title: Cancer Urothelia-28

description:
C-000028
Gene expression data from human urothelial cells in urine sediment.

source_name: Bladder barbotage, cancer


title: Muscle_PGC-1alpha-mTg_rep4

status: Public on Jan 08 2013

type: RNA

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description: Gene expression data from gastrocnemius muscle of adult male mice.

hyb_protocol: 85µl cocktail (containing 2µg labeled DNA) was loaded on Mouse Gene 1.0 ST Array (Affymetrix) and hybridized for 17 hours (45°C, 60rpm) in Hybridization oven 645 (Affymetrix).  The arrays were washed and stained on Fluidics Stations 450 (Affymetrix) by using the Hybridization Wash and Stain Kit (Affymetrix) under FS450_0007 protocol.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip Command Control 3.0.0.1214.
Affymetrix CEL files were normalized according to RMA method (Irizarry, 2003) and data were log 2.0 transformed. To select differently expressed genes a 1-way ANOVA model by using Method of Moments (Eisenhart, 1947) was applied using Partek Genomic Suite (version 6.6).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Gastrocnemius muscle from PGC-1alpha mTg mouse

label_protocol: Target synthesis was prepared starting from 250ng total RNA using the WT Expression kit (Ambion). Fragmentation and labeling of amplified cDNA were performed using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA from gastrocnemius was isolated with miRNeasy Mini Kit (QIAGEN)

tag: strain

tag: gender

value: Male

tag: genotype/variation


title: Spleen_BALB_TBI_300cGy_rep1

city: Salt Lake City

first: Thai

last: Cao

state: UT

address: 30 North 1900 East, SOM5C402

country: USA

institute: University of Utah

description: TBI - 300 cGy

hyb_protocol: Agilent One-color Heterologous GE Hybridization and Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Array images were processed with Agilent Feature Extraction software version 10.5.1.1. Array data files were filtered to remove positive and negative control features and any features flagged as non-uniform outliers or population outliers, as recommended by Agilent.  Log-transformed signal intensity values were then globally normalized using the percentile shift algorithm, shifting to the 75th percentile of each sample, followed by baseline shifting to the median of all samples.

source_name: Spleen

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: Total RNA was extracted from the spleens immediately after harvesting from mice 24 hours after total body irradiation, or from resting mice for un-irradiated controls.

extract_protocol: Total RNA was isolated from whole splenocytes homogenized with a rotor-stator device in TRIzol (Invitrogen) followed by RNeasy purification.  Samples quality was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated with total body irradiation using an XRAD320 Biological Irradiator (Precision X-Ray, North Branford, CT).

tag: total body irradiation dose

value: 300 cGy


title: Muscle_PGC-1alpha-mTg_rep1


title: Non-Cancer Urothelia-4

city: Orlando

first: Virginia

last: Urquidi

state: FL

address: 6900 Lake Nona Blvd

department: CRI

institute: MD Anderson Cancer Center Orlando

description:
NC-000004
Gene expression data from human urothelial cells in urine sediment.

hyb_protocol: Fragmented, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays. The Affymetrix GeneChip system used  includes an Affymetrix 450 fluidics station, 3000 scanner, hybridization oven and GeneChip Operating Software.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data was normalized using the MAS5 algorithm provided in Expression Console 1.1 of Affymetrix. The output are positive values.

label: biotin

organism: Homo sapiens

source_name: Bladder barbotage, non-cancer

label_protocol: Preparation of labeled cRNA was performed according to the Affymetrix Two-Cycle Target Labeling Assay.

extract_protocol: Total RNA was  extracted from urothelial cells using the Qiagen RNeasy protocol.

tag: cell type

value: non-cancer urothelial cells

tag: disease status

value: no bladder cancer


title: Spleen_BALB_TBI_300cGy_rep2

description: TBI - 300 cGy


title: Muscle_PGC-1alpha-mTg_rep2


title: Muscle_WT_rep5

source_name: Gastrocnemius muscle from WT mouse

value: wild type


title: Spleen_BALB_TBI_0cGy_rep3

description: TBI - 0 cGy

value: 0 cGy


title: Muscle_WT_rep4


title: Cancer Urothelia-27

description:
C-000027
Gene expression data from human urothelial cells in urine sediment.

value: urothelial cancer cells

value: bladder cancer


title: Cancer Urothelia-26

description:
C-000026
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_WT_rep1


title: Muscle_WT_rep3


title: Spleen_BALB_TBI_0cGy_rep2

description: TBI - 0 cGy


title: Muscle_WT_rep2


title: Cancer Urothelia-24

description:
C-000024
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-25

description:
C-000025
Gene expression data from human urothelial cells in urine sediment.


title: Spleen_BALB_TBI_0cGy_rep1

description: TBI - 0 cGy


title: Muscle_NCoR1-MKO_rep5

source_name: Gastrocnemius muscle from NCoR1 MKO mouse


title: Cancer Urothelia-23

description:
C-000023
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_NCoR1-MKO_rep2


title: Muscle_NCoR1-MKO_rep1


title: Cancer Urothelia-20

description:
C-000020
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_CON_rep2

source_name: Gastrocnemius muscle from CON mouse

tag: sample type

value: control


title: Cancer Urothelia-21

description:
C-000021
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-22

description:
C-000022
Gene expression data from human urothelial cells in urine sediment.


title: mutant 12-109C6 at 34oC for 24h rep2

city: Tampa

first: Elena

middle: S

last: Suvorova

address: 3720 Spectrum Blvd

institute: University of South Florida

description: gene expression data from mutant 12-109C6 grown 24h at permissive temperature

hyb_protocol: Fragmented cRNA (5μg) was hybridized to the Toxoplasma gondii Affymetrix microarray according to standard hybridization protocols (ToxoGeneChip: http://ancillary.toxodb.org/docs/Array-Tutorial.html).

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

data_processing: Hybridization data was preprocessed with Robust Multi-array Average (RMA) and normalized using per chip and per gene median polishing and analyzed using the software package GeneSpring GX (Agilent Technologies, Santa Clara CA).  t-Test was run in order to identify genes with significantly greater than random variation in RNA abundance across the data grouped by temperature and time of exposure.  Variances were calculated using cross-gene error model, with a p-value cutoff 0.05, and multiple testing correction: Benjamini and Hochberg False Discovery Rate.

organism: Toxoplasma gondii

source_name: mutant 12-109C6 grown for 24h at 34oC

label_protocol: A total of 500ng starting RNA was used to produce biotinilated cRNA using the Affymetrix One-Cycle Kit (Affymetrix, Santa Clara CA).

growth_protocol: Toxoplasma gonidii mutant 12-109C6 was grown in HFF monolayers for 24h at 34oC, then was either left at 34oC for another 24h or shifted to 40oC for 6h or 24h.

extract_protocol: RNA was extracted from parasites using the RNeasy kit with β-mercaptoethanol and DNase I treatment (Qiagen, Valencia, CA).   RNA quality was determined using the Agilent Bioanalyzer 2100 (Santa Clara, CA).

treatment_protocol: Parasites were separated by filtration and collected by centrifugation.

tag: developmental stage

value: tachyzoite

value: mutant 12-109C6


title: mutant 12-109C6 at 34oC for 24h rep1


title: Muscle_CON_rep3


title: mutant 12-109C6 at 40oC for 24h rep1

description: gene expression data from mutant 12-109C6 grown 24h at restricted temperature

source_name: mutant 12-109C6 grown for 24h at 40oC


title: Muscle_CON_rep5


title: mutant 12-109C6 at 40oC for 24h rep2


title: mutant 12-109C6 at 40oC for 6h rep1

description: gene expression data from mutant 12-109C6 grown 6h at restricted temperature

source_name: mutant 12-109C6 grown for 6h at 40oC


title: mutant 12-109C6 at 40oC for 6h rep2


title: Cancer Urothelia-19

description:
C-000019
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_NCoR1-MKO_rep3


title: Cancer Urothelia-17

description:
C-000017
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_NCoR1-MKO_rep4


title: Cancer Urothelia-18

description:
C-000018
Gene expression data from human urothelial cells in urine sediment.


title: Muscle_CON_rep4


title: EVI1 replicate 2

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description: Gene expression data from Lin- cells transduced with EVI1.IRES.EGFP

hyb_protocol: amplified, fragmented, biotin labeled cDNA was hybridized for 18 hr at 45C on Mouse GeneChip1.0 ST Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: Lin- hematopoietic progenitors

label_protocol: RNA was amplified by the Applause WT-Amp ST System (NuGEN Technologies, Bemmel, The Netherlands), amplified cDNA was fragmented and biotin labeled using the Encore Biotin Module (NuGEN Technologies)

growth_protocol: Lin- cells were cultured at 1x106 cells/ml in StemSpan serum-free medium (Stem Cell Technologies, Vancouver, Canada) supplemented with 2% penicillin/streptomycin, 1% glutamine (both PAA) and one of the following cytokine cocktail: S3F11: murine stem cell factor (mSCF) 50 ng/ml, murine interleukin 3 (mIL-3) 20 ng/ml, human FMS like tyrosine kinase 3 ligand (hFlt-3) 50 ng/ml, and human interleukin 11 (hIL-11) 50 ng/ml;

extract_protocol: Qiagen Rneasy Micro Kit according to manufacturers instructions

treatment_protocol: Transduction with Lentiviral Supernatants 24h after isolation; induction with Doxycyclin 1 ug /ml 24 h post transduction for 24 hrs than RNA Preparation

tag: transduction


title: EVI1 replicate 3


title: Muscle_CON_rep1

description: Gene expression data from gastrocnemius muscle of adult male mice.


