title: Uninfected cells from Medicago truncatula root nodules replicate 3

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

description:
Mt_MtGeneChip0189_A147_jbecker_IGC_PP _(Medicago)
Gene expression data from uninfected cells from Medicago truncatula root nodules

hyb_protocol: 30-40 μg of fragmented aRNA was added to a 250 μl hybridization cocktail also containing hybridization controls. 200 μl of the mixture was hybridized on GeneChips for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using packages from the Bioconductor project. Normalization was performed across all GeneChips using the Robust Multiarray Average (RMA) algorithm using the empirical Bayes approach to adjust for background in the Bioconductor library “gcrma.”. Only the 5 most 3’located probe sets on the GeneChip were used to account for observed 3’bias.

organism: Medicago truncatula

label_protocol: RNA samples were amplified according to the first amplification cycle of the Affymetrix Two-cycle Target Labeling kit user manual. Briefly, total RNA containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (Two-cycle Target Labeling kit; Affymetrix, Santa Clara, CA, USA) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (Two-cycle Target Labeling kit). The generated aRNA samples were than processed according to the Affymetrix GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of aRNA was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix, Santa Clara, CA, USA) to generate first-strand cDNA. Double-stranded cDNA obtained by second-strand synthesis was then used in a 16 h IVT reaction to generate aRNA (GeneChip 3’ IVT Express Kit). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer (Agilent, Böblingen, Germany), using an RNA 6000 Nano Assay. Assay.

growth_protocol: Medicago truncatula A17 plants were grown in (agra)perlite saturated with nitrate-free Fähraeus medium and inoculated with 2 ml a suspension (OD600 0.1) of Sinorhizobium meliloti strain Sm2011 per plant. Nodules were harvested 3 weeks after inoculation.

extract_protocol: Captured cells (3 biological replicates for each cell-/tissue type) were stored in 350 µl RLT buffer (containing β-mercaptoethanol and 50 ng poly-Inosine ) from the Qiagen RNeasy Micro kit and stored at - 80 0C until RNA extracion. RNA was extracted using the Qiagen Qiagen Rneasy Micro kit according to the manufacturers instructions, including an on column DNAse treatment.

treatment_protocol: Exised nodules were fixed in Farmer's fixative(3:1 ethanol:acetic acid),incubated at 4 0C overnigh tafter 30 min. vacuum. Fixed nodules were further dehydrated through an ethanol series: 75%, 85%, 100% (4x) for 15 min. each at room temperature (RT). At the first 100% ethanol step eosin B was added to facilitate the recognition of the nodule meristem during the sectioning steps. Nodules were subsequently infiltrated with xylene: ethanol  1:3, 1:1, 3:1 and finally 100% xylene (3x); 30 min at RT each. Next, the nodules were infiltrated with liquid filtered paraffin (Paraplast) at 60 0C for 2 days including 4 changes of paraffin. After solidification, 8 µm sections were cut using a microtome. Section were deparaffinized using 100% xylene 2x 5 min. each, air dryed and immediately used for laser capture using a PixCell II LCM system (Arcturus).

value: Root nodule

tag: genotype

value: Jemalong A17

tag: age

value: 21 days


title: MWCNT 48 h w/o IL-13 36__54

status: Public on May 29 2013

type: RNA

city: Raleigh

first: Stan

last: Martin

state: NC

address: 1404 Crete Dr.

country: USA

institute: Science Apps, L3C

hyb_protocol: The labeled cRNA was fragmented, hybridized to Affymetrix Human Genome U133A 2.0 arrays (Affymetrix, Santa Clara, CA), and stained using phycoerythreinconjugated streptavidin (Molecular Probes, Eugene, OR).

scan_protocol: Affymetrix Standard Protocol

data_processing: Data analysis: Affymetrix Cel files produced from the expression experiment were analyzed using JMP Genomics 4.1 software from SAS Institute. Data normalization was performed using a Standard Normalization implemented by the Data Standardize AP in JMP Genomics.  Expression values were standardized to the mean with a scale equivalent to the standard deviation.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: AT CC16Lu

label_protocol: stranded cDNA was synthesized from RNA using an oligo-dT24-T7. Biotinylated cRNA was synthesized from an aliquot of the cDNA template using the T7 RNA Transcript Labeling Kit (ENZO Diagnostics, Farmingdale NY).

growth_protocol: A separate, frozen stock was used for each experiment. Individual stocks were thawed and expanded by growth in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and antibiotic-antimycotic (Invitrogen, Carlsbad, CA).  Cells were passaged twice in 175 cm2 flasks, liberated with trypsin-EDTA, and seeded in 100 cm2 plates with 0.5-1x105 cells per plate.  Cells were grown to confluence and culture medium replaced with a serum-free defined medium (SFDM) comprised of Ham’s F12, 0.25% BSA, 1 g/L insulin, 0.55 g/L transferrin, 0.67 mg/L sodium selenite and antibiotic-antimycotic 24 h prior to treatment.

extract_protocol: A two-phase purification method was used to isolate mRNA with reduced nanoparticle contamination. RNALater® was removed by centrifugation and washing with DPBS.  RNA was isolated by adding 1 ml RNA STAT-60 reagent (Sigma-Alrich, St. Louis, MO) to microfuge tubes for 5-10 min, extraction with 0.2 ml chloroform, and isolation of the aqueous phase.  The majority of remaining MWCNT and CBNP were effectively trapped in the phenol/chloroform phase or were co-precipitated with denatured proteins.  The clear aqueous phase was isolated and RNA precipitated with isopropanol and washed with 70% ethanol.  The resulting pellet was resuspended in 100 µl RNAse-free water and 350 µl of buffer RLT added prior to transferring to an RNEasy spin column.  Purification then proceeded according to the manufacturer’s instructions for the RNEasy Mini Kit and included an on-column DNAse I digestion (Qiagen, Valencia, CA).  RNA quality verified spectrophotometrically on a Nano Drop 1000 (Nano Drop, Inc., Wilmonton, DE) and by gel electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell line

tag: treatment

value: MWCNT w/o IL-13

tag: time


title: vehicle control 4 h with IL-13 37__55

value: vehicle control with IL-13

value: 4 h


title: Uninfected cells from Medicago truncatula root nodules replicate 1

country: Germany

description:
Mt_MtGeneChip0187_A145_jbecker_IGC_PP _(Medicago)
Gene expression data from uninfected cells from Medicago truncatula root nodules

label: biotin

tag: tissue


title: CBNP 48 h with IL-13 33__51

value: CBNP with IL-13


title: CBNP 48 h w/o IL-13 34__52

value: CBNP w/o IL-13


title: CBNP 4 h with IL-13 39__57


title: Infected cells from Medicago truncatula root nodules replicate 1

description:
Mt_MtGeneChip0184_A142_jbecker_IGC_PP _(Medicago)
Gene expression data from infected cells from Medicago truncatula root nodules


title: Uninfected cells from Medicago truncatula root nodules replicate 2

description:
Mt_MtGeneChip0188_A146_jbecker_IGC_PP _(Medicago)
Gene expression data from uninfected cells from Medicago truncatula root nodules


title: Proximal infection zone cells from Medicago truncatula root nodules replicate 2

description:
Mt_MtGeneChip0182_A140_jbecker_IGC_PP _(Medicago)
Gene expression data from proximal infection zone cells from Medicago truncatula root nodules


title: MWCNT 48 h with IL-13 35__53

value: MWCNT with IL-13


title: Infected cells from Medicago truncatula root nodules replicate 2

description:
Mt_MtGeneChip0202_A169_jbecker_IGC_PP _(Medicago)
Gene expression data from infected cells from Medicago truncatula root nodules


title: CBNP 24 h w/o IL-13 28__46


title: vehicle control 48 h w/o IL-13 32__50

value: vehicle control w/o IL-13


title: Proximal infection zone cells from Medicago truncatula root nodules replicate 1

description:
Mt_MtGeneChip0181_A139_jbecker_IGC_PP _(Medicago)
Gene expression data from proximal infection zone cells from Medicago truncatula root nodules


title: Distal infection zone cells from Medicago truncatula root nodules replicate 3

description:
Mt_MtGeneChip0180_A138_jbecker_IGC_PP _(Medicago)
Gene expression data from distal infection zone cells from Medicago truncatula root nodules


title: Proximal infection zone cells from Medicago truncatula root nodules replicate 3

description:
Mt_MtGeneChip0183_A168_jbecker_IGC_PP _(Medicago)
Gene expression data from proximal infection zone cells from Medicago truncatula root nodules


title: Infected cells from Medicago truncatula root nodules replicate 3

description:
Mt_MtGeneChip0185_A143_jbecker_IGC_PP _(Medicago)
Gene expression data from infected cells from Medicago truncatula root nodules


title: MWCNT 24 h with IL-13 29__47


title: CBNP 24 h with IL-13 27__45


title: vehicle control 24 h w/o IL-13 26__44


title: MWCNT 24 h w/o IL-13 30__48


title: SAECs (PD = 18) treated with si-p53-#1 for 72 h rep2

city: Tokyo

first: Masato

last: Enari

address: 5-1-1 Tsukiji

country: Japan

institute: National Cancer Center

description: Gene expression data from SAECs treated with si-p53-#1 for 72 h

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: SAECs treated with si-p53-#1 for 72 h

label_protocol: Target cRNA was prepared from 3 μg of total RNA with a One-cycle cDNA Synthesis Kit and 3’-amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: SAECs were cultured at 37 °C in small airway epithelial basal medium supplemented with 52 μg/ml bovine pituitary extract, 0.5 ng/ml human recombinant epidermal growth factor, 0.5 μg/ml epinephrine, 1 μg/ml hydrocortisone, 10 μg/ml transferrin, 5 μg/ml insulin, 0.1 ng/ml retinoic acid , 6.5 ng/ml triiodothyronine, 50 μg/ml Gentamicin/Amphotericin-B, and 50 μg/ml fatty acid-free bovine serum albumin, according to the manufacturer's instructions (Lonza).

extract_protocol: Total RNA was purified using an RNeasy kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: SAECs (PD = 18) were transfected with the siRNAs (si-control, si-p53-#1 or si-p53-#2) using Lipofectamine 2000 (Invitrogen), and 24 h after transfection, the medium was replaced. The transfected cells were further incubated for 48 h.

