title: hcc_014.rep1 [tumor from HCC patient]

status: Public on Jan 31 2014

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

description: Sample name: hcc_014.rep1

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

label: biotin

molecule: total RNA

organism: Homo sapiens

extract_protocol: RNA was isolated with Triazol reagent (Invitrogen) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (10 micron-thick) sliced from 5~16-year-old FFPE blocks and archived for 6~7 years on glass slide

tag: disease state

value: hepatocellular carcinoma

tag: tissue

value: AS-FFPE tumor

tag: %p-call

tag: inter-sample correlation

tag: prediction in as-ffpe

value: S3 (HCC subclass:hepatocyte differentiation)

tag: prediction in as-ffpe (%p-call>20%)

tag: prediction confidence p-value in as-ffpe (%p-call>20%)

tag: prediction in fc-ffpe

tag: prediction confidence p-value in fc-ffpe

tag: geo accession of fc-ffpe profile


title: hcc_014.rep2 [tumor from HCC patient]

description: Sample name: hcc_014.rep2

scan_protocol: Refer to the Illumina beadarray Assay System Manual

tag: prediction confidence p-value in as-ffpe


title: RV A16-infected monocytes, 4 h after treatment

city: Madison

first: Maya

middle: R

last: Karta

state: WI

address: 1135 Biochemistry, 420 Henry Mall

department: Biomolecular Chemistry

institute: University Wisconsin-Madison

description: Gene expression data from RV A16-infected monocytes.

hyb_protocol: Fragmented cRNAs were hybridized to Affymetrix HuGeneFL arrays (Affymetrix) according to the standard protocol.

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

data_processing: The microarray images were analyzed by GeneChip software (Affymetrix) and values were normalized to the signal intensity of each chip. Quantification of each transcript's abundance in the sample was expressed as the normalized fluorescence intensity in arbitrary units . The algorithms of GeneChip software determined whether RV A16 exposure increased or decreased or did not affect transcript levels.

source_name: Purified human primary peripheral blood monocytes pooled from 5 different donors.

label_protocol: Biotin-labeled complementary RNA was synthesized from 5 ug total RNA transcribed to cDNA using BioArray High Yield RNA Transcript Kit (ENZO) according to the manufacturer's protocol.

growth_protocol: PBMCs were enriched from heparinized human whole blood via centrifugation with a Percoll bilayer. The mononuclear cells were resuspended in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin/streptomycin, 2 mM sodium pyruvate, 2 mM L-glutamine. Mononuclear cells were plated and allowed to adhere (2 h, 37 °C, 5% CO2), then washed twice with HBSS to deplete non-adherent contaminating cells.

extract_protocol: Cells were lysed in TRIzol reagent and RNA was isolated according to the manufacturer's instructions and total RNAs were pooled from the five different donors for each treatment condition.

treatment_protocol: Following overnight incubation (37 °C, 5% CO2), the cells from each patient were stimulated with medium (mock) or RV-A16 (MOI = 10) for 4 h (37 °C, 5% CO2).

value: primary peripheral blood monocytes

tag: infection

value: RV A16-infected


title: mock-infected monocytes, 4 h after treatment

description: Gene expression data from mock-infected monocytes.

value: mock-infected


title: hcc_005.rep2 [tumor from HCC patient]

description: Sample name: hcc_005.rep2

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: zebrafish embryo_hi2217 mutant_vs_WT_3

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

description:
CH1: WT sibling RNA
CH2: hi2217 mutant RNA

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) according to Agilent protocol G4140-90050 v.5.7 (www.Agilent.com) for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: Microarray data were processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies).

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of sequences. The significance cut-off for ratios of hi2217 mutant versus WT sibling was set at P ≤ 10-5 and absolute fold change equal or larger than 1.5.

organism: Danio rerio

source_name: D.rerio_RNA from WT sibling_3A

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 0.5 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye(GE Healthcare) and column purified.

growth_protocol: Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean see salts).

extract_protocol: Embryos were homogenized in RNA Stat60 (Teltest, Inc) and placed at -80C. Next, RNA was purified using standard chloroform phase separation, isopropanol precipitation, and ethanol wash steps. The RNA concentrations were determined using a Nano drop spectrophotometer, followed by DNAase treatment (Qiagen RNase-Free DNase set), and subsequent RNA cleanup (Qiagen RNA Minielute Cleanup kit). Final RNA concentrations were determined using a 1/10 dilution on the Nanodrop spectrophotometer.

treatment_protocol: Adults heterozygous for the hi2217 retroviral insertion within the HAI locus (Mathias et al 2007 JCS) were in-crossed for RNA samples from WT siblings zebrafish embryos

tag: genotype

value: wild type

source_name: D.rerio_RNA from hi2217 mutant_3B

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 0.5 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye(GE Healthcare) and column purified.

treatment_protocol: Adults heterozygous for the hi2217 retroviral insertion within the HAI locus (Mathias et al 2007 JCS) were in-crossed for RNA samples from hi2217 mutant zebrafish embryos.


title: zebrafish embryo_hi1520 mutant_vs_WT_4

description:
CH1: WT sibling RNA
CH2: hi1520 mutant RNA

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of sequences. The significance cut-off for ratios of hi1520 mutant versus WT sibling was set at P ≤ 10-5 and absolute fold change equal or larger than 1.5.

source_name: D.rerio_RNA from WT sibling_4A

treatment_protocol: Adults heterozygous for the hi1520 retroviral insertion within the Clint1 locus (Dodd et al in preparation) were in-crossed for RNA samples from WT siblings zebrafish embryos

source_name: D.rerio_RNA from hi1520 mutant_4B

treatment_protocol: Adults heterozygous for the hi1520 retroviral insertion within the Clint1 locus (Dodd et al in preparation) were in-crossed for RNA samples from hi1520 mutant zebrafish embryos


title: hcc_004.rep1 [tumor from HCC patient]

description: Sample name: hcc_004.rep1


title: prors1-2 leaves, replicate 1

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Gene expression data from 38-d-old prors1-2 leaves

hyb_protocol: Hybridisation, washing, staining, and scanning procedures were performed as described in the Affymetrix technical manual. A Hybridisation Oven 640 was used

scan_protocol: A GeneChip Scanner 3000 was used according to the Affymetrix protocol

data_processing: Normalization was done with gcRMA implemented in Flexarray.

organism: Arabidopsis thaliana

source_name: 38-d-old prors1-2 leaves

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

growth_protocol: A. thaliana plants were grown on potting soil (Stender) under controlled growth chamber conditions (16 h/8 h light/dark cycles with ~100 µmol photons m-2 s-1 on leaf surfaces). Wuxal Super fertilizer (8% N, 8% P2O5, and 6% K2O; MANNA) was used according to the manufacturer’s instructions.

extract_protocol: RNA was extracted with the Rneasy Kit (QIAGEN) according to the manufacturer’s instructions

value: leaves

tag: genotype/variation

tag: age

value: 38 day old


title: Col-0 leaves, replicate 3

description: Gene expression data from 4-week-old Col-0 leaves

source_name: 4-week-old Col-0 leaves

value: 4 week old


title: prors1-2 leaves, replicate 2


title: hcc_005.rep1 [tumor from HCC patient]

description: Sample name: hcc_005.rep1


title: zebrafish embryo_hi2217 mutant_vs_WT_2

source_name: D.rerio_RNA from WT sibling_2A

source_name: D.rerio_RNA from hi2217 mutant_2B


title: Col-0 leaves, replicate 1


title: zebrafish embryo_hi1520 mutant_vs_WT_5

source_name: D.rerio_RNA from WT sibling_5A

source_name: D.rerio_RNA from hi1520 mutant_5B


title: Col-0 leaves, replicate 2


title: prors1-2 leaves, replicate 3


title: zebrafish embryo_hi1520 mutant_vs_WT_6

source_name: D.rerio_RNA from WT sibling_6A

source_name: D.rerio_RNA from hi1520 mutant_6B


title: hcc_004.rep2 [tumor from HCC patient]

description: Sample name: hcc_004.rep2


title: zebrafish embryo_hi2217 mutant_vs_WT_1

source_name: D.rerio_RNA from WT sibling_1A

source_name: D.rerio_RNA from hi2217 mutant_1B


title: ATL sample 7

type: genomic

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: medical

country: Japan

institute: Miyazaki university

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files were processed by CNAG 3.0

label: Biotin

molecule: genomic DNA

source_name: ATL 7

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations from ATL patients  by using the standard phenol/chloroform method. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: acute-type ATL

tag: cell type

value: T lymphocyte

tag: gender

value: male


title: ATL sample 4

source_name: ATL 4

tag: disease state


title: ATL sample 9

source_name: ATL 9


title: hcc_003.rep1 [tumor from HCC patient]

description: Sample name: hcc_003.rep1

tag: tissue

value: S1 (HCC subclass:aberrant activation of the TGF-beta/WNT signaling pathways)