title: Cancer Urothelia-16

description:
C-000016
Gene expression data from human urothelial cells in urine sediment.


title: EVI1 replicate 1


title: Cancer Urothelia-15

description:
C-000015
Gene expression data from human urothelial cells in urine sediment.


title: 78B-Mmulticell_agi

type: genomic

city: Leuven

first: Niels

last: Van der Aa

address: Herestraat 49 bus 602

country: Belgium

institute: KU Leuven

hyb_protocol: Hybridization and washing of 24sure arrays followed the protocol provided by the manufacturer.

scan_protocol: Scanning was performed using a DNA-microarray scanner (Agilent Technologies)

data_processing: GenePix Pro 6.0 software (Axon - Molecular Devices) was used for feature extraction and to normalize the data so the ratio of means for all features equals 1. All further analyses were performed in R (version 2.13.2 – www.r-project.com). Log2 intensity ratios with a signal/noise ratio of less than 2 were excluded from the analyses. The remaining intensities were made consistent within each array using median correction as implemented in R using the limma package. Next, the log2 intensity ratios of replicate probes were averaged using the R-package snapCGH. Technical GC-bias correction was performed by subtracting from each probe’s log2 intensity ratio the corresponding value from a mean locally weighted regression between the log2 intensity ratios and the %GC-content of the corresponding micro-array probe locus for all G- and G2/M-phase samples per batch. Using the spline function in R missing data in this mean lowess regression curve were filled in before it was used for the correction of log2 intensity ratios.

molecule: genomic DNA

source_name: EBV-transformed lymphoblast cell line

label_protocol: 150ng of test-samples and reference were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen) using respectively Cy5- and Cy3-dCTPs (GE Healthcare).

growth_protocol: Epstein-Barr virus (EBV) immortalized lymphoid cells were cultured in DMEM/F12 medium (Gibco) with 10% fetal bovine Serum (Thermo Scientific) at 37°C at 5%CO2.

extract_protocol: Collected cells were lysed by overnight incubation at 50°C in lysisbuffer (0.25mM EDTA, 0.5% SDS and 0.1mg/ml protK in 1x PBS) and DNA was extracted using phenol/chloroform extraction and ethanol precipitation.

treatment_protocol: Cells were stained with DyeCycle Orange (Invitrogen) according to the manufacturer’s protocol. In short, cells were washed with 1xPBS and incubated at a concentration of 10^6 cells/ml at 37°C for 30 minutes after adding DyeCycle orange at 2µl/10^6 cells. Cells of lymphoblastoid cell lines at ~5*10^6cells/ml were sorted using a FACS Vantage SE or a FACSAria III with FACS DiVa software (BD Biosciences).

value: male

tag: cell line

value: EBV-transformed lymphoblast cell line

tag: cell cycle phase

tag: origin

value: male carrying 750kb amplification on the short arm of chromosome 4

source_name: Kreatech male reference DNA

value: reference DNA


title: 77B-S18_agi

description: whole genome amplified single-cell DNA

data_processing: GenePix Pro 6.0 software (Axon - Molecular Devices) was used  for feature extraction and to normalize the data so the ratio of means for all features equals 1. All further analyses were performed in R (version 2.13.2 – www.r-project.com). Log2 intensity ratios with a signal/noise ratio of less than 2 were excluded from the analyses. The remaining intensities were made consistent within each array using median correction as implemented in R using the limma package. Next, the log2 intensity ratios of replicate probes were averaged using the R-package snapCGH. Technical GC-bias correction was performed by subtracting from each probe’s log2 intensity ratio the corresponding value from a mean locally weighted regression between the log2 intensity ratios and the %GC-content of the corresponding micro-array probe locus for all G- and G2/M-phase samples per batch. Using the spline function in R missing data in this mean lowess regression curve were filled in before it was used for the correction of log2 intensity ratios.

source_name: EBV-transformed lymphoblast cell

extract_protocol: The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome).

value: S-phase

source_name: SureRef male reference DNA (BlueGnome)


title: G2/M-phase 175080A TOP M

description: whole genome amplified singel-cell DNA

value: female

tag: treatment

value: female normal control cell line 2

source_name: SureRef male reference DNA (BlueGnome

value: SureRef male reference DNA (BlueGnome


title: 74B-Smulticell_agi


title: S-phase 175083A TOP S

description: whole genome amplified singel-cell DNA


title: 81B-S8_agi

description: whole genome amplified single-cell DNA


title: Placenta_villi_weeks8_8

status: Public on Jan 09 2013

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

country: India

institute: All India Institute of Medical Sciences

description:
Fertile_hpv8w_SP7.7_20 years
This placental sample is of first  trimester normal pregnancy, underwent elective surgical termination. It is the eighth of eight, 8 weeks biological replicates sample, each from different individual woman.

hyb_protocol: The labeled cDNA probes were hybridized to the NimbelGen Human Gene Expression 12x135K (60-mer probes per target for latest 45,033 human genome builds) microarray in glass format (070925_HG18_expr_HX12) using the NimbleGen Expression protocol. See http://www.nimblegen.com/products/ expression/ eukarya/ human/ 12x135k/ index.html.

scan_protocol: Scanning was performed by Agilent G2505B microarray scanner system at 5 micron resolution, following the standard operating protocol.

data_processing:
The scanned images were processed to normalize the expression data using quantile normalization and Robust Multi-array analysis (RMA) algorithm using the NimbleScan2.5 software (Roche NimbleGen, Inc.).
The RMA  files containing normalized image analysis values for each detected probe along with accession number were imported into the GeneSpring11.5.0 software (Agilent Technologies) for further analysis on log transformed data and averaged gene-level signal intensity.

source_name: 8 weeks placental villi

label_protocol: Microarray experiments with individual samples were performed according to standard methodological guide lines (http://www.mged.org/ Workgroups/MIAME/miame.html). Total RNA (10 µg/sample) with RIN score >8.0 was converted to cDNA by reverse transcriptase enzymes and labeled with Cy3 dye. See www.nimblegen.com.

extract_protocol: Placental samples were collected in sterile ice-cold phosphate buffered saline (PBS, pH 7.4). The tissue samples were quickly washed in ice-cold PBS to remove blood and debris, and separated from surrounding membranes, and villous portions were dissected from decidual and embryonic tissue under a dissecting microscope and further washed with sterile, cold PBS. The total RNA was extracted using Trizol (Agilent Technologies Singapore Pvt. Ltd., Shung Avenue, Singapore) and cleaned up with DNase I (Sigma Chemical Co., St. Louis, Missouri, USA) and subjected to re-extraction when it was necessary. The yield and purity of the extracted RNA was checked using standard spectrophotometric method and 1% agarose gel electrophoresis. Furthermore, RIN score of individual sample was determined using Bioanalyzer, RNA Chip kit and Software from Agilent Technologies (Santa Clara, CA, USA).

tag: age

value: 20 years

tag: gestation stage

value: 8 weeks

tag: gestational history

value: term pregnancy_1; preterm_0; abortion_2; living children_1


title: 75B-S13_agi

description: whole genome amplified single-cell DNA


title: 76B-S14_agi

description: whole genome amplified single-cell DNA


title: Cancer Urothelia-12

description:
C-000012
Gene expression data from human urothelial cells in urine sediment.

source_name: Bladder barbotage, cancer


title: S-phase 175080A BOTTOM S

description: whole genome amplified singel-cell DNA


title: Cancer Urothelia-10

description:
C-000010
Gene expression data from human urothelial cells in urine sediment.


title: 74B-Gmulticell_agi


title: Cancer Urothelia-9

description:
C-000009
Gene expression data from human urothelial cells in urine sediment.


title: G2/M-phase PE 18 slide 24118 EBV C9 MG2 phase

hyb_protocol: Hybridization and washing of Perkin Elmer arrays followed the protocol provided by the manufacturer.

scan_protocol: Scanning was performed using a a Genepix 4000 B (Axon instruments - Molecular Devices).

label_protocol: 1µg of test-samples and reference were labeled for 2h by random primer labeling (BioPrime aCGH Genomic Labeling System; Invitrogen) using respectively Cy5- and Cy3-dCTPs (GE Healthcare).

value: female normal control 2

value: Kreatech male reference DNA


title: Cancer Urothelia-14

description:
C-000014
Gene expression data from human urothelial cells in urine sediment.

value: urothelial cancer cells

value: bladder cancer


title: EGFP replicate 2

description: Gene expression data from Lin- cells transduced with EGFP control vector

value: EGFP control vector


title: Cancer Urothelia-13

description:
C-000013
Gene expression data from human urothelial cells in urine sediment.


title: 80B-S4_agi

description: whole genome amplified single-cell DNA


title: 82B-S10_agi

description: whole genome amplified single-cell DNA


title: Cancer Urothelia-11

description:
C-000011
Gene expression data from human urothelial cells in urine sediment.


