title: Replica 2 - HIGH-translated_M0463

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in control cells
M0463

value: Replica 2 - HIGH-translated


title: Case L08A

status: Public on May 29 2015

type: genomic

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

country: China

institute: Shanghai Jiao Tong University

description: Genomic DNA was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Using the Genotyping Module of Illumina Genome Studio software version 2011.1.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: NT/T Tumor Cell

label_protocol: standard Illumina protocol

growth_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol  standard Illumina protocol

treatment_protocol: standard Illumina protocol

tag: disease state

value: natural killer/T-cell lymphoma

tag: individual

tag: gender

value: Male

tag: sample type

value: tumor


title: Replica 2 - NON-translated_M0464

status: Public on May 28 2015

type: RNA

city: Singapore

first: Igor

middle: V

last: Kurochkin

address: 30 Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute, A*STAR

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in MRC5 cells treated for 2hr with H2O2
M0464

hyb_protocol: The labeled cRNA was hybridized to the Agilent SurePrint G3 gene expression 8x60K microarray according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3μm resolution.

data_processing: The 24 Agilent features extraction results text files of both, stress and control in triplicates (as mentioned in the Sample section) were imported into Partek Genomics Suite. The gProcessed Signal parameter was imported into the Partek probe intensity spreadsheet and the data was further log2 transformed and quantile normalized.

molecule: total RNA

source_name: MRC5 cells

label_protocol: 100 ng of total RNA from whole cell extracts and polysome fractions was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions. Briefly, mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA.

growth_protocol: MRC5 fibroblasts were cultured in 5% CO2 atmosphere, at 37°C in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Cells were incubated with 150μg/ml of cycloheximide (Sigma-Aldrich) for 15 min prior to harvesting. Approximately, 1x10^7 cells were lysed in 500 μl of lysis buffer [5mM Tris-HCl, 2.5mM MgCl2, 1.5mM KCl, 0.5% Triton X, 0.5% Sodium deoxycholate, 2mM DTT, 40 U/µl of RNasin (Fermentas) and 1mM DTT]. Then cell lysates were subjected to centrifugation for 3 min at 14,000 rpm at 4°C to obtain clarified lysate.  The lysates were fractionated by centrifugation in 15-50% linear sucrose gradients at 36,000 x g in a SW41-Ti rotor (Beckman) for two hours at 80C. Twenty three fractions were collected using Piston Gradient Fractionator (Biocomp) and RNA was isolated from the fractions using phenol chloroform extraction. Briefly, RNA was extracted two times in equal volume of 25:24:1 phenol:chloroform:isoamyl alcohol followed by extraction in an equal volume of 49:1 chloroform:isoamyl alcohol. RNA was precipitated at -800C with 2.5 volumes of 100% ethanol and 1/10th volume of 3M sodium acetate, pH5.2.

treatment_protocol: MRC5 fibroblasts were seeded at sub-confluent density and treated the next day for 2 hr with 0.2mM H2O2.

tag: cell line

tag: group

value: STRESS

tag: rna translational categories

value: Replica 2 - NON-translated


title: Replica 2 - LOW-translated_M0462

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in control cells
M0462

value: Control

value: Replica 2 - LOW-translated


title: Replica 3 - NON-translated_M0467

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in control cells
M0467

value: Replica 3 - NON-translated


title: Replica 1 - NON-translated_M0458

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in MRC5 cells treated for 2hr with H2O2
M0458

value: Replica 1 - NON-translated


title: Replica 2 - NON-translated_M0455_2

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in control cells
M0455_2


title: Replica 2 - LOW-translated_M0465

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in MRC5 cells treated for 2hr with H2O2
M0465


title: Replica 2 - HIGH-translated_M0466

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in MRC5 cells treated for 2hr with H2O2
M0466


title: Replica 1 - HIGH-translated_M0460

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in MRC5 cells treated for 2hr with H2O2
M0460

value: Replica 1 - HIGH-translated


title: Case L03A


title: Replica 1 - LOW-translated_M0459

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in MRC5 cells treated for 2hr with H2O2
M0459

value: Replica 1 - LOW-translated


title: Case L01A


title: Replica 1 - NON-translated_M0455_1

description:
RNA from sucrose gradient fractions
RNA associated with non-translated fraction in control cells
M0455_1


title: Replica 1 - LOW-translated_M0456

description:
RNA from sucrose gradient fractions
RNA associated with low-translated fraction in control cells
M0456


title: Case L05A


title: Case L09A

value: Female


title: Case L04A


title: Replica 3 - Total RNA_M0454

description:
Total RNA
Total RNA extracted from MRC5 cells treated for 2hr with H2O2
M0454

value: Replica 3 - Total RNA


title: Replica 3 - Total RNA_M0451

description:
Total RNA
Total RNA extracted from control MRC5 cells
M0451


title: Replica 2 - Total RNA_M0453

description:
Total RNA
Total RNA extracted from MRC5 cells treated for 2hr with H2O2
M0453

value: Replica 2 - Total RNA


title: Replica 2 - Total RNA_M0450

description:
Total RNA
Total RNA extracted from control MRC5 cells
M0450


title: Replica 1 - HIGH-translated_M0457

description:
RNA from sucrose gradient fractions
RNA associated with high-translated fraction in control cells
M0457


title: MED_BG02_R1

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

country: USA

institute: Florida State University

description: House genomic data

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: DEVA (Nimblegen) software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias (limma package, R/Bioconductor) and early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: Differentiation of BG02 hESCs to mesendoderm (MED) was performed by switching from defined media to DMEM/F12, supplemented with 100 ng/ml Activin A and 20 ng/ml Fgf2 for two days with 25 ng/ml Wnt3a added on the first day (McLean et al. 2007. Stem Cells. 25:29-38).

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

tag: differentiation stage

value: Mesendoderm

source_name: Late-replicating DNA


title: Replica 1 - Total RNA_M0449

description:
Total RNA
Total RNA extracted from control MRC5 cells
M0449

value: Replica 1 - Total RNA


title: Splanc_BG02_R2

description: House genomic data

growth_protocol: Splanchnic mesoderm (PDGFRα+, GATA4+, FoxF1+, ISL1+ and Tbx20+) were derived from hESC in DMEM/F12, with 100 ng/ml Activin A, 20 ng/ml Fgf2, 25 ng/ml Wnt3a (R&D Systems) and BMP4 (R&D Systems) at 100 ng/ml for 4 days.

value: Splanchnic mesoderm


title: MED_BG02_R2

description: House genomic data


title: Gastric cancer 27

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

hyb_protocol: The aCGH was performed according to the manufacturer’s recommendations.

scan_protocol: After DNA hybridization and washing, slides were scanned immediately using an Agilent microarray scanner, and raw data were extracted using Feature Extraction Software at the default CGH parameter settings (Agilent Technologies).

data_processing:
Putative CNA intervals in each sample were identified using Agilent Genomic Workbench v7.0.4.0 software. Cy5/Cy3 ratios were converted into log2-transformed values. Centralization and fuzzy zero corrections were applied to the microarray. The Aberration Detection Method 2 (ADM-2) algorithm at threshold 6.0 was used to identify the CNAs in individual samples and to determine aberration frequencies in gastric cancer samples.
The following filters were employed: minimum number of probes in region >= 3, minimum absolute average log ratio of region > = 0.25. gIsSaturated = true OR rIsSaturated = true OR gIsFeatNonUnifOL = true OR rIsFeatNonUnifOL = true OR LogRatio = 0. Homology = 0 OR IsPseudoautosomal = 1

source_name: Gastric cancer tissue

label_protocol: Array CGH labeling kit (Invitrogen) using Cy5/Cy3

extract_protocol: A total of 30 patients, who had undergone curative surgical resection for gastric cancer at the Department of Surgery in the Samsung Medical Center, Seoul, Korea, participated in this study.  The tumors were snap-frozen in liquid nitrogen and stored at −80°C until needed. Before DNA was extracted from the fresh frozen tissues, the sections were placed on slides and stained with H&E to evaluate the admixture of tumorous and non-tumorous tissues. Tumor and non-tumor areas were microdissected carefully under a microscope. The microdissected tissues were digested with proteinase K, and the genomic DNA was isolated according to the instructions of the manufacturer (DNeasy Tissue kit, Qiagen, Valencia, CA).