title: hcc_003.rep2 [tumor from HCC patient]

description: Sample name: hcc_003.rep2

tag: %p-call


title: ATL sample 10

source_name: ATL 10


title: ATL sample 6

source_name: ATL 6

value: female


title: ATL sample 5

source_name: ATL 5


title: hcc_120 [tumor from HCC patient]

description: Sample name: hcc_120

tag: inter-sample correlation

value: S2 (HCC subclass:alpha-fetoprotein positivity as well as MYC and AKT activation)


title: ATL sample 2

source_name: ATL 2


title: ATL sample 3

source_name: ATL 3


title: hcc_114 [tumor from HCC patient]

description: Sample name: hcc_114

tag: prediction in as-ffpe


title: hcc_111 [tumor from HCC patient]

description: Sample name: hcc_111

tag: prediction in as-ffpe (%p-call>20%)


title: hcc_119 [tumor from HCC patient]

description: Sample name: hcc_119

tag: prediction confidence p-value in as-ffpe (%p-call>20%)


title: ATL sample 8

source_name: ATL 8


title: hcc_112 [tumor from HCC patient]

description: Sample name: hcc_112

tag: prediction in fc-ffpe


title: hcc_125 [tumor from HCC patient]

description: Sample name: hcc_125

tag: prediction confidence p-value in fc-ffpe


title: hcc_122 [tumor from HCC patient]

description: Sample name: hcc_122

tag: geo accession of fc-ffpe profile


title: hcc_115 [tumor from HCC patient]

description: Sample name: hcc_115

tag: prediction confidence p-value in as-ffpe


title: hcc_105 [tumor from HCC patient]

description: Sample name: hcc_105


title: ATL sample 1

source_name: ATL 1


title: hcc_001.rep1 [tumor from HCC patient]

description: Sample name: hcc_001.rep1


title: DTS-3 29°C Cy5/DTS-3 20°C Cy5

city: Szeged

first: Márton

last: Kiss

address: 52 Közép fasor

department: Genetics

country: Hungary

institute: University of Szeged

hyb_protocol: 2x GEx Hybridization buffer HI-RPM were added, and samples were applied to microarrays enclosed in hybridization chambers for 17 hours at 65°C, 10 RPM. After hybridization, slides were washed sequentially With GE Wash Buffer 1 and 2.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 8.5)

data_processing: GeneSpring GX was used to generate raw processed signal data. The raw processed signal intensities were normalized to total intensity to be comparable between subarrays and Cy5 and Cy3 dyes. Data was filtered for four features: green is positive and significant, red is positive and significant, green is well above background and red is well above background. Final values are shown only if all four constraints were true for all four samples. Log2 transformation of normalized values, two sample t-test with equal variances, filtering for p<0,01 and averaging of repeated log2 values followed.

organism: Drosophila melanogaster

source_name: DTS-3 29°C Cy5

label_protocol: 5 µg of total RNA for each sample was labeled in accordance with Agilent Two-color Quick Amp Kit protocol

growth_protocol: 0-24 hours old flies were maintained at 20 or 29°C for three days on standard yeast-cornmeal- sucrose-agar medium supplemented with propionic acid and hydroxymethylbenzoate.

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

value: adult 3 days

value: whole adult

tag: temperature

source_name: DTS-3 20°C Cy5


title: Normal oral keratinocytes (NOK), sample A

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C. Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany).

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

data_processing: The data was analyzed using Gene Chip Operating Software (Affymetrix), Expression Console (Affymetrix) or R/Bioconductor (for downstream analysis and quality control).

label: Affymetrix single-stage biotin

source_name: Normal oral keratinocytes in serum-free culture

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol: Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.

extract_protocol: We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.

value: normal oral keratinocytes (primary culture)


title: hcc_102 [tumor from HCC patient]

description: Sample name: hcc_102

value: hepatocellular carcinoma

value: AS-FFPE tumor

value: S3 (HCC subclass:hepatocyte differentiation)


title: hcc_099 [tumor from HCC patient]

description: Sample name: hcc_099


title: OreR 29°C Cy3/OreR 20°C Cy3

source_name: OreR 29°C Cy3

value: OreR

source_name: OreR 20°C Cy3


title: hcc_132 [tumor from HCC patient]

description: Sample name: hcc_132


title: Normal oral keratinocytes (NOK), sample B


title: hcc_103 [tumor from HCC patient]

description: Sample name: hcc_103


title: Normal oral keratinocytes (NOK), sample C


title: hcc_093 [tumor from HCC patient]

description: Sample name: hcc_093


title: hcc_091 [tumor from HCC patient]

description: Sample name: hcc_091


title: Oxali-2

city: ShangHai

first: Yang

last: Bu

address: 180 Fenglin Road

country: China

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

description: Oxaliplatin-resistant MHCC97H liver cell line demonstrated increased EMT, cell invasion, colony formation, etc.

hyb_protocol: The pre-hybridization of Agilent 4*44K arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy3-labeled aaRNA was hybridize on Agilent 4*44K in dulication  at 50℃ for 16 hour in the presentation of the Agilent hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Genespring System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: oxali, liver cell

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy3, Amershan) to uridine (dUTP).

growth_protocol: liver cell was selected and cultured for study.

extract_protocol: RNA extraction by Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) . RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: A liver cell line was cultured according to standard protocol. Total RNA was isolated from liver cell using the Qiagen RNeasy Mini kit (Qiagen, Chatsworth, CA, USA) according to manufacture’s protocols.

tag: cell line

tag: agent

value: Oxaliplatin


title: DTS-3 29°C Cy3/DTS-3 20°C Cy3

source_name: DTS-3 29°C Cy3

tag: genotype/variation

tag: age

source_name: DTS-3 20°C Cy3


title: Oxali-3

value: Oxaliplatin-resistant MHCC97H liver cell line


title: Oxali-1


title: hcc_110 [tumor from HCC patient]

description: Sample name: hcc_110


title: control-3

source_name: control, liver cell

value: control


title: hcc_086 [tumor from HCC patient]

description: Sample name: hcc_086


title: LK0412, sample B

description: The tongue squamous cell carcinoma cell line (LK0412) was derived and cultured under the same serum-free epithelial medium with high levels of amino acids (EMHA) as the normal cells (Roberg, K et al. Differentiation, 76:868-80, 2008 and Grafström, R.C., Culture of Epithelial cells, 2nd ed, John Wiley and Sonc Inc, NY, 2002). Cultures were transferred on regulat tissue culture plastic at 100% confluency and cells in passage 14-18 were used in the experiments.

source_name: Tongue squamous cell carcinoma derived and cultured under serum-free conditions

tag: cell type

value: tongue squamous cell carcinoma (cell line LK0412)


title: control-2


title: hcc_084 [tumor from HCC patient]

description: Sample name: hcc_084

tag: disease state


title: hcc_083 [tumor from HCC patient]

description: Sample name: hcc_083

tag: tissue


title: hcc_080 [tumor from HCC patient]

description: Sample name: hcc_080

tag: %p-call


title: hcc_076 [tumor from HCC patient]

description: Sample name: hcc_076

tag: inter-sample correlation


title: Macrophages_P14heart_3daysMI_2

first: Arin

middle: B

last: Aurora

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina bead studio software was used to analyze with quantile normalization

organism: Mus musculus

source_name: cardiac macrophages, P14, 3 days post-MI

label_protocol: cRNA was generated and labeled according to the protocols outlined at: http://microarray.swmed.edu/protocols/protocol/illumina-gene-expression-probe-labeling/

growth_protocol: All animals were maintained in compliance with the Institutional Animal Care and Use Committee at University of Texas Southwestern Medical Center

extract_protocol: Total RNA was isolated from mouse tissues and cell lines using Promega ReliaPrep RNA cell system according to the manufacturer’s protocol

treatment_protocol: no treatments applied

tag: age at mi

tag: strain

value: ICR

value: CD11b+Ly6G- cells sorted from heart

tag: gender

value: mixed


title: control-1


title: Macrophages_P1heart_3daysMI_2

source_name: cardiac macrophages, P1, 3 days post-MI


title: hcc_001.rep2 [tumor from HCC patient]

description: Sample name: hcc_001.rep2

tag: prediction in as-ffpe

tag: prediction in as-ffpe (%p-call>20%)

tag: prediction confidence p-value in as-ffpe (%p-call>20%)

tag: prediction in fc-ffpe


title: hcc_090 [tumor from HCC patient]

description: Sample name: hcc_090

tag: prediction confidence p-value in as-ffpe

tag: prediction confidence p-value in fc-ffpe

tag: geo accession of fc-ffpe profile


title: LK0412, sample A

growth_protocol: The tongue squamous cell carcinoma cell line (LK0412) was derived and cultured under the same serum-free epithelial medium with high levels of amino acids (EMHA) as the normal cells (Roberg, K et al. Differentiation, 76:868-80, 2008 and Grafström, R.C., Culture of Epithelial cells, 2nd ed, John Wiley and Sonc Inc, NY, 2002). Cultures were transferred on regulat tissue culture plastic at 100% confluency and cells in passage 14-18 were used in the experiments.