title: CD4

city: la jolla

first: Hilde

last: Cheroutre

state: California

address: 9420 athena circle

department: Developmental Immunology

institute: La Jolla Institute for Allergy and Immunology

description: CD4 IEL

hyb_protocol: hybridized to GeneChip Mouse Genome 430 2.0 arrays according to the Affymetrix protocols

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000

data_processing:
The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).
Data were analyzed in GeneSpring GX10.

source_name: Sorted from RAG knockout, recipients of naïve CD4 cells

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

growth_protocol: IELs were prepared using percol (density gradient centrifugation)

extract_protocol: RNA was prepared by TRIZol (Invitrogen, USA)

value: CD4 intraepthelial lymphocyte


title: Cancer Urothelia-6

description:
C-000006
Gene expression data from human urothelial cells in urine sediment.


title: Cancer Urothelia-8

description:
C-000008
Gene expression data from human urothelial cells in urine sediment.


title: G1-phase 175083A BOTTOM G

description: whole genome amplified singel-cell DNA

value: male


title: 76B-M9_agi

description: whole genome amplified single-cell DNA

value: EBV-transformed lymphoblast cell line


title: EGFP replicate 3


title: 78B-S1_agi

description: whole genome amplified single-cell DNA

value: male carrying 750kb amplification on the short arm of chromosome 4


title: CD4CD8aa

description: CD4CD8aa IEL

value: CD4CD8aa intraepthelial lymphocyte


title: S-phase PE 14 slide 024055 EBV Sphase

value: S-phase

value: female normal control 1


title: Cancer Urothelia-5

description:
C-000005
Gene expression data from human urothelial cells in urine sediment.


title: 81B-G3_agi

description: whole genome amplified single-cell DNA

value: reference DNA


title: 80B-G2_agi

description: whole genome amplified single-cell DNA


title: 82B-M1_agi

description: whole genome amplified single-cell DNA


title: G1-phase PE 17 slide 242216 EBV C9 G1 phase

value: female


title: G1-phase PE 13 slide 024050 EBV G1phase


title: Cancer Urothelia-4

description:
C-000004
Gene expression data from human urothelial cells in urine sediment.


title: Cow 7244 without carnitine infusion and fed normal diet

status: Public on Jan 07 2013

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description: A mixture of total RNA from several bovine tissues was used as reference (Cy5 in file1 and Cy3 in file2)

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 38 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Liver biopsy of cow without carnitine infusion and fed normal diet

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Cows were maintain in a normal farm management

extract_protocol: Biopsy tissue was weighted (~0.5-1.0 g) and immediately subjected to RNA extraction using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen).

tag: breed

value: Holstein dairy cow


title: Cow 7182 infused with carnitine and fed normal diet

source_name: Liver biopsy of cow infused with carnitine and fed normal diet

source_name: A mixture of total RNA from several bovine tissues


title: Cow 7244 infused with carnitine and feed restricted

source_name: Liver biopsy of cow infused with carnitine and feed restricted


title: Cow 7244 without carnitine infusion and feed restricted

source_name: Liver biopsy of cow without carnitine infusion and feed restricted


title: Cow 7146 without carnitine infusion and feed restricted


title: Cow 7162 without carnitine infusion and feed restricted


title: Cow 7182 without carnitine infusion and feed restricted


title: Cow 7162 without carnitine infusion and fed normal diet


title: EGFP replicate 1

tag: strain


title: Cancer Urothelia-1

description:
C-000001
Gene expression data from human urothelial cells in urine sediment.


title: G2/M-phase PE 15 slide 024054 EBV MG2phase

tag: gender


title: S-phase PE 16 slide 242217 EBV C9 S phase


title: Cow 7162 infused with carnitine and feed restricted


title: Cow 6993 without carnitine infusion and feed restricted


title: Cancer Urothelia-3

description:
C-000003
Gene expression data from human urothelial cells in urine sediment.


title: Cow 6993 without carnitine infusion and fed normal diet


title: Cow 7146 infused with carnitine and feed restricted


title: Cow 6993 infused with carnitine and fed normal diet


title: Cancer Urothelia-2

description:
C-000002
Gene expression data from human urothelial cells in urine sediment.


title: Cow 6922 infused with carnitine and feed restricted


title: Cow 6922 infused with carnitine and fed normal diet


title: Cow 6962 infused with carnitine and fed normal diet


title: Cow 6962 without carnitine infusion and fed normal diet


title: Cancer Urothelia-7

description:
C-000007
Gene expression data from human urothelial cells in urine sediment.


title: Cow 6962 without carnitine infusion and feed restricted


title: Cow 6922 without carnitine infusion and fed normal diet


title: UI-DBA BMDC_rep3

city: Paris

first: Thierry

last: Lang

address: 25 rue du Dr Roux

department: parasitology and Mycology

country: France

institute: Institut Pasteur

hyb_protocol: See standard Affymetrix protocols

scan_protocol: Following hybridization, the arrays were stained and scanned at 532 nm using an Affymetrix GeneChip Scanner 3000 which generates individual CEL files for each array.

data_processing: Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust Multichip Average algorithm (RMA) (Bolstad et al., 2003). RMA performs normalization, background correction and data summarization. An analysis is performed using the LPE test (Jain, 2003) to identify significant differences in gene expression between parasite-free and parasite-harbouring DLs, and a p-value threshold of p < 0.05 is used as the criterion for significant differential expression. The estimated false discovery rate (FDR) was calculated using the Benjamini and Hochberg approach (Benjamini et al., 1995) in order to correct for multiple comparisons.

source_name: DBA-2 BMDC

label_protocol: Two hundred ng of total RNA per sample were processed, labelled and hybridized to Affymetrix Mouse Gene ST 1.0 arrays, following Affymetrix Protocol (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

growth_protocol: DLs were differentiated from bone marrow cells of DBA/2 or C57BL/6 mice.On day 4 post the distribution of DLs in the 6 well plate culture, DLs were exposed to freshly isolated DsRed2-LV79 amastigotes.

extract_protocol: Mouse total RNA was extracted from either MHC class II+ BMD-DLs  using the RNeasy Plus Mini-Kit (Qiagen).The quality control (QC) and concentration of RNA were determined using the NanoDrop ND-1000 micro-spectrophotometer and the Agilent-2100 Bioanalyzer.

treatment_protocol: L. amazonensis amastigote-hosting DLs were sorted by selecting cells expressing both surface MHC Class II molecules and DsRed2 fluorescence and immediately used for further studies.

value: Dendritic Leucocyte (DL)

tag: infectious agent

value: None (control)


title: Normal mammary tissue, Normal4

city: Chiba

first: Daisuke

last: IIZUKA

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: Research Institutes for Quantum Science and Technology

hyb_protocol: Hybridization and post-hybridization wash were carried out essentially according to the manufacturers’ protocol (version 1.5).

scan_protocol: Microarray slides were scanned immediately using an Agilent microarray scanner.

data_processing: Data for individual features on the microarray were extracted from the scan image using Agilent’s Feature Extraction (FE) Software. Output files from FE were subsequently imported into GeneSpring. Normalization was not performed.

organism: Rattus norvegicus

source_name: normal mammary tissue No. 4 RNA

label_protocol: Total RNA (100 ng) was dephosphorylated using calf intestine alkaline phosphatase (Takara Bio Inc., Otsu, Japan), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase (New England Biolabs, Ipswich, MA).

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions.

tag: sprain

value: Sprague-Dawley

tag: tissue

value: normal mammary tissue


title: Normal mammary tissue, Normal2

source_name: normal mammary tissue No. 2 RNA


title: Normal mammary tissue, Normal6

source_name: normal mammary tissue No. 6 RNA


title: Normal mammary tissue, Normal7

source_name: normal mammary tissue No. 7 RNA


title: Normal mammary tissue, Normal5

source_name: normal mammary tissue No. 5 RNA


title: UI-C57 BMDC_rep3

source_name: C57 BMDC

tag: cell type


title: UI-DBA BMDC_rep2


title: Normal mammary tissue, Normal3

source_name: normal mammary tissue No. 3 RNA


title: Radiation-induced mammary carcinoma, M1467-1

source_name: mammary carcinoma No. M1467-Mt1 RNA

value: radiation-induced mammary carcinoma


title: Normal mammary tissue, Normal1

source_name: normal mammary tissue No. 1 RNA


title: I-C57 BMDC_rep3

source_name: C57 BMDC+LV79

value: Leishmania amazonensis amastigotes


title: I-DBA BMDC_rep3

source_name: DBA-2 BMDC+LV79


title: UI-C57 BMDC_rep1


title: UI-C57 BMDC_rep2


title: I-DBA BMDC_rep2


title: Radiation-induced mammary carcinoma, M1466-2

source_name: mammary carcinoma No. M1466-Mt2 RNA


title: Radiation-induced mammary carcinoma, M1413-1

source_name: mammary carcinoma No. M1413-Mt1 RNA


title: Radiation-induced mammary carcinoma, M1414-1

source_name: mammary carcinoma No. M1414-Mt1 RNA


title: Radiation-induced mammary carcinoma, M1415-3

source_name: mammary carcinoma No. M1415-Mt3 RNA


title: I-C57 BMDC_rep2


title: I-C57 BMDC_rep1


title: I-DBA BMDC_rep1


title: DMSO_3

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

hyb_protocol: An aliquot of cRNA was run in triplicate on a NanoDrop spectrophotometer to determine sample concentration and yield. Samples were normalised to 150ng/µl. An aliquot of normalised cRNA was run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality. 750ng of labelled cRNA was hybridised to Illumina BeadArrays overnight, and BeadArrays were washed and stained with streptavidin-Cy3, following the Illumina WGGX DirectHyb Assay Guide (11286331 RevA).