value: Human lung small airway epithelia

tag: gender

value: Male

value: treated with si-p53-#1 for 72 h


title: vehicle control 24 h with IL-13 25__43


title: SAECs (PD = 18) treated with si-p53-#2 for 72 h rep2

description: Gene expression data from SAECs treated with si-p53-#2 for 72 h

source_name: SAECs treated with si-p53-#2 for 72 h

value: treated with si-p53-#2 for 72 h


title: Distal infection zone cells from Medicago truncatula root nodules replicate 2

description:
Mt_MtGeneChip0179_A137_jbecker_IGC_PP _(Medicago)
Gene expression data from distal infection zone cells from Medicago truncatula root nodules


title: Distal infection zone cells from Medicago truncatula root nodules replicate 1

description:
Mt_MtGeneChip0178_A136_jbecker_IGC_PP _(Medicago)
Gene expression data from distal infection zone cells from Medicago truncatula root nodules


title: SAECs (PD = 18) treated with si-p53-#2 for 72 h rep1


title: MWCNT 4 h w/o IL-13 24__42


title: CBNP 4 h with IL-13 21__39


title: SAECs (PD = 18) treated with control siRNA for 72 h rep1

description: Gene expression data from SAECs treated with control siRNA for 72 h

value: control siRNA for 72 h


title: SAECs (PD = 18) treated with control siRNA for 72 h rep2

source_name: SAECs treated with control siRNA for 72 h


title: Meristem cells from Medicago truncatula root nodules replicate 1

description:
Mt_MtGeneChip0175_A133_jbecker_IGC_PP _(Medicago)
Gene expression data from meristem cells from Medicago truncatula root nodules


title: vehicle control 4 h w/o IL-13 20__38


title: Meristem cells from Medicago truncatula root nodules replicate 3

description:
Mt_MtGeneChip0177_A135_jbecker_IGC_PP _(Medicago)
Gene expression data from meristem cells from Medicago truncatula root nodules


title: CBNP 4 h w/o IL-13 22__40


title: SAECs (PD = 18) treated with si-p53-#1 for 72 h rep1


title: MWCNT 4 h with IL-13 23__41


title: Meristem cells from Medicago truncatula root nodules replicate 4

description:
Mt_MtGeneChip-test_A132_jbecker_IGC_PP_(Medicago)
Gene expression data from meristem cells from Medicago truncatula root nodules


title: HeLa cells transfected with siSp1 rep 1

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: Gene expression profile of HeLa cells transfected with 100nM siRNA against Sp1 (siSp1) for 48h.

hyb_protocol: Affymetrix protocol for HG U133A plus 2.0

data_processing: Summarization algorithm: RMA. Normalization: Quantile. Baseline transformation: median of control samples

source_name: HeLa cells with the decreased expression of Sp1

extract_protocol: RNAeasy Mini kit (Qiagen)

value: HeLa

tag: cell type

value: human Cervical Carcinoma

tag: transfected with

value: siRNA directed against Sp1 mRNA (siSp1)


title: HeLa cells transfected with siSp1 rep 2

scan_protocol: Affymetrix protocol for HG U133A plus 2.0


title: HeLa cells transfected with siSp1 rep 3

label_protocol: Affymetrix protocol for HG U133A plus 2.0


title: vehicle control 4 h with IL-13 19__37


title: MWCNT 48 h w/o IL-13 18__36


title: vehicle control 48 h w/o IL-13 14__32


title: CBNP 48 h with IL-13 15__33


title: VTA_18 months old_rep4

city: Seville

first: Lin

last: Gao

address: Avda Manuel Siurot, Hospital Virgen del Rocío

institute: Instituto de Biomedicina de Sevilla

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix AGCC software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma (v.3.4.5) package (affylmGUI interface v.1.22.0) of R/Bioconductor project.

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA Two-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

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

treatment_protocol: three age groups: 2, 10 18 months old C57 wild type mice

tag: strain

tag: genotype/variation

value: wild type

value: ventral tegmental area of brain

value: late-middle aged (18 months old)


title: vehicle control 48 h with IL-13 13__31

value: vehicle control with IL-13


title: MWCNT 48 h with IL-13 17__35


title: CBNP 48 h w/o IL-13 16__34


title: parental HeLa cells rep 3

description: Gene expression profile of parental HeLa cells

source_name: parental HeLa cells

value: parental


title: parental HeLa cells rep 1


title: MWCNT 24 h w/o IL-13 12__30

value: MWCNT w/o IL-13


title: MWCNT 24 h with IL-13 11__29


title: vehicle control 24 h w/o IL-13 8__26


title: VTA_18 months old_rep3


title: CBNP 24 h with IL-13 9__27

value: CBNP with IL-13


title: parental HeLa cells rep 2


title: vehicle control 24 h with IL-13 7__25


title: VTA_18 months old_rep2


title: CBNP 24 h w/o IL-13 10__28

value: CBNP w/o IL-13


title: VTA_18 months old_rep1


title: HT29-ICC-Replicate1

description: Gene expression profile of HT29 cells.

source_name: HT29 cells

extract_protocol: Speedtools Total RNA Extraction Kit® (Biotools)

tag: group

value: ICC

value: non cytotoxic concentrations of instant caffeinated coffee (7 µg/mL)

tag: cell line origin

value: colon cancer


title: VTA_10 months old_rep3

value: middle aged (10 months old)


title: HT29-ICC-Replicate2

description: Gene expression profile of HT29 cells.


title: HT29-ICC-Replicate3

description: Gene expression profile of HT29 cells.


title: MWCNT 4 h with IL-13 5__23

value: MWCNT with IL-13

value: 4 h


title: VTA_10 months old_rep4


title: HT29-CA-Replicate3

description: Gene expression profile of HT29 cells.

value: CA

value: non cytotoxic concentrations of caffeic acid (1.68 µg/mL)


title: CBNP 4 h with IL-13 3__21


title: CBNP 4 h w/o IL-13 4__22


title: MWCNT 4 h w/o IL-13 6__24


title: VTA_10 months old_rep2


title: vehicle control 4 h with IL-13 1__19


title: VTA_2 months old_rep4

value: young (2 months old)


title: vehicle control 4 h w/o IL-13 2__20

value: vehicle control w/o IL-13


title: EHEC+ B theta_mid-log_DMEM_anaerobic

city: Dallas

first: Meredith

middle: Mathis

last: Curtis

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: All data processed using GCOS v1.4

organism: Escherichia coli 8624

source_name: EHEC grown with B. theta anaerobically in DMEM to mid-log

label_protocol: standard Affymetrix protocol

growth_protocol: All strains grown in DMEM

extract_protocol: Ambion RiboPure RNA isolation protocol


title: VTA_10 months old_rep1

value: wild type

value: ventral tegmental area of brain


title: HT29-Control cells replicate 3

description: Gene expression profile of HT29 cells.

value: Control


title: SH1000 ΔthyA LL 9h rep3

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

hyb_protocol: The prepared targets were hybridized to Affymetrix GeneChip S. aureus Genome arrays. Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Partek Genomics Suite was used for data anlyses (RMA normalisation).

organism: Staphylococcus aureus

source_name: Staphylococcus aureus, grown in BHI

label_protocol: Microarray processing was performed as recommended by the manufacturer. Briefly, 10 μg of total RNA was reverse transcribed and the resulting cDNA was labeled and fragmented to produce oligonucleotide probes in accordance with the manufacturer’s instructions (Affymetrix).

growth_protocol: Bacterial strains were grown in BHI broth at 37°C on a rotary shaker at 160 rpm - 50ml in 500ml flasks

extract_protocol: For the RNA extraction from bacterial cultures, a combination of RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany), RNAiso (Segenetic, Borken, Germany), the RNeasy Mini Kit (Qiagen) and Lysing Matrix B (MP Biomedicals, Heidelberg, Germany) was used. Cells were mechanically disrupted by a Fast Prep FP120 instrument ( MP Biomedicals, Heidelberg, Germany). RNA quality was verified by a Bioanalyzer.

treatment_protocol: RNA was isolated at the timepoints given in the title of the microarray

value: SH1000 ΔthyA

value: 9 hr


title: SH1000 ΔthyA Stat 12h rep2

value: 12 hr


title: VTA_2 months old_rep3


title: HT29-CA-Replicate1

description: Gene expression profile of HT29 cells.


title: SH1000 ΔthyA EL 4h rep2

value: 4 hr


title: EHEC only_mid-log_DMEM_anaerobic

source_name: EHEC grown anaerobically in DMEM to mid-log

value: grown anaerobically in DMEM to mid-log


title: SH1000 ΔthyA Stat 12h rep3


title: HT29-CA-Replicate2

description: Gene expression profile of HT29 cells.


title: SH1000 ΔthyA LL 9h rep2


title: SH1000 ΔthyA EL 4h rep3


title: SH1000 ΔthyA LL 9h rep1


title: SH1000 ΔthyA Stat 12h rep1


title: VTA_2 months old_rep2


title: HT29-Control cells replicate 2

description: Gene expression profile of HT29 cells.


title: SH1000 ΔthyA EL 4h rep1


title: SH1000 WT Stat 9h rep1

value: SH1000 WT


title: SH1000 WT Stat 9h rep3


title: SNpc_18 months old_rep4

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix GCOS software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma (v.3.4.5) package (affylmGUI interface v.1.22.0) of R/Bioconductor project.

value: substantia nigra of brain

value: late-middle aged (18 months old)


title: ES2 NT-5 25nM

city: Indianapolis

first: Shannon

middle: M.

last: Hawkins

state: IN

address: 550 N University Blvd UH2440

institute: Indiana University School of Medicine

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization

source_name: Ovarian cancer cell line

label_protocol: Standard label protocol

growth_protocol: Cells were grown per ATCC recommendations

extract_protocol: RNA was extraction with the miRVana kit for total RNA, followed by Dnase I treatment (Ambion) all per kit instructions

treatment_protocol: Cells were transfected using RNAiMax and harvested 48 hours after transfection

tag: sirna

value: NT control

value: Ovarian cancer cell line


title: SNpc_18 months old_rep3


title: ES2 COUP-TFII-5 25nM

description: replicate 3

value: NR2F2 knockdown


title: ES2 NT-4 25nM

description: replicate 2


title: SH1000 WT Stat 9h rep2


title: VTA_2 months old_rep1


title: SNpc_18 months old_rep1


title: SH1000 WT LL 6h rep3

value: 6 hr


title: SH1000 WT LL 6h rep1


title: HT29-Control cells replicate 1

description: Gene expression profile of HT29 cells.