title: hcc_079 [tumor from HCC patient]

description: Sample name: hcc_079


title: hcc_078 [tumor from HCC patient]

description: Sample name: hcc_078


title: Macrophages_P14heart_3daysMI_3


title: hcc_085 [tumor from HCC patient]

description: Sample name: hcc_085


title: Macrophages_P1heart_3daysMI_3


title: Macrophages_P14heart_3daysMI_1


title: Macrophages_P1heart_3daysMI_1


title: hcc_072 [tumor from HCC patient]

description: Sample name: hcc_072


title: hcc_074 [tumor from HCC patient]

description: Sample name: hcc_074

value: S1 (HCC subclass:aberrant activation of the TGF-beta/WNT signaling pathways)


title: hcc_081 [tumor from HCC patient]

description: Sample name: hcc_081


title: hcc_070 [tumor from HCC patient]

description: Sample name: hcc_070


title: hcc_067 [tumor from HCC patient]

description: Sample name: hcc_067


title: hcc_065 [tumor from HCC patient]

description: Sample name: hcc_065


title: hcc_068 [tumor from HCC patient]

description: Sample name: hcc_068


title: hcc_063 [tumor from HCC patient]

description: Sample name: hcc_063


title: hcc_069 [tumor from HCC patient]

description: Sample name: hcc_069


title: Mouse 592 subcutaneous fat

city: Gothenburg

first: Erik

last: Larsson

address: Bruna stråket 16

department: Wallenberg Laboratory

institute: University of Gothenburg

description: RMA expression value derived from Expression Console software; gene level analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the Uppsala Array Platform microarray core facility (Sweden).

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

data_processing: Raw data were processed with the Expression Console software (Affymetrix) for background correction and normalization. Downstream data analysis and statistical evaluations were performed using customized matlab scripts.

source_name: Healthy male, autoclaved chow diet

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

extract_protocol: RNA was isolated using the RNeasy mini kit or the RNeasy Lipid tissue mini kit (QIAGEN), according to the manufacturer's instructions.

value: subcutaneous fat

value: CONV-R

tag: genotype

value: WT


title: Mouse 597 subcutaneous fat

value: GF


title: Mouse 601 subcutaneous fat


title: Mouse 594 subcutaneous fat


title: hcc_061 [tumor from HCC patient]

description: Sample name: hcc_061

value: S2 (HCC subclass:alpha-fetoprotein positivity as well as MYC and AKT activation)


title: hcc_060 [tumor from HCC patient]

description: Sample name: hcc_060

value: hepatocellular carcinoma


title: Mouse 600 subcutaneous fat


title: hcc_059 [tumor from HCC patient]

description: Sample name: hcc_059

value: AS-FFPE tumor


title: Mouse 593 subcutaneous fat


title: Mouse 599 subcutaneous fat


title: Mouse 587 subcutaneous fat


title: Mouse 588 subcutaneous fat


title: hcc_062 [tumor from HCC patient]

description: Sample name: hcc_062


title: hcc_058 [tumor from HCC patient]

description: Sample name: hcc_058


title: Mouse 596 subcutaneous fat


title: Mouse 602 subcutaneous fat


title: Mouse 589 subcutaneous fat


title: hcc_053 [tumor from HCC patient]

description: Sample name: hcc_053


title: hcc_054 [tumor from HCC patient]

description: Sample name: hcc_054


title: Mouse 590 subcutaneous fat


title: Mouse 586 subcutaneous fat


title: Mouse 585 subcutaneous fat


title: hcc_052 [tumor from HCC patient]

description: Sample name: hcc_052


title: hcc_047 [tumor from HCC patient]

description: Sample name: hcc_047

value: S3 (HCC subclass:hepatocyte differentiation)


title: Mouse 583 subcutaneous fat


title: hcc_050 [tumor from HCC patient]

description: Sample name: hcc_050


title: Mouse 584 subcutaneous fat


title: Mouse 596 epidimymal fat

value: epidimymal fat


title: Mouse 601 epidimymal fat


title: Mouse 593 epidimymal fat


title: Mouse 594 epidimymal fat


title: Mouse 600 epidimymal fat


title: Mouse 595 epidimymal fat


title: Mouse 602 epidimymal fat


title: Mouse 598 epidimymal fat


title: hcc_045 [tumor from HCC patient]

description: Sample name: hcc_045


title: Mouse 592 epidimymal fat


title: hcc_042 [tumor from HCC patient]

description: Sample name: hcc_042


title: Mouse 599 epidimymal fat


title: hcc_044 [tumor from HCC patient]

description: Sample name: hcc_044


title: OreR 29°C Cy5/OreR 20°C Cy5

source_name: OreR 29°C Cy5

tag: genotype/variation

value: OreR

tag: age

value: adult 3 days

value: whole adult

tag: temperature

source_name: OreR 20°C Cy5


title: hcc_038 [tumor from HCC patient]

description: Sample name: hcc_038

tag: disease state

tag: tissue


title: Mouse 590 epidimymal fat


title: hcc_039 [tumor from HCC patient]

description: Sample name: hcc_039

tag: %p-call

tag: inter-sample correlation


title: hcc_037 [tumor from HCC patient]

description: Sample name: hcc_037


title: hcc_035 [tumor from HCC patient]

description: Sample name: hcc_035


title: hcc_041 [tumor from HCC patient]

description: Sample name: hcc_041


title: hcc_043 [tumor from HCC patient]

description: Sample name: hcc_043


title: Mouse 591 epidimymal fat

tag: strain


title: hcc_049 [tumor from HCC patient]

description: Sample name: hcc_049


title: Mouse 588 epidimymal fat


title: hcc_034 [tumor from HCC patient]

description: Sample name: hcc_034


title: Mouse 586 epidimymal fat


title: hcc_032 [tumor from HCC patient]

description: Sample name: hcc_032


title: Mouse 585 epidimymal fat


title: hcc_033 [tumor from HCC patient]

description: Sample name: hcc_033


title: Mouse 597 liver

value: liver


title: Mouse 598 liver


title: Mouse 584 epidimymal fat


title: Mouse 593 liver


title: hcc_031 [tumor from HCC patient]

description: Sample name: hcc_031


title: hcc_028 [tumor from HCC patient]

description: Sample name: hcc_028


title: hcc_040 [tumor from HCC patient]

description: Sample name: hcc_040


title: Mouse 601 liver


title: Mouse 600 liver


title: hcc_027 [tumor from HCC patient]

description: Sample name: hcc_027


title: Mouse 595 liver


title: hcc_024 [tumor from HCC patient]

description: Sample name: hcc_024


title: Mouse 599 liver


title: Mouse 594 liver


title: hcc_021 [tumor from HCC patient]

description: Sample name: hcc_021


title: hcc_025 [tumor from HCC patient]

description: Sample name: hcc_025


title: hcc_020 [tumor from HCC patient]

description: Sample name: hcc_020


title: hcc_022 [tumor from HCC patient]

description: Sample name: hcc_022


title: Mouse 596 liver


title: Mouse 589 epidimymal fat


title: Mouse 590 liver


title: Mouse 591 liver


title: hcc_023 [tumor from HCC patient]

description: Sample name: hcc_023


title: hcc_017 [tumor from HCC patient]

description: Sample name: hcc_017


title: hcc_013 [tumor from HCC patient]

description: Sample name: hcc_013


title: hcc_015 [tumor from HCC patient]

description: Sample name: hcc_015


title: Mouse 592 liver


title: Mouse 589 liver


title: hcc_011 [tumor from HCC patient]

description: Sample name: hcc_011


title: hcc_012 [tumor from HCC patient]

description: Sample name: hcc_012


title: Mouse 588 liver


title: Mouse 585 liver


title: hcc_009 [tumor from HCC patient]

description: Sample name: hcc_009


title: bkg_122 [liver from HCC patient]

description: Sample name: bkg_122

value: AS-FFPE liver (cirrhotic)

value: poor

tag: prediction in as-ffpe (%p-call >20%)

tag: prediction confidence p-value in as-ffpe (%p-call >20%)

value: good


title: bkg_017.rep2 [liver from HCC patient]

description: Sample name: bkg_017.rep2

tag: prediction in as-ffpe


title: Mouse 586 liver


title: Mouse 583 liver


title: hcc_010 [tumor from HCC patient]

description: Sample name: hcc_010

tag: prediction in as-ffpe (%p-call>20%)

tag: prediction confidence p-value in as-ffpe (%p-call>20%)


title: bkg_017.rep1 [liver from HCC patient]