tag: Sex

tag: age (years)

source_name: Matched normal tissue


title: SM_BG02_R2

description: House genomic data

growth_protocol: Smooth muscle cells (SMA+, SM-MHC+, CALD1+, calponin+) were differentiated from hESC in DMEM/F12, with 100 ng/ml Activin A, 20 ng/ml Fgf2, 25 ng/ml Wnt3a and BMP4 at 100 ng/ml for 18 days.

value: Smooth Muscle


title: Replica 1 - Total RNA_M0452

description:
Total RNA
Total RNA extracted from MRC5 cells treated for 2hr with H2O2
M0452


title: DE_BG02_R2

description: House genomic data

growth_protocol: Differentiation of BG02 hESCs to definitive endoderm (DE) was performed by switching from defined media to DMEM/F12+100 ng/ml Activin A 20 ng/ml Fgf2 for four days with 25 ng/ml Wnt3a added on the first day. Cells were positive for DE markers CXCR4, SOX17, FOXA2, GSC (McLean et al. 2007. Stem Cells. 25:29-38).

value: Definitive Endoderm


title: Gastric cancer 30

value: Male


title: Splanc_BG02_R1

description: House genomic data


title: Gastric cancer 26


title: Gastric cancer 24


title: Gastric cancer 21


title: Gastric cancer 18


title: Gastric cancer 16


title: Gastric cancer 13


title: Gastric cancer 23


title: Gastric cancer 22


title: Gastric cancer 17


title: Gastric cancer 19


title: SM_BG02_R1

description: House genomic data


title: Gastric cancer 20


title: Gastric cancer 15


title: Gastric cancer 28


title: Gastric cancer 29


title: Gastric cancer 25


title: Gastric cancer 10


title: DE_BG02_R1

description: House genomic data


title: Gastric cancer 14


title: Gastric cancer 12


title: Gastric cancer 11


title: Gastric cancer 5


title: Gastric cancer 7


title: Gastric cancer 6


title: Gastric cancer 4


title: Gastric cancer 2


title: axil_9day_non-shaded 3

city: Umeå

first: Urs

last: Fischer

state: Schweden

address: Swedish Agricultural University

department: Forest Genetics and Plant Physiology

country: Sweden

institute: Umeå Plant Science Centre

description: Gene expression in leaf axil, 9 days after dark induction

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

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

data_processing: Robin affymetrix data analysis summary, normalization method: rma, P-value correction method: BH, analysis strategy: Limma, Multiple testing strategy: nestedF   P-value cut-off value for significant differential expression: 0.05  Genes that showed a log2-fold change smaller than two ignored: yes

label: biotin

organism: Populus tremula x Populus tremuloides

source_name: leaf axil, non-shaded

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

growth_protocol: Temperature was 22/18 °C (light/dark), photoperiod was 16 h, and lightTemperature was 22/18 °C (light/dark), photoperiod was 16 h, and light  intensity was 90 μmol·m-2·s-1  Temperature was 22/18 °C (light/dark), photoperiod was 16 h, and light  intensity was 90 μmol·m-2·s-1

extract_protocol: Total RNA was extracted from 3-mm-long petioles near the junction to the stem using RNeasy Plant Mini Kit (Qiagen).  spectrophotometer

treatment_protocol: For dark-induction experiments, fully expanded leaves with a petiolar angle of 75 ° to 90 ° from 1.5 m to 2 m tall trees were selected. Leaf blades were covered with aluminum bags for 9 days under standard greenhouse conditions. Control samples were bagged in transparent plastic bags of the same weight.

tag: clone

tag: treatment

value: 9 days after dark induction


title: axil_9day_shaded 4

description: Gene expression in leaf axil, 9 days non-shaded

source_name: leaf axil, shaded

value: 9 days non-shaded


title: axil_9day_non-shaded 1


title: axil_9day_non-shaded 4


title: Gastric cancer 3


title: axil_9day_shaded 3


title: axil_9day_non-shaded 2


title: Gastric cancer 8


title: Gastric cancer 1


title: axil_9day_shaded 1


title: Gastric cancer 9


title: axil_9day_shaded 2


title: NINJA murant, replica 2

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

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

data_processing: Data processing was done in R using GCRMA normalisation method

organism: Arabidopsis thaliana

source_name: NINJA murant_root

growth_protocol: Col-0 (WT) and ninja-1 seeds, both carrying the JAZ10pro-GUSPlus (JGP) reporter, were surface sterilized and equidistantly plated on a nylon mesh (200 μm pore size; product number AH03444, Lanz-Anliker AG, Rohrbach, Switzerland) resting on solid half-strength Murashige and Skoog solid medium (0.5XMS, 2.15 g/L, pH 5.7; Duchefa, Haarlem, The Netherlands) supplemented with 0.5 g/L of MES hydrate (Sigma, Buchs, Switzerland) and 0.7% agar. After seed stratification for 2 d at 4°C, plants were grown horizontally for 5 d at 21°C under 100 μE m-2 s-1 of light with 14 h light, 10 h dark photoperiod.

extract_protocol: Total RNA was extracted from 5-do roots and purified with RNeasy Plant Mini Kit (Qiagen). Three biological replicates, each consisting of 120 roots, were performed per genotype.

tag: ecotype background

tag: genotype/variation

value: ninja carrying the JAZ10pro-GUSPlus (JGP) reporter

tag: developmental stage

value: 5 days-old seedling

tag: tissue

value: root


title: NINJA murant, replica 1


title: Control, replica 2

value: WT carrying the JAZ10pro-GUSPlus (JGP) reporter


title: Panc_d12_CyT49_R4

description: Human genomic data

growth_protocol: CyT49 hESCs were differentiated in a four-step sequential process to mesendoderm (MIXL1+), definitive endoderm (SOX17+, FOXA2+); primitive gut tube (HNF1B+, HNF4A+); posterior foregut (PDX1+); and pancreatic endoderm (NKX6-1+, PTF1A+) and endocrine cells (NGN3+, NKX2-2+, PAX4+, PAX6+). Stage 1 (days 0-1): cells were maintained in RPMI 1640 (Mediatech), 0.2% FBS (HyClone), 1x GlutaMAX-1 (Life Technologies), 1% v/v penicillin/streptomycin. 1:5000 Insulin-Transferrin-Selenium (ITS) (Life Technologies), 100 ng/mL recombinant human Activin A (R&D Systems), 50 ng/mL recombinant mouse Wnt3A (R&D Systems). Stage 2 (days 1-4): addition of 25 ng/mL recombinant human KGF (R&D Systems) and 2.5 mM TGF-β RI Kinase inhibitor IV (EMD Bioscience). Stage 3 (days 5-7) cells were maintained in DMEM HI Glucose (HyClone) supplemented with 0.5x B-27 Supplement (Life Technologies), 1x GlutaMAX-1 and 1% v/v penicillin/streptomycin, 0.25 mM KAAD-Cyclopamine (Toronto Research Chemicals), 3 nM TTNPB (Sigma-Aldrich) and 50 ng/mL recombinant human Noggin (R&D Systems). Stage 4 (days 8-12): supplemented with 50 ng/mL recombinant human KGF (R&D Systems) and 50 ng/mL recombinant human EGF (R&D Systems) as previously described (Schulz et al. 2012. PLoS One. 7: e37004).

value: Pancreatic (pancreatic endoderm)


title: Splanc_CyT49_R1

description: Human genomic data


title: Mesothel_CyT49_R2

description: Human genomic data

growth_protocol: Mesothelial cells (Tbx5+, Raldh2+, WT1+) were derived from splanchnic mesoderm cells in the presence of Wnt3a (25ng/ml), BMP4 (50ng/ml) and all-trans retinoic acid (Sigma; 4μM) for 16 days.