value: colon cancer


title: SH1000 WT LL 6h rep2


title: SNpc_10 months old_rep4

value: middle aged (10 months old)


title: SNpc_10 months old_rep2

value: wild type


title: TOV112D COUP-TFII-4

description: replicate 3


title: ES2 NT-3 25nM

description: replicate 1


title: TOV112D NT-4

description: replicate 3


title: SNpc_2 months old_rep4

value: young (2 months old)


title: ES2 COUP-TFII-4 25nM

description: replicate 2


title: SH1000 WT EL 2h rep2

value: 2 hr


title: SH1000 WT EL 2h rep1


title: ES2 COUP-TFII-3 25nM

description: replicate 1


title: SNpc_10 months old_rep1


title: VCaP siERG

city: Chicago

first: Longtao

last: WU

state: IL

address: 303 E Superior St.

department: Hematology/Oncology

institute: Northwestern University

description: Replicate  1

hyb_protocol: The arrays were processed at Cleveland Clinic according to manufacturer’s protocol.

data_processing: The bead-level data were preprocessed using GenomeStudio (Illumina) and the expression data was analyzed using the beadarray package in Bioconductor, quantile normalized using the beadarray package.

source_name: VCaP cell line

growth_protocol: LNCap cell line was maintained in RPMI1640 supplemented with 10%FBS, VCaP cell line was maintained in DMEM supplemented with 10% FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

value: VCaP

value: ERG siRNA knockdown


title: SH1000 WT EL 2h rep3


title: TOV112D COUP-TFII-2

description: replicate 2


title: SNpc_10 months old_rep3


title: TOV112D NT-1

description: replicate 1


title: LNCaP ERG siCtrl

description: Replicate  1

scan_protocol: The arrays were processed at Cleveland Clinic according to manufacturer’s protocol.

source_name: LNCaP cell line

value: LNCaP

value: ERG overexpression


title: SNpc_2 months old_rep3


title: TOV112D NT-2

description: replicate 2


title: SNpc_2 months old_rep2


title: TOV112D COUP-TFII-1

description: replicate 1


title: SJL-ChrY^B10.S, young, CD4 T cell, rep2

status: Public on May 28 2013

city: Burlington

first: Laure

last: Case

address: 89 Beaumont Ave

institute: University of Vermont

hyb_protocol: After purification and fragmentation, biotinylated-cDNA targets were hybridized to the Mouse Gene 1.0 ST Arrays oligonucleotide arrays for 16 hours at 45oC. Hybridized arrays were washed and stained with streptavidin-phycoerythrin followed by sequential incubations with biotin-coupled polyclonal anti-streptavidin antibody and streptavidin phycoerythrin as a fluorescent amplification step.

scan_protocol: After staining, arrays were scanned (3000-7G Scanner, Affymetrix Inc., Santa Clara, CA) and data collected for statistical analysis.

data_processing:
Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip. Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample. Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites®, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv

source_name: SJL-ChrY^B10.S, CD4+TCRB+ cells, naive, young

label_protocol: Oligonucleotide microarray analysis of RNA expression levels was performed in the Vermont Genetics Network Microarray Facility using the Affymetrix GeneChip Platform (Affymetrix Inc., Santa Clara, CA) according to manufacturer's protocols. In brief, the Nugen Ovation system v.2 with SPIA® RNA amplification was employed to convert 50ng of total RNA to cDNA. This isothermal RNA amplification system produces 5-12 ug of anti-sense cDNA targets that is followed by several steps to produce sense strand cDNA to be fragmented, biotinylated and hybridized to the GeneChip.

extract_protocol: RNA was isolated from live cells using the Qiagen RNeasy® Plus Mini Kit following the manufacturer's instructions (Qiagen, Valencia, CA).

tag: strain/background

value: male

value: ≤ 4 weeks

value: CD4+TCRB+ cells

tag: cell purification

value: FACS


title: VCaP siCtrl

description: Replicate  1

label_protocol: The arrays were processed at Cleveland Clinic according to manufacturer’s protocol.

value: Control siRNA


title: SJL-ChrY^B10.S, young, CD4 T cell, rep1


title: SJL-ChrY^B10.S, old, CD4 T cell, rep3

source_name: SJL-ChrY^B10.S, CD4+TCRB+ cells, naive, old

value: ≥ 6 month


title: SJL-ChrY^B10.S, old, CD4 T cell, rep2


title: MGG8CSC ASCL1

type: SRA

city: Cambridge

first: Esther

last: Rheinbay

state: MA

address: 7 Cambridge Center

institute: Broad Institute

library_source: genomic

data_processing:
ChIP-Seq reads were aligned with Bowtie1; reads longer than 36 bases were truncated to 36 bases before alignment.
A filter to remove duplicate reads (identical starting position and direction) was applied
Peaks were identified as described in Rheinbay, Suva et al, Cell Reports 2013
Density maps were generated with IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: wig, density maps

molecule: genomic DNA

source_name: MGG8 human glioblastoma stem cell line

growth_protocol: MGG and NS cells were cultured and passaged using standard neural stem cell conditions as described in Wakimoto et al, 2009 (PMID: 19351838) and Conti et al, 2005 (PMID: 16086633)

extract_protocol:
As described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-1000 bp using Branson Sonifer. After IP and adapter ligation, library fragments of 200-600 bp were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Illumina Hiseq 2000 following the manufacturer's protocols.
After IP and adapter ligation, library fragments of 200-600 bp were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Illumina Hiseq 2000 following the manufacturer's protocols.

value: human glioblastoma stem cells

tag: chip-antibody

tag: chip-antibody vendor

value: Epitomics

tag: chip-antibody cat. #


title: MGG8CSC H3K27ac

tag: cell line

value: Active motif


title: MGG6serum Input

source_name: MGG6 human glioblastoma serum-grown cell line

value: human glioblastoma serum-grown cells


title: SJL, young, CD4 T cell, rep3

source_name: SJL, CD4+TCRB+ cells, naive, young

value: SJL

tag: age


title: LNCaP ERG siLEF1

description: Replicate  1

value: ERG overexpression and LEF1 knockdown


title: MGG6serum H3K4me3

value: Millipore


title: MGG6serum H3K36me3

value: Abcam


title: MGG6serum H3K4me1


title: SJL, young, CD4 T cell, rep2


title: LNCaP LacZ

description: Replicate  1

value: LacZ Control


title: SJL-ChrY^B10.S, young, CD4 T cell, rep3


title: SNpc_2 months old_rep1

value: wild type

value: substantia nigra of brain

value: young (2 months old)


title: SJL-ChrY^B10.S, old, CD4 T cell, rep1

value: male


title: MGG6serum H3K27me3


title: MGG4serum H3K4me3

source_name: MGG4 human glioblastoma serum-grown cell line


title: MGG4serum H3K4me1


title: SJL-ChrY^B10.S, young, macrophage, rep2

source_name: SJL-ChrY^B10.S, thioglycollate-elicited peritoneal macrophages, naïve, young

value: ≤ 4 weeks

value: adherent cells


title: SJL-ChrY^B10.S, young, macrophage, rep1


title: SJL-ChrY^B10.S, old, macrophage, rep3

source_name: SJL-ChrY^B10.S, thioglycollate-elicited peritoneal macrophages, naïve, old


title: SJL, old, CD4 T cell, rep3

source_name: SJL, CD4+TCRB+ cells, naive, old

value: CD4+TCRB+ cells

value: FACS


title: SJL-ChrY^B10.S, old, macrophage, rep1

value: ≥ 6 month


title: SJL-ChrY^B10.S, young, macrophage, rep3


title: SJL, young, CD4 T cell, rep1


title: SJL, old, CD4 T cell, rep1


title: SJL, old, CD4 T cell, rep2


title: SJL-ChrY^B10.S, old, macrophage, rep2


title: SJL, young, macrophage, rep3

source_name: SJL, thioglycollate-elicited peritoneal macrophages, naïve, young


title: MGG4CSC H3K4me1

source_name: MGG4 human glioblastoma stem cell line

value: human glioblastoma stem cells


title: MGG4serum H3K36me3


title: MGG4serum H3K27me3


title: MGG4serum Input


title: SJL, young, macrophage, rep2


title: SJL, old, macrophage, rep3

source_name: SJL, thioglycollate-elicited peritoneal macrophages, naïve, old


title: SJL, young, macrophage, rep1


title: SJL, old, macrophage, rep2


title: SJL, old, macrophage, rep1


title: G6Gm_iPSCs1

city: Beijing

first: Hongkui

last: Deng

address: 5th Yiheyuan Road

country: China

institute: Peking University

description: Induced pluripotent stem cells

hyb_protocol: Hybridized to a mouse Oligo Microarray (Phalanx Mouse OneArray® v2, Phalanx Biotech) according to the manufacturer's protocol.

scan_protocol: After hybridization, arrays were scanned using GenePix 4000B scanner (Molecular Devices) and processed using the GenePix Pro 6.0 software (Molecular Devices).

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech). R1_1, R2_2, G3_iPSCs1, G3_iPSCs2, G6_iPSCs1, G6_iPSCs2, MEF_expression_control1, MEF_expression_control2, Dlx3RNAi_iPSCs1, Dlx3RNAi_iPSCs2 were processed together for normalization.

source_name: Induced pluripotent stem cells

label_protocol: Total mRNAs of all samples were labeled with Cy5.

growth_protocol: Culture in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). 37℃. The dox-inducible lentiviral system used has been previously described (Maherali et al., 2008). iPSCs were cultured in mESC medium (a 1:1 mixture of Neurolbasal/B27 medium and DMEM/F12 medium supplemented with N2, plus nonessential amino acids, 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM L-glutamine, 55 μM β-mercaptoethanol, 1 μM PD0325901, and 3 μM CHIR99021) on mitomycin C-treated MEFs. PD0325901 and CHIR99021 could be replaced by LIF (Millipore). The medium was changed every day, and iPSCs were passaged using trypsin (Invitrogen).

extract_protocol: Total cellular RNA was extracted with TRIzol reagent (Sigma). Genomic DNA were removed with DNAase(Ambion). Total RNA was purified with RNeasy plus mini kit(Qiagen).

treatment_protocol: In brief, the limbs and tails of  mice were cut off, and the skin was carefully peeled. The isolated mouse skin was then incubated in Collagenase type Ⅳ (2mg/ml, Gibco) for 2hrs at 37℃. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated  skin fibroblasts were collected by flowing through cell strainers.

value: OGXICR

value: female

value: skin

value: IPS


title: MEF_expression_control2

description: None infected target cells

source_name: Mouse Embryonic Fibroblast D13.5

growth_protocol: Culture in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). 37℃.

value: MEF


title: G3_iPSCs1

description: Induced pluripotent stem cells


title: R1_1

description: Mouse embryonic stem cells line R1

source_name: Mouse Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells line R1 were cultured in mESC medium (a 1:1 mixture of Neurolbasal/B27 medium and DMEM/F12 medium supplemented with N2, plus nonessential amino acids, 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM L-glutamine, 55 μM β-mercaptoethanol, 1 μM PD0325901, and 3 μM CHIR99021) on mitomycin C-treated MEFs. PD0325901 and CHIR99021 could be replaced by LIF (Millipore). The medium was changed every day, and mESCs and iPSCs were passaged using trypsin (Invitrogen).