description: Sample name: bkg_017.rep1

tag: prediction confidence p-value in as-ffpe

tag: prediction in fc-ffpe


title: Mouse 584 liver


title: hcc_007 [tumor from HCC patient]

description: Sample name: hcc_007

tag: prediction confidence p-value in fc-ffpe

tag: geo accession of fc-ffpe profile


title: bkg_115 [liver from HCC patient]

description: Sample name: bkg_115


title: hcc_008 [tumor from HCC patient]

description: Sample name: hcc_008

value: S1 (HCC subclass:aberrant activation of the TGF-beta/WNT signaling pathways)


title: bkg_119 [liver from HCC patient]

description: Sample name: bkg_119


title: bkg_069 [liver from HCC patient]

description: Sample name: bkg_069


title: bkg_103 [liver from HCC patient]

description: Sample name: bkg_103


title: Mouse 587 liver

tag: genotype


title: bkg_086 [liver from HCC patient]

description: Sample name: bkg_086


title: bkg_062 [liver from HCC patient]

description: Sample name: bkg_062


title: bkg_080 [liver from HCC patient]

description: Sample name: bkg_080


title: bkg_065 [liver from HCC patient]

description: Sample name: bkg_065


title: bkg_067 [liver from HCC patient]

description: Sample name: bkg_067


title: bkg_093 [liver from HCC patient]

description: Sample name: bkg_093


title: bkg_090 [liver from HCC patient]

description: Sample name: bkg_090


title: bkg_091 [liver from HCC patient]

description: Sample name: bkg_091


title: bkg_053 [liver from HCC patient]

description: Sample name: bkg_053


title: bkg_059 [liver from HCC patient]

description: Sample name: bkg_059


title: bkg_079 [liver from HCC patient]

description: Sample name: bkg_079


title: bkg_084 [liver from HCC patient]

description: Sample name: bkg_084


title: bkg_083 [liver from HCC patient]

description: Sample name: bkg_083


title: bkg_058 [liver from HCC patient]

description: Sample name: bkg_058


title: bkg_052 [liver from HCC patient]

description: Sample name: bkg_052


title: bkg_047 [liver from HCC patient]

description: Sample name: bkg_047


title: bkg_045 [liver from HCC patient]

description: Sample name: bkg_045


title: bkg_050 [liver from HCC patient]

description: Sample name: bkg_050


title: bkg_040 [liver from HCC patient]

description: Sample name: bkg_040


title: bkg_041 [liver from HCC patient]

description: Sample name: bkg_041


title: hcc_036 [tumor from HCC patient]

description: Sample name: hcc_036


title: bkg_038 [liver from HCC patient]

description: Sample name: bkg_038


title: bkg_043 [liver from HCC patient]

description: Sample name: bkg_043


title: bkg_039 [liver from HCC patient]

description: Sample name: bkg_039


title: bkg_036 [liver from HCC patient]

description: Sample name: bkg_036


title: bkg_027 [liver from HCC patient]

description: Sample name: bkg_027


title: bkg_032 [liver from HCC patient]

description: Sample name: bkg_032


title: bkg_049 [liver from HCC patient]

description: Sample name: bkg_049


title: bkg_029 [liver from HCC patient]

description: Sample name: bkg_029


title: bkg_035 [liver from HCC patient]

description: Sample name: bkg_035


title: bkg_025 [liver from HCC patient]

description: Sample name: bkg_025


title: bkg_024 [liver from HCC patient]

description: Sample name: bkg_024


title: bkg_022 [liver from HCC patient]

description: Sample name: bkg_022


title: bkg_028 [liver from HCC patient]

description: Sample name: bkg_028


title: shRNA NC5 rep 3

city: Burnaby

first: Gratien

middle: G.

last: Prefontaine

state: British Columbia

address: 8888 University Drive

department: Faculty of Health Sciences

country: Canada

institute: Simon Fraser University

description: Gene expression upon shRNA Knock down

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004).

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution

data_processing: Data was processed with Agilent Feature Extraction 10.10. Green processed signal was quantile normalized with Agilent GeneSpring 11.5.1.

source_name: Cell Culture

label_protocol: An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA

growth_protocol: The stable lines have grown in DMEM in the presence of 10% FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Trizol/phenol chloroform plus an additional chloroform

treatment_protocol: no treatment

tag: cell line

tag: shRNA


title: bkg_031 [liver from HCC patient]

description: Sample name: bkg_031

tag: disease state


title: bkg_020 [liver from HCC patient]

description: Sample name: bkg_020

tag: tissue


title: bkg_033 [liver from HCC patient]

description: Sample name: bkg_033

tag: %p-call


title: bkg_023 [liver from HCC patient]

description: Sample name: bkg_023

tag: inter-sample correlation


title: hcc_029 [tumor from HCC patient]

description: Sample name: hcc_029


title: shRNA NC5 rep 2

description: Gene expression upon shRNA Knock down


title: Control and 24 hours after infection replicate 1

city: 6 October

first: Yasser

middle: Bahaa-ElDin

last: Morsy

address: Flat 24, building 30, region 7, district 11, 6th October City, Giza, Egypt

department: Plant molecular biology

country: Egypt

institute: AGERI

description:
Sample name: rice7_289
Technical replicate 1 of 2 control, and 24 hours

hyb_protocol: Lableing was performed using the same kit of lableing

scan_protocol: Agilent C Scanner was used to scan the microarray

data_processing: Feature Extraction software provided by Agilent Technologies was used to extract features

organism: Oryza sativa

source_name: Leaves, control

label_protocol: 200 ng of total RNA was labled with (Low Input Quick Amp Labeling) kit. (Agilent Technologies., Cat. No. G4140-90050) using manfucture instruction

growth_protocol: Rice seeds were grown in green house under normal condition

extract_protocol: Total RNA extraction using Trizol following manfuacture's instructions

treatment_protocol: Magnaporthe grisea spores were inoculated with 3 wweks old seedling and samples were isolated after 2 and 24 hours from treatment

value: Leaves

tag: infection

value: uninfected

source_name: Leaves, Magnaporthe grisea infection, 24 hours

value: Magnaporthe grisea spores

tag: time

value: 24 hours


title: Control and 2 hours after infection replicate 2

description:
Sample name: rice6_220
Technical replicate 2 of 2 control, and 2 hours

source_name: Leaves, Magnaporthe grisea infection, 2 hours

value: 2 hours


title: bkg_021 [liver from HCC patient]

description: Sample name: bkg_021

value: hepatocellular carcinoma

tag: prediction in as-ffpe (%p-call >20%)

tag: prediction confidence p-value in as-ffpe (%p-call >20%)


title: Control and 24 hours after infection replicate 2

description:
Sample name: rice8_291
Technical replicate 2 of 2 control, and 24 hours


title: Control and 2 hours after infection replicate 1

description:
Sample name: rice5_258
Technical replicate 1 of 2 control, and 2 hours


title: shRNA NC5 rep 1

description: Gene expression upon shRNA Knock down


title: bkg_003 [liver from HCC patient]

description: Sample name: bkg_003

tag: prediction in as-ffpe


title: bkg_015 [liver from HCC patient]

description: Sample name: bkg_015


title: Muscle_Duroc_F_Low_03

city: Dublin 15

first: Ruth

middle: Marie

last: Hamill

address: Teagasc Food Research Centre, Ashtown

department: Food Chemistry and Technology

country: Ireland

institute: Teagasc

hyb_protocol: Hybridisation was carried out by Almac Diagnostics according to their standard protocols. Fragmented and labelled cDNA was added to the hybridisation mix in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Post hybridisation washing and staining were carried out using GeneChip® Fluidics Station 450 (Affymetrix) followed by scanning according to standard Affymetrix protocols

scan_protocol: Gels were scanned commercially by Almac diagnostics (UK) according to standard Affymetrix protocols

data_processing: Microarray analysis including, pre-processing, normalisation and statistical analysis were performed using R (R, 2007) version 2.6 and Bioconductor version 2.1.The mmgMOS method was used for normalisation and the PPLR method was used for differential gene expression all within the  Propagating Uncertainty in Microarray Analysis (puma) method (Pearson et al., 2009 BMC Bioinformatics  10:211 doi:10.1186/1471-2105-10-211

organism: Sus scrofa

source_name: Semimembranosus muscle, low protein

label_protocol: The appropriate amount of amplified single-stranded cDNA was used as a template for biotin labelling using the FL-Ovation™ cDNA Biotin Module V2

growth_protocol: Standard protocol used in UCD Lyons Estate Farm

extract_protocol: RNA was extracted during standard phenol/guanidine isothiocyanate-based organic extraction method (TRIZOL) according to manufacturers instructions

treatment_protocol: Two isoenergetic diets contrasting in protein content were fed for 63 days during the finisher stage.

tag: diet

value: low protein

value: Semimembranosus muscle


title: Muscle_Duroc_F_Low_05


title: shRNA 4 rep 3

description: Gene expression upon shRNA Knock down


title: Muscle_Duroc_F_Low_01


title: Muscle_Duroc_F_High_06

source_name: Semimembranosus muscle, high protein

value: high protein


title: Muscle_Duroc_F_Low_02


title: shRNA 4 rep 2

description: Gene expression upon shRNA Knock down


title: Muscle_Duroc_F_High_04


title: Muscle_Duroc_F_High_03


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep8

city: Tokyo

first: Ayako

last: Oka

address: Hulic Kamiyacho Building 2F, Toranomon 4-3-13, Minato-ku

institute: Transdisciplinary Research Integration Center

description: Gene expression data from testes of 7dpp (B6-ChrXTMSM x B6-Chr1MSM)F1 males

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using theGenechip scanner 3000 (Affymetrix).

data_processing: The data were analyzed with RMA using GeneSrping GX software (Agilent).

