carcinoma metastatic to the liver


title: notte-00422: Sample_337


title: notte-00422: Sample_094

value: colon mucosa

value: normal colon mucosa


title: notte-00422: Sample_035


title: notte-00422: Sample_027


title: notte-00422: Sample_307


title: notte-00422: Sample_026


title: notte-00422: Sample_034


title: notte-00422: Sample_143


title: notte-00422: Sample_274


title: notte-00422: Sample_096


title: notte-00422: Sample_170


title: notte-00422: Sample_336


title: notte-00422: Sample_289


title: notte-00422: Sample_142


title: notte-00422: Sample_249


title: notte-00422: Sample_284


title: notte-00422: Sample_064


title: notte-00422: Sample_102

value: Lung

value: colon carcinoma metastatic to the lung


title: notte-00422: Sample_270

value: colon cancer


title: notte-00422: Sample_122


title: notte-00422: Sample_345


title: notte-00422: Sample_065


title: notte-00422: Sample_130


title: notte-00422: Sample_269


title: notte-00422: Sample_388


title: notte-00422: Sample_156


title: notte-00422: Sample_348


title: notte-00422: Sample_344


title: notte-00422: Sample_151


title: notte-00422: Sample_358


title: notte-00422: Sample_149


title: notte-00422: Sample_085


title: notte-00422: Sample_131


title: notte-00422: Sample_164


title: notte-00422: Sample_332


title: notte-00422: Sample_359


title: notte-00422: Sample_329


title: notte-00422: Sample_128

value: lung

value: normal lung


title: notte-00422: Sample_361

value: Colon


title: notte-00422: Sample_360


title: notte-00422: Sample_302


title: notte-00422: Sample_247


title: notte-00422: Sample_129


title: notte-00422: Sample_040


title: notte-00422: Sample_222


title: notte-00422: Sample_282


title: notte-00422: Sample_223


title: notte-00422: Sample_136


title: notte-00422: Sample_173


title: notte-00422: Sample_256


title: notte-00422: Sample_280


title: notte-00422: Sample_117


title: notte-00422: Sample_018


title: notte-00422: Sample_281


title: notte-00422: Sample_174


title: notte-00422: Sample_188


title: notte-00422: Sample_211


title: notte-00422: Sample_055


title: notte-00422: Sample_294


title: notte-00422: Sample_153


title: notte-00422: Sample_212


title: notte-00422: Sample_334


title: notte-00422: Sample_354


title: notte-00422: Sample_225


title: notte-00422: Sample_217


title: notte-00422: Sample_205


title: notte-00422: Sample_363


title: notte-00422: Sample_365


title: notte-00422: Sample_362


title: notte-00422: Sample_364


title: notte-00422: Sample_054


title: notte-00422: Sample_140


title: notte-00422: Sample_196


title: notte-00422: Sample_333


title: notte-00422: Sample_226


title: notte-00422: Sample_069


title: notte-00422: Sample_066


title: notte-00422: Sample_237


title: notte-00422: Sample_272


title: notte-00422: Sample_273


title: notte-00422: Sample_078


title: notte-00422: Sample_209


title: notte-00422: Sample_349


title: notte-00422: Sample_263


title: notte-00422: Sample_251


title: notte-00422: Sample_013


title: notte-00422: Sample_070


title: notte-00422: Sample_025


title: notte-00422: Sample_132


title: notte-00422: Sample_015


title: notte-00422: Sample_308


title: notte-00422: Sample_266


title: notte-00422: Sample_250


title: notte-00422: Sample_318


title: notte-00422: Sample_024


title: notte-00422: Sample_319


title: notte-00422: Sample_112


title: notte-00422: Sample_014


title: notte-00422: Sample_067


title: notte-00422: Sample_213


title: notte-00422: Sample_242


title: notte-00422: Sample_119


title: notte-00422: Sample_110


title: notte-00422: Sample_001


title: notte-00422: Sample_322


title: notte-00422: Sample_236


title: notte-00422: Sample_324

value: high grade dysplasia


title: notte-00422: Sample_133


title: notte-00422: Sample_383


title: notte-00422: Sample_155


title: notte-00422: Sample_036


title: notte-00422: Sample_124