treatment_protocol: In brief, mouse embryonic stem cells line R1 were cultured in mESC medium on mitomycin C-treated MEFs. PD0325901 and CHIR99021 could be replaced by LIF (Millipore). The medium was changed every day, and mESCs and iPSCs were passaged using trypsin (Invitrogen).

value: 129 cell type:Mouse embryonic stem cells


title: G6Gm_iPSCs2

description: Induced pluripotent stem cells


title: R1_2

description: Mouse embryonic stem cells line R1


title: MEF_expression_control1

description: None infected target cells


title: Mixl1SKM-1

description: MEF infected with MIXL1+SKM

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech). MEF1-1, MEF1-2, ESKM-1, ESKM-2, OSKM-1, OSKM-2, G6SKM-1, G6SKM-2, S7SKM-1, S7SKM-2, P1SKM-1, P1SKM-2, G4SKM-1, G4SKM-2, G4SKM-3, CEBPaSKM-1, CEBPaSKM-2, HNF4aSKM-1, HNF4aSKM-2, GRB2SKM-1, GRB2SKM, Mixl1SKM-1, Mixl1SKM-2 were processed together for normalization.

source_name: MEF infected with MIXL1+SKM

growth_protocol: Culture in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). 37℃. The dox-inducible lentiviral system used has been previously described (Maherali et al., 2008).

treatment_protocol: In brief, the limbs and tails of mice were cut off, and the skin was carefully peeled. The isolated mouse skin was then incubated in Collagenase type Ⅳ (2mg/ml, Gibco) for 2hrs at 37℃. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated skin fibroblasts were collected by flowing through cell strainers.

tag: treatment


title: G3_iPSCs2

description: Induced pluripotent stem cells

tag: tissue


title: Dlx3RNAi_iPSCs1

description: Induced stem cells

tag: gender

value: Dlx3 RNAi


title: Mixl1SKM-2

description: MEF infected with MIXL1+SKM

tag: cell type


title: GRB2SKM-1

description: MEF infected with GRB2+SKM

source_name: MEF infected with GRB2+SKM


title: CEBPaSKM-2

description: MEF infected with CEBPa+SKM

source_name: MEF infected with CEBPa+SKM

value: CEBPa+SKM


title: HNF4aSKM-2

description: MEF infected with HNF4a+SKM

source_name: MEF infected with HNF4a+SKM


title: GRB2SKM-2

description: MEF infected with GRB2+SKM


title: HNF4aSKM-1

description: MEF infected with HNF4a+SKM


title: CEBPaSKM-1

description: MEF infected with CEBPa+SKM


title: SNpc_18 months old_rep2

value: wild type

value: substantia nigra of brain

value: late-middle aged (18 months old)


title: G4SKM-2

description: MEF infected with GATA4+SKM

source_name: MEF infected with GATA4+SKM


title: Dlx3RNAi_iPSCs2

description: Induced stem cells


title: D58_G4_SARS_L_F058

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: Ferret lung with SARS on Day 57 post infection, Day 28 post challenge, biological rep2

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using ArrayAssist (Stratagene) default analysis settings.

organism: Mustela putorius furo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Influenza-free, castrated and descented male Fitch ferrets (Mustela putorius furo), 36 to 45 weeks of age, were purchased from Triple F Farms (Sayre, PA). On 0 days post infection (DPI) ferrets in the infection group (n=35) were anesthetized and then received 500 µL of serum free cell medium containing SARS-CoV TOR2 per nare for a total of 1 mL delivered intranasally and a dose of 103 TCID50. Ferrets in the mock-infected group (n=3) were treated in an identical manner but received 1 ml of the vehicle (serum free cell medium) alone intranasally. On 29 DPI, or 0 days post-challenge (DPC), 18 of the original SARS-CoV-infected ferrets were inoculated again (challenged) with 103 TCID50 SARS-CoV TOR2. The three mock-infected ferrets were sacrificed at 2 DPI. Three SARS-CoV-infected ferrets were also sacrificed at 2, 3, 5, 7, 14, and 28 DPI, as well as 2, 3, 5, 7, 14, and 28 DPC (or 31, 32, 34, 36, 43, and 57 DPI). Total RNA was isolated from fresh lung tissue collected during all sacrifice time points using TRIzol reagent by standard protocol (Invitrogen, Carlsbad, CA).

tag: Tissue

value: lung

tag: Virus Strain

value: SARS-CoV (TOR2)


title: D58_G4_SARS_L_F061

description: Ferret lung with SARS on Day 57 post infection, Day 28 post challenge, biological rep3


title: D58_G4_SARS_L_F049

description: Ferret lung with SARS on Day 57 post infection, Day 28 post challenge, biological rep1


title: D44_G4_SARS_L_F059

description: Ferret lung with SARS on Day 43 post infection, Day 14 post challenge, biological rep3


title: D44_G4_SARS_L_F056

description: Ferret lung with SARS on Day 43 post infection, Day 14 post challenge, biological rep2


title: G4SKM-1

description: MEF infected with GATA4+SKM

tag: strain


title: G4SKM-3

description: MEF infected with GATA4+SKM


title: P1SKM-2

description: MEF infected with PAX1+SKM

source_name: MEF infected with PAX1+SKM


title: G6SKM-1

description: MEF infected with GATA6+SKM

source_name: MEF infected with GATA6+SKM


title: G6SKM-2

description: MEF infected with GATA6+SKM


title: OSKM-2

description: MEF infected with OCT4+SKM

source_name: MEF infected with OCT4+SKM


title: S7SKM-1

description: MEF infected with SOX7+SKM

source_name: MEF infected with SOX7+SKM


title: D44_G4_SARS_L_F052

description: Ferret lung with SARS on Day 43 post infection, Day 14 post challenge, biological rep1


title: P1SKM-1

description: MEF infected with PAX1+SKM


title: D37_G4_SARS_L_F047

description: Ferret lung with SARS on Day 36 post infection, Day 7 post challenge, biological rep1


title: OSKM-1

description: MEF infected with OCT4+SKM


title: ESKM-2

description: MEF infected with EV+SKM

source_name: MEF infected with EV+SKM

treatment_protocol: In brief, the limbs and tails of  mice were cut off, and the skin was carefully peeled. The isolated mouse skin was then incubated in Collagenase type IV (2mg/ml, Gibco) for 2hrs at 37℃. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated  skin fibroblasts were collected by flowing through cell strainers.

value: EV+SKM


title: D37_G4_SARS_L_F048

description: Ferret lung with SARS on Day 36 post infection, Day 7 post challenge, biological rep2


title: S7SKM-2

description: MEF infected with SOX7+SKM


title: MEF1-1

description: MEF1 infected with EV used for comparison with OCT4 substitutes.

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech).  MEF1-1, MEF1-2, ESKM-1, ESKM-2, OSKM-1, OSKM-2, G6SKM-1, G6SKM-2, S7SKM-1, S7SKM-2, P1SKM-1, P1SKM-2, G4SKM-1, G4SKM-2, G4SKM-3, CEBPaSKM-1, CEBPaSKM-2, HNF4aSKM-1, HNF4aSKM-2, GRB2SKM-1, GRB2SKM, Mixl1SKM-1, Mixl1SKM-2 were processed together for normalization.

source_name: MEF infected with EV

value: EV


title: GmOKM-2

description: MEFs infected with OKM+GMNN

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech). S1OKM-1, S1OKM-2, S2OKM-1, S2OKM-2, S3OKM-1, S3OKM-2, GmOKM-1, GmOKM-2, EOKM-1, EOKM-2, EOKM-3 were processed together for normalization.

source_name: MEFs infected with OKM+GMNN

value: OKM+GMNN


title: MEF1-2


title: D37_G4_SARS_L_F062

description: Ferret lung with SARS on Day 36 post infection, Day 7 post challenge, biological rep3


title: ESKM-1

description: MEF infected with EV+SKM

growth_protocol: Culture in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). 37℃.. The dox-inducible lentiviral system used has been previously described (Maherali et al., 2008).


title: S3OKM-2

description: MEFs infected with OKM+SOX3

source_name: MEFs infected with OKM+SOX3


title: GmOKM-1

description: MEFs infected with OKM+GMNN


title: S2OKM-2

description: MEFs infected with OKM+SOX2

source_name: MEFs infected with OKM+SOX2


title: D35_G4_SARS_L_F054

description: Ferret lung with SARS on Day 34 post infection, Day 5 post challenge, biological rep2


title: S2OKM-1

description: MEFs infected with OKM+SOX2


title: S3OKM-1

description: MEFs infected with OKM+SOX3


title: S1OKM-1

description: MEFs infected with OKM+SOX1

source_name: MEFs infected with OKM+SOX1


title: D33_G4_SARS_L_F051

description: Ferret lung with SARS on Day 32 post infection, Day 3 post challenge, biological rep1


title: EOKM-3

description: MEFs infected with OKM+EV

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech). MEF2-1, MEF2-2, EOKM-1, EOKM-2, EOKM-3 were processed together for normalization.

source_name: MEFs infected with OKM+EV

value: OKM+EV


title: D32_G4_SARS_L_F060

description: Ferret lung with SARS on Day 31 post infection, Day 2 post challenge, biological rep3


title: B6-ChrY^SJL, CD4+ T cells, miRNA, rep3

hyb_protocol: Each sample was hybridized to a GeneChip® miRNA 2.0 Array (Affymetrix, Santa Clara, CA, USA) at 48°C and 60 rpm for 16 hours then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003).

data_processing:
Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip. Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample. Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites®, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).
probe group file: miRNA-2_0_v2.pgf
meta-probeset file: miRNA-2_0.annotations.20101222.csv

source_name: C57BL/6J-ChrY^SJL, CD4+TCRB+ cells, naive

label_protocol: Total RNA containing small RNA was labeled using the Flashtag RNA labeling kit (Genisphere, Hatfield, PA, USA) and performed in the Vermont Genetics Network Microarray Facility according to the manufacturer's instructions. Briefly, for each sample, 500ng of total RNA were subjected to a tailing reaction (2.5 mM MnCl2, ATP, Poly A Polymerase - incubation for 15 minutes at 37°) followed by ligation of the biotinylated signal molecule to the target RNA sample (1× Flash Tag ligation mix biotin, T4 DNA ligase - incubation for 30 minutes at 25oC) and addition of HSR stop solution.