scan_protocol: BeadArrays were scanned using the AutoLoader and BeadArray scanner at default settings following the BeadArray Reader User Guide (11179510 RevB). Metric files produced automatically save P95 and P05 readings and .xml files save scanner settings.

data_processing: Using the R beadarray package, the data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: Detection p-values are not available as the Bioconductor beadarray package was used to analyse raw bead-level data instead of the Illumina GenomeStudio software.

source_name: MCF-7 breast adenocarcinoma cells, control

label_protocol: An aliquot of total RNA was run in triplicate on a NanoDrop spectrophotometer to determine sample concentration, and an aliquot of total RNA was run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality. Good-quality samples were normalised to 22.7ng/µl. 250ng of quality total RNA was processed following the Ambion Illumina® TotalPrep™-96 RNA Amplification Kit standard protocols.

growth_protocol: The human MCF-7 cell line was obtained from the ECACC (European Collection of Animal Cell Cultures) and grown in DMEM supplemented with 10% FBS.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: Cells were grown to 60% confluence, and then treated with Thiostrepton (10μM) or DMSO (0.1%) for 6 hr.

value: ER-positive breast adenocarcinoma cells

value: DMSO

tag: treatment duration

tag: replicate


title: Thiostrepton_6

source_name: MCF-7 breast adenocarcinoma cells, thiostrepton

value: thiostrepton


title: Thiostrepton_5


title: DMSO_2


title: Radiation-induced mammary carcinoma, M1612-3

source_name: mammary carcinoma No. M1612-Mt3 RNA


title: Radiation-induced mammary carcinoma, M1233-1

source_name: mammary carcinoma No. M233-Mt1 RNA


title: Radiation-induced mammary carcinoma, M1177-1

source_name: mammary carcinoma No. M1177-Mt1 RNA


title: Spontaneous mammary carcinoma, K0265-3

source_name: mammary carcinoma No. K0265-Mt3 RNA

value: spontaneous mammary carcinoma


title: Spontaneous mammary carcinoma, K0179-1

source_name: mammary carcinoma No. K0179-Mt1 RNA


title: Spontaneous mammary carcinoma, K0672-2

source_name: mammary carcinoma No. K0672-Mt2 RNA


title: Spontaneous mammary carcinoma, K0677-1

source_name: mammary carcinoma No. K0677-Mt1 RNA


title: Spontaneous mammary carcinoma, K0679-2

source_name: mammary carcinoma No. K0679-Mt2 RNA


title: Spontaneous mammary carcinoma, M1596-1

source_name: mammary carcinoma No. M1596-Mt1 RNA


title: Spontaneous mammary carcinoma, M1695-1

source_name: mammary carcinoma No. M1695-Mt1 RNA


title: DMSO_4


title: Spontaneous mammary carcinoma, M1605-2

source_name: mammary carcinoma No. M1605-Mt2 RNA


title: Thiostrepton_2


title: C12 cell #3

city: Haifa

first: Maty

last: Tzukerman

address: Efron, 1

country: Israel

institute: Technion

description: SAMPLE 15

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data obtained from 3 independent microarray experiments were imported into genomics software (Genomics Suite; Partek Inc., St Louis, MO). By using default settings the data was normalized, and  removal of any non-biological, batch effects, which may interrupt with the results was performed

source_name: C12 cell

label_protocol: RNA was amplified into cRNA, and biotinylated by in vitro transcription using the TargetAmp Nano-g Biotin-aRNA Labeling kit for the Illumina system.

growth_protocol: Cell cultures were repeatedly initiated from frozen stock every 3-4 months and grew in RPMI-1640 supplamented with 20%FBS. i.m and i.t tumors were harvested 20-60 days following injection. Laser microdissection and pressure catapulting (LMPC) samples of identified tumor tissues were collected using the Palm® MicroLaser system.

extract_protocol: Total RNA was extracted from tissues of tumors generated i.m, and i.t using the RNeasy®Micro Kit, and from in vitro growing cells using the RNeasy®Mini Kit

treatment_protocol: Growing of two cancer cell supopulations derived from an individual tumor within a murine and a human tissues

value: ovarian clear cell carcinoma cells

tag: cell subpopulation

tag: protocol

value: in vitro grown cells


title: C13 i.t #3

description: SAMPLE 17

source_name: C13 i.t

value: tumors developed within a human (intra-teratoma)


title: DMSO_6


title: C13 i.m #3

description: SAMPLE 16

source_name: C13 i.m

value: tumors developed within a murine (intratumoral)


title: C12 i.m #3

description: SAMPLE 13

source_name: C12 i.m


title: DMSO_1

source_name: MCF-7 breast adenocarcinoma cells, control


title: Thiostrepton_3

source_name: MCF-7 breast adenocarcinoma cells, thiostrepton


title: 252800510959-2

city: Angers

first: Celine

last: Fassot-Lucht

address: Rue Haute de Reculée

department: BNMI

institute: INSERM U1083

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing

source_name: normal feeding group

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: total RNA (Chomzynski protocol)

value: heart

tag: developmental stage

value: 24 days postnatal

tag: rin number


title: C13 cell #3

description: SAMPLE 18

source_name: C13 cell


title: 252800510959-1


title: C12 i.t #3

description: SAMPLE 14

source_name: C12 i.t


title: C13 cell #1

description: SAMPLE 6


title: DMSO_5

tag: treatment


title: Thiostrepton_4


title: C13 i.m #1

description: SAMPLE 4


title: C13 i.t #1

description: SAMPLE 5


title: 252800510959-4


title: Thiostrepton_1


title: C13 cell #2

description: SAMPLE 12


title: C12 i.t #1

description: SAMPLE 2


title: C13 i.t #2

description: SAMPLE 11


title: C12 i.m #1

description: SAMPLE 1


title: C13 i.m #2

description: SAMPLE 10


title: C12 cell #2

description: SAMPLE 9


title: 252800510959-6

source_name: overfeeding group


title: C12 cell #1

description: SAMPLE 3


title: 252800510959-5


title: 252800510959-3


title: C12 i.t #2

description: SAMPLE 8


title: 252800510959-7


title: C12 i.m #2

description: SAMPLE 7


title: EA0724_02

city: Kobe

first: Toshiaki

last: Sakisaka

state: Hyogo

address: Kusunoki-cho 7-5-1, Chuou-ku

department: Physiology and Cell Biology

institute: Kobe University Graduate School of Medicine

description: Gene expression data from mutant mouse at P14

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Mutant mouse cerebrum at P14

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The mice were autopsied as a acknowledged protocol by ethical animal committee in Graduate School of Medicine of Kobe University . The cerebrum was dissected from each mouse and immediately frozen in -80 degree.

extract_protocol: Trizol extraction of total RNA and purification was performed with TRIzol Plus RNA purification Kit (Invirogen)  basically according to the manufacturer's instructions.

treatment_protocol: The brain tissue was minced into small pieces with scalpel on dry ice. The minced tissue were furtherly ground in the mortar with pestle, putting liquid nitrogen during that.

value: cerebrum

tag: genotype

value: Mutant

tag: age


title: EA0724_01

description: Gene expression data from wild type mouse at P14

source_name: Wild type mouse cerebrum at P14

value: Willd type


title: 78-C

status: Public on Jan 06 2013

city: Chungbuk

first: Kim

last: Hye-Ryun

address: Osong Health Technology Administration Comples

country: South Korea

institute: Korea Centers for Disease Control & Prevention

description: 2hr after glucose ingesion

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human-8 expression bead array for 16-18 h at 58C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8).

data_processing: The data were normalised using quantile normalisation

source_name: Subject 78-2hr

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: Subjects were recruited from the Korean Genome Epidemiology Study (KoGES), a longitudinal community-based prospective study, consisting of participants aged 40-69. Subjects with a previous history of diabetes or any malignant disease were excluded. A total of 60 subjects were included in the present study and underwent an OGTT.

extract_protocol: Total RNA was extracted from whole blood using LeukoLOCK Total RNA Isolation Kit (Ambion). The mRNA were assessed for concentration by NanoDrop (ND-1000 spectrophotometor) and integrity using the Agilent 2100 Bioanalyzer (Agilent Technologies) and stored at -80C until use.

treatment_protocol: Subjects were given 75g glucose dissolved in 300mL water (Glucola; Allegiance Healthcare Corporation, McGaw Park, IL) to drink within 5min. Blood samples were obtained at 0, 1 and 2 hours.