title: notte-00422: Sample_192


title: notte-00422: Sample_043


title: notte-00422: Sample_008


title: notte-00422: Sample_325


title: notte-00422: Sample_044


title: notte-00422: Sample_006


title: notte-00422: Sample_147


title: notte-00422: Sample_076


title: notte-00422: Sample_020


title: notte-00422: Sample_187


title: notte-00422: Sample_057


title: notte-00422: Sample_033


title: notte-00422: Sample_323


title: notte-00422: Sample_058


title: notte-00422: Sample_037


title: notte-00422: Sample_075


title: notte-00422: Sample_195


title: notte-00422: Sample_007


title: notte-00422: Sample_157


title: notte-00422: Sample_224


title: notte-00422: Sample_179


title: notte-00422: Sample_083


title: notte-00422: Sample_283


title: notte-00422: Sample_116


title: notte-00422: Sample_099


title: notte-00422: Sample_221

value: microadenoma


title: notte-00422: Sample_181


title: notte-00422: Sample_271


title: notte-00422: Sample_056


title: notte-00422: Sample_084


title: notte-00422: Sample_052


title: notte-00422: Sample_051


title: notte-00422: Sample_166


title: notte-00422: Sample_010

value: Liver


title: notte-00422: Sample_248


title: notte-00422: Sample_134


title: notte-00422: Sample_241


title: notte-00422: Sample_088


title: notte-00422: Sample_100


title: notte-00422: Sample_031


title: notte-00422: Sample_158


title: notte-00422: Sample_180


title: notte-00422: Sample_244


title: notte-00422: Sample_159


title: notte-00422: Sample_090


title: notte-00422: Sample_011


title: notte-00422: Sample_219


title: notte-00422: Sample_086


title: notte-00422: Sample_301


title: notte-00422: Sample_220


title: notte-00422: Sample_012


title: notte-00422: Sample_091


title: notte-00422: Sample_291


title: notte-00422: Sample_321


title: notte-00422: Sample_053


title: notte-00422: Sample_309


title: notte-00422: Sample_030


title: notte-00422: Sample_261


title: notte-00422: Sample_203


title: notte-00422: Sample_373


title: notte-00422: Sample_372

value: normal liver


title: notte-00422: Sample_262


title: notte-00422: Sample_310


title: notte-00422: Sample_216


title: notte-00422: Sample_252


title: notte-00422: Sample_061


title: notte-00422: Sample_214


title: notte-00422: Sample_062


title: notte-00422: Sample_370


title: notte-00422: Sample_115


title: notte-00422: Sample_382


title: notte-00422: Sample_331

value: colon


title: notte-00422: Sample_201


title: notte-00422: Sample_135


title: notte-00422: Sample_197


title: notte-00422: Sample_215


title: notte-00422: Sample_355


title: notte-00422: Sample_231


title: notte-00422: Sample_371


title: notte-00422: Sample_339


title: notte-00422: Sample_073


title: notte-00422: Sample_169


title: notte-00422: Sample_074


title: notte-00422: Sample_089


title: notte-00422: Sample_101


title: notte-00422: Sample_191

value: colon polyp


title: notte-00422: Sample_330


title: notte-00422: Sample_245


title: notte-00422: Sample_265


title: notte-00422: Sample_356


title: notte-00422: Sample_168


title: notte-00422: Sample_081


title: notte-00422: Sample_267


title: notte-00422: Sample_206


title: notte-00422: Sample_264


title: notte-00422: Sample_208


title: notte-00422: Sample_207


title: notte-00422: Sample_125


title: notte-00422: Sample_381

value: Colon Carcinoma


title: notte-00422: Sample_005


title: notte-00422: Sample_292


title: notte-00422: Sample_379


title: notte-00422: Sample_077


title: notte-00422: Sample_193


title: notte-00422: Sample_047


title: notte-00422: Sample_326


title: notte-00422: Sample_293


title: notte-00422: Sample_114


title: notte-00422: Sample_139


title: notte-00422: Sample_016


title: notte-00422: Sample_233


title: notte-00422: Sample_172


title: notte-00422: Sample_218


title: notte-00422: Sample_048


title: notte-00422: Sample_376


title: notte-00422: Sample_154