value: Mesothelium


title: Mesothel_H9_R2

description: Human genomic data


title: Mesothel_H9_R3

description: Human genomic data


title: Control, replica 3


title: LPM_H9_R2

description: Human genomic data

growth_protocol: Lateral plate mesoderm cells (T+, Nanog-) were derived from hESC in DMEM/F12, with 100 ng/ml Activin A, 20 ng/ml Fgf2, 25 ng/ml Wnt3a (R&D Systems) and BMP4 (R&D Systems) at 100 ng/ml for 2 days.

value: Lateral Plate Mesoderm


title: LPM_H9_R5

description: Human genomic data


title: NC_CyT49_R2

description: Human genomic data

growth_protocol: For direct neural crest differentiation, hES cells were plated in defined media lacking Activin A and supplemented with 2 micromolar GSK3 inhibitor IX (BIO) and 20 micromolar SB 431542 (SB media). Neural crest identity was confirmed by immunocytochemistry and RT-PCR positive detection of p75, Hnk1, AP2 and FoxD3 NC markers, as well as negative detection of hESCs markers (Sox2, Oct4, Nanog) and neural progenitor markers (Pax6, Sox2) as previously described (Menendez et al. 2011; 2013).

value: Neural Crest


title: Control, replica 1


title: Panc_d12_CyT49_R3

description: Human genomic data


title: Mesothel_CyT49_R1

description: Human genomic data


title: NPC_H9_R2

description: Human genomic data

growth_protocol: Neural progenitors were derived in DM containing Noggin and SB431542 to induced neural differentiation. Cultures were split at day 7 and 14. FGF2 was added at day 14 to promote neural progenitor expansion. On day 28 the culture was split and neural progenitors expanded in DMEM/F12/B27 containing heregulin and FGF2. Q-PCR analysis demonstrated that these NP cells expressed SOX1, PAX6, and Musashi, but were negative for OCT4, Rex1, Nanog, and CD9, in comparison to undifferentiated cells. Immunofluorescence confirmed that these progenitors were negative for OCT4, but expressed Sox2 and Nestin. This population can be expanded and maintained for >3 months in defined conditions (Schulz et al. 2003. BMC Neuroscience 4: 27; Schulz et al. 2004. Stem Cells 22: 1218-1238).

value: Neural progenitors


title: Serum_ 3 months after ethanol sclerotherapy_rep3

city: Harbin

first: xiaoqiu

last: dong

address: Yiyuan Str 37, Harbin, Heilongjiang Province

department: Ultrasonography

institute: the Fourth Hospital of Harbin Medical University

description:
gene expression 3 months after ethanol sclerotherapy in  human blood(which patients of C)
Cb

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: Serum,3 months after ethanol sclerotherapy

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: The serum from the patients were collected before treatment and three months after treatment

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

value: female

value: blood serum


title: Serum_ before ethanol sclerotherapy_rep3

description:
gene expression before ethanol sclerotherapy in patients with ovarian endometriomas
C

source_name: Serum,before ethanol sclerotherapy


title: LPM_H9_R1

description: Human genomic data


title: ESC_CyT49_R2

description: Human genomic data

growth_protocol: Human embryonic stem cell (hESC) cultures were routinely maintained using defined media (DM) as previously described (Wang et al. 2007. Blood. 110:4111-9).

value: Embrionic stem cells


title: NINJA murant, replica 3


title: MSC_H9_R1

description: Human genomic data

growth_protocol: For mesenchymal differentiation, neural crest (NC) cells were cultured in media containing 10% FBS and passed every 4–5 d, MSCs were CD73+, CD44+ and CD13+ by day 5 (Menendez et al. 2011; 2013).

value: Mesenchimal stem cells


title: Serum_ 3 months after ethanol sclerotherapy_rep2

description:
gene expression 3 months after ethanol sclerotherapy in  human blood(which patients of B)
Bb


title: Serum_ before ethanol sclerotherapy_rep2

description:
gene expression before ethanol sclerotherapy in patients with ovarian endometriomas
B


title: Serum_ before ethanol sclerotherapy_rep1

description:
gene expression before ethanol sclerotherapy in patients blood with ovarian endometriomas
A


title: NC_H9_R1

description: Human genomic data


title: NC_CyT49_R1

description: Human genomic data


title: Serum_ 3 months after ethanol sclerotherapy_rep1

description:
gene expression 3 months after ethanol sclerotherapy in human blood(which patients of A)
Ab


title: LPM_H9_R4

description: Human genomic data


title: Liver_d16_CyT49_R1

description: Human genomic data

growth_protocol: Liver differentiation of CyT49 hESCs was carried out using modifications to pancreatic differentiation (medium supplemented with 100 ng/mL BMP4 (R&D Systems) and 25 ng/mL FGF2 (Sigma) to stages 2-4 resulting in an APF+, Albumin+ and TAT+ cell population (Schulz et al. 2012. PLoS One. 7: e37004).

value: Liver day 16


title: ESC_CyT49_R1

description: Human genomic data


title: DE_CyT49_R4

description: Human genomic data

growth_protocol: CyT49 hESCs were differentiated to definitive endoderm (SOX17+, FOXA2+) by rotational suspension culture in RPMI 1640 (Mediatech), 0.2% FBS (HyClone), 1x GlutaMAX-1 (Life Technologies), 1% v/v penicillin/streptomycin, 1:5000 Insulin-Transferrin-Selenium (ITS) (Life Technologies), 100 ng/mL recombinant human Activin A (R&D Systems), 50 ng/mL recombinant mouse Wnt3A (R&D Systems) as previously described (Schulz et al. 2012. PLoS One. 7: e37004).

value: Definitive Endoderm


title: DE_CyT49_R1

description: Human genomic data


title: Bladder tumor UC_0495_1

city: Lund

first: Mattias

last: Aine

address: Klinikgatan 28

department: Oncology

institute: Lund University

hyb_protocol: According to manufacturers specifications at the Nimblegen genomics facility

data_processing: Control hybridization probes as well as all probes not mapping to hg18 autosomes were removed and raw intensities were log2 transformed, the resulting individual dye channels were lowess normalized with respect to probe GC content, ratios were formed by subtracting the Cy3 channel intensities from the Cy5 intensities and the resulting matrix was quantile normalized. Replicate probes were median merged and a PCA-based method for removal of technical variation was applied (Lauss et al. 2013, Cancer informatics).

source_name: Input DNA

growth_protocol: Primary tumor DNA

extract_protocol: Genomic DNA was extracted using DNeasy/Allprep (QIAGEN)  spin columns acording to manufacturers specifications, 1250ng genomic DNA was subjected to sonication followed by MeDIP (Diagenode), WGA whole genome amplification (Sigma-Aldrich) and WGA2 re-amplification (Sigma-Aldrich), yielding sufficient amounts of DNA for hybridization to Nimblegen arrays. All sample and input reactions were treated in parallel and (where possible) subjected to the same protocol steps.

treatment_protocol: MeDIP (WGA)

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: B

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation

source_name: MeDIP DNA

treatment_protocol: Input Control (WGA)


title: Bladder tumor UC_0611_1

scan_protocol: According to manufacturers specifications at the Nimblegen genomics facility

tag: Sex

value: F


title: genomic DNA from whole blood of subject Sample112

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values in Series supplementary file

label: Cy3 and Cy5

source_name: Whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from EDTA tubes using the RecoverEase DNA Isolation Kit.

value: whole blood

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband

value: sister


title: genomic DNA from whole blood of subject Sample110

tag: tissue

value: mother


title: Bladder tumor UC_0438_1

label_protocol: According to manufacturers specifications at the Nimblegen genomics facility

