title: Stimulated uterine horn

city: Urbana

first: Juanmahel

last: Davila

state: Illinois

address: 2001 S. Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois

description: Gene expression data from 72h ADR Stimulated horn.

hyb_protocol: 10 micrograms of labeled cRNA were hybridized to an Affymetrix Murine Genome U74A Version 2 Array. Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center, Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics, the Keck Center generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

organism: Mus musculus

source_name: Mouse uterus 72h ADR, stimulated

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals.

extract_protocol: Trizol extraction of total RNA was performed followed by RNA clean-up using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: CD-1 adult female mice (n=3) were subjected to the experimentally induced decidualization protocol.

tag: gender

value: female

tag: age

value: adult

tag: tissue

value: uterus

tag: treatment

value: 72h post-ADR stimulated


title: IFNg 6.5ng 48h_3

status: Public on Feb 09 2017

type: RNA

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

country: USA

institute: CC/DTM/NIH

description: IFNg 6.5ng 48h

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

molecule: total RNA

organism: Homo sapiens

source_name: IFNg 6.5ng 48h

growth_protocol: BMSCs were isolated at Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland. These cells were expanded and characterized as described in our previous work27. Briefly, cells from the bone marrow aspirates were seeded in complete media (α-minimal essential medium [α-MEM], 2mM glutamine, 10µg/ml gentamicin and 20% fetal bovine serum) for 24 hours, and the non-adherent cells were removed. The adherent cells were expanded until 70-80% confluence was reached. Cells were sub-cultured and kept in complete media. These BMSCs were >70% viable and expressed CD73, CD90, CD105 and CD146 but not CD11b, CD14, CD19, CD34 or CD45.

extract_protocol: Total RNA from stimulated and control BMSC samples were isolated and purified by using miRNeasyKit (Qiagen, Germantown, MD, USA). The RNA concentration was determined using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: BMSCs (passage 4) were stimulated with 6.5 or 65 ng/ml of IFN-g (R&D System Minneapolis, MN, USA), and with 1.5 or 15 ng/ml of TNF-a (R&D System Minneapolis, MN, USA), or the combination of IFN-g and TNF-a   (1.5 ng/ml of TNF-a + 6.5 ng/ml of IFN-g or 15 ng/ml of TNF-a + 65 ng/ml of IFN-g).  After the adherent BMSCs were incubated with the cytokines for 48 hours, the BMSCs were harvested using trypsin and they were then evaluated by gene expression profiling. Prior to harvesting the BMSCs, the supernatant was collected, frozen and stored at -80oC for protein analysis.

tag: cell type

value: BMSC cell line

source_name: universal human reference RNA

tag: reference type

value: pooled whole human RNA


title: IFNg 65ng 48h_3

description: IFNg 65ng 48h

source_name: IFNg 65ng 48h

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)


title: IFNg 65ng 48h_2

description: IFNg 65ng 48h


title: genomic DNA from 9701417057_R06C01

type: genomic

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

institute: Yale University

description: 9701417057_R06C01: Sample 109

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407210093_R06C01

description: 9407210093_R06C01: Sample 108


title: genomic DNA from 9701417057_R02C02

description: 9701417057_R02C02: Sample 111


title: IFNg 6.5ng 48h_2

description: IFNg 6.5ng 48h


title: NLS 12_251109.CEL

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

hyb_protocol: GeneChips were washed and stained with Fluidics Script FS450-004 in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G. The data were analyzed with Affymetrix GeneChip Operating Software version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

data_processing: The raw data (CELL files) were subjected to GCRMA.

label: Biotin

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA was prepared according to a standard Ambion protocol from 1 μg total RNA (MessageAmp II-Biotin Enhanced Kit; Ambion). After amplification and fragmentation, 12.5 μg of cRNA was hybridized for 16 h at 45°C on GeneChip ATH1-121501 Genome Array.

growth_protocol: Arabidopsis seedlings were grown on soil for 4 weeks under 10h light/14h dark conditions.

extract_protocol: Total RNA was isolated with RNeasy Plant Mini kit according to the manufacturer's instructions.

tag: genotype

value: EDS1-NLS (eds1-2)

value: untreated

tag: time


title: genomic DNA from 9701417031_R06C01

description: 9701417031_R06C01: Sample 107


title: IFNg 6.5ng 48h_1

description: IFNg 6.5ng 48h


title: BMSC control 48h_9

description: BMSC control 48h

source_name: BMSC control 48h


title: genomic DNA from 9701417035_R03C02

description: 9701417035_R03C02: Sample 106

value: White


title: BMSC control 48h_8

description: BMSC control 48h


title: NLS 11_261109.CEL


title: genomic DNA from 9701417053_R06C02

description: 9701417053_R06C02: Sample 105


title: genomic DNA from 9407210029_R02C02

description: 9407210029_R02C02: Sample 104


title: IFNg 65ng 48h_1

description: IFNg 65ng 48h


title: mir-35-41(nDf50) embryo, 20 degrees, rep 1

city: Bethesda

first: Katherine

last: McJunkin

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

description:
mir-35-41_20_rep1
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Hybridization was carried out according to GeneChip instructions in a GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using a GeneChip Scanner.

data_processing: Linear and log2 signals were generated as pivot files in Expression Console from Affymetrix. Further analysis was conducted in GeneSpring from Agilent.

label: biotin

organism: Caenorhabditis elegans

source_name: whole mixed-stage embryos, mir-35-41(nDf50) mutant, 20C

label_protocol: Biotinylated aRNA was generated using the Enzo Single-Round RNA Amplification and Biotin Labeling System, according to instructions.

growth_protocol: Cultures were grown on NGM supplemented with chicken egg yolk at 20 degrees Celsius.

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

treatment_protocol: Mixed-stage embryos samples were obtained by hypochlorite treatment of mixed-stage C. elegans cultures.

tag: strain/background

value: VT2935 lacking nEx1187

tag: genotype/variation

value: mir-35-41(nDf50) mutant

tag: developmental stage

value: mixed-stage embryos

value: whole body

tag: temperature


title: BMSC control 48h_7

description: BMSC control 48h


title: Col 3_261109.CEL

value: Wild-type (Col-0)

tag: treatment


title: BMSC control 48h_4

description: BMSC control 48h

tag: cell type


title: BMSC control 48h_6

description: BMSC control 48h

tag: reference type


title: Col 2_261109.CEL


title: genomic DNA from 9701417057_R01C01

description: 9701417057_R01C01: Sample 102

tag: hiv


title: genomic DNA from 9701417035_R01C01

description: 9701417035_R01C01: Sample 101

tag: agebl


title: Brain_Wildtype-3

city: Callaghan

first: Adrienne

middle: E

last: Milward

state: NSW

address: Medical Science Building MSB

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: University of Newcastle

hyb_protocol: Standard Illumina hybridization protocol was used (Illumina Sentrix MouseRef-8 v2.0 Expression BeadChips).

scan_protocol: Beadchips were scanned using the Illumina BeadArray Reader and BeadScan software (V2.2.7).

data_processing: Data were extracted in GenomeStudio Gene Expression Module (Illumina, v2010.3) background subtracted and Cubic Spline,  Average or no normalisation were performed. We routinely use two different normalization methods as we have previously published a paper (Johnstone et al. Microarray 2013) showing that normalization can affect this kind of data. Depending on the context, our analyses typically use both the intersection and the union of the two methods (here Cubic Spline and Average normalization). The intersection set contains probes that are selected using both methods and are therefore less likely to be an artefact of either method. Conversely the union set includes probes that are selected by either one or both methods and therefore makes it less likely that we will miss probes which are false negatives by either method.  Normalized data using each method are available on the series record. The sample data table contains the Cubic Spline-normalized data.

source_name: mouse, brain, wildtype

label_protocol: RNA samples were biotin-labelled and amplified using the TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was isolated from Hfe-/-xTfr2mut and wildtype mice (n≥4/group) using TRI reagent (Ambion) then purified and concentrated using the RNeasy MinElute Kit (QIAGEN).

value: Wildtype

tag: strain

value: AKR mice

tag: gender

value: male

tag: age

tag: tissue

value: brain

tag: diet

value: standard diet


title: BMSC control 48h_5

description: BMSC control 48h


title: NLS 10_261109.CEL


title: BMSC control 48h_3

description: BMSC control 48h


title: Col 1_261109.CEL


title: Unstimulated uterine horn

description: Gene expression data from 72h ADR Unstimulated horn.

source_name: Mouse uterus 72h ADR, unstimulated

value: female

value: adult

value: uterus

value: 72h post-ADR unstimulated


title: genomic DNA from 9701417053_R03C01

description: 9701417053_R03C01: Sample 103

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417053_R04C01

description: 9701417053_R04C01: Sample 100


title: BMSC control 48h_1

description: BMSC control 48h

value: BMSC cell line

value: pooled whole human RNA


title: IFNg+TNFa 6.5+1.5ng 48h_1

description: IFNg+TNFa 6.5+1.5ng 48h

source_name: IFNg+TNFa 6.5+1.5ng 48h


title: genomic DNA from 9407210073_R05C01

description: 9407210073_R05C01: Sample 99


title: Brain_Wildtype-1

tag: genotype


title: Leukocyte  TP13-S0459

city: Pittsburgh

first: Shuchang

last: Liu

state: Pennsylvania

address: 130 De Soto Street

institute: University of Pittsburgh

description: Affymetrix SNP 6.0

hyb_protocol: Two hundred fifty micrograms of fragmented DNA were hybridized with a pre-equilibrated Affymetrix chip SNP 6.0 at 50oC for 18 hours.  Procedures of washing and scanning of SNP 6.0 chips followed the manuals provided by Affymetrix, Inc.