title: notte-00422: Sample_378


title: notte-00422: Sample_082


title: notte-00422: Sample_377


title: notte-00422: Sample_312


title: notte-00422: Sample_087


title: notte-00422: Sample_374


title: notte-00422: Sample_167


title: notte-00422: Sample_109


title: notte-00422: Sample_375


title: notte-00422: Sample_177


title: notte-00422: Sample_137


title: notte-00422: Sample_092


title: notte-00422: Sample_311


title: notte-00422: Sample_340


title: notte-00422: Sample_313


title: notte-00422: Sample_161


title: notte-00422: Sample_150


title: notte-00422: Sample_046


title: notte-00422: Sample_255


title: notte-00422: Sample_160


title: notte-00422: Sample_286


title: notte-00422: Sample_288


title: notte-00422: Sample_353


title: notte-00422: Sample_295


title: notte-00422: Sample_254


title: notte-00422: Sample_287


title: notte-00422: Sample_253


title: notte-00422: Sample_285


title: notte-00422: Sample_352


title: notte-00422: Sample_369


title: notte-00422: Sample_002


title: notte-00422: Sample_368


title: notte-00422: Sample_347


title: notte-00422: Sample_240


title: notte-00422: Sample_141


title: notte-00422: Sample_003


title: notte-00422: Sample_063


title: notte-00422: Sample_182


title: notte-00422: Sample_004


title: notte-00422: Sample_346


title: notte-00422: Sample_304


title: notte-00422: Sample_366


title: notte-00422: Sample_144


title: notte-00422: Sample_123


title: notte-00422: Sample_104


title: notte-00422: Sample_232


title: notte-00422: Sample_367


title: notte-00422: Sample_106


title: notte-00422: Sample_032


title: notte-00422: Sample_105


title: notte-00422: Sample_145


title: notte-00422: Sample_194


title: notte-00422: Sample_186


title: notte-00422: Sample_290


title: notte-00422: Sample_080


title: notte-00422: Sample_227


title: notte-00422: Sample_228


title: notte-00422: Sample_306


title: notte-00422: Sample_234


title: notte-00422: Sample_121


title: notte-00422: Sample_079


title: notte-00422: Sample_243


title: notte-00422: Sample_380


title: notte-00422: Sample_163


title: notte-00422: Sample_229


title: notte-00422: Sample_045


title: notte-00422: Sample_068


title: notte-00422: Sample_060


title: notte-00422: Sample_178


title: notte-00422: Sample_335


title: notte-00422: Sample_299


title: notte-00422: Sample_095


title: notte-00422: Sample_230


title: notte-00422: Sample_260


title: notte-00422: Sample_303


title: notte-00422: Sample_059


title: notte-00422: Sample_305


title: notte-00422: Sample_210


title: notte-00422: Sample_384

value: Prostate Adenocarcinoma

value: Prostate

value: LNCaP


title: notte-00422: Sample_320


title: notte-00422: Sample_246

value: colon carcinoma metastatic to the liver


title: notte-00422: Sample_148


title: notte-00422: Sample_023


title: notte-00422: Sample_296


title: notte-00422: Sample_386

value: breast cancer

value: Breast


title: notte-00422: Sample_315

value: colon cancer

value: colon mucosa

value: normal colon mucosa


title: notte-00422: Sample_049

value: Colon


title: notte-00422: Sample_171


title: notte-00422: Sample_165


title: notte-00422: Sample_098


title: notte-00422: Sample_118


title: notte-00422: Sample_190


title: notte-00422: Sample_113


title: notte-00422: Sample_202


title: notte-00422: Sample_189


title: NCI_control18_U133.mas5

source_name: Stratagene

value: Normal


title: NCI_control16_U133A.mas5


title: notte-00422: Sample_300


title: NCI_control19_U133A.mas5


title: NCI_control14_U133A.mas5


title: NCI_Control6_U133A.mas5


title: NCI_Control12_U133A.mas5


title: NCI_control9_U133A.mas5


title: NCI_control8_U133A.mas5


title: NCI_control15_U133A.mas5


title: notte-00422: Sample_314


title: NCI_control7_U133A.mas5


title: notte-00422: Sample_327


title: Moff_Strat5.mas5


title: Moff_Strat6.mas5


title: jacob-00182: 632

source_name: MI

value: Lung Adenocarcinoma