value: circulating leukocytes

tag: sampling timepoint

value: 2hr after glucose ingesion


title: SACMV-[ZA:99]-infected vs control_36 dpi

city: Braamfontein

first: Chrissie

last: Rey

state: Johannesburg, Gauteng

address: 1 Jan Smuts Avenue

department: School of Molecular and Cell Biology

country: South Africa

institute: University of the Witswatersrand

description:
3 biological replicates and 1 technical replicate, direct comparison with a dye swap.
Raw file dye assignments:
Biological Replicate 1 (BR1): Cy3_Control, Cy5_Infected
Biological Replicate 1 Reverse (Technical Replicate)  (BR1 R): Cy3_Infected, Cy5_Control
Biological Replicate 2 (BR 2): Cy3_Control, Cy5_Infected
Biological Replicate 3 (BR 3): Cy3_Infected, Cy5_Control

hyb_protocol: Microarray hybridization was carried out according to manufacturer’s instructions (Agilent). 100 pmol of each cyanine dye, linearly amplified cRNA was added to a hybridization mix containing 10 X blocking agent and 25 X fragmentation buffer were incubated for 30 mins at 60°C to fragment the RNA. Fifty five microliters of 2 X GE buffer was then added to the solution, spun gently and placed on ice, ready for hybridization.  One hundred and ten microliters  of solution was added onto three Arabidopsis Agilent 4 X 44 slides (Version 3), and placed in a rotating hybridization chamber (Agilent) set at 65°C for 18 h. Slides were then washed using Agilent‘s Gene Expression Wash Buffers 1 and 2.

scan_protocol: Genepix 4000B scanner using Genepix Pro 6 software

data_processing:
Fluorescence data obtained from the microarray was imported into Limma in the R computing environment, where the data was normalized (‘within-array’ global loess normalization and ‘between-array’ quantile normalization), and linear models were fitted in order to contrast SACMV-[ZA:99] - infected expression values with those of mock-inoculated controls.
Dye swap experiments were carried out for each replicate. Normalized Log2 fold change ratios showing direct comparison of data representing infection/control are shown below.

organism: Arabidopsis thaliana

source_name: [infection] Apical leaf tissue

label_protocol: Total RNA (1 ug) was amplified using the Amino Allyl MessageAmp™II aRNA Amplification Kit (Ambion) following manufacturer’s instructions. During aRNA:Dye coupling, 4 ug of aRNA was vacuum dried at 45°C and resuspended in 5 ul of 0.2M NAHCO3 (pH 9.0) at RT for 20 min. Two microlitres of each dye (Cy5 or Cy3) was added to the sample.

extract_protocol: Total RNA was extracted from pooled SACMV-[ZA;99] - infected and healthy Arabidopsis plants at 14, 24, and 36 dpi using a QIAzol lysis reagent method

tag: infection

value: South African cassava mosaic virus [ZA-99]

tag: time

value: 36 dpi

value: Apical leaf tissue

source_name: [control] Apical leaf tissue

value: mock-inoculation


title: 73-C

description: 2hr after glucose ingesion

source_name: Subject 73-2hr


title: 70-C

description: 2hr after glucose ingesion

source_name: Subject 70-2hr


title: 73-B

description: 1hr after glucose ingestion

source_name: Subject 73-1hr

value: 1hr after glucose ingestion


title: 73-A

description: baseline

source_name: Subject 73-0hr

value: before glucose ingestion (baseline)


title: SACMV-[ZA:99]-infected vs control_24 dpi

value: 24 dpi


title: 69-A

description: baseline

source_name: Subject 69-0hr


title: 71-C

description: 2hr after glucose ingesion

source_name: Subject 71-2hr


title: 78-B

description: 1hr after glucose ingestion

source_name: Subject 78-1hr


title: 70-A

description: baseline

source_name: Subject 70-0hr


title: 69-B

description: 1hr after glucose ingestion

source_name: Subject 69-1hr


title: SACMV-[ZA:99]-infected vs control_14 dpi

value: 14 dpi


title: 66-B

description: 1hr after glucose ingestion

source_name: Subject 66-1hr


title: 66-C

description: 2hr after glucose ingesion

source_name: Subject 66-2hr


title: 70-B

description: 1hr after glucose ingestion

source_name: Subject 70-1hr


title: 78-A

description: baseline

source_name: Subject 78-0hr


title: 67-B

description: 1hr after glucose ingestion

source_name: Subject 67-1hr


title: 66-A

description: baseline

source_name: Subject 66-0hr


title: 65-C

description: 2hr after glucose ingesion

source_name: Subject 65-2hr


title: 71-B

description: 1hr after glucose ingestion

source_name: Subject 71-1hr


title: 252800510959-8

source_name: overfeeding group

tag: strain


title: 67-C

description: 2hr after glucose ingesion

source_name: Subject 67-2hr


title: UI-DBA BMDC_rep1

source_name: DBA-2 BMDC

value: Dendritic Leucocyte (DL)

tag: infectious agent

value: None (control)