scan_protocol: The hybridized chips were scanned by 7G Affymetrix scanner.

data_processing:
CEL files were analyzed with Genotyping Console for quality control analysis. Samples with QC call above 80% and QC contrast ratio above 0.4 were admitted into the analysis. To analyze CNV, CEL files were imported into Partek GenomeSuite 6.6 to generate copy number from raw intensity.
Each CEL file represents data from one patient. Deletion or amplification of genomes were analyzed by first limiting to the regions with p-value less than 0.001. The selected regions were subsequently filtered by limiting to the regions with at least 10 markers and 2 kb in size.

source_name: Leukocyte  TP13-S0459

label_protocol: The fragmented DNA was labeled with biotinylated nucleotides through terminal deoxynucleotide transferase for 4 hours at 37oC, following the manual provided by Affymetrix, Inc.

extract_protocol: DNA was extracted using Qiagen blood DNA extraction kit.

value: Leukocyte

tag: patient


title: Brain_Double mut_4

source_name: mouse, brain, Hfe-/-xTfr2mut Mutant

value: iron diet


title: BMSC control 48h_2

description: BMSC control 48h

tag: cell type


title: Brain_Double mut_3


title: Brain_Wildtype-2


title: Brain_Wildtype-4


title: Leukocyte  TP13-S0439

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0439


title: Leukocyte  TP13-S0342_2

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0342


title: genomic DNA from 9701417053_R05C01

description: 9701417053_R05C01: Sample 96


title: Leukocyte  TP13-S0383

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0383


title: genomic DNA from 9701417048_R02C02

description: 9701417048_R02C02: Sample 95


title: Hop3B Sh SIRT6 vs. Hop3B Sh Cont 4day

city: Toronto

first: Dae-Kyum

last: Kim

state: ON

address: 88 Wellesley Street East

department: Donnelly centre

country: Canada

institute: University of Toronto

description: Replicate #2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: Hop3B Sh SIRT6

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: The cells were cultured at 37 ℃ under 5% CO2 in DMEM supplemented with 10% FBS, 100 units/ml of penicillin and 100 µg/ml streptomycin.

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

treatment_protocol: Stable cell lines were established by transduction with lentiviral shRNA targeting SIRT6 or scrambled control (Sigma).

value: HCC cells

source_name: Hop3B Sh Cont 4day


title: Leukocyte  TP13-S0318

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0318


title: genomic DNA from 9701417031_R05C02

description: 9701417031_R05C02: Sample 98


title: thymus_control_CT8

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from thymus explant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering up to 3 NAs for each group (DS or CT) and  the expression values in Log (base 2).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Thymus explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: subject status

value: karyotipically normal individual

tag: age at surgery (yr/mo/d)

value: thymus


title: SIRT6 4day vs. Cont 4day

description: Replicate #1

source_name: SIRT6 4day

source_name: Cont 4day


title: Leukocyte  TP13-S0314

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0314


title: PT supplemented group [after PT_4]

type: SRA

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

country: South Korea

institute: Kyungpook National University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 1.3.3, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.0.2 software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "PT" sample.

source_name: after_PT_ PBMCs

growth_protocol: Fifty subjects with mild metabolic syndrome were enrolled in this study. Subjects excluded were pregnant women, type 1 diabetic, those treated with insulin and any drugs for the control of blood glucose, blood lipids and body weight and those using functional food products, since they may affect the results of the this study. This was performed in accordance with the Declaration of Helsinki, and all subjects provide written informed consent prior to participating in this study.

extract_protocol:
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: All subjects were randomly divided into two nutritional intervention groups: placebo (n=25) and PT (n=25). Subjects consumed either six capsules containing starch (3 g per day; placebo group), PT (2 g per day) in the morning, afternoon and evening daily for 12 weeks.

value: mild metabolic syndrome

tag: subject id

tag: nutritional intervention group

value: pterocarpan-rich extract soybean leaf (PT)

tag: time point

value: after PT-supplemented

value: pheripheral mononuclear cells


title: PT supplemented group [after PT_3]


title: genomic DNA from 9701417031_R05C01

description: 9701417031_R05C01: Sample 93

source_name: whole blood

tag: hiv

tag: agebl

value: White


title: Leukocyte  TP13-S0273

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0273


title: PT supplemented group [after PT_8]


title: thymus_control_CT10

description: Gene expression from thymus explant

tag: gender

value: male

tag: tissue


title: Leukocyte  TP13-S0569

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0569


title: thymus_control_CT9

description: Gene expression from thymus explant

value: female


title: genomic DNA from 9407210074_R03C02

description: 9407210074_R03C02: Sample 92

tag: racecomg

tag: dmgsex


title: genomic DNA from 9701417047_R06C02

description: 9701417047_R06C02: Sample 91

tag: gran

tag: nk


title: thymus_control_CT6

description: Gene expression from thymus explant


title: Leukocyte  TP13-S0557

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0557


title: thymus_control_CT5

description: Gene expression from thymus explant


title: Brain_Double mut_2

tag: strain

value: AKR mice

tag: age

value: brain

tag: diet


title: genomic DNA from 9407210065_R05C01

description: 9407210065_R05C01: Sample 90

value: Other

tag: bcell

tag: mono


title: Leukocyte  TP13-S0546

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0546

tag: cell type

tag: patient


title: Brain_Double mut_1

tag: genotype


title: thymus_control_CT7

description: Gene expression from thymus explant

tag: subject status

tag: age at surgery (yr/mo/d)


title: thymus_control_CT2

description: Gene expression from thymus explant


title: thymus_control_CT3

description: Gene expression from thymus explant


title: genomic DNA from 9407210016_R06C02

description: 9407210016_R06C02: Sample 89

tag: hiv

tag: agebl

value: Black


title: Leukocyte  TP13-S0543

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0543


title: Leukocyte  TP13-S0570

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0570


title: genomic DNA from 9407210029_R03C02

description: 9407210029_R03C02: Sample 87


title: genomic DNA from 9407210065_R03C01

description: 9407210065_R03C01: Sample 88


title: thymus_control_CT4

description: Gene expression from thymus explant

tag: gender

tag: tissue


title: Leukocyte  TP13-S0404

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0404


title: thymus_down-syndrome_DS9

description: Gene expression from thymus explant

value: Down syndrome (DS)


title: Leukocyte  TP13-S0342

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0342

value: Leukocyte


title: genomic DNA from 9407210107_R02C01

description: 9407210107_R02C01: Sample 84

tag: racecomg

tag: dmgsex


title: thymus_down-syndrome_DS8

description: Gene expression from thymus explant


title: genomic DNA from 9407210016_R04C01

description: 9407210016_R04C01: Sample 85

tag: gran

tag: nk


title: Leukocyte  TP13-S0297

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0297


title: thymus_down-syndrome_DS10

description: Gene expression from thymus explant


title: genomic DNA from 9701417048_R01C02

description: 9701417048_R01C02: Sample 83


title: thymus_control_CT1

description: Gene expression from thymus explant


title: genomic DNA from 9701417031_R03C01

description: 9701417031_R03C01: Sample 82


title: genomic DNA from 9407210065_R03C02

description: 9407210065_R03C02: Sample 81


title: thymus_down-syndrome_DS4

description: Gene expression from thymus explant


title: genomic DNA from 9701417047_R04C01

description: 9701417047_R04C01: Sample 86


title: genomic DNA from 9701417053_R02C01

description: 9701417053_R02C01: Sample 80


title: Leukocyte  TP13-S0947

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0947

tag: age


title: Leukocyte  TP13-S0586

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0586


title: Leukocyte  TP13-S0501

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0501


title: genomic DNA from 9407210074_R01C01

description: 9407210074_R01C01: Sample 79


title: thymus_down-syndrome_DS5

description: Gene expression from thymus explant


title: thymus_down-syndrome_DS3

description: Gene expression from thymus explant


title: thymus_down-syndrome_DS2

description: Gene expression from thymus explant


title: Leukocyte  TP13-S0494

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0494


title: genomic DNA from 9701417048_R03C02

description: 9701417048_R03C02: Sample 77


title: Leukocyte  TP13-S0484

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0484


title: thymus_down-syndrome_DS7

description: Gene expression from thymus explant


title: genomic DNA from 9407210029_R01C02

description: 9407210029_R01C02: Sample 76


title: Leukocyte  TP13-S0661

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0661


title: Leukocyte  TP13-S0483

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0483


title: thymus_down-syndrome_DS6

description: Gene expression from thymus explant


title: HY1

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

data_processing:
Sequencing reads were mapped to the UCSC Genome Browser dm6 (NCBI genome/47) Drosophila melanogaster genome with Bowtie version 1.0.
Small RNA sequencing reads were analyzed with miRDeep2.
Differential expression of miRNAs was analyzed with the Bioconductor package edgeR.
Genome_build: Drosophila dm6 (NCBI genome/47)
Supplementary_files_format_and_content: tab-delimited text file that includes the miRNA read counts generated by miRDeep2. FASTA file contains trimmed read sequences.