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch


title: genomic DNA from whole blood of subject Sample108

tag: Sex

value: male

value: brother


title: genomic DNA from whole blood of subject Sample111

tag: age

value: father


title: genomic DNA from whole blood of subject Sample107

tag: dna methylation age


title: DE_CyT49_R2

description: Human genomic data

tag: differentiation stage

tag: cell line


title: Bladder tumor UC_0779_1

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample106

tag: tissue

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Bladder tumor UC_0554_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: Sex


title: Bladder tumor UC_0237_1

value: DNeasy

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: Bladder tumor UC_0193_1

tag: tissue

tag: tp53 mutation


title: Bladder tumor UC_0608_1


title: genomic DNA from whole blood of subject Sample113

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number


title: genomic DNA from whole blood of subject Sample105

tag: relation to proband


title: IPS-TIP-3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: 07-28-11_C_Deng_YL#9_Mo_Gene1_0_ST_IPS-TIP-3

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

data_processing: RMA by software Partek

organism: Mus musculus

source_name: differentiated inducible pluripotent stem cells derived from tail tip fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted by RNA STAT-60TM solution according to manufacturer's instruction (Tel-Test, INC).

tag: cell type


title: genomic DNA from whole blood of subject Sample109

tag: Sex


title: Bladder tumor UC_0780_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch


title: Bladder tumor UC_0614_1

tag: tissue

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0753_1


title: genomic DNA from whole blood of subject Sample103

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Bladder tumor UC_0726_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: Sex


title: Bladder tumor UC_0106_2

tag: tissue

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: DE_CyT49_R3

description: Human genomic data

tag: differentiation stage

tag: cell line


title: genomic DNA from whole blood of subject Sample102

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Bladder tumor UC_0591_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: Sex

tag: tp53 mutation


title: Bladder tumor UC_0238_1

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: Bladder tumor UC_0257_1


title: Bladder tumor UC_0548_1


title: IPS-MEP_3

description: 07-28-11_C_Deng_YL#6_Mo_Gene1_0_ST_IPS-MEP_3

source_name: differentiated inducible pluripotent stem cells derived from mammary epithelial cells

tag: cell type


title: genomic DNA from whole blood of subject Sample104

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample101

tag: tissue

tag: Sex


title: IPS-TIP-2

description: 07-28-11_C_Deng_YL#8_Mo_Gene1_0_ST_IPS-TIP-2

value: differentiated inducible pluripotent stem cells derived from tail tip fibroblasts


title: IPS-MEP_2

description: 07-28-11_C_Deng_YL#5_Mo_Gene1_0_ST_IPS-MEP_2

value: differentiated inducible pluripotent stem cells derived from mammary epithelial cells


title: genomic DNA from whole blood of subject Sample99


title: IPS-MEP_1

description: 07-28-11_C_Deng_YL#4_Mo_Gene1_0_ST_IPS-MEP_1


title: Bladder tumor UC_0589_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: tp53 mutation


title: MEP_C2

description: 07-28-11_C_Deng_YL#2_Mo_Gene1_0_ST_MEP_C2

source_name: Freshly isolated mammary epithelial cells

tag: cell type


title: Bladder tumor UC_0705_1

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: genomic DNA from whole blood of subject Sample100

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: MEP_C3

description: 07-28-11_C_Deng_YL#3_Mo_Gene1_0_ST_MEP_C3

value: Freshly isolated mammary epithelial cells


title: Bladder tumor UC_0584_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: Sex


title: AH017 control iPSc clone 7

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
single replicate
AH017 control iPSc clone 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor AH017, clone 7

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

growth_protocol: culture conditions: mTeSR-1 + matrigel

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: cell type

tag: gender


title: genomic DNA from whole blood of subject Sample97

tag: age

tag: dna methylation age


title: Bladder tumor UC_0778_1

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Normal Urothelium N_036_Urothel

tag: hoglund lab uid

tag: tissue

value: Normal Urothelium

tag: sjodahl 2012 molecular subtype

value: Ctrl

value: N


title: MEP_C1

description: 07-28-11_C_Deng_YL#1_Mo_Gene1_0_ST_MEP_C1


title: genomic DNA from whole blood of subject Sample98

value: whole blood

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: IPS-TIP-1

description: 07-28-11_C_Deng_YL#7_Mo_Gene1_0_ST_IPS-TIP-1

tag: cell type


title: genomic DNA from whole blood of subject Sample95

tag: Sex

tag: age

tag: dna methylation age

value: Control


title: BPAF-3.3m

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after long-time (3 months) exposure at 10 nM concentration, replicate 3.

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.10.0). It was vst transformed and normalized using Robust Spline Normalization (RSN) method.

label_protocol: Illumina Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v 2.0).

extract_protocol: Total RNA was extracted with QIAzol Lysis Reagent and purified automatically on QIAcube with RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, USA).

tag: compound

value: bisphenol AF (BPAF)

tag: exposure time

value: 3 months

tag: replicate


title: BPAF-2.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after long-time (3 months) exposure at 10 nM concentration, replicate 2.


title: AH017 control iPSc clone 3

description:
single replicate
AH017 control iPSc clone 3

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor AH017, clone 3

tag: gender


title: Bladder tumor UC_0770_1

tag: hoglund lab uid

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample96

tag: tissue

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband

value: mother


title: genomic DNA from whole blood of subject Sample93

value: Turner Syndrome and possibly Syndrome X

value: proband


title: BPAF-1.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after long-time (3 months) exposure at 10 nM concentration, replicate 1.

tag: compound

tag: exposure time

tag: replicate


title: genomic DNA from whole blood of subject Sample94

value: female

value: sister


title: Bladder tumor UC_0574_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade


title: Bladder tumor UC_0607_1

tag: tissue

tag: Sex

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample92

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband

value: father


title: BPS-3.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol S after long-time (3 months) exposure at 10 nM concentration, replicate 3.

tag: compound

value: bisphenol S (BPS)

tag: exposure time

tag: replicate


title: BPS-2.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol S after long-time (3 months) exposure at 10 nM concentration, replicate 2.


title: BPS-1.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol S after long-time (3 months) exposure at 10 nM concentration, replicate 1.


title: Bladder tumor UC_0577_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade


title: genomic DNA from whole blood of subject Sample91

tag: tissue

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

value: Down Syndrome and possibly Syndrome X


title: genomic DNA from whole blood of subject Sample90

value: whole blood

tag: disease status

tag: family number

tag: relation to proband


title: BPA-3.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol A after long-time (3 months) exposure at 10 nM concentration, replicate 3.

tag: compound

value: bisphenol A (BPA)

tag: exposure time

tag: replicate


title: Bladder tumor UC_0762_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: BPA-2.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol A after long-time (3 months) exposure at 10 nM concentration, replicate 2.


title: genomic DNA from whole blood of subject Sample89

tag: tissue

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

value: Control


title: BPA-1.3m

description: Human osteosarcoma (HOS) cells induced by bisphenol A after long-time (3 months) exposure at 10 nM concentration, replicate 1.

tag: compound

tag: exposure time

value: 3 months

tag: replicate


title: Bladder tumor UC_0721_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: F


title: Bladder tumor UC_0536_1

tag: tissue

value: B

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample87

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Syndrome X

tag: family number

tag: relation to proband

value: proband


title: C-3.3m

description: Human osteosarcoma (HOS) cells used as a control for long-time (3 months) exposure, replicate 3.

tag: compound

value: none (control)

tag: exposure time

tag: replicate


title: genomic DNA from whole blood of subject Sample88

tag: tissue

value: male


title: Bladder tumor UC_0113_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade


title: Bladder tumor UC_0518_1

tag: Sex

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: C-2.3m

description: Human osteosarcoma (HOS) cells used as a control for long-time (3 months) exposure, replicate 2.

tag: compound

tag: exposure time


title: genomic DNA from whole blood of subject Sample86

tag: tissue

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband

value: mother


title: C-1.3m

description: Human osteosarcoma (HOS) cells used as a control for long-time (3 months) exposure, replicate 1.

tag: replicate


title: genomic DNA from whole blood of subject Sample83


title: genomic DNA from whole blood of subject Sample84


title: Bladder tumor UC_0345_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: D

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade


title: Bladder tumor UC_0094_1

tag: tissue

tag: Sex

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: BPAF-3.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after short-time (8 hours) exposure at 10 nM concentration, replicate 3.