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by using GeneChip 3’IVT express kit (Affymetrix) according to the standard Affymetrix protocol.

extract_protocol: Testes were immersed in RNAlater (life technologies) and stored at -20C. Total RNA was extracted by RNeasy Microarray Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: organ

value: testis

tag: genotype/variation

value: (B6-ChrXTMSM x B6-Chr1MSM)F1

tag: age


title: shRNA 4 rep 1

description: Gene expression upon shRNA Knock down


title: anti-CSF1R Ab (M279) treated mouse liver sample replicate 1

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

country: United Kingdom

institute: Roslin Institute/The University of Edinburgh

hyb_protocol: Samples were hybridised according to the Nugen protocol for Affymetrix Gene Titan hybridisation, using the Affymetrix Gene Titan Hybridization Wash & Stain Kit for WT Array Plates (PN 901622)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using the Affymetrix Expression Console software version 1.1

source_name: liver

label_protocol: Samples were biotin labelled using the Nugen Encore labelling kit using the half volume protocol

growth_protocol: Mouse livers dissected from adult C57Bl6 mice

extract_protocol: All livers were dissected and stored in RNA later prior to preparation of RNA with Trizol, cDNA synthesis and amplification was performed using the Nugen Pico SL kit

treatment_protocol: Mice were injected ip thrice weekly for  6 weeks with300ug rat IgG Control or anti-CSF1R Ab (M279)  before cull

tag: strain

value: adult

tag: treatment

value: anti-CSF1R Ab (M279)


title: Control mouse liver sample replicate 3.

value: liver

value: control


title: L. donovai culture_resistant_rep2

city: Varanasi

first: PUJA

last: TIWARY

state: India

address: C/O Prof. Shyam Sundar, Dept of Medicine

department: MEDICINE

country: India

institute: Banaras Hindu University

description: Gene expression in Miltefosine resistant strain

hyb_protocol: 600 ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed Leishmania GXP 8X15K (G2509F_035638) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner, Model G2565BA using one color scan setting , Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%.

data_processing: The scanned images were analyzed with GeneSpring GX Version 10.0.1 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Leishmania donovani

source_name: Miltefosine non-responders, splenic aspirate, parasite culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent One-Color Spike-Mix  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 c Spectrophotometer.

growth_protocol: Splenic aspirates was drawn from patients and confirmed Leishmania donovani by microscopy and allowed to grow in M199 media and incubated in BOD incubator at 26 c until logarithmic phase achieved.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop 2000c spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Logarithmic phase culture was centrifused at 5000 rpm. Pallet was washed 2 times with 1XPBS and mixed with RNALater and stored in -80 deep freezer

value: parasite culture

tag: isolate

tag: Stage

value: Promastigote


title: Muscle_Duroc_F_High_05


title: L. donovai culture_resistant_rep1


title: shRNA 3 rep 1

description: Gene expression upon shRNA Knock down

tag: cell line

tag: shRNA


title: shRNA 3 rep 3

description: Gene expression upon shRNA Knock down


title: Muscle_Duroc_F_High_01

tag: tissue


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep7


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep3


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep6


title: shRNA 3 rep 2

description: Gene expression upon shRNA Knock down


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep5


title: anti-CSF1R Ab (M279) treated mouse liver sample replicate 2


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep1


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep4


title: Control mouse liver sample replicate 1.


title: Control mouse liver sample replicate 2.


title: Muscle_Duroc_F_High_02


title: B6-ChrXTMSM testes at 7dpp, biological rep3

description: Gene expression data from testes of 7dpp B6-ChrXTMSM males

source_name: B6-ChrXTMSM testes at 7dpp


title: L. donovai culture_sensitive_rep1

description: Gene expression in Miltefosine sensitive strain

source_name: Miltefosine responders, splenic aspirate, parasite culture

value: BHU 681


title: L. donovai culture_sensitive_rep2

value: BHU 776


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 7dpp, biological rep2


title: B6-ChrXMSM testes at 7dpp, biological rep1

description: Gene expression data from testes of 7dpp B6-ChrXMSM males

source_name: B6-ChrXMSM testes at 7dpp


title: Wild type Arabidopsis control

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description:
WT Control
Seedling of Arabidopsis thaliana (wild type) grown on MS media supplemented with 0 mM NaCl for two weeks.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between control and test sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Arabidopsis thaliana, uninduced with salt

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 0.5 µg total RNA samples that were first subject to dephosphorylation reaction to remove 5' phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3' end of sample (3'OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contains a tag segment for capturing fluorescent dye during a later Cy3 dye staining process.

growth_protocol: Surface-sterilized seeds of transgenic A. thaliana expressing the cDNA encoding ABR17, along with the WT control, were germinated on Murashige and Skoog (MS) medium supplemented with 100 mM NaCl, along with no-salt control (0 mM NaCl), for two weeks under light/dark (16h/8 h) regime for 7 days at 22±1 º C.

extract_protocol: Total RNA from both WT and ABR17 transgenic A. thaliana seedlings was isolated using the TRI-Reagent (Ambion, USA). The isolated RNA was enriched for small RNA using PEG and NaCl (Accerbi et al. 2010), and was subsequently used in the miRNA-microarray experiment.

value: wild type

value: seedling


title: B6-ChrXTMSM testes at 7dpp, biological rep2


description:
ABR17
Seedling of Arabidopsis thaliana (expressing abscisic acid-responsive (ABR17) gene) grown on MS media supplemented with 0 mM NaCl for two weeks.

source_name: Arabidopsis plant expressing abscisic acid-responsive (ABR17) gene, uninduced with salt

value: abscisic acid-responsive (ABR17) transgenic


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) 4

city: Badajoz

first: Angel

middle: Carlos

last: Roman

address: Avda. de Elvas s/n

department: Bioquimica y Biologia Molecular y Genetica

country: Spain

institute: Universidad de Extremadura

description:
Patient Noonan Syndrome and JMML
NS/JMML3

hyb_protocol: Biotinylated RNAs were hybridized to Illumina HT-12v4 Expression BeadChips

scan_protocol: scanned with an Illumina HiScan Bead Array Scanner

data_processing: quality controlled in GenomeStudio and the lumi R/Bioconductor package. In GenomeStudio, probes were filtered for those detected with a P value of 0.01 in at least one sample and exported for normalization in R

source_name: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan/JMML syndrome patient (#4)

label_protocol: RNA samples were amplified using the Illumina Total Prep RNA Amplification Kit

growth_protocol: HES2 and all the iPSC samples were grown in HES2 medium: DMEM/F12 containing 20% KSR, 5% MEF-conditioned medium, Penicillin/Streptomycin, L-glutamine, non-essential amino acids, β-mercaptoethanol and bFGF. The hematopoietic differentiation media consisted of StemPro-34 and nutrient complement (Invitrogen) with penicillin/streptomycin, 2 mM glutamine, 4x10-4 M monothioglycerol, 150 µg/ml transferrin (Roche) and 50 µg/mL ascorbic acid (Sigma-Aldrich) with specific citokynes according to the day of differentiation.

extract_protocol: Total RNA was extracted from sorted CD33+ cells using Trizol (Invitrogen) and RNeasy plus mini kit (Qiagen). RNA quality (RNA6000 Nano Kit; Agilent) was evaluated.

treatment_protocol: Cells were grown in non-treated conditions.

tag: cell type

tag: gender

value: MALE


title: Wild type Arabidopsis induced with salt stress (100 mM)

description:
WT salt
Seedling of Arabidopsis thaliana (wild type) grown on MS media supplemented with 100 mM NaCl for two weeks.

source_name: Arabidopsis thaliana, induced with salt stress (100 mM)

value: salt stress (100 mM NaCl)


title: HL60_shSYK_2_Replicate1

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: The samples were profiled using the HT U133A Gene Expression Arrays (Affymetrix) at the Broad Institute of MIT and Harvard (Cambridge, MA, USA).

hyb_protocol: GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454)