organism: Drosophila melanogaster

source_name: young

growth_protocol: Young (2 days old) and old (25 days old) males flies were anesthetized and used to collect samples of hemolymph and body tissues.

extract_protocol:
Total RNA, including small RNA, was extracted from hemolymph and body tissues using Qiagen miRNeasy Serum/Plasma Kit and miRNeasy kit, respectively.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit (#RS-200-0012). Illumina HiSeq2000 was used to sequence the libraries (50bp, single-end)

tag: tissue type

value: Hemolymph

value: 2 days

tag: Sex


title: genomic DNA from 9407210016_R06C01

description: 9407210016_R06C01: Sample 75

source_name: whole blood

tag: bcell

tag: mono


title: HY3


title: HY4


title: thymus_down-syndrome_DS1

description: Gene expression from thymus explant


title: HY2


title: HO7

source_name: Old

value: 25 days


title: HO6


title: Leukocyte  TP13-S0468

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0468

tag: cell type

tag: patient


title: genomic DNA from 9407210029_R01C01

description: 9407210029_R01C01: Sample 73


title: genomic DNA from 9701417035_R02C02

description: 9701417035_R02C02: Sample 72


title: genomic DNA from 9701417048_R01C01

description: 9701417048_R01C01: Sample 74


title: HO8


title: genomic DNA from 9407210016_R05C02

description: 9407210016_R05C02: Sample 71


title: HO5


title: Leukocyte  TP13-S0458B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0458B


title: Leukocyte  TP13-S0465

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0465


title: Leukocyte  TP13-S0289

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0289


title: HO4


title: genomic DNA from 9407210063_R03C02

description: 9407210063_R03C02: Sample 70


title: Leukocyte  TP13-S0456

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0456

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes

tag: fast relapase label

value: f


title: genomic DNA from 9407210029_R02C01

description: 9407210029_R02C01: Sample 78

tag: hiv

tag: agebl


title: PBMC_sample116

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted

hyb_protocol: bisulphite-converted DNA was subjected to whole-genome amplification after which the DNA was enzymatically fragmented and hybridised to the Infinium HumanMethylation450 BeadChip

scan_protocol: The BeadChips were scanned with the Illumina iScan reader

data_processing: 1st) The data (N=122) was preprocessed as methylumiset object by using R package wateRmelon(normalization&background correction with dasen; pfilter with default settings). Unspecific probes were excluded.  The batch effect of the Infinium chemistries was adjusted with BMIQ algorithm and the batch effect of two different run series was adjusted with EB-based algorithm by using R package Combat.    2nd) The preprosessed beta values were regressed in the variable dispersion beta regression model (implemented in R package betareg) with gender and cell type proportions as predictors after which the standardized weighted residuals were extracted and used in all statistical analyses --> There were 7 samples without information about cell type characterization and thus the total number of samples after residual extraction was 115. (The final statistical analysis was made with N=111 samples because there were 4 samples without information about BMI or MMSE)

source_name: PBMC from fresh blood

label_protocol: Standard Illumina protocol using Cy5 and Cy3

growth_protocol: Fresh blood sampleswere collected to EDTA-tubes. The peripheral blood mononuclear cells (PBMCs) were separated with Ficoll-Paque density gradient

extract_protocol: DNA was extracted from PBMCs using the QIAamp DNA Mini kit (Qiagen, CA, USA)

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: HO3

tag: tissue type

tag: age

tag: Sex


title: Leukocyte  TP13-S0481

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0481

tag: cell type

tag: patient


title: genomic DNA from 9701417031_R06C02

description: 9701417031_R06C02: Sample 69

tag: hiv

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: HO2


title: Leukocyte  TP13-S0370

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0370


title: genomic DNA from 9701417048_R06C01

description: 9701417048_R06C01: Sample 67

tag: agebl


title: genomic DNA from 9701417057_R03C02

description: 9701417057_R03C02: Sample 66


title: HO1


title: Leukocyte  TP13-S0359

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0359


title: Leukocyte  TP13-S0438

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0438


title: genomic DNA from 9701417057_R01C02

description: 9701417057_R01C02: Sample 65


title: FY3

value: Body tissue


title: FY4


title: genomic DNA from 9407210016_R03C01

description: 9407210016_R03C01: Sample 64


title: FY1


title: FY2


title: Leukocyte  TP13-S0244

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0244


title: Leukocyte  TP13-S0482

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0482


title: genomic DNA from 9701417047_R03C01

description: 9701417047_R03C01: Sample 63


title: FO8


title: Leukocyte  TP13-S0232

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0232


title: FO7


title: Leukocyte  TP13-S0455

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0455


title: genomic DNA from 9701417047_R04C02

description: 9701417047_R04C02: Sample 62


title: genomic DNA from 9701417047_R05C02

description: 9701417047_R05C02: Sample 68


title: Leukocyte  TP13-S0179

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0179


title: genomic DNA from 9407210016_R05C01

description: 9407210016_R05C01: Sample 60

source_name: whole blood


title: Leukocyte  TP13-S0147

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0147

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label


title: genomic DNA from 9701417031_R04C01

description: 9701417031_R04C01: Sample 59


title: FO5

source_name: Old

tag: tissue type


title: Leukocyte  TP13-S0134

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0134

tag: age


title: genomic DNA from 9701417047_R05C01

description: 9701417047_R05C01: Sample 61


title: Leukocyte  TP13-S0109

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0109

tag: fast relapase label


title: FO3

tag: Sex


title: Leukocyte  TP13-S0388

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0388

tag: cell type

tag: patient


title: genomic DNA from 9701417047_R02C01

description: 9701417047_R02C01: Sample 57

tag: hiv

tag: racecomg


title: FO6


title: FO2


title: Leukocyte  TP13-S0048

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0048


title: FO4


title: genomic DNA from 9407201108_R02C01

description: 9407201108_R02C01: Sample 55

tag: dmgsex

tag: gran


title: Leukocyte  TP13-S0022

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0022


title: Leukocyte  TP13-S0035

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0035


title: genomic DNA from 9701417053_R04C02

description: 9701417053_R04C02: Sample 97

tag: nk

tag: bcell


title: FO1


title: genomic DNA from 9701417035_R06C01

description: 9701417035_R06C01: Sample 54

tag: agebl

tag: mono


title: genomic DNA from 9701417047_R01C01

description: 9701417047_R01C01: Sample 53


title: genomic DNA from 9407210029_R04C02

description: 9407210029_R04C02: Sample 94


title: genomic DNA from 9701417035_R01C02

description: 9701417035_R01C02: Sample 58


title: Leukocyte  TP12-S1406

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1406


title: genomic DNA from 9701417047_R03C02

description: 9701417047_R03C02: Sample 56


title: Skeletal_muscle_wt_biological_rep5

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

description: Gene expression data from quadriceps samples from Mut+/+ mice on a high-fat diet.

hyb_protocol: 15ug cRNA was used to make 300ul hyb cocktail, of which 200ul were injected into GeneChip Mouse 430 2.0 arrays and hybridized for 16 hours at 45C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with user-prepared reagents.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were analyzed using MAS 5.0, and scaled to all probesets with a scale factor of 1 and target signal of 1500.

source_name: quadriceps muscle, WT, high-fat diet

label_protocol: Simultaneous cRNA synthesis and biotin labeling via 3' IVT Express protocol.

growth_protocol: Male mice were fed a high-fat diet (45% kcal from fat) for 4 months.

treatment_protocol: Mice were fasted overnight prior to sacrifice and tissue collection.

tag: strain/background

tag: genotype/variation

value: Mut+/+

tag: gender

value: 5 months

tag: tissue

value: quadriceps muscle

tag: treatment

value: high-fat diet


title: Leukocyte  TP12-S1387

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1387

tag: age


title: Skeletal_muscle_wt_biological_rep3

value: male


title: Skeletal_muscle_het_biological_rep5

description: Gene expression data from quadriceps samples from Mut+/- mice on a high-fat diet.