tag: compound

value: bisphenol AF (BPAF)

tag: exposure time

value: 8 hours


title: Bladder tumor UC_0210_2

tag: hoglund lab uid

value: Ta


title: genomic DNA from whole blood of subject Sample82

value: whole blood

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample85

value: father


title: Bladder tumor UC_0757_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: F


title: BPAF-2.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after short-time (8 hours) exposure at 10 nM concentration, replicate 2.

tag: compound

tag: exposure time

tag: replicate


title: Bladder tumor UC_0579_1

tag: hoglund lab uid

tag: tissue

tag: Sex

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: BPAF-1.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol AF after short-time (8 hours) exposure at 10 nM concentration, replicate 1.


title: Bladder tumor UC_0622_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: M


title: genomic DNA from whole blood of subject Sample79

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample81


title: BPS-2.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol S after short-time (8 hours) exposure at 10 nM concentration, replicate 2.

tag: compound

value: bisphenol S (BPS)

tag: exposure time

tag: replicate


title: genomic DNA from whole blood of subject Sample78

tag: tissue

tag: Sex

value: Syndrome X

value: proband


title: Bladder tumor UC_0626_1

tag: hoglund lab uid

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: Bladder tumor UC_0561_1a

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: B

tag: tp53 mutation


title: Bladder tumor UC_0287_1

value: DNeasy


title: genomic DNA from whole blood of subject Sample77

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband

value: mother


title: Bladder tumor UC_0782_1

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: Sex


title: Bladder tumor UC_0335_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation


title: BPS-3.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol S after short-time (8 hours) exposure at 10 nM concentration, replicate 3.

tag: compound

tag: exposure time

tag: replicate


title: BPS-1.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol S after short-time (8 hours) exposure at 10 nM concentration, replicate 1.


title: genomic DNA from whole blood of subject Sample75

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample80

tag: tissue

tag: Sex


title: AH017 control fibroblasts

description: HDF AH017

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: dermal fibroblasts, control donor AH017

label_protocol: Standard Illumina labelling protocol

growth_protocol: culture conditions: ADMEM + 10% FCS

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: cell type

value: dermal fibroblasts

tag: gender


title: BPA-3.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol A after short-time (8 hours) exposure at 10 nM concentration, replicate 3.

value: bisphenol A (BPA)

value: 8 hours


title: Bladder tumor UC_0751_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: tp53 mutation


title: Bladder tumor UC_0580_1

tag: pik3ca mutation


title: Bladder tumor UC_0348_1

tag: tissue

value: D


title: AH017 control iPSc clone 7

value: induced pluripotent stem cell line derived from dermal fibroblasts


title: BPA-2.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol A after short-time (8 hours) exposure at 10 nM concentration, replicate 2.

tag: compound

tag: exposure time

tag: replicate


title: BPA-1.8h

description: Human osteosarcoma (HOS) cells induced by bisphenol A after short-time (8 hours) exposure at 10 nM concentration, replicate 1.


title: Bladder tumor UC_0336_2

tag: hoglund lab uid

tag: Sex


title: genomic DNA from whole blood of subject Sample74

value: whole blood

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample72

value: sister


title: Bladder tumor UC_0537_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: M

tag: fgfr3 mutation


title: genomic DNA from whole blood of subject Sample76

tag: tissue

tag: Sex

tag: age

tag: dna methylation age


title: genomic DNA from whole blood of subject Sample73

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status


title: Splanc_H9_R2

description: Human genomic data

source_name: Early-replicating DNA

growth_protocol: Splanchnic mesoderm (PDGFRα+, GATA4+, FoxF1+, ISL1+ and Tbx20+) were derived from hESC in DMEM/F12, with 100 ng/ml Activin A, 20 ng/ml Fgf2, 25 ng/ml Wnt3a (R&D Systems) and BMP4 (R&D Systems) at 100 ng/ml for 4 days.

tag: differentiation stage

value: Splanchnic mesoderm

tag: cell line

source_name: Late-replicating DNA


title: C-3.8h

description: Human osteosarcoma (HOS) cells used as a control for short-time (8 hours) exposure, replicate 3.

tag: compound

value: none (control)

tag: exposure time

tag: replicate


title: Normal Urothelium N_035_Urothel

tag: hoglund lab uid

value: Normal Urothelium

tag: sjodahl 2012 molecular subtype

value: Ctrl

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

value: N

tag: pik3ca mutation

tag: tp53 mutation


title: Splanc_CyT49_R2

description: Human genomic data


title: C-2.8h

description: Human osteosarcoma (HOS) cells used as a control for short-time (8 hours) exposure, replicate 2.


title: Splanc_H9_R1

description: Human genomic data


title: genomic DNA from whole blood of subject Sample71

tag: tissue

tag: Sex

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: family number

tag: relation to proband

value: mother


title: C-1.8h

description: Human osteosarcoma (HOS) cells used as a control for short-time (8 hours) exposure, replicate 1.

tag: compound

tag: exposure time

tag: replicate


title: genomic DNA from whole blood of subject Sample70

value: male

tag: disease status

value: brother


title: Bladder tumor UC_0398_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

value: F

tag: fgfr3 mutation


title: AH017 control iPSc clone 3

tag: cell type

value: induced pluripotent stem cell line derived from dermal fibroblasts

tag: gender


title: Bladder tumor UC_0493_1

tag: tissue

tag: wga reamplification batch

tag: Sex

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0393_1

tag: hoglund lab uid


title: genomic DNA from whole blood of subject Sample69

value: whole blood

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample68


title: SM_H9_R1

description: Human genomic data

growth_protocol: Smooth muscle cells (SMA+, SM-MHC+, CALD1+, calponin+) were differentiated from hESC in DMEM/F12, with 100 ng/ml Activin A, 20 ng/ml Fgf2, 25 ng/ml Wnt3a and BMP4 at 100 ng/ml for 18 days.

tag: differentiation stage

value: Smooth Muscle

tag: cell line


title: Bladder tumor UC_0506_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation


title: genomic DNA from whole blood of subject Sample66

tag: tissue

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

value: sister


title: genomic DNA from whole blood of subject Sample65

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Bladder tumor UC_0556_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: wga reamplification batch

value: M

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0694_1

tag: tissue

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation


title: genomic DNA from whole blood of subject Sample67

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Syndrome X

value: proband


title: genomic DNA from whole blood of subject Sample63

tag: family number

tag: relation to proband

value: grandmother


title: genomic DNA from whole blood of subject Sample64

value: father


title: Panc_d12_CyT49_R1

description: Human genomic data

tag: differentiation stage

value: Pancreatic (pancreatic endoderm)

tag: cell line


title: Panc_d5_CyT49_R1

description: Human genomic data

value: Pancreatic (foregut endoderm)


title: NPC_H9_R1

description: Human genomic data

value: Neural progenitors


title: Bladder tumor UC_0563_1

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: wga reamplification batch

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0279_1

value: DNeasy

tag: sonication batch

tag: ip-batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: Sex

tag: fgfr3 mutation


title: Panc_d8_CyT49_R1

description: Human genomic data

tag: differentiation stage

value: Pancreatic (pre-pancreatic endoderm)


title: Bladder tumor UC_0575_1


title: Bladder tumor UC_0713_1


title: genomic DNA from whole blood of subject Sample61

value: whole blood

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Panc_d12_CyT49_R2

description: Human genomic data

tag: cell line


title: NC_H9_R3

description: Human genomic data

value: Neural Crest


title: genomic DNA from whole blood of subject Sample62

tag: tissue

value: Control


title: Bladder tumor UC_0055_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: D