title: 65-B

description: 1hr after glucose ingestion

source_name: Subject 65-1hr


title: 69-C

description: 2hr after glucose ingesion

source_name: Subject 69-2hr


title: 63-A

description: baseline

source_name: Subject 63-0hr


title: 61-B

description: 1hr after glucose ingestion

source_name: Subject 61-1hr


title: 62-B

description: 1hr after glucose ingestion

source_name: Subject 62-1hr


title: 67-A

description: baseline

source_name: Subject 67-0hr


title: 63-B

description: 1hr after glucose ingestion

source_name: Subject 63-1hr


title: 60-C

description: 2hr after glucose ingesion

source_name: Subject 60-2hr


title: 63-C

description: 2hr after glucose ingesion

source_name: Subject 63-2hr


title: 61-C

description: 2hr after glucose ingesion

source_name: Subject 61-2hr


title: 62-C

description: 2hr after glucose ingesion

source_name: Subject 62-2hr


title: 60-A

description: baseline

source_name: Subject 60-0hr


title: 59-C

description: 2hr after glucose ingesion

source_name: Subject 59-2hr


title: 59-A

description: baseline

source_name: Subject 59-0hr


title: 60-B

description: 1hr after glucose ingestion

source_name: Subject 60-1hr


title: 58-C

description: 2hr after glucose ingesion

source_name: Subject 58-2hr


title: 61-A

description: baseline

source_name: Subject 61-0hr


title: 58-A

description: baseline

source_name: Subject 58-0hr


title: 58-B

description: 1hr after glucose ingestion

source_name: Subject 58-1hr


title: 56-C

description: 2hr after glucose ingesion

source_name: Subject 56-2hr


title: 55-C

description: 2hr after glucose ingesion

source_name: Subject 55-2hr


title: 57-A

description: baseline

source_name: Subject 57-0hr


title: 56-B

description: 1hr after glucose ingestion

source_name: Subject 56-1hr


title: 57-B

description: 1hr after glucose ingestion

source_name: Subject 57-1hr


title: 62-A

description: baseline

source_name: Subject 62-0hr


title: 59-B

description: 1hr after glucose ingestion

source_name: Subject 59-1hr


title: 57-C

description: 2hr after glucose ingesion

source_name: Subject 57-2hr


title: 55-B

description: 1hr after glucose ingestion

source_name: Subject 55-1hr


title: 54-A

description: baseline

source_name: Subject 54-0hr


title: 54-C

description: 2hr after glucose ingesion

source_name: Subject 54-2hr


title: 54-B

description: 1hr after glucose ingestion

source_name: Subject 54-1hr


title: 53-A

description: baseline

source_name: Subject 53-0hr


title: 56-A

description: baseline

source_name: Subject 56-0hr


title: 55-A

description: baseline

source_name: Subject 55-0hr


title: 53-B

description: 1hr after glucose ingestion

source_name: Subject 53-1hr


title: 53-C

description: 2hr after glucose ingesion

source_name: Subject 53-2hr


title: 50-B

description: 1hr after glucose ingestion

source_name: Subject 50-1hr


title: 51-B

description: 1hr after glucose ingestion

source_name: Subject 51-1hr


title: 52-A

description: baseline

source_name: Subject 52-0hr


title: 50-A

description: baseline

source_name: Subject 50-0hr


title: 51-A

description: baseline

source_name: Subject 51-0hr


title: 50-C

description: 2hr after glucose ingesion

source_name: Subject 50-2hr


title: 49-B

description: 1hr after glucose ingestion

source_name: Subject 49-1hr


title: 52-C

description: 2hr after glucose ingesion

source_name: Subject 52-2hr


title: 52-B

description: 1hr after glucose ingestion

source_name: Subject 52-1hr


title: 51-C

description: 2hr after glucose ingesion

source_name: Subject 51-2hr


title: 47-C

description: 2hr after glucose ingesion

source_name: Subject 47-2hr


title: 47-A

description: baseline

source_name: Subject 47-0hr


title: 47-B

description: 1hr after glucose ingestion

source_name: Subject 47-1hr


title: 46-B

description: 1hr after glucose ingestion

source_name: Subject 46-1hr


title: 46-C

description: 2hr after glucose ingesion

source_name: Subject 46-2hr


title: 46-A

description: baseline

source_name: Subject 46-0hr


title: 71-A

description: baseline

source_name: Subject 71-0hr


title: 45-C

description: 2hr after glucose ingesion

source_name: Subject 45-2hr


title: 44-C

description: 2hr after glucose ingesion

source_name: Subject 44-2hr


title: 45-B

description: 1hr after glucose ingestion

source_name: Subject 45-1hr


title: 44-B

description: 1hr after glucose ingestion

source_name: Subject 44-1hr


title: 45-A

description: baseline

source_name: Subject 45-0hr


title: 49-C

description: 2hr after glucose ingesion

source_name: Subject 49-2hr


title: 38-B

description: 1hr after glucose ingestion

source_name: Subject 38-1hr


title: 38-C

description: 2hr after glucose ingesion

source_name: Subject 38-2hr


title: 40-C

description: 2hr after glucose ingesion

source_name: Subject 40-2hr


title: 41-B

description: 1hr after glucose ingestion

source_name: Subject 41-1hr


title: 44-A

description: baseline

source_name: Subject 44-0hr


title: 39-B

description: 1hr after glucose ingestion

source_name: Subject 39-1hr


title: 37-C

description: 2hr after glucose ingesion

source_name: Subject 37-2hr


title: 36-C

description: 2hr after glucose ingesion

source_name: Subject 36-2hr


title: 41-A

description: baseline

source_name: Subject 41-0hr


title: 40-B

description: 1hr after glucose ingestion

source_name: Subject 40-1hr


title: 65-A

description: baseline

source_name: Subject 65-0hr


title: 35-B

description: 1hr after glucose ingestion

source_name: Subject 35-1hr


title: 39-A

description: baseline

source_name: Subject 39-0hr


title: 39-C

description: 2hr after glucose ingesion

source_name: Subject 39-2hr


title: 40-A

description: baseline

source_name: Subject 40-0hr


title: 36-A

description: baseline

source_name: Subject 36-0hr


title: 37-A

description: baseline

source_name: Subject 37-0hr


title: 37-B

description: 1hr after glucose ingestion

source_name: Subject 37-1hr


title: 49-A

description: baseline

source_name: Subject 49-0hr


title: 38-A

description: baseline

source_name: Subject 38-0hr


title: 34-C

description: 2hr after glucose ingesion

source_name: Subject 34-2hr


title: 36-B

description: 1hr after glucose ingestion

source_name: Subject 36-1hr


title: 33-A

description: baseline

source_name: Subject 33-0hr


title: 35-C

description: 2hr after glucose ingesion

source_name: Subject 35-2hr


title: 33-C

description: 2hr after glucose ingesion

source_name: Subject 33-2hr


title: 41-C

description: 2hr after glucose ingesion

source_name: Subject 41-2hr


title: 34-A

description: baseline

source_name: Subject 34-0hr


title: 33-B

description: 1hr after glucose ingestion

source_name: Subject 33-1hr


title: 35-A

description: baseline

source_name: Subject 35-0hr


title: 34-B

description: 1hr after glucose ingestion

source_name: Subject 34-1hr


title: 32-C

description: 2hr after glucose ingesion

source_name: Subject 32-2hr


title: 28-C

description: 2hr after glucose ingesion

source_name: Subject 28-2hr


title: 29-A

description: baseline

source_name: Subject 29-0hr


title: 30-C

description: 2hr after glucose ingesion

source_name: Subject 30-2hr


title: 32-B

description: 1hr after glucose ingestion

source_name: Subject 32-1hr


title: 29-C

description: 2hr after glucose ingesion

source_name: Subject 29-2hr


title: 27-B

description: 1hr after glucose ingestion

source_name: Subject 27-1hr


title: 29-B

description: 1hr after glucose ingestion

source_name: Subject 29-1hr


title: 30-A

description: baseline

source_name: Subject 30-0hr


title: 27-C

description: 2hr after glucose ingesion

source_name: Subject 27-2hr


title: 28-B

description: 1hr after glucose ingestion

source_name: Subject 28-1hr


title: 26-B

description: 1hr after glucose ingestion

source_name: Subject 26-1hr


title: 26-A

description: baseline

source_name: Subject 26-0hr


title: 24-C

description: 2hr after glucose ingesion

source_name: Subject 24-2hr


title: 23-C

description: 2hr after glucose ingesion

source_name: Subject 23-2hr


title: 22-A

description: baseline

source_name: Subject 22-0hr


title: 30-B

description: 1hr after glucose ingestion

source_name: Subject 30-1hr


title: 21-B

description: 1hr after glucose ingestion

source_name: Subject 21-1hr


title: 20-C

description: 2hr after glucose ingesion

source_name: Subject 20-2hr


title: 22-B

description: 1hr after glucose ingestion

source_name: Subject 22-1hr


title: 20-B

description: 1hr after glucose ingestion

source_name: Subject 20-1hr


title: 23-A

description: baseline

source_name: Subject 23-0hr


title: 24-B

description: 1hr after glucose ingestion

source_name: Subject 24-1hr


title: 27-A

description: baseline

source_name: Subject 27-0hr


title: 28-A

description: baseline

source_name: Subject 28-0hr


title: 32-A

description: baseline

source_name: Subject 32-0hr


title: 24-A

description: baseline

source_name: Subject 24-0hr


title: 26-C

description: 2hr after glucose ingesion

source_name: Subject 26-2hr


title: 19-C

description: 2hr after glucose ingesion

source_name: Subject 19-2hr


title: 21-C

description: 2hr after glucose ingesion

source_name: Subject 21-2hr


title: 22-C

description: 2hr after glucose ingesion

source_name: Subject 22-2hr


title: 23-B

description: 1hr after glucose ingestion

source_name: Subject 23-1hr


title: 20-A

description: baseline

source_name: Subject 20-0hr


title: 17-C

description: 2hr after glucose ingesion

source_name: Subject 17-2hr


title: 19-A

description: baseline

source_name: Subject 19-0hr


title: 17-B

description: 1hr after glucose ingestion

source_name: Subject 17-1hr


title: 21-A

description: baseline

source_name: Subject 21-0hr


title: 16-B

description: 1hr after glucose ingestion

source_name: Subject 16-1hr


title: 17-A

description: baseline

source_name: Subject 17-0hr


title: 16-C

description: 2hr after glucose ingesion

source_name: Subject 16-2hr


title: 15-B

description: 1hr after glucose ingestion

source_name: Subject 15-1hr


title: 14-C

description: 2hr after glucose ingesion

source_name: Subject 14-2hr


title: 12-A

description: baseline

source_name: Subject 12-0hr


title: 19-B

description: 1hr after glucose ingestion

source_name: Subject 19-1hr


title: 11-C

description: 2hr after glucose ingesion

source_name: Subject 11-2hr


title: 14-B

description: 1hr after glucose ingestion

source_name: Subject 14-1hr


title: 12-C

description: 2hr after glucose ingesion

source_name: Subject 12-2hr


title: 16-A

description: baseline

source_name: Subject 16-0hr


title: 14-A

description: baseline

source_name: Subject 14-0hr


title: 13-A

description: baseline

source_name: Subject 13-0hr


title: 15-A

description: baseline

source_name: Subject 15-0hr


title: 12-B

description: 1hr after glucose ingestion

source_name: Subject 12-1hr


title: 11-A

description: baseline

source_name: Subject 11-0hr


title: 15-C

description: 2hr after glucose ingesion

source_name: Subject 15-2hr


title: 11-B

description: 1hr after glucose ingestion

source_name: Subject 11-1hr


title: 13-B

description: 1hr after glucose ingestion

source_name: Subject 13-1hr


title: 10-C

description: 2hr after glucose ingesion

source_name: Subject 10-2hr


title: 10-A

description: baseline

source_name: Subject 10-0hr


title: esiOgt_rep2

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used to prepare the Hybridization Cocktail. The kit contains mix for target  dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat  #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. These control oligos serve as positive controls for  hybridization. Biotin-labeled sense targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes.  Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to loading into the GeneChip® array cartridge. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60 RPM. Upon hybridization, GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol. The cartridge is then loaded into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are scanned using default parameters. Affymetrix GeneChip Command Console software (AGCC) was used to acquire GeneChip images and generate .DAT and .CEL files.

data_processing: Microarray data is analyzed using Affy (quantile-normalized with rma method) and Limma packages in R. For annotating affy IDs, mogene10sttranscriptcluster.db is used.

source_name: ES cell RNA

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA. Double stranded cDNA synthesis and related cRNA amplification was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the protocol were performed according to manufacturer’s specifications. Efficacy of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

growth_protocol: ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

extract_protocol: Total RNA was cleaned -up with RNAesy Qiagen purification kit.

treatment_protocol: Total RNA was extracted from exponentially growing ES cells previously tryptinizied and collected.

value: Embryonic Stem Cells

tag: genotype/variation

value: Ogt silencing


title: 8-A

description: baseline

source_name: Subject 8-0hr

tag: tissue


title: 8-C

description: 2hr after glucose ingesion

source_name: Subject 8-2hr


title: 8-B

description: 1hr after glucose ingestion

source_name: Subject 8-1hr


title: 5-B

description: 1hr after glucose ingestion

source_name: Subject 5-1hr


title: 10-B

description: 1hr after glucose ingestion

source_name: Subject 10-1hr


title: 5-A

description: baseline

source_name: Subject 5-0hr


title: Muscle from WT, biological rep2

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description:
Muscle_DS20
Gene-level analysis.