source_name: quadriceps muscle, Mut+/-, high-fat diet

value: Mut+/-


title: Skeletal_muscle_wt_biological_rep4


title: genomic DNA from 9407210107_R06C01

description: 9407210107_R06C01: Sample 51


title: Skeletal_muscle_het_biological_rep2


title: Skeletal_muscle_wt_biological_rep2


title: Leukocyte  TP13-S0248

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0248

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

tag: fast relapase label


title: Leukocyte  TP12-S1308

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1308

tag: cell type

tag: patient


title: Leukocyte  TP12-S1408

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1408


title: Leukocyte  TP12-S1303

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1303


title: genomic DNA from 9407210107_R01C02

description: 9407210107_R01C02: Sample 48

source_name: whole blood

tag: hiv

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk


title: Leukocyte  TP12-S1300

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1300


title: genomic DNA from 9407210073_R04C02

description: 9407210073_R04C02: Sample 47

tag: agebl

tag: bcell

tag: mono


title: genomic DNA from 9407201108_R04C01

description: 9407201108_R04C01: Sample 52


title: Skeletal_muscle_het_biological_rep4

tag: strain/background

tag: genotype/variation

tag: gender

tag: tissue

tag: treatment


title: Skeletal_muscle_het_biological_rep3

tag: age


title: Skeletal_muscle_het_biological_rep1


title: Skeletal_muscle_wt_biological_rep1


title: genomic DNA from 9407210107_R02C02

description: 9407210107_R02C02: Sample 46


title: genomic DNA from 9407210016_R04C02

description: 9407210016_R04C02: Sample 50

value: Other


title: genomic DNA from 9407210073_R05C02

description: 9407210073_R05C02: Sample 45

value: Black


title: Leukocyte  TP12-S1257

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1257

value: Leukocyte


title: Leukocyte  TP12-S1256

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1256


title: genomic DNA from 9701417031_R04C02

description: 9701417031_R04C02: Sample 44


title: APC+/-/Olfm4-/-_T_107879T2

first: WeiPing

last: Chen

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

department: GCL

institute: NIDDK/NIH

description: 07-26-12_GRodgers_15_HL_Mouse430_2_15#107879T2

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

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

data_processing: RMA by software Partek (v.6.5)

source_name: APC/Olfm4 mutant_colon

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

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4-5 animals per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food and water ad libitum. Age and sex matched littermate cohorts were used for all the experiments to account for potential strain differences.

tag: strain background

value: C57BL/6 and 129 hybrid

value: APC/Olfm4 mutant; APC+/-/Olfm4-/-

value: 3 months

value: colon

tag: tissue subtype

value: tumor tissue


title: genomic DNA from 9407210063_R04C01

description: 9407210063_R04C01: Sample 49


title: genomic DNA from 9701417035_R05C01

description: 9701417035_R05C01: Sample 43


title: genomic DNA from 9407210093_R02C02

description: 9407210093_R02C02: Sample 42


title: Leukocyte  TP12-S1255

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1255

tag: cell type

tag: patient


title: APC+/-/Olfm4-/-_T_107879T1

description: 07-26-12_GRodgers_14_HL_Mouse430_2_14#107879T1


title: Leukocyte  TP12-S1253

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1253


title: Leukocyte  TP12-S1271

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1271


title: Leukocyte  TP12-S1227

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1227


title: genomic DNA from 9407210073_R06C02

description: 9407210073_R06C02: Sample 41

tag: hiv

tag: racecomg


title: Leukocyte  TP12-S1226

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1226


title: genomic DNA from 9407210061_R02C02

description: 9407210061_R02C02: Sample 40

tag: dmgsex

tag: gran


title: APC+/-/Olfm4-/-_N_107879N2

description: 07-26-12_GRodgers_12_HL_Mouse430_2_12#107879N2

value: adjacent normal tissue


title: Leukocyte  TP12-S1224

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1224


title: APC+/+/Olfm4-/-_107855

description: 07-26-12_GRodgers_08_HL_Mouse430_2_8#107855

source_name: Olfm4 mutant_colon

value: Olfm4 mutant; APC+/+/Olfm4-/-


title: APC+/-/Olfm4-/-_N_107879N1

description: 07-26-12_GRodgers_11_HL_Mouse430_2_11#107879N1


title: APC+/+/Olfm4-/-_825855

description: 07-26-12_GRodgers_09_HL_Mouse430_2_9#825855


title: APC+/-/OLFM4(+/+)_107831

description: 07-26-12_GRodgers_06_HL_Mouse430_2_6#107831

source_name: APC mutant_colon

value: APC mutant; APC+/-/OLFM4(+/+)


title: APC+/-/Olfm4-/-_T_107848T

description: 07-26-12_GRodgers_13_HL_Mouse430_2_13#107848T


title: APC+/-/Olfm4-/-_N_107848N

description: 07-26-12_GRodgers_10_HL_Mouse430_2_10#107848N


title: genomic DNA from 9407210016_R02C01

description: 9407210016_R02C01: Sample 39

tag: agebl

tag: nk


title: genomic DNA from 9407210093_R06C02

description: 9407210093_R06C02: Sample 38

tag: bcell

tag: mono


title: Leukocyte  TP12-S1197

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1197


title: APC+/-/OLFM4(+/+)_107826

description: 07-26-12_GRodgers_05_HL_Mouse430_2_5#107826

tag: genotype/variation


title: Leukocyte  TP12-S1189

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1189


title: genomic DNA from 9407210073_R03C01

description: 9407210073_R03C01: Sample 37


title: genomic DNA from 9701417031_R02C01

description: 9701417031_R02C01: Sample 35


title: Leukocyte  TP12-S1176

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1176


title: Leukocyte  TP12-S1175

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1175


title: APC+/+/Olfm4+/+_107829

description: 07-26-12_GRodgers_03_HL_Mouse430_2_3#107829

source_name: wild type_colon

value: wild type; APC+/+/Olfm4+/+

tag: gender


title: APC+/+/Olfm4-/-_107825

description: 07-26-12_GRodgers_07_HL_Mouse430_2_7#107825

tag: tissue


title: genomic DNA from 9701417057_R05C01

description: 9701417057_R05C01: Sample 34

source_name: whole blood


title: Leukocyte  TP12-S1147

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1147


title: Leukocyte  TP12-S1146

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1146


title: genomic DNA from 9407210073_R02C01

description: 9407210073_R02C01: Sample 36


title: genomic DNA from 9701417031_R03C02

description: 9701417031_R03C02: Sample 33


title: genomic DNA from 9407210073_R04C01

description: 9407210073_R04C01: Sample 32


title: Leukocyte  TP12-S1144

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1144


title: genomic DNA from 9407210093_R04C01

description: 9407210093_R04C01: Sample 31


title: Leukocyte  TP12-S1124

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1124


title: genomic DNA from 9407210065_R01C02

description: 9407210065_R01C02: Sample 30


title: Leukocyte  TP12-S1111

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1111


title: genomic DNA from 9407210093_R03C01

description: 9407210093_R03C01: Sample 29


title: APC+/+/Olfm4+/+_107822

description: 07-26-12_GRodgers_02_HL_Mouse430_2_2#107822


title: genomic DNA from 9407210065_R06C01

description: 9407210065_R06C01: Sample 28


title: Leukocyte  TP12-S1109

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1109


title: APC+/-/OLFM4(+/+)_107813

description: 07-26-12_GRodgers_04_HL_Mouse430_2_4#107813


title: Leukocyte  TP12-S1100

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1100


title: APC+/+/Olfm4+/+_107814

description: 07-26-12_GRodgers_01_HL_Mouse430_2_1#107814


title: genomic DNA from 9701417031_R01C01

description: 9701417031_R01C01: Sample 27


title: Pt4458

city: New York

first: Samir

last: Parekh

state: NY

address: 1470 Madison Ave, 5th FL, Room 114

department: Hematology and Medical Oncology

institute: Icahn School of Medicine at Mount Sinai

description: Genomic DNA was pruified from RNeasy (Qiagen) flow-through by standard phenol/Chloroform extraction protocol

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as  'failed.' These 'failed' loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, 'Methylated' loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either 'methylated' or 'failed') were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding  windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

source_name: MCL patient_before Bortezomib treatment_MspI

label_protocol: Random 9-mers pre-labeled with either Cy5 or Cy3

extract_protocol: Genomic DNA from RNeasy (Qiagen) flow-through was first precipitated with Ethanol, then purified following proteinase K digestion and standard phenol/choloroform extraction protocol.  Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: subject id

value: patient #4

tag: subject group

value: Patient diagnosed with leukemic mantle cell lymphoma (MCL)

tag: time point

value: before Bortezomib treatment

value: whole blood

value: magnetic beads enriched CD19+ fractions

tag: restriction enzyme

value: MspI representation of genomic DNA

source_name: MCL patient_before Bortezomib treatment_HpaII

value: HpaII representation of genomic DNA


title: Leukocyte  TP12-S1099

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1099

tag: cell type

value: Leukocyte

tag: age


title: SP4535

source_name: MCL patient_96-hour after Bortezomib treatment_MspI

value: patient #3

value: 96-hour after Bortezomib treatment

tag: tissue subtype

source_name: MCL patient_96-hour after Bortezomib treatment_HpaII


title: phoP-flea-rep1

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from phoP-flea-rep1

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing:
The data were analyzed with Expression Console
MAS5.0 signal intensity

organism: Yersinia pestis

label_protocol: Total RNA (100 ng) was amplified and labeled with biotin-16-UTP (Roche Molecular Biochemicals, Pleasanton, CA) by using the Message-Amp II-Bacteria amplified antisense RNA (aRNA) kit (Ambion; Austin, TX). Amplified RNA was then fragmented using Ambion’s Fragmentation reagent (Applied Biosystems)