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: wga reamplification batch

value: F

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0213_1

tag: ip-batch

tag: who1999 stage simple

tag: who 1999 grade

tag: Sex

value: M

tag: fgfr3 mutation


title: genomic DNA from whole blood of subject Sample60

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Bladder tumor UC_0103_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch


title: NC_H9_R2

description: Human genomic data

tag: differentiation stage

tag: cell line


title: genomic DNA from whole blood of subject Sample56

tag: Sex

value: male

tag: age


title: Bladder tumor UC_0760_1

value: AllPrep

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: genomic DNA from whole blood of subject Sample59

tag: tissue

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: SM_H9_R2

description: Human genomic data

tag: differentiation stage

value: Smooth Muscle

tag: cell line


title: MSC_H9_R2

description: Human genomic data

value: Mesenchimal stem cells


title: Normal Urothelium N_037_Urothel

tag: hoglund lab uid

value: Normal Urothelium

tag: sjodahl 2012 molecular subtype

value: Ctrl

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

value: N

tag: Sex


title: genomic DNA from whole blood of subject Sample54

tag: tissue

tag: age

tag: dna methylation age


title: genomic DNA from whole blood of subject Sample55

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard


title: genomic DNA from whole blood of subject Sample53

tag: disease status

tag: family number

tag: relation to proband


title: Mesothel_H9_R1

description: Human genomic data

tag: differentiation stage

value: Mesothelium

tag: cell line


title: Bladder tumor UC_0491_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: B

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0415_1

tag: tissue

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: Sex


title: Bladder tumor UC_0781_1


title: Bladder tumor UC_0542_2

value: DNeasy


title: genomic DNA from whole blood of subject Sample50

value: whole blood

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample52

value: Control


title: genomic DNA from whole blood of subject Sample51


title: 8hrsTri6_WT-C

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

hyb_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

data_processing: The probe-level data for the whole profiling experiment were assembled into one dataset using the Just RMA protocol implemented in the software FlexArray 1.6.1 (Genome Quebec, Montreal, Canada) using the default parameters.

organism: Triticum aestivum

source_name: Roblin, spk 0 Tri6Δ, spk 2 WT for 8 hrs

growth_protocol: Plants were grown in growth cabinets at 20 C/16 hrs daylight; 16 C/8 hrs night until heads reached mid anthesis; then they were moved to the misting room.

extract_protocol: Total RNA from each sample was isolated using a modified version of the Trizol method (Invitrogen Life Technologh, ON, Canada).  The RNA samples were treated with an RNase-free DNase (Qiagen, Mississauga, Canada) and cleaned up using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Wheat heads at mid-anthesis were inoculated as follow: 10 µl of either water (mock inoculation) or a 100,000 spores/ml suspension of the Fusarium graminearum mutant strain NoxABΔ (DAOM 239571) or Tri6Δ (DAOM 237993) was point-inoculated into each of two basal florets of one developed spikelet (spk 0) of 16 wheat heads.  The inoculated plants were mist-irrigated for 10 second intervals every 15 minutes for 24 hours to maintain high humidity, at a temperature of 25 oC. After 24 hrs of misting, a spikelet (spk 2) close to spk 0 was inoculated in the same manner with either water or  a 100,000 spores/ml suspension of the pathogenic Fusarium graminearum strain DAOM 233423. Eight treated heads were used for each three biological replicates, and inoculated spikelets spk 2 were sampled at 8 and 24 hours after the second inoculation.  The sampled tissues were immediately frozen in liquid nitrogen and stored at -80 C until used.

tag: genotype

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg Tri6Δ

tag: inoculation treatment 2 on spk 2

value: Fg WT

tag: hours after inoculation 2


title: Bladder tumor UC_0530_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0712_1

tag: sonication batch

tag: ip-batch

tag: Sex

value: F


title: genomic DNA from whole blood of subject Sample58

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 8hrsTri6_WT-B

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

scan_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.

tag: genotype

tag: tissue

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: genomic DNA from whole blood of subject Sample57

value: male


title: 8hrsTri6_WT-A

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

label_protocol: According to Affymetrix instructions for the GeneChip® 3' IVT Express Kit. All samples were processed in one experimental batch.


title: Bladder tumor UC_0583_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Liver_d8_CyT49_R1

description: Human genomic data

tag: differentiation stage

value: Liver day 8

tag: cell line


title: NSC_#3

city: Houston

first: Xin

last: HU

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: MD Anderson Cancer Center

description:
EP:TagBFPnls-V5, pBase
5_Dyn2-BFP-Sorted-NoCre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

scan_protocol: standard protocols for Affymetrix GeneChip™3000 7G laser confocal slide scanner

data_processing: Expression levels of 20,716 genes were extracted from Affymetrix Mouse Gene 1.0 ST Array using AROMA package with MoGene-1_0-st-v1,r3.cdf probe definition file and mogene10sttranscriptcluster.db annotation file.

source_name: EGFP purified neural stem and progenitor cells

label_protocol: standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array

growth_protocol: The SVZ on the left side of the mouse brain (site of EP) was then sub-dissected using scissors and placed into a 10 cm petri dish containing 1 mL of media (as described in Cell Culture Methods below). Using a sterile utility razor blade, tissue was chopped for approximately 30 seconds or until pieces were 1 mm3 or smaller. Using a P1000, the cell suspension was carefully and slowly pipetted against the wall of the petri dish 5 times and then transferred into a 15 mL conical tube. Additionally, 1 mL of media was used to wash off the petri dish to pick up any cells left behind and placed into the collecting conical tube. Cells were spun down at 1350 rpm for 2 minutes. Supernatant was aspirated and the pellet was resuspended in 4-6 mL (depending on pellet size) of accutase (Millipore SCR005) and incubated at 37°C in 5% CO2 for 10 minutes. During this incubation, tubes were inverted approximately 5 times, disrupting the cell suspension, every 3 minutes. An equal volume of fresh media was then added to neutralize the accutase and cells were spun down at 1350 rpm for 3 minutes. Supernatant was then removed and pellets were resuspended in fresh media and placed into T75 cm2 flasks coated with CELLstart (Life Technologies A10142-01). Cells were grown in media containing Neurobasal-A Medium (Life Technologies 10888-022) supplemented with B-27 without vitamin A (Life Technologies 12587-010), GlutaMAX (Life Technologies 35050-061), Anti-biotic Anti-mycotic (Life Technologies 15240-062), Epidermal Growth Factor (EGF, Sigma E9644), heparin (Sigma), and Fibroblast Growth Factor (FGF, Millipore GF003). Media was changed every two days.

extract_protocol: RNA from EGFP+ NSCs and EGFP+ tumor cells was isolated using RNeasy+ Kits according to manufacturer’s protocols

treatment_protocol: Once harvested cells reached approximately 80% confluency, media was removed and T75 cm2 flasks were passaged with 2 mL of accutase at 37°C in 5% CO2 for 3 minutes. Accutase was neutralized with 2mL of media and cells were spun down at 1350 rpm for 3 minutes. Supernatant was removed and cells were resuspended in 2 mL of fresh media, using a P1000 in order to disrupt the cells in a careful yet vigorous manner. In increments of approximately 200 μL, cells were filtered through a 100 μm filter. The collected filtrate was then passed through a 70 μm filter. This filtrate was then placed on ice. Cells were then FACS sorted for GFP with tight gates making sure only the cells highly expressing GFP were collected, indicative of either membrane UFEK-PB or HRAS-GFP-PB plasmid expression. Cells were collected into fresh media kept cold and on ice. Once all cells were sorted, the collected cells were pelleted and placed into new T75 cm2 flasks coated with CELLstart.