extract_protocol: Three biological replicates were pooled from the axillary, brachial, and inguinal lymph nodes from 5 mice for each replicate. Cells were washed with PBS/1%FCS, pelleted at 300g for 5 min at 4oC. A working stock of Live/Dead-775 dye (Invitrogen L10119) was made by adding 1ul of reconstituted dye to 1ml PBS and cells were resuspended in 100ul of working stock per 1x10^6 cells. Cells were incubated for 30 minutes on ice in the dark. Cells were washed with cold PBS/1%FCS, pelleted, and resuspended in 100ul of an antibody mixture containing 1ug/ml PerCp-Cy5.5 anti-mouse TCRβ chain and 1ug/ml Alexa Flour® 488 anti-mouse CD4 antibodies in PBS/1%FCS. Cells were incubated on ice in the dark for 30 minutes then washed with cold PBS/1%FCS, pelleted, and resuspended at a concentration of 10x106 cells per 1ml of PBS/10%FCS. Cells were filtered through 50um nylon mesh and sorted using BD FACSAria to collect ~3x10^6 CD4+ T cells per sample. RNA was isolated using the miVana miRNA isolation Kit following the manufacturer's instructions (Ambion).

value: male

value: 8 weeks

value: lymph nodes

value: CD4+ T cells


title: EOKM-2

description: MEFs infected with OKM+EV

value: OGXICR

value: female

value: skin

value: MEF


title: D33_G4_SARS_L_F053

description: Ferret lung with SARS on Day 32 post infection, Day 3 post challenge, biological rep2


title: B6-ChrY^SJL, CD4+ T cells, miRNA, rep1


title: B6, CD4+ T cells, miRNA, rep3

source_name: C57BL/6J, CD4+TCRB+ cells, naive


title: D35_G4_SARS_L_F046

description: Ferret lung with SARS on Day 34 post infection, Day 5 post challenge, biological rep1


title: D29_G2_SARS_L_F035

description: Ferret lung with SARS on Day 28 post infection, biological rep3


title: D32_G4_SARS_L_F055

description: Ferret lung with SARS on Day 31 post infection, Day 2 post challenge, biological rep2


title: S1OKM-2

description: MEFs infected with OKM+SOX1


title: EOKM-1

description: MEFs infected with OKM+EV


title: D29_G2_SARS_L_F011

description: Ferret lung with SARS on Day 28 post infection, biological rep2


title: D32_G4_SARS_L_F050

description: Ferret lung with SARS on Day 31 post infection, Day 2 post challenge, biological rep1


title: D35_G4_SARS_L_F057

description: Ferret lung with SARS on Day 34 post infection, Day 5 post challenge, biological rep3


title: B6, CD4+ T cells, miRNA, rep2


title: B6-ChrY^SJL, CD4+ T cells, miRNA, rep2


title: B6, CD4+ T cells, miRNA, rep1


title: MEF2-1

description: MEF2 infected with EV used for comparison with SOX2 substitutes.

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech).  MEF2-1, MEF2-2, EOKM-1, EOKM-2, EOKM-3 were processed together for normalization.


title: D29_G2_SARS_L_F003

description: Ferret lung with SARS on Day 28 post infection, biological rep1


title: MEF2-2


title: B6_rep2

description: Mouse embryonic stem cells line B6

data_processing: After removing control probes, the data were analyzed according to the manufacturer's protocol (Phalanx Mouse OneArray® v2, Phalanx Biotech). B6_rep1, B6_rep2, B6_rep3 were processed together for normalization.

source_name: Mouse Embryonic Stem Cells B6

growth_protocol: Mouse embryonic stem cells line B6 were cultured in mESC medium (a 1:1 mixture of Neurolbasal/B27 medium and DMEM/F12 medium supplemented with N2, plus nonessential amino acids, 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM L-glutamine, 55 μM β-mercaptoethanol, 1 μM PD0325901, and 3 μM CHIR99021) on mitomycin C-treated MEFs. PD0325901 and CHIR99021 could be replaced by LIF (Millipore). The medium was changed every day, and mESCs and iPSCs were passaged using trypsin (Invitrogen).

treatment_protocol: In brief, mouse embryonic stem cells line B6 were cultured in mESC medium on mitomycin C-treated MEFs. PD0325901 and CHIR99021 could be replaced by LIF (Millipore). The medium was changed every day, and mESCs and iPSCs were passaged using trypsin (Invitrogen).

value: C57BL\6 cell type:Mouse embryonic stem cells


title: D15_G2_SARS_L_F005

description: Ferret lung with SARS on Day 14 post infection, biological rep1


title: B6_rep1

description: Mouse embryonic stem cells line B6

value: Mouse embryonic stem cells


title: B6_rep3

description: Mouse embryonic stem cells line B6


title: D8_G2_SARS_L_F010

description: Ferret lung with SARS on Day 7 post infection, biological rep1


title: D15_G2_SARS_L_F028

description: Ferret lung with SARS on Day 14 post infection, biological rep3


title: D6_G2_SARS_L_F034

description: Ferret lung with SARS on Day 5 post infection, biological rep3


title: D8_G2_SARS_L_F030

description: Ferret lung with SARS on Day 7 post infection, biological rep3


title: 3XTPA-Day 1 (D6 KO3_d1)

city: London

first: Helen

last: Baldwin

address: 5 University Street

country: United Kingdom

institute: University College London

description: Backskin, Day 1 after 3 applications of TPA, 24 hours apart

hyb_protocol: Please refer to GeneChipExpression Analysis Technical Manual (version P/N 702232 Rev. 3) for more detailed instructions.  Fragmented, biotinylated cRNA was hybridised with oligonucleotides, heated for 99C for 4 mins and hybridised onto the probe array for 16 hours at 45C.

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

data_processing:
Data were processed using GeneSpring GXI using robust multi-array analysis (RMA) and baseline transformed to the median of the control samples (untreated D6 deficient or WT mice).
Software: Normalised data files generated from GeneSpring GXI.
Normalisation: RMA Normalisation and Baseline to Median Transformation of Specified control samples. (D6 KO or WT d0)
Details: Normalised data files generated from GeneSpring GXI. Raw data was imported into GeneSpring GXI and RMA normalisation was applied.  Data was transformed using the 'baseline to median transformation of specified control samples'. RMA normalisation constituted of three steps: background correction, quantile normalisation and summarisation. Background correction was performed firstly to remove the background signal generated from the mismatch probes for each gene on the chip. Quantile normalisation was used to adjust for the differences in probe intensity across the chips and correct for chip to chip variation. Summarisation was perfomed to amalgomate the intensity values for each probe set on the chip to generate an overall signal for a particular gene. This step involved transforming the data onto a log2 scale and summarising the data according to the median polish method to remove outliers. To enable visualisation of the data on a scale to include both lowly and highly expressed genes, the algorithm 'baseline to median transformation of the control samples' was used. This involved taking the median intensity of each gene from the specified control samples (in this case D6 KO d0 or WT d0) away from the intensity for each gene. For example: Log2Gene A (WT1_d1)- Log2 Median Intensity (WT1d0, WT2d0, WT3d0).

source_name: D6 deficient (Day 1 after 3XTPA), Biological Rep 3

label_protocol: Please refer to GeneChipExpression Analysis Technical Manual (version P/N 702232 Rev. 3)  for more detailed instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: TPA treated backskin from D6 deficient or Wild Type Mice

extract_protocol: Backskin was removed from mice at each of these time points and stored in RNAlater® for 24 hours at 4C after which skin was removed from RNAlater® and stored at -80°C until processing.  To extract RNA, back skin was ground into a powder in liquid N2 and RNA was extracted using Trizol® and the PureLink® RNA kit (Ambion, #12183018A) according to the manufacturer’s instructions.  RNA concentrations were quantified using the Nanodrop (Thermo Scientific) and stored at -80 °C.

treatment_protocol: Backskin of D6 null deficient or Wild Type mice were treated with 3X TPA 24 hours apart. Pathology was left to develop for 1, 2, 4 or 6 days.  Whole backskin from D6 deficient or Wild Type mice was taken for microarray analysis at each time point.

value: 8-12 weeks

tag: genotype/variation

value: D6 Deficient

value: TPA (3 applications, 24 hours apart)

tag: time

value: Day 1

value: Female

value: Shaved Backskin


title: D8_G2_SARS_L_F029

description: Ferret lung with SARS on Day 7 post infection, biological rep2

value: lung

value: SARS-CoV (TOR2)


title: Untreated (D6 KO3_d0)

description: Acetone treated backskin

source_name: D6 deficient (Untreated), Biological Rep 3

value: control

value: Day 0


title: 3XTPA-Day 2 (WT3_d2)

description: Backskin, Day 2 after 3 applications of TPA, 24 hours apart

source_name: Wild Type (Day 2 after 3XTPA), Biological Rep 3

value: Wild Type

value: Day 2


title: 3XTPA-Day 4 (D6 KO3_d4)

description: Backskin, Day 4 after 3 applications of TPA, 24 hours apart

source_name: D6 deficient (Day 4 after 3XTPA), Biological Rep 3

value: Day 4


title: 3XTPA-Day 6 (D6 KO3_d6)

description: Backskin, Day 6 after 3 applications of TPA, 24 hours apart

source_name: D6 deficient (Day 6 after 3XTPA), Biological Rep 3

value: Day 6


title: 3XTPA-Day 6 (D6 KO2_d6)

source_name: D6 deficient (Day 6 after 3XTPA), Biological Rep 2


title: D6_G2_SARS_L_F012

description: Ferret lung with SARS on Day 5 post infection, biological rep1


title: 3XTPA-Day 6 (WT3_d6)

source_name: Wild Type (Day 6 after 3XTPA), Biological Rep 3


title: 3XTPA-Day 4 (WT3_d4)

source_name: Wild Type (Day 4 after 3XTPA), Biological Rep 3


title: 3XTPA-Day 1 (WT3_d1)

source_name: Wild Type (Day 1 after 3XTPA), Biological Rep 3


title: 3XTPA-Day 4 (D6 KO2_d4)

source_name: D6 deficient (Day 4 after 3XTPA), Biological Rep 2


title: D6_G2_SARS_L_F027

description: Ferret lung with SARS on Day 5 post infection, biological rep2


title: Untreated (WT3_d0)

description: Acetone treated backskin

source_name: Wild Type (Untreated), Biological Rep 3


title: 3XTPA-Day 2 (D6 KO3_d2)

source_name: D6 deficient (Day 2 after 3XTPA), Biological Rep 3


title: MGG6_rep2

type: genomic

hyb_protocol: Bisulfite conversion with Zymo EZ DNA methylation kit followed by standard Illumina protocol