growth_protocol: The bacterial100 strains used in this study were Y. pestis KIM6+, which lacks the 70-kb virulence plasmid that is not required for flea infection or blockage, and an isogenic mutant deleted of functional phoP.  For in vitro planktonic samples, bacteria were grown from frozen stocks in Brain Heart Infusion (BHI) broth at 28°C, followed by two successive transfers in Luria Bertani broth supplemented with 100 mM MOPS, pH 7.4 (LB/MOPS) at 21°C. An inoculum of 104 cells/ml was added to 50 ml of LB/MOPS and incubated at 21°C with shaking at 250 rpm until exponential (OD600 = 2.5) or stationary phase (OD600 = 4.5)

extract_protocol: RNA was isolated from five independent samples from in vitro and flow cell cultures and from pooled fleas two weeks post-infection, using the RNeasy Mini Kit (Qiagen)

treatment_protocol: no treatments, just strain differences

tag: genotype

value: phoP mutant

tag: strain

tag: treatment

value: flea


title: phoP-flea-rep4

description: Gene expression data from phoP-flea-rep4


title: phoP-flea-rep2

description: Gene expression data from phoP-flea-rep2


title: phoP-flea-rep3

description: Gene expression data from phoP-flea-rep3


title: phoP-flea-rep5

description: Gene expression data from phoP-flea-rep5


title: Leukocyte  TP13-S0243

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP13-S0243

tag: patient


title: Pt4530


title: Pt4523

value: patient #5


title: genomic DNA from 9407210063_R01C02

description: 9407210063_R01C02: Sample 26

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk


title: Leukocyte  TP12-S1097

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1097


title: Leukocyte  TP12-S1096

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1096


title: genomic DNA from 9407210029_R06C01

description: 9407210029_R06C01: Sample 24

tag: bcell

tag: mono


title: Leukocyte  TP12-S1094

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1094


title: Leukocyte  TP12-S1090

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1090


title: genomic DNA from 9407210074_R04C02

description: 9407210074_R04C02: Sample 25

source_name: whole blood


title: genomic DNA from 9701417053_R03C02

description: 9701417053_R03C02: Sample 23


title: genomic DNA from 9407210029_R05C01

description: 9407210029_R05C01: Sample 22

value: White


title: SP4526

tag: subject id

tag: subject group

tag: time point

tag: tissue


title: Pt3073

value: patient #2

tag: tissue subtype

tag: restriction enzyme


title: Leukocyte  TP12-S1089

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1089

tag: cell type

tag: age


title: SP4463


title: genomic DNA from 9407210074_R02C02

description: 9407210074_R02C02: Sample 21


title: Pt4040

value: patient #1


title: wild type-flea-rep5

description: Gene expression data from wild type-flea-rep5

source_name: wild type-flea-rep5

tag: genotype

value: wild type

tag: strain

tag: treatment


title: wild type-flea-rep2

description: Gene expression data from wild type-flea-rep2

source_name: wild type-flea-rep2


title: wild type-flea-rep3

description: Gene expression data from wild type-flea-rep3

source_name: wild type-flea-rep3


title: SP2686

value: patient #6

value: Patient diagnosed with leukemic mantle cell lymphoma (MCL)


title: wild type-flea-rep4

description: Gene expression data from wild type-flea-rep4

source_name: wild type-flea-rep4


title: Leukocyte  TP12-S1086

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1086

tag: patient


title: genomic DNA from 9407210063_R05C02

description: 9407210063_R05C02: Sample 20

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex


title: wild type-flea-rep1

description: Gene expression data from wild type-flea-rep1

source_name: wild type-flea-rep1


title: Pt2681

source_name: MCL patient_before Bortezomib treatment_MspI

value: before Bortezomib treatment

value: whole blood

source_name: MCL patient_before Bortezomib treatment_HpaII


title: wild type-stationary phase-rep4

description: Gene expression data from wild type-stationary phase-rep4

source_name: wild type-stationary phase-rep4

value: stationary phase


title: Leukocyte  TP12-S1309

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1309


title: genomic DNA from 9407210065_R01C01

description: 9407210065_R01C01: Sample 19

value: Other

tag: gran

tag: nk

tag: bcell

tag: mono


title: SP4052

source_name: MCL patient_96-hour after Bortezomib treatment_MspI

tag: subject id

tag: subject group

tag: time point

tag: tissue

value: magnetic beads enriched CD19+ fractions

value: MspI representation of genomic DNA

source_name: MCL patient_96-hour after Bortezomib treatment_HpaII

value: HpaII representation of genomic DNA


title: Leukocyte  TP12-S1085

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1085

tag: cell type

value: Leukocyte

tag: age


title: wild type-stationary phase-rep5

description: Gene expression data from wild type-stationary phase-rep5

source_name: wild type-stationary phase-rep5

tag: genotype

tag: strain


title: Leukocyte  TP12-S1073

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1073

tag: patient


title: wild type-stationary phase-rep3

description: Gene expression data from wild type-stationary phase-rep3

source_name: wild type-stationary phase-rep3

tag: treatment


title: X6T

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: lung tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: lung adenocarcinoma

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

tag: Stage

value: IB

tag: tnm stage

tag: differentiation grades

value: poorly

tag: surgery

value: lobectomy of LLL

tag: ppd x years

tag: ex-smokers or not

value: not

tag: expire

value: Death

tag: 1st regimen

value: Tarceva

tag: 1st response

value: PD

tag: 2nd regimen

value: NVB

tag: 2nd response


title: SP3083

tag: subject id

value: patient #2

tag: subject group

value: Patient diagnosed with leukemic mantle cell lymphoma (MCL)

tag: time point

value: 96-hour after Bortezomib treatment

tag: tissue

tag: tissue subtype

tag: restriction enzyme


title: X5T

description: lung tumor sample

tag: age

tag: gender

tag: Stage

value: lobectomy LUL

value: NVBCDDP

value: SD


title: wild type-stationary phase-rep2

description: Gene expression data from wild type-stationary phase-rep2

source_name: wild type-stationary phase-rep2

tag: genotype

value: wild type

tag: strain

tag: treatment

value: stationary phase


title: wild type-stationary phase-rep1

description: Gene expression data from wild type-stationary phase-rep1

source_name: wild type-stationary phase-rep1


title: genomic DNA from 9407210063_R04C02

description: 9407210063_R04C02: Sample 18

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: X12T

description: lung tumor sample

value: Male

value: IB

tag: tnm stage

tag: differentiation grades

value: moderately

tag: surgery

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Live

tag: 1st regimen

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: genomic DNA from 9407210016_R03C02

description: 9407210016_R03C02: Sample 17

tag: hiv

tag: agebl

value: Black


title: Leukocyte  TP12-S1072

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1072

tag: cell type

value: Leukocyte

tag: patient

tag: age


title: Leukocyte  TP12-S1061

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1061


title: Leukocyte  TP12-S1060

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1060


title: Leukocyte  TP12-S1058

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1058


title: Leukocyte  TP12-S1059

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1059

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes

tag: fast relapase label

value: f


title: genomic DNA from 9407210063_R03C01

description: 9407210063_R03C01: Sample 16

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: BR

city: Taichung

first: Tzu-Hung

last: Hsiao

address: 1650 Taiwan Boulevard Sect. 4

department: Department of Medical Research

institute: Taichung Veterans General Hospital

description: Gene expression data from BR

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

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

data_processing: raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf). Background-adjusted signals were normalized by Robust Multichip Analysis (RMA) and quantile normalization algorithm.

source_name: pooled samples of pre-treatment liver biopsies from responder

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: Total RNA from the tissue specimens were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA)  according to the manufacturer's instructions.

tag: response

value: responder

tag: tissue

value: liver


title: Leukocyte  TP12-S1145

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1145


title: genomic DNA from 9407210063_R02C01

description: 9407210063_R02C01: Sample 14

tag: hiv

tag: agebl


title: genomic DNA from 9407210016_R01C01

description: 9407210016_R01C01: Sample 12


title: X4T

description: lung tumor sample

tag: gender

value: Female

tag: tnm stage

tag: differentiation grades

tag: surgery

value: lobectomy LML

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Death

tag: 1st regimen

value: no

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: genomic DNA from 9407210074_R01C02

description: 9407210074_R01C02: Sample 15

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell


title: genomic DNA from 9407210065_R02C02

description: 9407210065_R02C02: Sample 11

tag: hiv

tag: agebl

tag: mono


title: X10T

description: lung tumor sample

tag: age

tag: gender

tag: Stage

tag: tnm stage

tag: differentiation grades

value: poorly

value: lobectomyRUL

value: PacCar

value: PD

value: Iressa


title: wild type-log phase-rep2

description: Gene expression data from wild type-log phase-rep2

source_name: wild type-log phase-rep2

tag: genotype

value: wild type

tag: strain

tag: treatment

value: log phase


title: X9T

description: lung tumor sample

value: Male

value: IA

value: moderately

tag: surgery

value: Lobectoy LLL

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Live

tag: 1st regimen

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: phoP-stationary phase-rep5