hyb_protocol: Labeled cDNA was hybridized on the Mouse Gene ST array for 18 hours at 45C. Arrays were washed and stained on an Affymetrix Fluidics Station 450 using protocol FS_450_0007.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 7G Plus.

data_processing: Data were analyzed using Expression Console version 1.1 (Affymetrix) using the default RMA algorithm.

source_name: Soleus muscle, basal state, WT

label_protocol: Biotinylated cDNA was prepared using the NuGEN Technologies Ovation Pico WTA System, WT Ovation Exon Module, and Biotin Module according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit.

value: B6EiC3SnF1/J (mix of B6 and C3H background)

value: wild-type

value: skeletal muscle

tag: Sex

value: male

value: 5 months


title: 4-C

description: 2hr after glucose ingesion

source_name: Subject 4-2hr

value: circulating leukocytes

value: 2hr after glucose ingesion


title: Muscle from WT, biological rep3

description:
Muscle_DS29
Gene-level analysis.


title: esiOgt_rep1

tag: cell type


title: Muscle from WT, biological rep1

description:
Muscle_DS15
Gene-level analysis.


title: 1-C

description: 2hr after glucose ingesion

source_name: Subject 1-2hr


title: CTRL_esiGFP_rep2

value: control


title: Muscle from DS, biological rep4

description:
Muscle_DS6
Gene-level analysis.

source_name: Soleus muscle, basal state, Ts65Dn


title: 5-C

description: 2hr after glucose ingesion

source_name: Subject 5-2hr


title: Muscle from DS, biological rep3

description:
Muscle_DS28
Gene-level analysis.


title: 4-B

description: 1hr after glucose ingestion

source_name: Subject 4-1hr


title: 4-A

description: baseline

source_name: Subject 4-0hr


title: Muscle from DS, biological rep1

description:
Muscle_DS14
Gene-level analysis.


title: Muscle from WT, biological rep4

description:
Muscle_DS8
Gene-level analysis.


title: Vehicle-117.Lisa.rma-Signal

city: Columbus

first: Lisa

last: Berman-Booty

state: OH

address: 500 West 12th Avenue

department: Division of Medicinal Chemistry

institute: The Ohio State University

description: Gene expression data from the dorsal and lateral lobes of the prostate of 10 week old TRAMP mice treated for 4  weeks with vehicle

hyb_protocol: Samples were hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix) for 16 hours at 45ºC.

scan_protocol: Array scanning was performed according to the standard Affymetrix protocol. An Affymetrix 7000G GeneChip Scanner was used.

data_processing: The data was analyzed using the Bioconductor microarray analysis package (http://bioconductor.org/). Data was normalized using Robust Multiarray Averaging  (RMA) Fold changes and differences in gene expression profiles were considered significant at P < 0.05.

source_name: dorsal and lateral lobes of the prostate of 10 week old TRAMP mice after 4-weeks of daily treatment with vehicle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

extract_protocol: Trizol extraction of total RNA from the dorsal and lateral lobes of the prostate was performed according to the manufacturer's instructions.

treatment_protocol: 6 week old intact male TRAMP mice were treated with either a vehicle or 100 mg/kg/day OSU-CG5 for 4-weeks. At the end of the study, animals were euthanized via carbon dioxide asphyxiation approximately 2-4 hours after their last dose. The urogenital tracts were removed, and the dorsal and lateral lobes of the prostate microdissected in RNAlater (Qiagen), then stored at -80 degrees C.

value: (C57BL/6 TRAMP x FvB) F1


title: 13-C

description: 2hr after glucose ingesion

source_name: Subject 13-2hr


title: CTRL_esiGFP_rep1


title: Vehicle-99.Lisa.rma-Signal

value: dorsal and lateral lobes of the prostate


title: 1-B

description: 1hr after glucose ingestion

source_name: Subject 1-1hr

value: 1hr after glucose ingestion


title: Vehicle-115.Lisa.rma-Signal


title: CG5-100-141.Lisa.rma-Signal

description: Gene expression data from the dorsal and lateral lobes of the prostate of 10 week old TRAMP mice treated for 4  weeks with OSU-CG7

source_name: dorsal and lateral lobes of the prostate of 10 week old TRAMP mice after 4-weeks of daily treatment with OSU-CG5


title: CG5-100-121.Lisa.rma-Signal

description: Gene expression data from the dorsal and lateral lobes of the prostate of 10 week old TRAMP mice treated for 4 weeks with OSU-CG5


title: Meningioma #47 tumor

status: Public on Jan 05 2013

city: Salamanca

first: MariaDolores

last: Tabernero

address: Paseo San Vicente 58-182

country: Spain

institute: Hospital Universitario de Salamanca y Centro del Cáncer

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133A microarray, after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing:
CEL files were analyzed using R and Bioconductor software tools. The Bioconductor packages used for RMA normalization were:
library(limma)
library(affy)
library(hgu133plus2)

source_name: Meningioma tumor

label_protocol: Labeling were performed according to protocols from Affymetrix. Briefly,total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Quiagen, Valencia, CA). The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: gender

value: Female

tag: cytogenetic group

value: del 1p/Loss 1p

tag: who grade

value: I

tag: histology

value: Meningothelial

tag: patientcodeoncologistms

tag: code samplebrainpatholms

value: not included


title: posterior limb bud at E10.5

city: Nashville

first: jiang

last: liu

state: TN

address: 465 21st ave south, MRB3 RM4114

department: cell and dvelopmental biology

institute: vanderbilt university

description: posterior havles of limb buds pooled litter, RMA expression value derived from Expression Console software; core-gene level analysis

hyb_protocol: Targets were hybridized following Nugen Kit specifications to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the Vanderbilt Microarray CORE facility.

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

data_processing:
Raw data was processed with Expression Console for core gene level RMA normalization.  Fold change cutoff of 1.3 was used.
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: wild-type, posterior limb

label_protocol: Samples were amplified using Nugen's WT-Pico kit (Cat#3300) and then the ss cDNA was fragmented and biotinylated using the Nugen FL-Ovation Kit (Cat#4200).

growth_protocol: Mouse limb buds dissected from day 10.5 mouse embryos

extract_protocol: 8 litter of E10.5 embryo limb buds were bisected at the midline in cold PBS. Total RNA was extracted from anterior and posterior halves by Trizol and purified by RNeasy Mini kit (Qiagen, CA).

value: posterior limb

tag: genotype


title: Sample#3 normal meninges

source_name: Normal meninge US Biological

value: Male

tag: age

value: Normal meninge lot nº L5102059

value: Not applicable

value: normal meninge

value: Not included


title: Meningioma #44 tumor

value: Fibroblastic


title: Meningioma #46 tumor

value: Psammomatous


title: Sample#4 normal meninges

value: Normal meninge lot nº A503203


title: CG5-100-123.Lisa.rma-Signal

description: Gene expression data from the dorsal and lateral lobes of the prostate of 10 week old TRAMP mice treated for 4  weeks with OSU-CG6

value: (C57BL/6 TRAMP x FvB) F1


title: anterior limb bud at E10.5

description: anterior halves of limb buds pooled litter, RMA expression value derived from Expression Console software; core-gene level analysis

source_name: wild-type, anterior limb

value: anterior limb

value: wild-type


title: Meningioma #41 tumor

value: Complex karyotype

value: Transitional


title: Meningioma #40 tumor

value: I


title: Meningioma #45 tumor

value: Female

value: del 1p/Loss 1p

value: Meningothelial


title: Meningioma #42 tumor

value: Male

value: II

value: Atypical


title: Muscle from DS, biological rep2

description:
Muscle_DS19
Gene-level analysis.

value: skeletal muscle

value: male

value: 5 months


title: Meningioma #39 tumor

value: III

value: Anaplastic


title: Meningioma #36 tumor


title: Meningioma #43 tumor

value: Not included


title: 1-A

description: baseline

source_name: Subject 1-0hr

value: circulating leukocytes

tag: sampling timepoint

value: before glucose ingestion (baseline)


title: Meningioma #38 tumor

value: Complex karyotype


title: Meningioma #37 tumor


title: Sample#2 normal meninges

source_name: Normal meninge BioChain Institute

value: Normal meninge lot nº A602330

value: Not applicable

value: normal meninge

value: not included


title: Meningioma #34 tumor

value: Female

value: I

value: Meningothelial


title: Meningioma #33 tumor

value: II

value: Atypical


title: Meningioma #31 tumor


title: Meningioma #29 tumor

value: del22q/Monosomy 22

value: Psammomatous


title: Meningioma #35 tumor

value: Male


title: Meningioma #28 tumor

value: Fibroblastic


title: Meningioma #30 tumor


title: Meningioma #25 tumor


title: Meningioma #17 tumor

value: Diploid


title: Meningioma #16 tumor


title: Meningioma #15 tumor


title: Meningioma #14 tumor

value: Transitional


title: Meningioma #32 tumor

value: III

value: Atypical-Papillary


title: Meningioma #24 tumor


title: Meningioma #26 tumor


title: Meningioma #18 tumor

value: Diploid (autosomes) with -Y

value: Not included


title: Meningioma #21 tumor


title: Meningioma #27 tumor


title: Meningioma #23 tumor


title: Meningioma #19 tumor


title: Meningioma #20 tumor


title: Meningioma #22 tumor


title: Meningioma #10 tumor


title: Meningioma #12 tumor


title: Meningioma #6 tumor


title: Meningioma #7 tumor


title: Meningioma #9 tumor


title: Meningioma #8 tumor

value: Secretory


title: Meningioma #2 tumor


title: Meningioma #13 tumor


title: Meningioma #1 tumor


title: Meningioma #11 tumor


title: Meningioma #3 tumor


title: Meningioma #5 tumor


title: Metastatic breast cancer sample 1024

city: Woburn

first: Christos

last: Hatzis

state: MA

address: 400 West Cummings Park, Suite 5350

institute: Nuvera Biosciences

description: Metastatic breast cancer biopsy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