tag: strain

value: C57/Bl6 Dnm2 floxed mice


title: Panc_d5_CyT49_R2

description: Human genomic data

growth_protocol: CyT49 hESCs were differentiated in a four-step sequential process to mesendoderm (MIXL1+), definitive endoderm (SOX17+, FOXA2+); primitive gut tube (HNF1B+, HNF4A+); posterior foregut (PDX1+); and pancreatic endoderm (NKX6-1+, PTF1A+) and endocrine cells (NGN3+, NKX2-2+, PAX4+, PAX6+). Stage 1 (days 0-1): cells were maintained in RPMI 1640 (Mediatech), 0.2% FBS (HyClone), 1x GlutaMAX-1 (Life Technologies), 1% v/v penicillin/streptomycin. 1:5000 Insulin-Transferrin-Selenium (ITS) (Life Technologies), 100 ng/mL recombinant human Activin A (R&D Systems), 50 ng/mL recombinant mouse Wnt3A (R&D Systems). Stage 2 (days 1-4): addition of 25 ng/mL recombinant human KGF (R&D Systems) and 2.5 mM TGF-β RI Kinase inhibitor IV (EMD Bioscience). Stage 3 (days 5-7) cells were maintained in DMEM HI Glucose (HyClone) supplemented with 0.5x B-27 Supplement (Life Technologies), 1x GlutaMAX-1 and 1% v/v penicillin/streptomycin, 0.25 mM KAAD-Cyclopamine (Toronto Research Chemicals), 3 nM TTNPB (Sigma-Aldrich) and 50 ng/mL recombinant human Noggin (R&D Systems). Stage 4 (days 8-12): supplemented with 50 ng/mL recombinant human KGF (R&D Systems) and 50 ng/mL recombinant human EGF (R&D Systems) as previously described (Schulz et al. 2012. PLoS One. 7: e37004).

value: Pancreatic (foregut endoderm)


title: 8hrsTri6_dh20-B

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 8 hrs after inoculation 2

source_name: Roblin, spk 0 Tri6Δ, spk 2 water for 8 hrs

tag: genotype

tag: tissue

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

value: water


title: NSC_#2

description:
EP:Histone 3.3-EGFP, TagBFPnls-V5, pBase
4_WT-H3.3-GFP-Sorted


title: genomic DNA from whole blood of subject Sample48

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: 8hrsTri6_dh20-A

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 8 hrs after inoculation 2

tag: hours after inoculation 2


title: 8hrsTri6_dh20-C

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 8 hrs after inoculation 2


title: Liver_d5_CyT49_R1

description: Human genomic data

tag: differentiation stage

value: Liver day 5

tag: cell line


title: LPM_H9_R3

description: Human genomic data

value: Lateral Plate Mesoderm


title: NSC_#1

description:
EP:Membrane EGFP, TagBFPnls-V5, pBase
4_Control

tag: strain


title: genomic DNA from whole blood of subject Sample49

tag: tissue

value: whole blood

value: female


title: Bladder tumor UC_0565_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0576_1

tag: Sex


title: genomic DNA from whole blood of subject Sample46

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: Bladder tumor UC_0421_1

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch


title: DE_CyT49_R5

description: Human genomic data

tag: differentiation stage

value: Definitive Endoderm

tag: cell line


title: 8hrs_NoxAB_WT_C

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

source_name: Roblin, spk 0 NoxABΔ, spk 2 WT for 8 hrs

tag: genotype

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg NoxABΔ

tag: inoculation treatment 2 on spk 2

value: Fg WT

tag: hours after inoculation 2


title: 8hrs_NoxAB_WT_B

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2


title: genomic DNA from whole blood of subject Sample45

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status


title: Hras_Line_#3

description:
EP:EGFP-Hras G12V, TagBFPnls-V5, pBase
3_HRAS_4

source_name: EGFP purified Hras G12V Glioma

tag: strain


title: Liver_d16_CyT49_R2

description: Human genomic data

value: Liver day 17


title: Liver_d16_CyT49_R3

description: Human genomic data

value: Liver day 18


title: Bladder tumor UC_0429_1a

tag: hoglund lab uid

tag: tissue

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Hras_Line_#2

description:
EP:EGFP-Hras G12V, TagBFPnls-V5, pBase
2_HRAS_2


title: genomic DNA from whole blood of subject Sample44

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample47

tag: tissue

tag: cor sample vs gold standard

tag: disease status


title: NC_H9_R4

description: Human genomic data

tag: differentiation stage

value: Neural Crest

tag: cell line


title: 8hrs_NoxAB_WT_A

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

tag: genotype

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: Erbb2_Line_#2

description:
EP:EGFP-P2A-Erbb2 V664E, TagBFPnls-V5, pBase
2_Erbb2_Tumor_2

source_name: EGFP purified Erbb2 V664E Glioma

tag: strain


title: 8hrs_NoxAB_dH20_C

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 8 hrs after inoculation 2

source_name: Roblin, spk 0 NoxABΔ, spk 2 water for 8 hrs

value: water


title: Hras_Line_#1

description:
EP:EGFP-Hras G12V, TagBFPnls-V5, pBase
1_HRAS_1


title: 8hrs_NoxAB_dH20_B

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 8 hrs after inoculation 2


title: Bladder tumor UC_0154_2

source_name: Input DNA

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: D

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: Sex

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation

source_name: MeDIP DNA


title: genomic DNA from whole blood of subject Sample42

source_name: Whole Blood

tag: tissue

value: whole blood

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: HFC_Male_LKO_rep3

description: Gene expression data from a male LKO mouse X624 on a high-fat diet with cholesterol

hyb_protocol: 150 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to the manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Male LKO mouse X624 on a high-fat diet with cholesterol

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Cyp51 KO (LKO) mice and their control littermates (LWT) were bred at the Medical Experimental Centre, Faculty of Medicine, University of Ljubljana, Slovenia and maintained in a temperature and humidity controlled environment under 12h light/dark cycle (lights were on from 7.00 am to 7.00 pm). Animals had ad libitum access to food and acidified tap water (pH = 3).

extract_protocol: Mice were euthanized after a 5 h fast with cervical dislocation at the same time of the light period (11.30 am – 3.00 pm) in order to avoid diurnal variability as much as possible. Liver was removed, weighed, cut to thin slices and snap-frozen in liquid nitrogen and stored at - 80° C for subsequent analysis. Liver samples were first pulverized and then isolated using QuickGene Tissue Kit S II and QuickGene-810 (Fujifilm, Singapore) according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments. All samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

treatment_protocol: After the weaning period, 3-week LKO and LWT mice of both sexes were randomly assigned to one of the three diets: standard laboratory chow (1324, Altromin, Lage, Germany) regarded as a low-fat no-cholesterol diet (LFnC); high-fat diet without cholesterol (HFnC) (D12108C, Research Diets, Inc., New Brunswick, NJ, USA) and high-fat diet with 1.25% (w/w) of cholesterol (HFC) (D12106C, Research Diets, Inc., New Brunswick, NJ, USA). A total of 136 mice (9 to 13 animals per group) were fed the specified diets for 16 weeks.

tag: strain

value: liver

tag: diet

value: HFC

tag: genotype

value: Cyp51 KO LKO

tag: batch

tag: animal

tag: treatment

value: high-fat diet with cholesterol


title: Erbb2_Line_#1

description:
EP:EGFP-P2A-Erbb2 V664E, TagBFPnls-V5, pBase
1_Erbb2_Tumor_1


title: genomic DNA from whole blood of subject Sample43

tag: Sex

value: Control


title: 8hrs_NoxAB_dH20_A

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed NoxABΔ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg NoxABΔ in spk 0 then water in spk 2, 8 hrs after inoculation 2