scan_protocol: ChIPs were scanned on Illumina iScans

data_processing: Data processing performed with Illumina BeadStudio software (v. 3.1.3.0). The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy3 and Cy5

source_name: MGG6 human glioblastoma stem cell line

label_protocol: Standard Illumina protocol

growth_protocol: MGG cells were cultured and passaged using standard neural stem cell conditions as described Wakimoto et al, 2009 (PMID: 19351838)

extract_protocol: DNA was extracted using the QiaAMP DNA mini kit per the manufacturer's instructions

value: human glioblastoma stem cells


title: MGG8_rep1

source_name: MGG8 human glioblastoma stem cell line


title: 3XTPA-Day 2 (D6 KO2_d2)

source_name: D6 deficient (Day 2 after 3XTPA), Biological Rep 2


title: D4_G2_SARS_L_F007

description: Ferret lung with SARS on Day 3 post infection, biological rep3


title: D4_G2_SARS_L_F002

description: Ferret lung with SARS on Day 3 post infection, biological rep1


title: D3_G2_SARS_L_F032

description: Ferret lung with SARS on Day 2 post infection, biological rep3


title: D3_G2_SARS_L_F013

description: Ferret lung with SARS on Day 2 post infection, biological rep2


title: MGG6_rep1


title: 3XTPA-Day 1 (D6 KO2_d1)

source_name: D6 deficient (Day 1 after 3XTPA), Biological Rep 2


title: MGG8_rep2


title: MGG4_rep2

source_name: MGG4 human glioblastoma stem cell line


title: Untreated (D6 KO2_d0)

description: Acetone treated backskin

source_name: D6 deficient (Untreated), Biological Rep 2


title: MGG4_rep1


title: 3XTPA-Day 2 (WT2_d2)

source_name: Wild Type (Day 2 after 3XTPA), Biological Rep 2


title: 3XTPA-Day 6 (WT2_d6)

source_name: Wild Type (Day 6 after 3XTPA), Biological Rep 2


title: 3XTPA-Day 1 (WT2_d1)

source_name: Wild Type (Day 1 after 3XTPA), Biological Rep 2


title: Untreated (WT2_d0)

description: Acetone treated backskin

source_name: Wild Type (Untreated),  Biological Rep 2


title: D3_G1_SARS_L_F022

description: Ferret lung with serum free cell media, health control, biological rep3


title: D4_G2_SARS_L_F004

description: Ferret lung with SARS on Day 3 post infection, biological rep2


title: 3XTPA-Day 4 (WT2_d4)

source_name: Wild Type (Day 4 after 3XTPA), Biological Rep 2


title: D3_G2_SARS_L_F001

description: Ferret lung with SARS on Day 2 post infection, biological rep1


title: D3_G1_SARS_L_F016

description: Ferret lung with serum free cell media, health control, biological rep1


title: TTTS_AF_sample_13

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description:
WIH3_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package (v.1.28.5) in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: AF cell free mRNA from recipient fetus with TTTS

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-30 mL AF supernatant.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: gestational age (wks)

value: female

tag: ttts stage

value: IIIR/D


title: TTTS_AF_sample_12

description:
UT6.2_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: male

value: IIIR


title: 3XTPA-Day 6 (D6 KO1_d6)

source_name: D6 deficient (Day 6 after 3XTPA), Biological Rep 1

value: 8-12 weeks

value: D6 Deficient

value: TPA (3 applications, 24 hours apart)


title: TTTS_AF_sample_10

description:
B23_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: II


title: D3_G1_SARS_L_F018

description: Ferret lung with serum free cell media, health control, biological rep2

value: lung


title: TTTS_AF_sample_11

description:
B33_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS


title: 3XTPA-Day 2 (D6 KO1_d2)

description: Backskin, Day 2 after 3 applications of TPA, 24 hours apart

source_name: D6 deficient (Day 2 after 3XTPA), Biological Rep 1

value: Female

value: Shaved Backskin


title: 3XTPA-Day 4 (D6 KO1_d4)

description: Backskin, Day 4 after 3 applications of TPA, 24 hours apart

source_name: D6 deficient (Day 4 after 3XTPA), Biological Rep 1


title: 3XTPA-Day 1 (D6 KO1_d1)

description: Backskin, Day 1 after 3 applications of TPA, 24 hours apart

source_name: D6 deficient (Day 1 after 3XTPA), Biological Rep 1

value: Day 1


title: 3XTPA-Day 6 (WT1_d6)

description: Backskin, Day 6 after 3 applications of TPA, 24 hours apart

source_name: Wild Type (Day 6 after 3XTPA), Biological Rep 1

value: Wild Type


title: TTTS_AF_sample_5 [re-analysis]

description:
B2_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS


title: TTTS_AF_sample_4 [re-analysis]

description:
B11_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS


title: 3XTPA-Day 4 (WT1_d4)

source_name: Wild Type (Day 4 after 3XTPA), Biological Rep 1


title: Control keratinocyte, biological rep 1

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: normal

hyb_protocol: Labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray chips

scan_protocol: CEL files were generated using Expresison Console v1.1.1

data_processing: Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.

source_name: Keratinocyte from individual without keloid scar

growth_protocol: Normal full thickness skin samples and excised keloid scars were incubated overnight at 4 degrees in Dispase II.  Fibroblasts were isolated by mincing dermal components followed by collagenase digestion.  Keratinocytes were released from epidermis using 0.025% trypsin.  Fibroblasts were cultered in Dubecco's modified Eagle's medium supplemented with 10ng/ml EGF, f ug/ml insulin, 0.5 ug/ml hydrocortisone, 0.1 mM ascorbic acid-2=phosphate, 4% fetal bovine serum, and 1X penicillin-streptomucin-fungizone.  Primary keratinocyte cultures were initiated using tissue culture flasks coated with collagen, in medium containing reduced calcium.  Keratinocyte medium consisted of MCDB153 supplemented with 0.2% bovine pituitary extract, 1ng/ml EGF, 5ug/ml insulin, 0.5ug/ml hydrocortisone, 0.1mM AA2P, and 1X PPSF.  All cells were subcultured or harvested at 80-90% confluence.

extract_protocol: RNA was isolated using Rneasy and quality verified by Agilent 2100 Bioanalyzer

treatment_protocol: Keloid skars were exised from pediatric and young adult patients undergoing elective scar excision surgeries; for some patients adjacent non-lesional skin samples were also obtained.  Non-keloid skin biopsies were not collected due to ethical concerns of further keloid scar development.  Normal skin samples were obtained from pateints undergoing elective plastic surgery.

value: Control keratinocyte

value: F

tag: ethnicity

value: African American

tag: excision location

value: Breast


title: Control keratinocyte, biological rep 3

description: normal

label_protocol: Labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray chips


title: 3XTPA-Day 2 (WT1_d2)

source_name: Wild Type (Day 2 after 3XTPA), Biological Rep 1

value: Day 2


title: Untreated (D6 KO1_d0)

description: Acetone treated backskin

source_name: D6 deficient (Untreated), Biological Rep 1

value: control

value: Day 0


title: NS H3K36me3

source_name: ES-derived neural stem cells

value: ES-derived neural stem cells

tag: chip-antibody

tag: chip-antibody vendor

value: Abcam


title: TTTS_AF_sample_6 [re-analysis]

description:
B1_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: male

value: IIIR/D


title: 3XTPA-Day 1 (WT1_d1)

source_name: Wild Type (Day 1 after 3XTPA), Biological Rep 1

value: 8-12 weeks

value: TPA (3 applications, 24 hours apart)


title: TTTS_AF_sample_2 [re-analysis]

description:
B3_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: female

value: II


title: NS H3K27me3

value: Millipore

tag: chip-antibody cat. #


title: TTTS_AF_sample_9

description:
B6_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS


title: Singleton control_AF_sample_7

description:
N12_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus

source_name: AF cell free mRNA from euploid singleton fetus


title: Singleton control_AF_sample_6

description:
N13_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: D15_G2_SARS_L_F006

description: Ferret lung with SARS on Day 14 post infection, biological rep2

value: lung

value: SARS-CoV (TOR2)


title: Untreated (WT1_d0)

description: Acetone treated backskin

source_name: Wild Type (Untreated), Biological Rep 1

tag: age

value: Wild Type

value: Female

value: Shaved Backskin


title: Singleton control_AF_sample_8

description:
N8_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: NS H3K4me3


title: MGG8serum Input

source_name: MGG8 human glioblastoma serum-grown cell line

tag: cell line

value: human glioblastoma serum-grown cells


title: Singleton control_AF_sample_4

description:
N6_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: TTTS_AF_sample_1 [re-analysis]

description:
B12_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS


title: MGG8serum H3K4me3


title: MGG8serum H3K36me3


title: MGG8serum H3K4me1


title: MGG8serum H3K27me3


title: MGG8CSC LEF1

source_name: MGG8 human glioblastoma stem cell line

value: human glioblastoma stem cells


title: MGG8CSC H3K4me3


title: Control keratinocyte, biological rep 2

description: normal

value: Control keratinocyte

value: M

value: Caucasian

value: Torso


title: MGG8CSC H3K4me1

value: Abcam


title: MGG8CSC H3K36me3


title: MGG8CSC Input


title: MGG8CSC H3K27me3


title: Singleton control_AF_sample_2

description:
N1_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: MGG6CSC Input

source_name: MGG6 human glioblastoma stem cell line


title: TTTS_AF_sample_8

description:
B10_(HG-U133_Plus_2)_2.CEL
gene expression data from  fetus with TTTS

source_name: AF cell free mRNA from recipient fetus with TTTS

value: male

value: IIID


title: Singleton control_AF_sample_3

description:
N4_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: Singleton control_AF_sample_1

description:
N11_(HG-U133_Plus_2).CEL
gene expression data from normal term fetus


title: TTTS_AF_sample_7

description:
B8_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: female


title: TTTS_AF_sample_5

value: IIIR


title: Keloid keratinocyte, biological rep8

description: Subject with keloid scar

source_name: Keratinocyte from keloid scar

value: Keloid keratinocyte

value: F

value: African American

value: Neck


title: Singleton control_AF_sample_5

description:
N2_(HG-U133_Plus_2).CEL
gene expression data from normal second trimester fetus


title: Keloid keratinocyte, biological rep9

description: Subject with keloid scar

value: Face


title: Keloid keratinocyte, biological rep7

description: Subject with keloid scar


title: MGG6CSC H3K4me1


title: TTTS_AF_sample_4

value: II


title: TTTS_AF_sample_2


title: TTTS_AF_sample_1


title: NS_rep2

hyb_protocol: As recommended by Affymetrix

scan_protocol: As recommended by Affymetrix

data_processing: GenePattern RMA, default parameters

label_protocol: As recommended by Affymetrix

growth_protocol: MGG and NS cells were cultured and passaged using standard neural stem cell conditions as described in the references