source_name: Metastatic breast cancer sample 1024

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA) or  core biopsy (CBX) prior to any systemic therapy, and to the future assessment of pathologic  response and/or survival endpoints

tag: sample id

tag: sample cohort

tag: percent liver

value: Metastatic breast cancer biopsy


title: Metastatic breast cancer sample ER 50

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 50


title: Metastatic breast cancer sample ER 82

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 82


title: Meningioma #4 tumor

value: Female


title: Metastatic breast cancer sample 1025

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1025


title: Metastatic breast cancer sample ER 37

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 37


title: Metastatic breast cancer sample 1010

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1010


title: Metastatic breast cancer sample ER 113

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 113


title: Metastatic breast cancer sample ER 34

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 34


title: Metastatic breast cancer sample ER 149

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 149


title: Metastatic breast cancer sample 1027

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1027


title: Metastatic breast cancer sample ER 94

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 94


title: Metastatic breast cancer sample 1000

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1000


title: Metastatic breast cancer sample 1006

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1006


title: Metastatic breast cancer sample ER 10

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 10


title: Metastatic breast cancer sample 1004

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 1004


title: Metastatic breast cancer sample ER 101

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample ER 101


title: Metastatic breast cancer sample 993

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 993


title: Metastatic breast cancer sample 992

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 992


title: Metastatic breast cancer sample 991

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 991


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL90-7KT10

description: Liver/breast cancer RNA mixture

value: breast cancer tumor and liver mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL15-7KT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL100-7KT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL20-7KT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL25-7KT75

description: Liver/breast cancer RNA mixture


title: Metastatic breast cancer sample 964

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 964


title: Metastatic breast cancer sample 974

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 974


title: Metastatic breast cancer sample 980

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 980


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL50-7KT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL90-7JT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL10-7KT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL50-7JT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL75-7KT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL25-7JT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL5-7KT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL20-7JT80

description: Liver/breast cancer RNA mixture


title: Metastatic breast cancer sample 984

description: Metastatic breast cancer biopsy

source_name: Metastatic breast cancer sample 984


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL10-7JT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL90-7IT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL100-7IT0

description: Liver/breast cancer RNA mixture


title: Sample#1 normal meninges

source_name: Normal meninge BioChain Institute

value: Normal meninge lot nº A6903225

value: Not applicable

value: normal meninge

value: not included


title: Mixture of RNA from liver and breast cancer (Pair 11) 6WL0-7KT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL100-7JT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL0-7JT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL75-7JT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL5-7JT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL75-7IT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 10) 6VL15-7JT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL50-7IT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL0-7IT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL15-7IT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL10-7IT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL25-7IT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL20-7IT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML100-7HT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML90-7HT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML75-7HT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML25-7HT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL15-5JT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML15-7HT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 9) 6OL5-7IT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL100-5JT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL75-5JT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML50-7HT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML0-7HT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML20-7HT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL25-5JT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML10-7HT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 8) 6ML5-7HT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL50-5JT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL90-5JT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL10-5JT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL20-5JT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL90-MD100C10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL20-MD100C80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL75-MD100C25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL15-MD100C85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL100-MD100C0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL0-5JT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL0-MD100C100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL25-MD100C75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL50-MD100C50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 7) 5JL5-5JT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL100-5AT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL90-5AT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL10-MD100C90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL10-5AT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL75-5AT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL15-5AT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL75-MD99C25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL90-MD99C10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL20-5AT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL100-MD99C0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL25-5AT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 6) 6JL5-MD100C95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL15-MD99C85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL5-5AT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL0-MD99C100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL15-MD94C85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL50-MD99C50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL5-MD99C95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL0-MD94C100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL10-MD99C90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL100-MD94C0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL50-MD94C50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL25-MD99C75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL75-MD94C25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL5-MD94C95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL90-MD94C10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL0-5AT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL90-MD71C10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 4) 6IL20-MD99C80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL100-MD71C0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL75-MD71C25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 5) 5AL50-5AT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL10-MD94C90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL25-MD94C75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL25-MD71C75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL15-MD71C85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL5-MD71C95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL15-4GT85

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL50-MD71C50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL100-4GT0

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL90-4GT10

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL0-4GT100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL10-4GT90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL5-4GT95

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL0-MD71C100

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL25-4GT75

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL20-4GT80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L5C95R3

description: Liver/breast cancer RNA mixture; technical replicate 3


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL20-MD71C80

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L10C90R3


title: Mixture of RNA from liver and breast cancer (Pair 2) 5LL10-MD71C90

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL50-4GT50

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from liver and breast cancer (Pair 1) 4GL75-4GT25

description: Liver/breast cancer RNA mixture


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L15C85R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L75C25R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L0C100R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L25C75R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L70C30R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L85C15R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L50C50R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L90C10R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L5C95R2

description: Liver/breast cancer RNA mixture; technical replicate 2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L100R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L20C80R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L10C90R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L85C15R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L5C95R1

description: Liver/breast cancer RNA mixture; technical replicate 1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L70C30R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L90C10R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L0C100R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L50C50R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L100R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L15C85R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L20C80R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L80C20R3


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L75C25R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L0C100R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L25C75R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L20C80R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L80C20R2


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L15C85R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L25C75R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L50C50R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L10C90R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L70C30R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L80C20R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L100R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L90C10R1


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L75C25R1


title: Mixture of RNA from liver and breast cancer (Pair 3) 6CL20-MD94C80

description: Liver/breast cancer RNA mixture


title: Liver ANON5I-L

description: Liver biopsy

source_name: Liver ANON5I-L

value: Liver biopsy


title: Liver ANON5K-L

description: Liver biopsy

source_name: Liver ANON5K-L


title: Liver ANON5Z-L

description: Liver biopsy

source_name: Liver ANON5Z-L


title: Mixture of RNA from first pair of liver and breast cancer samples (Pair 0) L85C15R1


title: Liver ANON3J-L

description: Liver biopsy

source_name: Liver ANON3J-L


title: Liver ANON5H-L

description: Liver biopsy

source_name: Liver ANON5H-L


title: Liver ANON4M-L

description: Liver biopsy

source_name: Liver ANON4M-L


title: Liver ANON2V-L

description: Liver biopsy

source_name: Liver ANON2V-L


title: Liver ANONS-L

description: Liver biopsy

source_name: Liver ANONS-L


title: Liver ANON5C-L

description: Liver biopsy

source_name: Liver ANON5C-L


title: Liver ANON4I-L

description: Liver biopsy

source_name: Liver ANON4I-L


title: Liver ANON2L-L

description: Liver biopsy

source_name: Liver ANON2L-L


title: Liver ANON4N-L

description: Liver biopsy

source_name: Liver ANON4N-L


title: Liver ANON4Q-L

description: Liver biopsy

source_name: Liver ANON4Q-L


title: Liver ANONT-L

description: Liver biopsy

source_name: Liver ANONT-L


title: Liver ANON4V-L

description: Liver biopsy

source_name: Liver ANON4V-L


title: Liver ANON3P-L

description: Liver biopsy

source_name: Liver ANON3P-L


title: Liver ANON4X-L

description: Liver biopsy

source_name: Liver ANON4X-L


title: Liver ANON3F-L

description: Liver biopsy

source_name: Liver ANON3F-L


title: Liver ANON3X-L

description: Liver biopsy

source_name: Liver ANON3X-L


title: Liver ANON4Y-L

description: Liver biopsy

source_name: Liver ANON4Y-L


title: Liver ANON4P-L

description: Liver biopsy

source_name: Liver ANON4P-L


title: Liver ANON3G-L

description: Liver biopsy

source_name: Liver ANON3G-L


title: Liver ANON2Z-L

description: Liver biopsy

source_name: Liver ANON2Z-L


title: Liver ANON2U-L

description: Liver biopsy

source_name: Liver ANON2U-L


title: Liver ANON2W-L

description: Liver biopsy

source_name: Liver ANON2W-L


title: Liver ANON2R-L

description: Liver biopsy

source_name: Liver ANON2R-L


title: Liver ANON2S-L

description: Liver biopsy

source_name: Liver ANON2S-L


title: Liver ANON2T-L

description: Liver biopsy

source_name: Liver ANON2T-L


title: Liver ANON2K-L

description: Liver biopsy

source_name: Liver ANON2K-L


title: Liver ANONQ-L

description: Liver biopsy

source_name: Liver ANONQ-L