description: Gene expression data from phoP-stationary phase-rep5

source_name: phoP-stationary phase-rep5

value: phoP mutant

value: stationary phase


title: wild type-log phase-rep3

description: Gene expression data from wild type-log phase-rep3

source_name: wild type-log phase-rep3


title: X11T

description: lung tumor sample

value: IB

value: lobectomy RUL


title: wild type-log phase-rep4

description: Gene expression data from wild type-log phase-rep4

source_name: wild type-log phase-rep4


title: X3T

description: lung tumor sample

value: Female

value: lobectomy RML

value: Death

value: SD

value: NVB+cisplatin


title: X8T

description: lung tumor sample

value: bilobectomy RUL


title: Leukocyte  TP12-S1029

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1029

tag: cell type

value: Leukocyte

tag: patient


title: wild type-log phase-rep1

description: Gene expression data from wild type-log phase-rep1

source_name: wild type-log phase-rep1

value: wild type

value: log phase


title: genomic DNA from 9407201108_R05C02

description: 9407201108_R05C02: Sample 10

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: X2T

description: lung tumor sample

source_name: lung adenocarcinoma

tag: age

tag: gender

value: Male

tag: Stage

tag: tnm stage

tag: differentiation grades

value: poorly

tag: surgery

value: wecge resection of RLL

tag: ppd x years


title: X1T

description: lung tumor sample

value: moderately

value: wedge resection of RLL

tag: ex-smokers or not

tag: expire

tag: 1st regimen

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: wild type-log phase-rep5

description: Gene expression data from wild type-log phase-rep5

source_name: wild type-log phase-rep5

tag: genotype

tag: strain

tag: treatment


title: Leukocyte  TP12-S0997

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0997

tag: cell type

tag: patient


title: genomic DNA from 9407210061_R01C02

description: 9407210061_R01C02: Sample 9

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407210061_R06C01

description: 9407210061_R06C01: Sample 8


title: BN

description: Gene expression data from BN

source_name: pooled samples of pre-treatment liver biopsies from non-responder

tag: response

value: non-responder

tag: tissue

value: liver


title: Leukocyte  TP12-S0996

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0996

tag: age

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes

tag: fast relapase label

value: f


title: Leukocyte  TP12-S0995

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0995

tag: cell type

tag: patient


title: genomic DNA from 9701417048_R05C01

description: 9701417048_R05C01: Sample 7

tag: hiv

tag: agebl


title: phoP-stationary phase-rep2

description: Gene expression data from phoP-stationary phase-rep2

source_name: phoP-stationary phase-rep2

tag: genotype

value: phoP mutant

tag: strain

tag: treatment

value: stationary phase


title: X7T

description: lung tumor sample

tag: gender

value: Female

value: IB

tag: tnm stage

tag: differentiation grades

tag: surgery

value: Lobectomy LUL

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Live

tag: 1st regimen

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: Leukocyte  TP12-S0988

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0988

tag: cell type

value: Leukocyte

tag: patient

tag: age


title: genomic DNA from 9407201108_R06C02

description: 9407201108_R06C02: Sample 6

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: Leukocyte  TP12-S0985

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0985


title: T210

description: lung tumor sample

tag: gender

value: Male

tag: Stage

value: IIB

tag: tnm stage

tag: differentiation grades

tag: surgery

value: lobectomy of LUL

tag: ppd x years

tag: ex-smokers or not

value: Death

value: NVBCDDP

value: SD

value: Iressa

value: PD


title: genomic DNA from 9407210063_R06C02

description: 9407210063_R06C02: Sample 5

value: Black


title: phoP-stationary phase-rep3

description: Gene expression data from phoP-stationary phase-rep3

source_name: phoP-stationary phase-rep3

tag: genotype

tag: strain

tag: treatment


title: phoP-stationary phase-rep4

description: Gene expression data from phoP-stationary phase-rep4

source_name: phoP-stationary phase-rep4


title: phoP-stationary phase-rep1

description: Gene expression data from phoP-stationary phase-rep1

source_name: phoP-stationary phase-rep1


title: genomic DNA from 9407201108_R03C01

description: 9407201108_R03C01: Sample 4

tag: hiv

tag: agebl

value: White


title: phoP-log phase-rep5

description: Gene expression data from phoP-log phase-rep5

source_name: phoP-log phase-rep5

value: phoP mutant

value: log phase


title: phoP-log phase-rep4

description: Gene expression data from phoP-log phase-rep4

source_name: phoP-log phase-rep4


title: T152

description: lung tumor sample

tag: age

value: IA

value: moderately

value: lobectomy RLL

tag: expire

tag: 1st regimen

value: PacCar

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: Leukocyte  TP12-S0967

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0967

tag: cell type

value: Leukocyte

tag: patient


title: T144

description: lung tumor sample

tag: gender

value: Male

tag: Stage

tag: tnm stage

tag: differentiation grades

value: poorly

value: lobectomy LUL


title: genomic DNA from 9407210093_R05C02

description: 9407210093_R05C02: Sample 3

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: Leukocyte  TP12-S0966

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0966

tag: age


title: phoP-log phase-rep2

description: Gene expression data from phoP-log phase-rep2

source_name: phoP-log phase-rep2

tag: genotype

tag: strain

tag: treatment


title: genomic DNA from 9407201108_R04C02

description: 9407201108_R04C02: Sample 2

tag: hiv

tag: agebl


title: T118

description: lung tumor sample

source_name: lung adenocarcinoma

value: IB

tag: surgery

value: wedge resection of RUL

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Death

tag: 1st regimen

value: no

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: Leukocyte  TP12-S0950

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0950

tag: cell type

tag: patient


title: Leukocyte  TP12-S0981

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0981


title: genomic DNA from 9407210093_R04C02

description: 9407210093_R04C02: Sample 1

source_name: whole blood

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: Leukocyte  TP12-S0946

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0946

tag: age


title: Leukocyte  TP12-S0945

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0945

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes

tag: fast relapase label

value: f


title: Leukocyte  TP12-S0941

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0941


title: phoP-log phase-rep3

description: Gene expression data from phoP-log phase-rep3

source_name: phoP-log phase-rep3

tag: genotype

tag: strain

tag: treatment


title: phoP-log phase-rep1

description: Gene expression data from phoP-log phase-rep1

source_name: phoP-log phase-rep1


title: Leukocyte  TP12-S0929

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0929

tag: cell type


title: T104

description: lung tumor sample

tag: gender

value: IIB

tag: tnm stage

tag: differentiation grades

tag: surgery

value: penumonectomy LUL

tag: ppd x years

tag: ex-smokers or not

tag: expire

tag: 1st regimen

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: Leukocyte  TP12-S0928

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0928

tag: patient

tag: age


title: T119

description: lung tumor sample

tag: Stage

value: well

value: lobectomy LUL:

value: GemCDDP

value: SD

value: Alimta


title: T112

description: lung tumor sample

value: Live


title: wild type-biofilm-rep 5

description: Gene expression data from wild type-biofilm-rep 5

source_name: wild type-biofilm-rep 5

tag: genotype

value: wild type

tag: strain

value: biofilm


title: Leukocyte  TP12-S0927

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0927

tag: cell type

value: Leukocyte


title: T96

description: lung tumor sample

tag: gender

value: Male

value: IB

value: poorly

value: lobectomy RUL

value: Tarceva


title: wild type-biofilm-rep 3

description: Gene expression data from wild type-biofilm-rep 3

source_name: wild type-biofilm-rep 3

tag: treatment


title: wild type-biofilm-rep 4

description: Gene expression data from wild type-biofilm-rep 4

source_name: wild type-biofilm-rep 4


title: T156

description: lung tumor sample

tag: tnm stage

tag: differentiation grades

value: more than one pack*30

value: TXT


title: Leukocyte  TP12-S0926

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0926


title: wild type-biofilm-rep 2

description: Gene expression data from wild type-biofilm-rep 2

source_name: wild type-biofilm-rep 2


title: T89

description: lung tumor sample

source_name: lung adenocarcinoma

tag: surgery

value: lobectomy RML

tag: ppd x years

value: Death


title: T95

description: lung tumor sample

value: IA

value: moderately

value: Lobectomy RUL

tag: ex-smokers or not

tag: expire


title: Leukocyte  TP12-S0925

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0925


title: T97

description: lung tumor sample

value: Locectomy RLL

tag: 1st regimen

value: PacCDDP

tag: 1st response

value: PD

value: TXTEpi


title: T79

description: lung tumor sample

value: Wedge resection of RUL

tag: 2nd regimen

tag: 2nd response


title: phoP-biofilm-rep 3

description: Gene expression data from phoP-biofilm-rep 3

source_name: phoP-biofilm-rep 3

value: phoP mutant

value: biofilm


title: Leukocyte  TP12-S0919

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0919

value: Leukocyte

tag: patient

tag: age


title: T91

description: lung tumor sample

value: Male

tag: Stage

value: IB

value: lobectomy RUL

value: unknown


title: T85

description: lung tumor sample

value: poorly

value: lobectomy RUL and RML


title: phoP-biofilm-rep 4

description: Gene expression data from phoP-biofilm-rep 4

source_name: phoP-biofilm-rep 4

tag: genotype

tag: strain


title: wild type-biofilm-rep 1

description: Gene expression data from wild type-biofilm-rep 1

source_name: wild type-biofilm-rep 1

value: wild type


title: phoP-biofilm-rep 5

description: Gene expression data from phoP-biofilm-rep 5

source_name: phoP-biofilm-rep 5


title: T75

description: lung tumor sample

tag: gender

value: bilobectomy RUL& RML, and Rll wedge resection

value: Live


title: Leukocyte  TP12-S0918

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0918

tag: cell type

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes

tag: fast relapase label

value: f


title: Leukocyte  TP12-S0917

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0917


title: phoP-biofilm-rep 2

description: Gene expression data from phoP-biofilm-rep 2

source_name: phoP-biofilm-rep 2

tag: treatment


title: Leukocyte  TP12-S0916

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0916


title: Leukocyte  TP12-S0915

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0915


title: Leukocyte  TP12-S0914

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0914


title: Leukocyte  TP12-S0869

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0869


title: Leukocyte  TP12-S0868

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0868


title: T54

description: lung tumor sample

tag: tnm stage

tag: differentiation grades

value: moderately

tag: surgery

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Tarceva

value: NE


title: T53

description: lung tumor sample

tag: age

value: IA

value: wedge resection RML and completion lobectomy

tag: 1st regimen

value: no

tag: 1st response

tag: 2nd regimen

tag: 2nd response


title: T23

description: lung tumor sample

tag: gender

value: Male

tag: Stage

value: lobectomy

value: some weeks


title: phoP-biofilm-rep 1

description: Gene expression data from phoP-biofilm-rep 1

source_name: phoP-biofilm-rep 1

tag: genotype

value: phoP mutant

tag: strain

value: biofilm


title: Leukocyte  TP12-S0862

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0862

tag: cell type

value: Leukocyte

tag: patient


title: Leukocyte  TP12-S0860

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0860


title: Leukocyte  TP12-S1032

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1032


title: genomic DNA from 9701417053_R01C01

description: 9701417053_R01C01: Sample 13

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: Leukocyte  TP12-S0830

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0830

tag: age


title: Leukocyte  TP12-S0867

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0867


title: Leukocyte  TP12-S0839

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0839


title: Leukocyte  TP12-S1030

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S1030


title: T12

description: lung tumor sample

source_name: lung adenocarcinoma

value: Female

value: IIB

tag: tnm stage

tag: differentiation grades

tag: surgery

value: lobectomy RLL

tag: ppd x years

tag: ex-smokers or not

tag: expire

value: Death

tag: 1st regimen

value: NVBCDDP

tag: 1st response

value: SD

tag: 2nd regimen

value: TXT

value: PD


title: T18

description: lung tumor sample

tag: gender

tag: Stage

value: IB

value: lobectomy RUL

value: Live

tag: 2nd response


title: T14

description: lung tumor sample

value: Male

value: poorly

value: Wedge resection of RML


title: Leukocyte  TP12-S0814

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0814

tag: cell type

tag: patient


title: Leukocyte  TP12-S0816

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0816


title: T8

description: lung tumor sample

value: moderately

value: lobectomy


title: T37

description: lung tumor sample

value: IA


title: T4

description: lung tumor sample

value: Female

value: Loectomy LLL , Ecploratory thoracotomy LT

value: no

value: paclitaxel+carboplatin

value: Iressa

value: PR


title: Leukocyte  TP12-S0813

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0813

value: Leukocyte


title: T9

description: lung tumor sample

value: lobectomy LLL

value: Death

value: cisplatin+docetaxel


title: T6

description: lung tumor sample

value: Lobectomy RLL


title: Cancer_tissue_Lung_cancer_patient_19

city: Beijing

first: Jiao

last: Yuan

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were subjected to for background subtraction, quality control, log2 transformation and quantile normalization by the GeneSpring software V11.5 (Agilent).

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

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

tag: disease

value: lung cancer

tag: tissue

value: Lung

tag: tissue type

value: Cancer tissue


title: Lactose versus Ribose dye swap

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: Biological replicate 2

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 LNT or LNnT or LNB or lactosamine HCl or lactose/ribose ratios from a single array experiment.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown on Lactose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of Lactose, LNT, LNnT, LNB Lactosamine HCl  or Ribose as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) untill OD600 was 0.5. Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: strain

source_name: Bifidobacterium breve UCC2003 grown on Ribose


title: Leukocyte  TP12-S0805

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0805

tag: age

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: yes


title: LNnT versus Ribose dye swap

description: Biological replicate 2

source_name: Bifidobacterium breve UCC2003 grown on LNnT


title: Lactosamine HCl versus Ribose

description: Biological replicate 1

source_name: Bifidobacterium breve UCC2003 grown on Lactosmine HCl


title: Lactosamine HCl versus Ribose dye swap

description: Biological replicate 2


title: LNB versus Ribose

description: Biological replicate 1

source_name: Bifidobacterium breve UCC2003 grown on LNB


title: Cancer_tissue_Lung_cancer_patient_18


title: LNT versus Ribose

description: Biological replicate 1

source_name: Bifidobacterium breve UCC2003 grown on LNT


title: Cancer_tissue_Lung_cancer_patient_20


title: LNnT versus Ribose

description: Biological replicate 1


title: Lactose versus Ribose

description: Biological replicate 1


title: Leukocyte  TP12-S0803

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0803


title: Normal_tissue_Lung_cancer_patient_19

value: Normal tissue


title: Normal_tissue_Lung_cancer_patient_20


title: Normal_tissue_Lung_cancer_patient_18


title: Leukocyte  TP12-S0799

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0799


title: Cancer_tissue_Lung_cancer_patient_17


title: Leukocyte  TP12-S0795

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0795


title: LNT versus Ribose dye swap

description: Biological replicate 2


title: Leukocyte  TP12-S0794

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0794


title: genomic DNA from white adipose tissue Obese_4615

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

label_protocol: 1 μg of genomic DNA was subjected to bisulphite conversion with the EZ DNA Methylation kit (Zymo research, Orange, CA)

extract_protocol: Genomic DNA was extracted and purified from adipose tissue using standard protocol.

value: abdominal subcutaneous adipose tissue

tag: disease state

value: Obese


title: genomic DNA from white adipose tissue Obese_1116

value: Female


title: genomic DNA from white adipose tissue nonobese_828

value: Nonobese


title: genomic DNA from white adipose tissue Obese_3725


title: genomic DNA from white adipose tissue nonobese_134


title: Leukocyte  TP12-S0790

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0790

tag: fast relapase label

value: f


title: Normal_tissue_Lung_cancer_patient_17


title: genomic DNA from white adipose tissue Obese_3731


title: LNB versus Ribose dye swap

description: Biological replicate 2


title: Cancer_tissue_Lung_cancer_patient_16


title: Leukocyte  TP12-S0789

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0789


title: Normal_tissue_Lung_cancer_patient_16


title: Leukocyte  TP12-S0786

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0786


title: genomic DNA from white adipose tissue Obese_4639


title: Leukocyte  TP12-S0770

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0770


title: Leukocyte  TP12-S0769

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0769


title: genomic DNA from white adipose tissue Obese_795


title: Leukocyte  TP12-S0768

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0768


title: Normal_tissue_Lung_cancer_patient_15


title: genomic DNA from white adipose tissue Obese_48


title: genomic DNA from white adipose tissue Obese_1529


title: Cancer_tissue_Lung_cancer_patient_15


title: Leukocyte  TP12-S0765

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0765


title: genomic DNA from white adipose tissue nonobese_4873


title: Leukocyte  TP12-S0745

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0745


title: genomic DNA from white adipose tissue nonobese_469


title: Normal_tissue_Lung_cancer_patient_14


title: genomic DNA from white adipose tissue Obese_3825


title: stable clone shRNA4-18 replicate 3

city: Madrid

first: Maria Angeles

last: Pajares

address: Arturo Duperier 4

department: Metabolismo y Señalizacion Celular

country: Spain

institute: Instituto de Investigaciones Biomedicas Alberto Sols (CSIC-UAM)

description: gene expression upon stable transfection with shRN4 silencing plasmid

hyb_protocol: Preparation of probes was carried out as described in the One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5 (Agilent Technologies). Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ml of 10X Blocking Agent, 1 ml of 25X Fragmentation Buffer and Nuclease free water in a 25 ml reaction, incubated a 60ºC for 30 minutes to fragment RNA and stopped with 25 ml 2X Hybridization buffer. The samples were kept on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation.