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

value: NS


title: TTTS_AF_sample_6

value: IIIR/D


title: MGG6CSC H3K4me3

value: human glioblastoma stem cells

value: Millipore


title: MGG6CSC H3K27me3


title: MGG4CSC Input

source_name: MGG4 human glioblastoma stem cell line


title: MGG4CSC H3K4me3


title: MGG6CSC H3K36me3


title: Keloid keratinocyte, biological rep6

description: Subject with keloid scar

value: M

value: Ear


title: MGG4CSC H3K27me3


title: NS_rep1


title: Keloid keratinocyte, biological rep4

description: Subject with keloid scar

value: Caucasian

value: Chin


title: MGG23CSC Input

source_name: MGG23 human glioblastoma stem cell line


title: Keloid keratinocyte, biological rep3

description: Subject with keloid scar


title: MGG23CSC H3K4me3


title: MGG23CSC H3K36me3

value: Abcam


title: MGG8_rep3


title: MGG8_rep4


title: Keloid keratinocyte, biological rep5

description: Subject with keloid scar

value: Face-cheek


title: TTTS_AF_sample_3

description:
B5_(HG-U133_Plus_2).CEL
gene expression data from  fetus with TTTS

value: male


title: MGG23CSC H3K27me3


title: MGG6_rep2


title: MGG6_rep1


title: MGG4CSC H3K36me3


title: MGG4_rep2


title: control CD4 replicate 2 vs Cocaine treated CD4 replicate 2

city: Nashville

first: Chandravanu

last: Dash

state: TN

address: 1005 Dr. DB Todd Jr Blvd

department: Center for AIDS Health Disparities Research

institute: Meharry Medical College School of Medicine

hyb_protocol: The Cy5 /Cy3 labeled targets were combined per hyb order instructions, then mixed with 2x Hyb Buffer, heat denatured at 95C for 2 minutes and quick-chilled on ice. The targets were loaded on an Agilent 1plex coverslip in an Agilent hyb chamber. The targets were then covered with the Exiqon arrays (Item # 20-1122; Lot#34001.03, 6th generation (product#208401-A Lot#6000) and the hybridization chamber was sealed. The hybridizations were performed per protocol specifications, for ~16 - 18 hours (17), 56C, 20rpm in an Agilent Hybridizaiton oven

scan_protocol: Scanned on Axon 4000B using GenePix Pro v. 6.1 at 5 microns

data_processing: GenePix Pro v. 6.1

source_name: Primary CD4+ T cell from healthy donor

label_protocol: Exiqon Hi-Power Labeling Kit (Cat#208035, lot#3000) protocol on 06232011

growth_protocol: Cells grown in RPMI with 20% FBS

extract_protocol: Total RNA isolated using Qiagen miRNAeasy miRNA kit

value: CD4+ T cells

tag: treatment

treatment_protocol: Treated with 1 uM cocaine

value: Treated with 1 uM cocaine


title: MGG4_rep1


title: MGG23_rep1


title: MGG8_rep2


title: MGG23_rep2


title: control CD4 replicate 1 vs Cocaine treated CD4 replicate 1


title: Keloid keratinocyte, biological rep1

description: Subject with keloid scar

value: Keloid keratinocyte

tag: gender


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 193

status: Public on May 27 2013

city: L'Hospitalet del Llobregat

first: Antonio

last: Berenguer-Llergo

address: Gran Via 199-203

department: Cancer Prevention Program

institute: Catalan Institute of Oncology (ICO)

hyb_protocol: After bisulfite treatment of DNA, the Illumina GoldenGate Methylation Cancer Panel I genotyping assay protocol was followed using Illumina-supplied reagents and conditions.

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting.

data_processing: Pre-processing and initial quality assessment of hybridizations was performed using the Illumina BeadStudio Methylation Module software, version 3.2 (Illumina, Inc.). Negative controls bead types were used to obtain an estimation of the background intensity level that was subtracted from the loci probe signals. Moreover, the distribution of intensities at negative controls was used to compute detection p-values which were assigned to each probe as a measure of the signal-to-noise ratio. As quality criteria, loci showing a detection p-value greater than 0.01 in at least 10% of arrays and samples with a detection p-value greater than 0.01 in more than 5% of loci were considered defective. Beta values were computed from methylated and unmethylated signals for each microarray assay, and potential bias of dye in the array was corrected using the methylumi R Bioconductor package. Finally, a Principal Component Analysis was performed on the Beta values in order to identify potential outliers regarding the global methylation pattern of samples.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA from fresh-frozen tissues was extracted using fenol-clorophorm.

tag: array identifier

tag: array position

tag: patient code

value: Patient 92

value: Male

tag: age at surgery

tag: tumor location

value: Rectum

tag: tumor grade

value: Low

tag: tumor stage

value: Stage IV

tag: type of surgery

value: Radical

tag: neoadjuvant chemotherapy

value: No

tag: adjuvant chemotherapy

value: Si

tag: radiotherapy

tag: metastasis

value: Synchronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 191

value: Patient 91

value: Left colon

value: Stage IIA

value: Metachronic


title: control CD4 replicate 3 vs Cocaine treated CD4 replicate 3

tag: cell type


title: genomic DNA from colorectal tumor 188

description: colorectal tumor

source_name: colorectal tumor 188

value: Patient 89


title: genomic DNA from colorectal tumor 186

description: colorectal tumor

source_name: colorectal tumor 186

value: Patient 88

value: Female


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 187


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 183

value: Patient 87


title: genomic DNA from colorectal tumor 184

description: colorectal tumor

source_name: colorectal tumor 184


title: MGG8_rep1


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 181

value: Patient 86


title: genomic DNA from colorectal tumor 180

description: colorectal tumor

source_name: colorectal tumor 180

value: Patient 85

value: Male

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 189

value: Patient 90

value: Low

value: Stage IV


title: genomic DNA from colorectal tumor 178

description: colorectal tumor

source_name: colorectal tumor 178

value: Patient 84


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 179

value: Radical

value: No

value: Synchronic


title: Keloid keratinocyte, biological rep2

description: Subject with keloid scar

value: Keloid keratinocyte

value: M

tag: ethnicity

value: Caucasian

tag: age

tag: excision location

value: Ear


title: genomic DNA from colorectal tumor 182

description: colorectal tumor

source_name: colorectal tumor 182

tag: gender

value: Left colon


title: genomic DNA from colorectal tumor 194

description: colorectal tumor

source_name: colorectal tumor 194

tag: array identifier

value: Patient 92

value: Rectum

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 177

tag: array position

value: Female


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 175

tag: patient code

value: Patient 83

value: Male

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 173

value: Patient 82

tag: age at surgery

value: Low

value: Stage IV

value: Palliative


title: genomic DNA from colorectal tumor 174

description: colorectal tumor

source_name: colorectal tumor 174

tag: tumor location

value: No

value: Synchronic


title: genomic DNA from colorectal tumor 192

description: colorectal tumor

source_name: colorectal tumor 192

value: Patient 91

tag: tumor grade

value: Stage IIA

value: Radical

value: Metachronic


title: genomic DNA from colorectal tumor 176

description: colorectal tumor

source_name: colorectal tumor 176

tag: tumor stage


title: genomic DNA from colorectal tumor 190

description: colorectal tumor

source_name: colorectal tumor 190

value: Patient 90

value: Left colon

tag: type of surgery


title: genomic DNA from colorectal tumor 172

description: colorectal tumor

source_name: colorectal tumor 172

value: Patient 81

tag: neoadjuvant chemotherapy


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 185

value: Patient 88

value: Female

value: Rectum

tag: adjuvant chemotherapy


title: genomic DNA from colorectal tumor 170

description: colorectal tumor

source_name: colorectal tumor 170

value: Patient 80

tag: radiotherapy


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 169

tag: metastasis


title: genomic DNA from colorectal tumor 168

description: colorectal tumor

source_name: colorectal tumor 168

value: Patient 79


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 167

value: Low


title: genomic DNA from colorectal tumor 166

description: colorectal tumor

source_name: colorectal tumor 166

value: Patient 78

value: Male

value: High

value: Stage IV

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 163

value: Patient 77

value: Palliative

value: No

value: Synchronic


title: genomic DNA from colorectal tumor 164

description: colorectal tumor

source_name: colorectal tumor 164


title: genomic DNA from colorectal tumor 162

description: colorectal tumor

source_name: colorectal tumor 162

value: Patient 76

value: Right colon

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 171

value: Patient 81


title: genomic DNA from colorectal tumor 160

description: colorectal tumor

source_name: colorectal tumor 160

value: Patient 75

value: Female

value: Rectum

value: Stage IIIC


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 153

value: Patient 72

value: Low

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 159

value: High


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 165

value: Patient 78

value: Male

value: Stage IV

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 157

value: Patient 74

value: Left colon

value: Palliative

value: No

value: Synchronic


title: genomic DNA from colorectal tumor 158

description: colorectal tumor

source_name: colorectal tumor 158


title: genomic DNA from colorectal tumor 154

description: colorectal tumor

source_name: colorectal tumor 154

value: Right colon

value: Radical


title: genomic DNA from colorectal tumor 156

description: colorectal tumor

source_name: colorectal tumor 156

value: Patient 73

value: Rectum

value: Stage IIIB


title: genomic DNA from colorectal tumor 152

description: colorectal tumor

source_name: colorectal tumor 152

value: Patient 71

value: Female

value: Low


title: genomic DNA from colorectal tumor 150

description: colorectal tumor

source_name: colorectal tumor 150

value: Patient 70

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 161

value: Patient 76

value: Male

value: Stage IV


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 149

value: Left colon

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 155

value: No


title: genomic DNA from colorectal tumor 148

description: colorectal tumor

source_name: colorectal tumor 148

value: Patient 69


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 147


title: genomic DNA from colorectal tumor 146

description: colorectal tumor

source_name: colorectal tumor 146

value: Patient 68

value: Stage IIIC


title: genomic DNA from colorectal tumor 144

description: colorectal tumor

source_name: colorectal tumor 144

value: Patient 67

value: High

value: Radical


title: genomic DNA from colorectal tumor 142

description: colorectal tumor

source_name: colorectal tumor 142

value: Patient 66

value: Rectum


title: genomic DNA from colorectal tumor 140

description: colorectal tumor

source_name: colorectal tumor 140

value: Patient 65

value: Female

value: Right colon

value: Low

value: Stage IIIB


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 143

value: Male

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 151

value: Patient 71

value: Left colon

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 141

value: No


title: GN29 vs CONTROL

city: Madrid

first: Santiago

last: Rodriguez de Cordoba

state: Madrid

address: Ramiro de Maeztu, 9

department: Medicina Celular y Molecular

institute: Centro de Investigaciones Biologicas

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Microarray data were extracted and visualized using the Feature Extraction Software v10.7 and Genomic Workbench Standard Edition 7.0 (Agilent Corp, Santa Clara, CA). Copy number altered regions were detected using ADM-2 (set as 5) statistic provided by DNA Analytics, with a minimum number of 5 consecutive probes. Genomic build hg19 was used for the experiment.