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg NoxABΔ

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: Bladder tumor UC_0456_2

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: B

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: 8hrs_dH20_WT-B

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

source_name: Roblin, spk 0 water, spk 2 WT for 8 hrs

tag: genotype

tag: tissue age

tag: inoculation treatment 1 on spk 0

value: water

value: Fg WT


title: Bladder tumor UC_0525_1

tag: hoglund lab uid

value: AllPrep

tag: Sex

value: M


title: genomic DNA from whole blood of subject Sample40

tag: tissue

value: whole blood

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: Erbb2_Line_#3

description:
EP:EGFP-P2A-Erbb2 V664E, TagBFPnls-V5, pBase
3_Erbb2_Tumor_3

tag: strain


title: genomic DNA from whole blood of subject Sample41


title: 8hrs_dH20_WT-C

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: genomic DNA from whole blood of subject Sample38

value: male


title: Bladder tumor UC_0545_1

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: HFC_Male_LWT_rep3

description: Gene expression data from a male LWT mouse X524 on a high-fat diet with cholesterol

source_name: Male LWT mouse X524 on a high-fat diet with cholesterol

tag: tissue

value: liver

tag: diet

value: HFC

tag: genotype

value: LWT

tag: Sex

tag: batch

tag: animal

tag: treatment

value: high-fat diet with cholesterol


title: Bladder tumor UC_0195_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: F


title: HFC_Female_LWT_rep3

description: Gene expression data from a female LWT mouse X513 on a high-fat diet with cholesterol

source_name: Female LWT mouse X513 on a high-fat diet with cholesterol

tag: strain


title: 8hrs_dH20_dH20-B

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 8 hrs after inoculation 2

source_name: Roblin, spk 0 water, spk 2 water for 8 hrs

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: HFnC_Male_LKO_rep3

description: Gene expression data from a male LKO mouse X535 on a high-fat no-cholesterol diet

source_name: Male LKO mouse X535 on a high-fat no-cholesterol diet

value: HFnC

value: Cyp51 KO LKO

value: high-fat no-cholesterol diet


title: Bladder tumor UC_0601_1

value: Bladder tumor

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: 8hrs_dH20_dH20-A

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 8 hrs after inoculation 2

tag: genotype

tag: tissue

value: water


title: genomic DNA from whole blood of subject Sample37

value: whole blood

tag: Sex

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: genomic DNA from whole blood of subject Sample36

value: female


title: 8hrs_dH20_dH20-c

description:
Roblin, 8 hrs after water inoculation in spk 2, which followed water inoculation in spk 0, rep c
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then water in spk 2, 8 hrs after inoculation 2

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: Bladder tumor UC_0720_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation


title: genomic DNA from whole blood of subject Sample39

tag: tissue

tag: Sex

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: HFnC_Female_LKO_rep3

description: Gene expression data from a female LKO mouse X711 on a high-fat no-cholesterol diet

source_name: Female LKO mouse X711 on a high-fat no-cholesterol diet

tag: strain

value: liver

tag: diet

tag: genotype

tag: batch

tag: animal

tag: treatment


title: genomic DNA from whole blood of subject Sample35


title: Normal Urothelium N_034_Urothel

tag: hoglund lab uid

value: Normal Urothelium

tag: sjodahl 2012 molecular subtype

value: Ctrl

tag: lauss 2012 epitype

tag: dna extraction method

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: N

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: 24hTri6_Wt-C

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

source_name: Roblin, spk 0 Tri6Δ, spk 2 WT for 24 hrs

tag: genotype

value: spring wheat cv Roblin

tag: tissue

value: inoculated spikelet spk 2

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg Tri6Δ

tag: inoculation treatment 2 on spk 2

value: Fg WT

tag: hours after inoculation 2


title: HFnC_Male_LWT_rep3

description: Gene expression data from a male LWT mouse X426 on a high-fat no-cholesterol diet

source_name: Male LWT mouse X426 on a high-fat no-cholesterol diet

tag: strain

tag: diet

value: HFnC

value: LWT

tag: Sex

tag: batch

tag: animal

tag: treatment

value: high-fat no-cholesterol diet


title: 24hTri6_Wt-B

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2


title: HFnC_Female_LWT_rep3

description: Gene expression data from a female LWT mouse X632 on a high-fat no-cholesterol diet

source_name: Female LWT mouse X632 on a high-fat no-cholesterol diet

value: F


title: genomic DNA from whole blood of subject Sample34

value: whole blood

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: HFC_Female_LKO_rep3

description: Gene expression data from a female LKO mouse X706 on a high-fat diet with cholesterol

source_name: Female LKO mouse X706 on a high-fat diet with cholesterol

tag: tissue

value: HFC

tag: genotype

value: Cyp51 KO LKO

value: high-fat diet with cholesterol


title: Bladder tumor UC_0405_1

tag: hoglund lab uid

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: 24hTri6_Wt-A

description:
Roblin, 24 hrs after WT inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then Fg WT in spk 2, 24 hrs after inoculation 2

value: spring wheat cv Roblin

value: inoculated spikelet spk 2

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

tag: hours after inoculation 2


title: Bladder tumor UC_0619_1

tag: hoglund lab uid

tag: tissue

tag: Sex


title: LFnC_Male_LKO_rep3

description: Gene expression data from a male LKO mouse X406 on a low-fat no-cholesterol diet

source_name: Male LKO mouse X406 on a low-fat no-cholesterol diet

tag: strain

value: liver

tag: diet

value: LFnC

tag: genotype

tag: batch

tag: animal

tag: treatment

value: low-fat no-cholesterol diet


title: genomic DNA from whole blood of subject Sample32

value: female

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

value: Control

tag: family number

tag: relation to proband


title: 24hTri6_H20-C

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep C
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 24 hrs after inoculation 2

source_name: Roblin, spk 0 Tri6Δ, spk 2 water for 24 hrs

tag: tissue age

value: heads after mid-anthesis

tag: inoculation treatment 1 on spk 0

value: Fg Tri6Δ

tag: inoculation treatment 2 on spk 2

value: water

tag: hours after inoculation 2


title: genomic DNA from whole blood of subject Sample33

tag: tissue

value: whole blood

tag: Sex


title: Bladder tumor UC_0384_1

tag: hoglund lab uid

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

tag: dna extraction method

value: DNeasy

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

tag: who 1999 grade

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation


title: Bladder tumor UC_0746_1


title: 8hrs_dH20_WT-A

description:
Roblin, 8 hrs after WT inoculation in spk 2, which followed water inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of water in spk 0 then Fg WT in spk 2, 8 hrs after inoculation 2

tag: genotype

tag: tissue age

tag: inoculation treatment 1 on spk 0

tag: inoculation treatment 2 on spk 2

value: Fg WT


title: 24hTri6_H20-B

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep B
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 24 hrs after inoculation 2

tag: tissue

tag: hours after inoculation 2


title: 24hTir6_H20-A

description:
Roblin, 24 hrs after water inoculation in spk 2, which followed Tri6Δ inoculation in spk 0, rep A
Gene expression data from Roblin spikelet 2, after inoculation of Fg Tri6Δ in spk 0 then water in spk 2, 24 hrs after inoculation 2


title: genomic DNA from whole blood of subject Sample31

tag: Sex

value: male

tag: age

tag: dna methylation age

tag: age acceleration vs controls

tag: age acceleration vs controls in children

tag: cor sample vs gold standard

tag: disease status

tag: family number

tag: relation to proband


title: LFnC_Male_LWT_rep3

description: Gene expression data from a male LWT mouse X614 on a low-fat no-cholesterol diet

source_name: Male LWT mouse X614 on a low-fat no-cholesterol diet

tag: strain

tag: diet

value: LWT

tag: batch

tag: animal

tag: treatment


title: LFnC_Female_LWT_rep3

description: Gene expression data from a female LWT mouse X505 on a low-fat no-cholesterol diet

source_name: Female LWT mouse X505 on a low-fat no-cholesterol diet

tag: genotype

value: F


title: Bladder tumor UC_0598_1

source_name: Input DNA

tag: hoglund lab uid

tag: tissue

value: Bladder tumor

tag: sjodahl 2012 molecular subtype

tag: lauss 2012 epitype

value: B

tag: dna extraction method

value: AllPrep

tag: nimblegen slide id

tag: sonication batch

tag: ip-batch

tag: wga reamplification batch

tag: who1999 stage simple

value: Ta

tag: who 1999 grade

value: M

tag: fgfr3 mutation

tag: pik3ca mutation

tag: tp53 mutation

source_name: MeDIP DNA


title: LFnC_Female_LKO_rep3

description: Gene expression data from a female LKO mouse X701 on a low-fat no-cholesterol diet

source_name: Female LKO mouse X701 on a low-fat no-cholesterol diet

tag: strain

value: liver

tag: diet

value: LFnC

value: Cyp51 KO LKO

tag: Sex

tag: batch

tag: animal

value: low-fat no-cholesterol diet