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Data were extracted from the  CEL files and preprocessed through  the ExpressionFileCreator module implemented  in  GenePattern 3.5.0  software platform (Broad Institute, http://www.broadinstitute.org/cancer/software/genepattern/),  by applying  RMA and the quantile normalization procedures.  The computational analysis of the gene expression data was performed through the Genome Space bioinformatics platform (http://www.genomespace.org).

source_name: HL-60 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection

label_protocol: Biotin

growth_protocol: HL-60, MOLM-14, and U937 were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum (FBS, Sigma-Aldrich) at 37 °C with 5% CO2

extract_protocol: RNA was extracted using Qiagen Rneasy Mini Kit (74104) at 5 days post infection.

treatment_protocol: HL-60, MOLM-14, and U937 cell lines were transduced in triplicate with a control luciferase-directed shRNA (target sequence CCTAAGGTTAAGTCGCCCTCG), and in duplicate with two SYK-directed shRNAs:  shSYK_1 (clone ID TRCN0000197257,  target sequence  GCAGCAGAACAGACATGTCAA)   and shSYK_2  (clone ID TRCN0000003163 , target sequence  GCAGGCCATCATCAGTCAGAA),  and were then selected with 1 µg/ml puromycin 48 hours post-infection.

tag: replicate


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) DUPLICATE 3

description:
Replicate of NS/JMML1
NS/JMML1 DUPLICATE

source_name: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan/JMML syndrome patient (#3)


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) DUPLICATE 4

description:
Replicate of NS/JMML3
NS/JMML3 DUPLICATE

value: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan/JMML syndrome patient (#4)


title: B6-ChrXMSM testes at 7dpp, biological rep3


description:
Control
CTRL5

source_name: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from healthy individual

value: UNKNOWN


title: B6-ChrXTMSM testes at 7dpp, biological rep1

value: testis


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) DUPLICATE 1

description:
Replicate of CTRL1
CTRL1 DUPLICATE

value: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from healthy individual


title: bkg_119 [liver from HCC patient]

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: standard NanoString nCounter Assay protocol

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated with High Pure RNA paraffin kit (Roche) according to manufacturer’s protocol.

tag: prediction in as-ffpe (ncounter)

value: good

tag: prediction confidence p-value in as-ffpe (ncounter)

tag: prediction in fc ffpe (dasl)

tag: prediction in fc ffpe (re-prediction within these 24 samples)

value: poor

tag: prediction confidence p-value in fc ffpe  (re-prediction within these 24 samples)

tag: geo accession of fc-ffpe profile

tag: disease state

value: hepatocellular carcinoma

value: AS-FFPE liver (cirrhotic)


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) DUPLICATE 2

description:
Replicate of NS2
NS2 DUPLICATE

source_name: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan syndrome patient (#2)

value: FEMALE


title: B6-ChrXMSM testes at 7dpp, biological rep2

tag: organ

tag: genotype/variation

tag: age


title: bkg_122 [liver from HCC patient]

scan_protocol: standard NanoString nCounter Assay protocol


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) 2

description:
Patient Noonan Syndrome
NS2

value: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan syndrome patient (#2)


title: bkg_090 [liver from HCC patient]

label_protocol: standard NanoString nCounter Assay protocol


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) 3

description:
Patient Noonan Syndrome and JMML
NS/JMML1

value: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) from Noonan/JMML syndrome patient (#3)


title: Arabidopsis plant expressing abscisic acid-responsive (ABR17) gene and induced with salt stress (100 mM)

description:
ABR17 salt
Seedling of Arabidopsis thaliana (expressing abscisic acid-responsive (ABR17) gene) grown on MS media supplemented with 100 mM NaCl for two weeks.

source_name: Arabidopsis plant expressing abscisic acid-responsive (ABR17) gene, induced with salt stress (100 mM)

tag: treatment


title: MSM testes at 7dpp, biological rep1

description: Gene expression data from testes of 7dpp MSM males

source_name: MSM testes at 7dpp

value: MSM


title: Larval_Brain complexes_scrib mutant_9day AED_rep3

city: East Melbourne

first: Helena

middle: Elizabeth

last: Richardson

state: Victoria

address: 7 St Andrew's place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Center

description: tumours

hyb_protocol: Hybridization was carried out following standard Affymetrix protocols

scan_protocol: Gene-Chips were washed and stained in the Affymetrix Fluidics Station 400 and scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was gcrma normalised using the R Bioconductor package gcrma

source_name: Drosophila larval brain complexes scrib mutant day 9

label_protocol: Biotinylated cRNA were prepared according to the standardAffymetrix protocol from 6 ug total RNA.

growth_protocol: Larvae were incubated at 25oC and grown on standard fly media

extract_protocol: Samples were prepared in triplicate, and the RNA isolated using TRIZOL, before being column purified (Qiagen)

treatment_protocol: wing discs or brain complexes were dissected from 3rd instar larvae at day 5 (for wildtype) or day 9 (for mutants) after egg deposition

tag: genotype

value: scrib mutant

value: larval brain complexes

value: 9 d AED

tag: developmental stage

value: 3rd instar larvae


title: MSM testes at 7dpp, biological rep2


title: Larval_Brain complexes_scrib mutant_9day AED_rep2

description: tumours

tag: tissue


title: Larval_Brain complexes_scrib mutant_9day AED_rep1

description: tumours


title: bkg_083 [liver from HCC patient]


title: bkg_069 [liver from HCC patient]


title: bkg_079 [liver from HCC patient]


title: MSM testes at 7dpp, biological rep3


title: B6 testes at 7dpp, biological rep3

description: Gene expression data from testes of 7dpp B6 males

source_name: B6 testes at 7dpp


title: bkg_086 [liver from HCC patient]


title: Larval_Wing discs_scrib mutant_9day AED_rep3

description: tumours

source_name: Drosophila larval wing discs scrib mutant day 9

value: larval wing discs


title: B6 testes at 7dpp, biological rep2


title: B6 testes at 7dpp, biological rep1


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 5dpp, biological rep3

description: Gene expression data from testes of 5dpp (B6-ChrXTMSM x B6-Chr1MSM)F1 males

value: (B6-ChrXTMSM x B6-Chr1MSM)F1


title: Larval_Wing discs_scrib mutant_9day AED_rep1

description: tumours


title: hiPSC-derived CD33+ myeloid cells (DAY 14 OF DIFFERENTIATION) 1

description:
Control
CTRL1

tag: cell type

value: MALE


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 5dpp, biological rep2

value: testis


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYDROME/JMML PATIENT N#4 1

source_name: hIPS generated from skin fibroblasts

value: hIPS generated from skin fibroblasts

tag: gender


title: bkg_065 [liver from HCC patient]


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYDROME/JMML PATIENT N#3

description:
Patient Noonan Syndrome and JMML
NS/JMML2


title: Muscle_Duroc_F_Low_04

source_name: Semimembranosus muscle, low protein

tag: diet

value: low protein

value: Semimembranosus muscle


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYDROME/JMML PATIENT N#4 3

description:
Patient Noonan Syndrome and JMML
NS/JMML5


title: bkg_062 [liver from HCC patient]

tag: prediction in as-ffpe (ncounter)

value: poor

value: good

value: hepatocellular carcinoma


title: bkg_052 [liver from HCC patient]

tag: prediction confidence p-value in as-ffpe (ncounter)

value: AS-FFPE liver (cirrhotic)


title: Larval_Brain complexes_lgl mutant_9day AED_rep2

description: tumours

source_name: Drosophila larval brain complexes lgl mutant day 9

value: lgl mutant


title: Larval_Wing discs_scrib mutant_9day AED_rep2

description: tumours


title: bkg_049 [liver from HCC patient]

tag: prediction in fc ffpe (dasl)


title: XS39-tel testes at 5dpp, biological rep3

description: Gene expression data from testes of 5dpp XS39-tel males

source_name: XS39-tel testes at 5dpp


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYNDROME PATIENT #2

description:
Patient Noonan Syndrome
NS3

value: FEMALE


title: Larval_Wing discs_lgl mutant_9day AED_rep3

description: tumours

source_name: Drosophila larval wing discs lgl mutant day 9


title: bkg_045 [liver from HCC patient]

tag: prediction in fc ffpe (re-prediction within these 24 samples)


title: Larval_Brain complexes_lgl mutant_9day AED_rep3

description: tumours


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYNDROME PATIENT N#2

description:
Patient Noonan Syndrome
NS2


title: XS39-tel testes at 5dpp, biological rep2


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYNDROME/JMML PATIENT N#3


title: bkg_043 [liver from HCC patient]

tag: prediction confidence p-value in fc ffpe  (re-prediction within these 24 samples)


title: Larval_Brain complexes_lgl mutant_9day AED_rep1

description: tumours


title: bkg_041 [liver from HCC patient]

tag: geo accession of fc-ffpe profile


title: bkg_040 [liver from HCC patient]