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing:
Background correction and normalization of expression data were performed using LIMMA.
Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjimani and Hochberg. The expected false discovery rate was controlled to be less than 5%.

organism: Rattus norvegicus

source_name: hepatoma H35 cells

label_protocol: Four biological replicates were independently hybridized for each transcriptomic comparison. Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). Preparation of probes and hybridization was performed as described One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies, using Rat Gene Expression Microarray v3 Agilent 4x44K.

growth_protocol: Rat hepatoma H35 cells were grown in DMEM supplemented with 10% (v/v) fetal bovine serum and 2 mM glutamine

extract_protocol: RNA was prepared from 4 biological replicates for each condition using RNeasy Mini kit (Qiagen) with DNase treatment. The quantity and quality of the RNA was determined spectrophotometrically using NanoDrop and by automated electrophoretogram on a Bioanalyzer 2100.

treatment_protocol: Cells were transfected with SureSilencing shRNA plasmids designed for Pdrg1 silencing and a negative control using Lipofectamine. Initial selection was started 48 hours after transfection using G418 1.8 mg/ml and carried out for two weeks. Pools of shRNA3 transfected cells after this enrichment constitute the shRNA-trans samples. Further selection to obtain stable clones was carried out for two additional weeks using 4 mg/ml G418. Only clones exhibiting reproducible behaviour according to RT-qPCR were selected.

tag: plasmid

value: shRNA4 silencing sequence

tag: transfection

value: stable

tag: cell line


title: Cancer_tissue_Lung_cancer_patient_12


title: Normal_tissue_Lung_cancer_patient_13


title: Cancer_tissue_Lung_cancer_patient_13


title: enriched pool shRNA3-trans replicate 4

description: gene expression upon transient transfection with shRN3 silencing plasmid

value: shRNA3 silencing sequence

value: transient


title: genomic DNA from white adipose tissue nonobese_202

tag: gender


title: genomic DNA from white adipose tissue nonobese_13


title: stable clone shRNA4-18 replicate 4


title: enriched pool shRNA3-trans replicate 1


title: genomic DNA from white adipose tissue nonobese_136


title: enriched pool shRNA3-trans replicate 3


title: Normal_tissue_Lung_cancer_patient_12


title: Cancer_tissue_Lung_cancer_patient_14


title: Leukocyte  TP12-S0744

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0744

value: Leukocyte


title: stable clone shRNA4-18 replicate 2


title: Leukocyte  TP12-S0742

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0742


title: Normal_tissue_Lung_cancer_patient_11


title: stable clone shRNA4-18 replicate 1


title: Leukocyte  TP12-S0741

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0741


title: Cancer_tissue_Lung_cancer_patient_11


title: Leukocyte  TP12-S0740

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0740

tag: Stage


title: enriched pool shRNA3-trans replicate 2


title: Leukocyte  TP12-S0725

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0725

tag: cell type


title: genomic DNA from white adipose tissue Obese_4648


title: Leukocyte  TP12-S0724

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0724

tag: patient


title: genomic DNA from white adipose tissue Obese_3655


title: Cancer_tissue_Lung_cancer_patient_10

tag: disease


title: stable clone shRNA3-44 replicate 4

description: gene expression upon stable transfection with shRN3 silencing plasmid


title: Leukocyte  TP12-S0723

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP12-S0723


title: genomic DNA from white adipose tissue Obese_4595


title: genomic DNA from white adipose tissue Obese_126


title: genomic DNA from white adipose tissue Obese_3651


title: Cancer_tissue_Lung_cancer_patient_09

tag: tissue


title: stable clone shRNA3-44 replicate 3


title: genomic DNA from white adipose tissue nonobese_3604

tag: tissue type


title: genomic DNA from white adipose tissue Obese_4872


title: stable clone CN-10 replicate 4

description: gene expression upon stable transfection with negative control plasmid

value: shRNA negative control sequence


title: Leukocyte  TP10-S093B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP10-S093B

value: nf


title: stable clone shRNA3-44 replicate 2


title: genomic DNA from white adipose tissue nonobese_43


title: Normal_tissue_Lung_cancer_patient_10

value: lung cancer


title: stable clone CN-10 replicate 3


title: Normal_tissue_Lung_cancer_patient_09

value: Lung


title: stable clone shRNA3-44 replicate 1


title: Leukocyte  TP09-S0928

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0928


title: Normal_tissue_Lung_cancer_patient_08


title: Cancer_tissue_Lung_cancer_patient_08

value: Cancer tissue


title: Leukocyte  TP09-S0638B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0638B

value: yes


title: Cancer_tissue_Lung_cancer_patient_07


title: stable clone CN-10 replicate 2


title: Normal_tissue_Lung_cancer_patient_07

value: Normal tissue


title: Leukocyte  TP09-S0420B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0420B2


title: stable clone CN-10 replicate 1


title: genomic DNA from white adipose tissue nonobese_1732

value: abdominal subcutaneous adipose tissue


title: Cancer_tissue_Lung_cancer_patient_06


title: Leukocyte  TP09-S0420B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0420B


title: genomic DNA from white adipose tissue nonobese_398


title: genomic DNA from white adipose tissue Obese_4645

value: Obese


title: Leukocyte  TP09-S0721B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0721B


title: Leukocyte  TP09-S0408B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0408B


title: Normal_tissue_Lung_cancer_patient_06


title: Leukocyte  TP09-S0006B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP09-S0006B


title: Leukocyte  TP08-S00542B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP08-S00542B


title: Replicate 1

first: Ian

middle: Cameron

last: Scott

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: The Hospital for Sick Childen

description: Biological replicate 1 of 2

scan_protocol: Scanned on an Agilent G2565C DNA scanner.  Images were quantified using Agilent Feature Extraction Software (version 10.7.1.3).  Extraction Protocol GE2_107_Sept07.

data_processing: Results analyzed using Genespring v11.0.1 and normalized using Agilent’s Spatial Detrending Lowess normalization. All data analysis was performed on log2-transformed data. Standard single factor ttests were used followed by ranking with fold changes. After normalization and averaging the two chips, data was filtered to remove the probes that showed no signal in order to avoid confounding effects on subsequent analysis. Only probes between the 20th and 100th percentile of the distribution of intensities in both samples for either group were allowed to pass through this filtering. Statistical significance for differential expression between sample groups was set at p<0.05. This set of probes was then filtered to leave only probes with either 2 fold over or 2 fold under changes in expression

organism: Danio rerio

source_name: mut c

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label (Labelling Protocol version GE2 v6.0)

extract_protocol: Total RNA was isolated by chloroform/isopropanol  extraction of 20 pooled 2.25 dpf mutant or control embryos homogenization in Trizol.

tag: developmental stage

value: 2.25 dpf embryo

tag: genotype/variation

value: med14 mutant

source_name: ctrl c

value: wildtype


title: genomic DNA from white adipose tissue nonobese_24

value: Female

value: Nonobese

tag: age


title: Replicate 2

description: Biological replicate 2 of 2

source_name: mut f

source_name: ctrl f


title: genomic DNA from white adipose tissue nonobese_4082


title: Leukocyte  TP08-S00530B

first: Shuchang

last: Liu

address: 130 De Soto Street

institute: University of Pittsburgh

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP08-S00530B

tag: gleason

tag: nomogram 5 years

value: f


title: genomic DNA from white adipose tissue nonobese_1892

tag: disease state


title: Cancer_tissue_Lung_cancer_patient_05


title: genomic DNA from white adipose tissue Obese_4625


title: Normal_tissue_Lung_cancer_patient_04


title: Leukocyte  TP08-S00268B

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP08-S00268B

tag: recurrence label

tag: fast relapase label


title: Normal_tissue_Lung_cancer_patient_05


title: Leukocyte  TP08-S00262

description: Affymetrix SNP 6.0

source_name: Leukocyte  TP08-S00262


title: genomic DNA from white adipose tissue nonobese_3712


title: Cancer_tissue_Lung_cancer_patient_03


title: Cancer_tissue_Lung_cancer_patient_04


title: liver of control mice Replicate 3

city: Guangzhou

first: Lin

last: Xiaolin

address: Tonghe

department: Southern Medical University

institute: Cancer reseach institute

description:
Biological replicate 3 of 3.
Control mice liver, untreated.
Raw data can be found on sample record: GSM1567090

hyb_protocol: Labeled cDNA was then hybridized to 32K mouse genome arrays.

scan_protocol: Hybridization signals were scanned with a Lux-Scan 3.0 scanner.The resultant images were digitized with Lux-Scan 3.0 image analyzer software

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

source_name: liver of control mice

label_protocol: cDNA was fluorescently labeled by Cy5-dCTP or Cy3-dCTP (GE Healthcare Cat. No. PA 55021/PA 53021) with Klenow enzyme.

value: liver

value: male


title: liver of miR-155 transgenic mice and control mice Replicate 3

description: Biological replicate 3 of 3.

source_name: liver of miR-155 transgenic mice


title: genomic DNA from white adipose tissue Obese_2343


title: genomic DNA from white adipose tissue nonobese_399


title: Leukocyte  PR542

description: Affymetrix SNP 6.0

data_processing:
CEL files were analyzed with Genotyping Console for quality control analysis. Samples with QC call above 80% and QC contrast ratio above 0.4 were admitted into the analysis. To analyze CNV, CEL files were imported into Partek GenomeSuite 6.6 to generate copy number from raw intensity.
Each CEL file represents data from one patient. Deletion or amplification of genomes were analyzed by first limiting to the regions with p-value less than 0.001. The selected regions were subsequently filtered by limiting to the regions with at least 10 markers and 2 kb in size.

source_name: Leukocyte  PR542

value: Leukocyte

value: no


title: Leukocyte  PR543

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR543

value: nf


title: genomic DNA from white adipose tissue Obese_4264