tag: Sex

value: Male

tag: race

value: Unknown

value: Dead

value: No

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Lung

value: POORLY DIFFERENTIATED


title: NCI_control17_U133.mas5


title: CL2004113027AA.mas5


title: NCI_control13_U133A.mas5


title: jacob-00182: 635

value: Yes


title: NCI_Control11_U133A.mas5


title: jacob-00182: 633

value: Alive

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE

value: Moderate Differentiation


title: jacob-00182: 637


title: Moff_Strat1.mas5


title: Moff_Strat3.mas5


title: NCI_Control10_U133A.mas5


title: jacob-00182: 628


title: jacob-00182: 630


title: jacob-00182: 627


title: jacob-00182: 626


title: jacob-00182: 622

value: WELL DIFFERENTIATED


title: jacob-00182: 621


title: jacob-00182: 620


title: jacob-00182: 631


title: jacob-00182: 624

value: Female


title: jacob-00182: 623


title: jacob-00182: 629


title: jacob-00182: 619


title: jacob-00182: 625


title: jacob-00182: 610


title: jacob-00182: 609


title: jacob-00182: 616


title: jacob-00182: 618


title: jacob-00182: 615


title: jacob-00182: 617


title: jacob-00182: 614


title: jacob-00182: 606


title: jacob-00182: 605


title: jacob-00182: 613


title: jacob-00182: 612


title: jacob-00182: 611


title: jacob-00182: 608


title: jacob-00182: 607


title: jacob-00182: 604


title: jacob-00182: 602


title: jacob-00182: 603


title: jacob-00182: 601


title: jacob-00182: 543

source_name: HLM

value: White

value: Smoked in the past


title: jacob-00182: 544


title: jacob-00182: 545


title: jacob-00182: 548

value: Never smoked


title: jacob-00182: 542

value: Lung Adenocarcinoma

value: Currently smoking


title: jacob-00182: 538

value: Male


title: jacob-00182: 537

value: Dead

value: Unknown


title: jacob-00182: 536

value: No

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 535

value: Lung

value: POORLY DIFFERENTIATED


title: jacob-00182: 529

value: Alive


title: jacob-00182: 533

value: Yes


title: jacob-00182: 527

value: Moderate Differentiation


title: jacob-00182: 540


title: jacob-00182: 539

value: Black or African American


title: jacob-00182: 526

value: Asian


title: jacob-00182: 517

value: Female

value: White


title: jacob-00182: 521

value: Smoked in the past


title: jacob-00182: 511

value: Lung Adenocarcinoma

value: WELL DIFFERENTIATED


title: jacob-00182: 525

value: Male


title: jacob-00182: 531

value: Dead


title: jacob-00182: 513

value: Unknown

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: jacob-00182: 516

value: No

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 519

value: Lung


title: jacob-00182: 515


title: jacob-00182: 509

value: Never smoked


title: jacob-00182: 508

value: Yes

value: POORLY DIFFERENTIATED


title: jacob-00182: 514

value: Alive

value: Moderate Differentiation


title: jacob-00182: 506

value: Female


title: jacob-00182: 501

value: White


title: jacob-00182: 507

value: Smoked in the past


title: jacob-00182: 502

value: Lung Adenocarcinoma

value: Currently smoking


title: jacob-00182: 499

value: Male


title: jacob-00182: 636


title: jacob-00182: 505


title: jacob-00182: 494

value: Dead


title: jacob-00182: 500


title: jacob-00182: 503

value: Unknown


title: jacob-00182: 493


title: jacob-00182: 495


title: jacob-00182: 492

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: jacob-00182: 491


title: jacob-00182: 490

value: No


title: jacob-00182: 498

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 483

value: Lung


title: jacob-00182: 486


title: jacob-00182: 488

value: Never smoked

value: WELL DIFFERENTIATED


title: jacob-00182: 484

value: Black or African American

value: Yes


title: jacob-00182: 482

value: POORLY DIFFERENTIATED


title: jacob-00182: 480

value: Female

value: Moderate Differentiation


title: jacob-00182: 638


title: jacob-00182: 481

value: White