tag: disease state


title: HUMAN INDUCED PLURIPOTENT STEM CELL_HEALTHY 3

description:
Control
CTRL5

value: UNKNOWN


title: Larval_Brain complexes_wild type_5day AED_rep2

description: no tumours

source_name: Drosophila larval brain complexes day 5

value: wild type

value: larval brain complexes

value: 5 d AED


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYNDROME PATIENT N#1 1

description:
Patient Noonan Syndrome
NS1


title: HUMAN INDUCED PLURIPOTENT STEM CELL_HEALTHY 2

description:
Control
CTRL2


title: Larval_Brain complexes_wild type_5day AED_rep1

description: no tumours

value: 3rd instar larvae


title: B6-ChrXTMSM testes at 5dpp, biological rep2

description: Gene expression data from testes of 5dpp B6-ChrXTMSM males

source_name: B6-ChrXTMSM testes at 5dpp

tag: organ


title: Larval_Wing discs_lgl mutant_9day AED_rep1

description: tumours

value: larval wing discs

value: 9 d AED


title: HUMAN INDUCED PLURIPOTENT STEM CELL_HEALTHY 1

description:
Control
CTRL1

value: MALE


title: bkg_039 [liver from HCC patient]


title: XS39-tel testes at 5dpp, biological rep1

value: testis

tag: genotype/variation


title: bkg_038 [liver from HCC patient]


title: B6-ChrXTMSM testes at 5dpp, biological rep1

tag: age


title: Larval_Wing discs_wild type_5day AED_rep2

description: no tumours

source_name: Drosophila larval wing discs day 5


title: B6-ChrXTMSM testes at 5dpp, biological rep3


title: Larval_Wing discs_lgl mutant_9day AED_rep2

description: tumours


title: Larval_Wing discs_wild type_5day AED_rep1

description: no tumours


title: B6-ChrXMSM testes at 5dpp, biological rep2

description: Gene expression data from testes of 5dpp B6-ChrXMSM males

source_name: B6-ChrXMSM testes at 5dpp


title: B6-ChrXMSM testes at 5dpp, biological rep3


title: bkg_036 [liver from HCC patient]


title: B6-ChrXMSM testes at 5dpp, biological rep1


title: Healthy control 3

city: Moscow

first: Anelya

last: Alieva

address: 2 Kurchatova sq.

country: Russia

institute: IMG RAS

hyb_protocol: Standard Illumina  protocol

scan_protocol: Standard Illumina  protocol

data_processing:
The software package Genome Studio (Illumina, San Diego, California, USA) and the DAVID Bioinformatics Resources 6.7 database (http://david.abcc.ncifcrf.gov/home.jsp) were used for the statistical processing.
Normalized signal intensity was used for further investigation. A volcano plot was used to identify differentially expressed genes (using n-fold > 1.5 and P < 0.01 as the threshold of statistical significance). For further investigations, we selected transcripts that were common among all the pairs and pools.

source_name: peripheral blood

label_protocol: Standard Illumina  protocol

extract_protocol: The isolation of total RNA from whole blood was performed using the ZR Whole-Blood Total RNA Kit™ (Zymo Research Corp., Irvine, CA, USA) according to the manufacturer’s recommendations.

value: peripheral blood

tag: diagnosis

value: healthy


title: Healthy control 4


title: bkg_029 [liver from HCC patient]

value: poor


title: bkg_025 [liver from HCC patient]

value: good


title: RNA pool from PD controls1-5


title: bkg_022 [liver from HCC patient]

value: hepatocellular carcinoma


title: bkg_005 [liver from HCC patient]

description: Sample name: bkg_005

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

extract_protocol: RNA was isolated with Triazol reagent (Invitrogen) according to manufacturer’s protocol.

value: AS-FFPE liver (cirrhotic)

tag: %p-call

tag: inter-sample correlation

tag: prediction in as-ffpe

tag: prediction in as-ffpe (%p-call >20%)

tag: prediction confidence p-value in as-ffpe (%p-call >20%)

tag: prediction in fc-ffpe

tag: prediction confidence p-value in fc-ffpe


title: MSM testes at 5dpp, biological rep1

description: Gene expression data from testes of 5dpp MSM males

source_name: MSM testes at 5dpp

value: MSM


title: RNA pool from PD patients 1-5

tag: tissue

value: Parkinson's disease


title: bkg_020 [liver from HCC patient]

tag: prediction in as-ffpe (ncounter)

tag: prediction confidence p-value in as-ffpe (ncounter)

tag: prediction in fc ffpe (dasl)


title: bkg_003 [liver from HCC patient]

tag: prediction in fc ffpe (re-prediction within these 24 samples)

tag: prediction confidence p-value in fc ffpe  (re-prediction within these 24 samples)

tag: geo accession of fc-ffpe profile


title: PD patient 4


title: WT Atria_5 vs TGFB1 Tg Aria_7

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: equal amounts of Cy3 and Cy5 labeled probe were hybridized in Ambion hyb solution #1, at 65 degrees for 20 hrs. Slides were prewashed with 0.2% SDS for 10 minutes and blocked with 5% BSA for 15min at 42 degrees before hybridization,and washed with sequentially in 1XSSC, 0.03% SDS; 42 degrees; .2XSSC RT; 0.05XSSC  RT

scan_protocol: Scanned on an Axon 4000AB scanner.

data_processing: LOWESS normalized, no background subtraction was used

source_name: Mouse Atria (WT)

label_protocol: Total RNA was amplified (using the Ambion aRNA kit) and indirectly labeled with amino-allyl Cy3 or Cy5

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, Resulting RNA was then put through a second round of purification, using Qiuagen RNEasy clumns, following the manufacturer's instructions.

value: Atria

tag: genotype

value: WT

tag: genetic background

source_name: Mouse Atria (Tg)

value: TGFB1 Tg


title: MSM testes at 5dpp, biological rep3

tag: organ

tag: genotype/variation

tag: age


title: bkg_015 [liver from HCC patient]

tag: disease state


title: HUMAN INDUCED PLURIPOTENT STEM CELL_NOONAN SYDROME/JMML PATIENT N#4 2

description:
Patient Noonan Syndrome and JMML
NS/JMML4

tag: cell type

value: hIPS generated from skin fibroblasts

tag: gender


title: PD patient 2

tag: diagnosis


title: (B6-ChrXTMSM x B6-Chr1MSM)F1 testes at 5dpp, biological rep1

value: (B6-ChrXTMSM x B6-Chr1MSM)F1


title: WT Atria_5 vs WT Ventricle_10

source_name: Mouse Ventricle (WT)

value: Ventricle


title: TGFB1 Tg Aria_1 vs WT Atria_3


title: Healthy control 1


title: MSM testes at 5dpp, biological rep2


title: Healthy control 2


title: TGFB1 Tg Aria_11 vs TGFB1 Tg Ventricle_12

source_name: Mouse Ventricle (Tg)


title: PD patient 1


title: WT Atria_13 vs WT Ventricle_14


title: PP_OP_18D_R1

status: Public on Jan 30 2014

city: Las Vegas

first: Allen

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

description:
171_PP_OP_18D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Eighteen day old females were collected.

hyb_protocol: Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.

scan_protocol: Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA.  Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: fly source

value: Punta Prieta 2008; PP08

value: Wild-type

tag: origin

value: Punta Prieta, Baja California

tag: host diet

value: Organ pipe (OP)

tag: life stage

value: 18 Day old adult (18D)

tag: phenotype

value: normal


title: B6 testes at 5dpp, biological rep3

description: Gene expression data from testes of 5dpp B6 males

source_name: B6 testes at 5dpp

value: testis


title: PP_OP_24D_R1

description:
172_PP_OP_24D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Twenty-four day old females were collected.

value: 24 Day old adult (24D)


title: B6 testes at 5dpp, biological rep1


title: PP_OP_14D_R1

description:
169_PP_OP_14D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Fourteen day old females were collected.

value: 14 Day old adult (14D)


title: PP_OP_10D_R2

description:
168_PP_OP_10D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Ten day old females were collected.

value: 10 Day old adult (10D)


title: B6 testes at 5dpp, biological rep2


title: TGFB1 Tg Ventricle_8 vs Wt Ventricle_6

tag: tissue


title: PP_OP_14D_R2

description:
170_PP_OP_14D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Fourteen day old females were collected.


title: PP_OP_10D_R1

description:
167_PP_OP_10D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Ten day old females were collected.


title: PP_OP_6D_R2

description:
164_PP_OP_6D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.

value: 6 Day old adult (6D)


title: PP_OP_0D_R4

description:
156_PP_OP_0D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.

value: 0 Day old adult (0D)


title: PP_OP_6D_R4

description:
166_PP_OP_6D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.


title: PP_OP_6D_R3

description:
165_PP_OP_6D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.


title: TGFB1 Tg Ventricle_16 vs TGFB1 Tg Aria_15

value: Atria


title: PP_OP_EP_R2

description:
146_PP_OP_EP_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.