label_protocol: standard Agilent protocol

extract_protocol: Trizol

tag: tissue

value: blood

tag: disease state

value: C3 glomeropathy

value: unknown

source_name: Male DNA

value: male

value: healthy control reference


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 137

value: Patient 64

value: Radical


title: genomic DNA from colorectal tumor 138

description: colorectal tumor

source_name: colorectal tumor 138

value: Female


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 139

value: Patient 65

value: Right colon


title: genomic DNA from colorectal tumor 136

description: colorectal tumor

source_name: colorectal tumor 136

value: Patient 41

value: Low

value: Stage IIIB


title: genomic DNA from colorectal tumor 134

description: colorectal tumor

source_name: colorectal tumor 134

value: Patient 63

value: Male

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 135

value: Left colon

value: No

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 145

value: Patient 68

value: Stage IIIC


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 133


title: genomic DNA from colorectal tumor 132

description: colorectal tumor

source_name: colorectal tumor 132

value: Patient 62

value: Rectum

value: Yes


title: genomic DNA from colorectal tumor 128

description: colorectal tumor

source_name: colorectal tumor 128

value: Patient 30

value: Stage IIIA

value: Radical


title: genomic DNA from colorectal tumor 130

description: colorectal tumor

source_name: colorectal tumor 130

value: Patient 61

value: Female


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 129

value: Low

value: Stage IIIB


title: genomic DNA from colorectal tumor 120

description: colorectal tumor

source_name: colorectal tumor 120

value: Patient 58

value: Male

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 121

value: Patient 59

value: Left colon

value: No

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 131

value: Patient 62

value: Stage IIIC

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 111

value: Patient 56

value: Rectum

value: Yes

value: Metachronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 119

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 123

value: Patient 25

value: Low


title: genomic DNA from colorectal tumor 122

description: colorectal tumor

source_name: colorectal tumor 122

value: Female

value: Stage IIIB


title: genomic DNA from colorectal tumor 124

description: colorectal tumor

source_name: colorectal tumor 124

value: Male

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 125

value: Patient 60

value: Left colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 117

value: Patient 17

value: High

value: No

value: No metastasis


title: genomic DNA from colorectal tumor 112

description: colorectal tumor

source_name: colorectal tumor 112

value: Patient 56

value: Si


title: genomic DNA from colorectal tumor 116

description: colorectal tumor

source_name: colorectal tumor 116

value: Patient 13

value: Stage IIIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 113

value: Patient 57

value: Radical

value: Metachronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 115

value: Female

value: Low


title: genomic DNA from colorectal tumor 114

description: colorectal tumor

source_name: colorectal tumor 114

value: Male

value: Stage IIIB


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 109

value: Patient 55

value: Rectum


title: genomic DNA from colorectal tumor 110

description: colorectal tumor

source_name: colorectal tumor 110


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 127

value: Patient 30

value: Right colon


title: genomic DNA from colorectal tumor 126

description: colorectal tumor

source_name: colorectal tumor 126

value: Patient 60

value: Left colon

value: No


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 107

value: Patient 54

value: Stage IV

value: Synchronic


title: genomic DNA from colorectal tumor 106

description: colorectal tumor

source_name: colorectal tumor 106

value: Patient 53

value: Si


title: genomic DNA from colorectal tumor 118

description: colorectal tumor

source_name: colorectal tumor 118

value: Patient 17

value: High

value: Radical

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 103

value: Patient 52

value: Male

value: Low

value: Stage IIIB

value: Metachronic


title: genomic DNA from colorectal tumor 104

description: colorectal tumor

source_name: colorectal tumor 104


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 105


title: genomic DNA from colorectal tumor 102

description: colorectal tumor

source_name: colorectal tumor 102

value: Patient 51

value: Female

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 101

value: Left colon

value: No


title: genomic DNA from colorectal tumor 100

description: colorectal tumor

source_name: colorectal tumor 100

value: Patient 50


title: genomic DNA from colorectal tumor 108

description: colorectal tumor

source_name: colorectal tumor 108

value: Patient 54

value: Stage IV

value: Synchronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 99

value: Si


title: genomic DNA from colorectal tumor 84

description: colorectal tumor

source_name: colorectal tumor 84

value: Patient 42

value: Stage IIB

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 95

value: Patient 48

value: Stage IIIC


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 97

value: Patient 49

value: Low

value: Stage IIIB


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 81

value: Patient 41

value: Female

value: No metastasis


title: genomic DNA from colorectal tumor 96

description: colorectal tumor

source_name: colorectal tumor 96

value: Left colon

value: No

value: Metachronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 83


title: genomic DNA from colorectal tumor 98

description: colorectal tumor

source_name: colorectal tumor 98


title: genomic DNA from colorectal tumor 94

description: colorectal tumor

source_name: colorectal tumor 94

value: Patient 47

value: Male

value: High


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 87

value: Patient 44

value: Right colon


title: genomic DNA from colorectal tumor 88

description: colorectal tumor

source_name: colorectal tumor 88

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 89

value: Patient 45

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 93

value: Stage IIIC

value: Si


title: genomic DNA from colorectal tumor 90

description: colorectal tumor

source_name: colorectal tumor 90


title: genomic DNA from colorectal tumor 86

description: colorectal tumor

source_name: colorectal tumor 86

value: Patient 43

value: Rectum

value: Low

value: Yes


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 91

value: Patient 46

value: Left colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 85

value: No

value: Metachronic


title: genomic DNA from colorectal tumor 80

description: colorectal tumor

source_name: colorectal tumor 80

value: Patient 40

value: Male


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 75

value: Patient 38

value: No metastasis


title: genomic DNA from colorectal tumor 74

description: colorectal tumor

source_name: colorectal tumor 74

value: Patient 37

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 79

value: High


title: genomic DNA from colorectal tumor 78

description: colorectal tumor

source_name: colorectal tumor 78

value: Patient 39

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 73

value: Stage IIIC

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 77

value: Rectum

value: Low


title: genomic DNA from colorectal tumor 92

description: colorectal tumor

source_name: colorectal tumor 92

value: Patient 46


title: genomic DNA from colorectal tumor 76

description: colorectal tumor

source_name: colorectal tumor 76

value: Left colon


title: genomic DNA from colorectal tumor 82

description: colorectal tumor

source_name: colorectal tumor 82

value: Patient 41

value: Female

value: Stage IIIB

value: No


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 69

value: Patient 35


title: genomic DNA from colorectal tumor 70

description: colorectal tumor

source_name: colorectal tumor 70


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 63

value: Patient 32

value: Stage IV

value: Synchronic


title: genomic DNA from colorectal tumor 64

description: colorectal tumor

source_name: colorectal tumor 64

value: Radical


title: genomic DNA from colorectal tumor 68

description: colorectal tumor

source_name: colorectal tumor 68

value: Patient 34

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 65

value: Patient 33

value: Stage IIIC

value: Yes


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 67

value: Rectum

value: Low

value: Stage IIA


title: genomic DNA from colorectal tumor 66

description: colorectal tumor

source_name: colorectal tumor 66

value: Si


title: genomic DNA from colorectal tumor 72

description: colorectal tumor

source_name: colorectal tumor 72

value: Patient 36

value: Female

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 71

value: No


title: genomic DNA from colorectal tumor 62

description: colorectal tumor

source_name: colorectal tumor 62

value: Patient 31

value: Male

value: Left colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 57

value: Patient 29

value: Radical


title: genomic DNA from colorectal tumor 56

description: colorectal tumor

source_name: colorectal tumor 56

value: Patient 28

value: No metastasis


title: genomic DNA from colorectal tumor 54

description: colorectal tumor

source_name: colorectal tumor 54

value: Patient 27

value: Metachronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 61


title: genomic DNA from colorectal tumor 50

description: colorectal tumor

source_name: colorectal tumor 50

value: Patient 25

value: Stage IIIB


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 55

value: Low

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 59

value: Patient 30

value: Stage IIIA

value: Si


title: genomic DNA from colorectal tumor 44

description: colorectal tumor

source_name: colorectal tumor 44

value: Patient 22

value: Rectum

value: Stage IIB

value: No

value: Yes


title: genomic DNA from colorectal tumor 46

description: colorectal tumor

source_name: colorectal tumor 46

value: Patient 23

value: Male

value: Left colon

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 45


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 47

value: Patient 24

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 53

value: Patient 27

value: Metachronic


title: genomic DNA from colorectal tumor 58

description: colorectal tumor

source_name: colorectal tumor 58

value: Patient 29

value: Right colon

value: Low

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 43

value: Patient 22

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 51

value: Patient 26

value: Stage IIIC


title: genomic DNA from colorectal tumor 48

description: colorectal tumor

source_name: colorectal tumor 48

value: Stage IIIB

value: No


title: genomic DNA from colorectal tumor 52

description: colorectal tumor

source_name: colorectal tumor 52

value: Male


title: genomic DNA from colorectal tumor 42

description: colorectal tumor

source_name: colorectal tumor 42

value: Patient 21

value: Female

value: Left colon

value: Stage IIIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 41

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 49

value: Patient 25

value: No metastasis


title: genomic DNA from colorectal tumor 60

description: colorectal tumor

source_name: colorectal tumor 60

value: Patient 30

value: Right colon


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 37

value: Patient 19

value: Low

value: Stage IIA


title: genomic DNA from colorectal tumor 38

description: colorectal tumor

source_name: colorectal tumor 38

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 35

value: Patient 18

value: Rectum

value: Stage I


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 39

value: Patient 20

value: No

value: Yes


title: genomic DNA from colorectal tumor 36

description: colorectal tumor

source_name: colorectal tumor 36

value: Male


title: genomic DNA from colorectal tumor 34

description: colorectal tumor

source_name: colorectal tumor 34

value: Patient 17

value: High

value: Stage IIIB


title: genomic DNA from colorectal tumor 40

description: colorectal tumor

source_name: colorectal tumor 40

value: Female

value: Radical

value: No metastasis