value: Smoked in the past


title: jacob-00182: 476

value: Lung Adenocarcinoma


title: jacob-00182: 485

value: Alive


title: jacob-00182: 478

value: Dead


title: jacob-00182: 473

value: Male

value: Unknown


title: jacob-00182: 475

value: No

value: Currently smoking


title: jacob-00182: 472

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Lung


title: jacob-00182: 468


title: jacob-00182: 474


title: jacob-00182: 470

value: Never smoked


title: jacob-00182: 479


title: jacob-00182: 477


title: jacob-00182: 504


title: jacob-00182: 469


title: jacob-00182: 464

value: pp


title: jacob-00182: 462

value: Yes


title: jacob-00182: 458


title: jacob-00182: 466

value: MICROSCOPICALLY POSITIVE MARGINS OR MICROSCOPIC RESIDUAL DISEASE


title: jacob-00182: 465

value: Female


title: jacob-00182: 467

value: POORLY DIFFERENTIATED


title: jacob-00182: 460

value: White

value: WELL DIFFERENTIATED


title: jacob-00182: 459

value: Lung Adenocarcinoma

value: Smoked in the past

value: Moderate Differentiation


title: jacob-00182: 456

value: Dead


title: jacob-00182: 454


title: jacob-00182: 455

value: Male

value: Unknown


title: jacob-00182: 451

value: Black or African American

value: No


title: jacob-00182: 381

source_name: DFCI

value: Not Reported

value: ALL MARGINS PATHOLOGICALLY NEGATIVE

value: Lung


title: jacob-00182: 379

value: Alive


title: jacob-00182: 378


title: jacob-00182: 380

value: Yes

value: Never smoked


title: jacob-00182: 375

value: Female


title: jacob-00182: 376

value: POORLY DIFFERENTIATED


title: jacob-00182: 377


title: jacob-00182: 371

value: Currently smoking


title: jacob-00182: 369

value: Lung Adenocarcinoma


title: jacob-00182: 368

value: Smoked in the past


title: jacob-00182: 365


title: jacob-00182: 372


title: jacob-00182: 374


title: jacob-00182: 363

value: Moderate Differentiation


title: jacob-00182: 361

value: WELL DIFFERENTIATED


title: jacob-00182: 452

value: Male

value: White

value: Dead


title: jacob-00182: 366

value: No


title: jacob-00182: 364

value: Not Reported


title: jacob-00182: 373

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 382

value: Lung


title: jacob-00182: 370

value: Alive


title: jacob-00182: 359

value: Unknown

value: Yes


title: jacob-00182: 362

value: Female


title: jacob-00182: 358

value: Never smoked

value: POORLY DIFFERENTIATED


title: jacob-00182: 360

value: Lung Adenocarcinoma


title: jacob-00182: 356

value: Currently smoking


title: jacob-00182: 367

value: Moderate Differentiation


title: jacob-00182: 357

value: Smoked in the past


title: jacob-00182: 355


title: jacob-00182: 354

value: WELL DIFFERENTIATED


title: jacob-00182: 352


title: jacob-00182: 353

value: Male


title: jacob-00182: 351


title: jacob-00182: 348


title: jacob-00182: 349


title: jacob-00182: 350


title: jacob-00182: 341

value: White


title: jacob-00182: 346

value: Dead

value: No


title: jacob-00182: 342

value: ALL MARGINS PATHOLOGICALLY NEGATIVE


title: jacob-00182: 344

value: Not Reported

value: Lung


title: jacob-00182: 345

value: Alive


title: jacob-00182: 338

value: Unknown

value: Yes


title: jacob-00182: 340


title: jacob-00182: 337

value: Female


title: jacob-00182: 336


title: jacob-00182: 347


title: jacob-00182: 333

value: POORLY DIFFERENTIATED


title: jacob-00182: 332

value: Lung Adenocarcinoma

value: Never smoked


title: jacob-00182: 339


title: jacob-00182: 343

value: Moderate Differentiation


title: jacob-00182: 334

value: Smoked in the past


title: jacob-00182: 497


title: jacob-00182: 330


title: jacob-00182: 331

value: WELL DIFFERENTIATED


title: jacob-00182: 487

value: Male


title: jacob-00182: 335


title: jacob-00182: 325


title: jacob-00182: 328


title: jacob-00182: 326

value: Native Hawaiian or Other Pacific Islander


title: jacob-00182: 327

value: Dead


title: jacob-00182: 329

value: No