value: Early pupal stage (EP)


title: PP_OP_LP_R3

description:
151_PP_OP_LP_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Late stage pupae were collected.

value: Late pupal stage (LP)


title: PP_OP_EP_R3

description:
147_PP_OP_EP_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.


title: PP_OP_3D_R4

description:
161_PP_OP_3D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.

value: 3 Day old adult (3D)


title: PP_OP_0D_R5

description:
157_PP_OP_0D_R5
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.


title: PP_OP_LP_R1

description:
149_PP_OP_LP_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Late stage pupae were collected.


title: PP_OP_3D_R2

description:
159_PP_OP_3D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: PP_OP_3D_R1

description:
158_PP_OP_3D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: PP_OP_0D_R3

description:
155_PP_OP_0D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.


title: PP_OP_EP_R1

description:
145_PP_OP_EP_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.


title: PP_OP_EP_R4

description:
148_PP_OP_EP_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.


title: PP_OP_0D_R2

description:
154_PP_OP_0D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.


title: PP_OP_L3_R1

description:
144_PP_OP_L3_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. Third instar larvae were collected.

value: 3rd instar larvae (L3)


title: PP_OP_4D_R1

description:
162_PP_OP_4D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Four day old females were collected.

value: Punta Prieta 2008; PP08

value: 4 Day old adult (4D)


title: PP_OP_LP_R4

description:
152_PP_OP_LP_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Late stage pupae were collected.

value: Wild-type

value: Punta Prieta, Baja California


title: PP_OP_0D_R1

description:
153_PP_OP_0D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.

value: Organ pipe (OP)


title: PP_OP_6D_R1

description:
163_PP_OP_6D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.

value: normal


title: PP_OP_L2_R3

description:
143_PP_OP_L2_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.

value: 2nd instar larvae (L2)


title: PP_OP_E6_R3

description:
136_PP_OP_E6_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.

value: 6hr egg (E6)


title: PP_OP_L1_R1

description:
139_PP_OP_L1_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.

value: 1st instar larvae (L1)


title: PP_OP_E6_R5

description:
138_PP_OP_E6_R5
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: Wt Ventricle_4 vs TGFB1 Tg Ventricle_2

value: Ventricle

value: WT

value: TGFB1 Tg


title: PP_OP_3D_R3

description:
160_PP_OP_3D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: PP_OP_LP_R2

description:
150_PP_OP_LP_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Late stage pupae were collected.


title: PP_OP_L1_R2

description:
140_PP_OP_L1_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.


title: PP_OP_L2_R2

description:
142_PP_OP_L2_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.


title: PP_OP_E6_R4

description:
137_PP_OP_E6_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: PP_OP_L2_R1

description:
141_PP_OP_L2_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.


title: PP_AG_24D_R2

description:
133_PP_AG_24D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Twenty-four day old females were collected.

value: Agria (AG)

value: 24 Day old adult (24D)


title: PP_OP_E6_R2

description:
135_PP_OP_E6_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: PP_OP_E6_R1

description:
134_PP_OP_E6_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: PP_AG_18D_R1

description:
128_PP_AG_18D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.

value: 18 Day old adult (18D)


title: PD patient 3

value: peripheral blood

value: Parkinson's disease


title: human embryonic stem cells

description:
Cell line
HES2

source_name: embryonic cell line

tag: cell line

value: FEMALE


title: PP_AG_18D_R4

description:
131_PP_AG_18D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.

value: Punta Prieta 2008; PP08


title: PP_AG_18D_R3

description:
130_PP_AG_18D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.

value: Wild-type


title: PP_AG_24D_R1

description:
132_PP_AG_24D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Twenty-four day old females were collected.

value: Punta Prieta, Baja California


title: PP_AG_14D_R3

description:
127_PP_AG_14D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.

value: 14 Day old adult (14D)


title: PP_AG_18D_R2

description:
129_PP_AG_18D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.

value: normal


title: PP_AG_14D_R1

description:
125_PP_AG_14D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.


title: PP_AG_10D_R4

description:
124_PP_AG_10D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.

value: 10 Day old adult (10D)


title: PP_AG_10D_R2

description:
122_PP_AG_10D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: PP_AG_10D_R1

description:
121_PP_AG_10D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: PP_AG_10D_R3

description:
123_PP_AG_10D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: PP_AG_6D_R3

description:
118_PP_AG_6D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.

value: 6 Day old adult (6D)


title: PP_AG_6D_R4

description:
119_PP_AG_6D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.


title: PP_AG_14D_R2

description:
126_PP_AG_14D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.


title: 8895 adjacent non-tumor tissue

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

description: DNA methylation in HCC

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

label: Cy5 and Cy3

source_name: adjacent non-tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 66 frozen tumor/adjacent tissues by standard proteinase K/RNase treatment and phenol/chloroform extraction.

value: Female

tag: tissue type

value: Liver

value: hepatocellular carcinoma (HCC)


title: PP_AG_6D_R2

description:
117_PP_AG_6D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.

tag: genotype


title: PP_AG_6D_R5

description:
120_PP_AG_6D_R5
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.


title: 8896 adjacent non-tumor tissue

description: DNA methylation in HCC


title: PP_AG_4D_R1

description:
115_PP_AG_4D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Four day old females were collected.

value: 4 Day old adult (4D)


title: PP_AG_6D_R1

description:
116_PP_AG_6D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.

value: Agria (AG)


title: PP_AG_3D_R2

description:
113_PP_AG_3D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.

value: 3 Day old adult (3D)


title: PP_AG_3D_R3

description:
114_PP_AG_3D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.


title: 8894 HCC tumor

description: DNA methylation in HCC

source_name: HCC tumor


title: PP_AG_3D_R1

description:
112_PP_AG_3D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.


title: PP_AG_0D_R5

description:
111_PP_AG_0D_R5
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.

value: 0 Day old adult (0D)


title: 8892 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Male


title: PP_AG_0D_R4

description:
110_PP_AG_0D_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: 8893 HCC tumor

description: DNA methylation in HCC


title: 8803 adjacent non-tumor tissue

description: DNA methylation in HCC


title: PP_AG_0D_R3

description:
109_PP_AG_0D_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: PP_AG_0D_R2

description:
108_PP_AG_0D_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: 8674 HCC tumor

description: DNA methylation in HCC


title: PP_AG_0D_R1

description:
107_PP_AG_0D_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: 8797 HCC tumor

description: DNA methylation in HCC


title: 8802 HCC tumor

description: DNA methylation in HCC


title: PP_AG_LP_R4

description:
106_PP_AG_LP_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.

value: Late pupal stage (LP)


title: 8796 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8798 HCC tumor

description: DNA methylation in HCC


title: 8795 HCC tumor

description: DNA methylation in HCC


title: 8673 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8672 HCC tumor

description: DNA methylation in HCC


title: 8794 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8660 HCC tumor

description: DNA methylation in HCC


title: PP_AG_LP_R2

description:
104_PP_AG_LP_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.


title: PP_AG_LP_R1

description:
103_PP_AG_LP_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.


title: PP_AG_LP_R3

description:
105_PP_AG_LP_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.


title: PP_AG_EP_R3

description:
102_PP_AG_EP_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.

value: Early pupal stage (EP)


title: 8669 adjacent non-tumor tissue

description: DNA methylation in HCC


title: PP_AG_EP_R2

description:
101_PP_AG_EP_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.

value: Punta Prieta 2008; PP08


title: 8662 HCC tumor

description: DNA methylation in HCC


title: PP_AG_EP_R1

description:
100_PP_AG_EP_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.

value: Wild-type


title: 8661 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8670 HCC tumor

description: DNA methylation in HCC


title: 8671 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8799 adjacent non-tumor tissue

description: DNA methylation in HCC


title: PP_AG_L3_R5

description:
99_PP_AG_L3_R5
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.

value: Punta Prieta, Baja California

value: 3rd instar larvae (L3)


title: PP_AG_L3_R4

description:
98_PP_AG_L3_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.

value: normal


title: 8897 HCC tumor

description: DNA methylation in HCC


title: 8657 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8658 HCC tumor

description: DNA methylation in HCC


title: 8656 adjacent non-tumor tissue

description: DNA methylation in HCC


title: PP_AG_L3_R3

description:
97_PP_AG_L3_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: PP_AG_L3_R1

description:
95_PP_AG_L3_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: PP_AG_L3_R2

description:
96_PP_AG_L3_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: PP_AG_L2_R4

description:
94_PP_AG_L2_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.

value: 2nd instar larvae (L2)


title: 8654 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8655 HCC tumor

description: DNA methylation in HCC


title: PP_AG_L2_R3

description:
93_PP_AG_L2_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.


title: PP_AG_L2_R2

description:
92_PP_AG_L2_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.


title: 8650 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8651 HCC tumor

description: DNA methylation in HCC