title: genomic DNA from blood 9611518097_R04C02

status: Public on Aug 19 2015

first: Carolina

last: Soriano-Tarraga

address: Calle Doctor Aiguader 88

department: Department of Neurology

institute: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM).Hospital del Mar

description: stroke blood sample

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: GenomeStudio 2011.1 software and R version 3.1.2. Processed data: raw Average Beta obtained from GenomeStudio, quality controls were done by MINFI Bioconductor package and probe type correction by SWAN bioconductor package.  Raw data: Unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: blood

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA samples were extracted from whole peripheral blood collected in 10 mL EDTA tubes. The Chemagic Magnetic Separation Module I system (Chemagen)

treatment_protocol: no treatment

tag: stroke subtype

value: cardio emobolic

value: blood

tag: disease state

value: stroke


title: genomic DNA from blood 9611518097_R03C02

type: genomic

city: Barcelona

state: Barcelona

country: Spain

description: stroke blood sample

molecule: genomic DNA

organism: Homo sapiens

tag: gender

value: Female

tag: sample type


title: U3005

status: Public on Aug 20 2015

city: Uppsala

first: Sven

last: Nelander

address: Rudbecklab

country: Sweden

institute: Uppsala Universitet

hyb_protocol: standard protocols for Affymetrix Cytoscan™ HD arrays (Affymetrix® Cytoscan User Guide (P/N 703038 Rev4.) Hybridized probes were captured by streptavidin-phycoerythrin conjugates using the GeneChip® Fluidics Station 450.

scan_protocol: scanned using the GeneChip® Scanner 3000 7G

data_processing: Data processing of CEL files was performed using Rawcopy software

label: biotin

label_protocol: 250 ng total genomic DNA was digested with the restriction enzyme Nsp I, then ligated to an Nsp I adaptor and further subjected to PCR amplification using a single primer. After fragmentation, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase (TdT)

growth_protocol: adherent cultures on laminin-coated dishes using neural stem cell media

extract_protocol: Dneasy blood and tissue kit (Qiagen)

treatment_protocol: not applicable

tag: cell line


title: genomic DNA from blood 9611518097_R02C01

description: stroke blood sample

value: Male

value: Large-artery atherosclerosis


title: genomic DNA from blood 9611518097_R03C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R06C01

description: stroke blood sample

value: lacunar


title: genomic DNA from blood 9611518097_R05C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R05C02

description: stroke blood sample


title: genomic DNA from blood 9611518097_R01C01

description: stroke blood sample


title: U3004


title: genomic DNA from blood 9611518097_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518063_R03C02

description: stroke blood sample


title: genomic DNA from blood 9611518063_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518097_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518063_R05C01

description: stroke blood sample


title: genomic DNA from blood 9611518097_R02C02

description: stroke blood sample


title: genomic DNA from blood 9611518063_R04C02

description: stroke blood sample


title: genomic DNA from blood 9611518097_R04C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R03C01

description: stroke blood sample


title: U3002


title: genomic DNA from blood 9611518097_R06C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R04C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R02C01

description: stroke blood sample


title: genomic DNA from blood 9611518097_R05C02

description: stroke blood sample


title: genomic DNA from blood 9611518063_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518062_R04C02

description: stroke blood sample


title: genomic DNA from blood 9611518062_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518062_R02C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R02C02

description: stroke blood sample


title: genomic DNA from blood 9611518062_R05C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R06C01

description: stroke blood sample


title: genomic DNA from blood 9611518063_R01C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R04C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R01C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R06C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R04C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R05C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R04C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R02C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R01C01

description: stroke blood sample


title: genomic DNA from blood 9611518062_R03C01

description: stroke blood sample


title: genomic DNA from blood 9611518007_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R02C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R05C01

description: stroke blood sample


title: genomic DNA from blood 9611518007_R06C01

description: stroke blood sample


title: genomic DNA from blood 9611518007_R03C02

description: stroke blood sample


title: genomic DNA from blood 9611518062_R03C02

description: stroke blood sample


title: genomic DNA from blood 9611518007_R03C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R03C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R02C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R05C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518003_R01C01

description: stroke blood sample


title: genomic DNA from blood 9611518003_R04C02

description: stroke blood sample


title: genomic DNA from blood 9611518003_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518003_R03C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R06C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R05C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R02C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R03C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R04C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R05C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R02C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R02C01

description: stroke blood sample


title: genomic DNA from blood 9611518002_R02C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R03C01

description: stroke blood sample


title: genomic DNA from blood 9611518002_R04C01

description: stroke blood sample


title: genomic DNA from blood 9611518002_R04C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R05C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R06C02

description: stroke blood sample


title: genomic DNA from blood 9403904115_R04C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R01C01

description: stroke blood sample


title: genomic DNA from blood 9611518002_R01C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R06C01

description: stroke blood sample


title: genomic DNA from blood 9610361002_R04C02

description: stroke blood sample


title: genomic DNA from blood 9610361002_R02C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R05C01

description: stroke blood sample


title: genomic DNA from blood 9611518002_R03C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R03C01

description: stroke blood sample


title: genomic DNA from blood 9610361002_R04C01

description: stroke blood sample


title: genomic DNA from blood 9403904115_R01C02

description: stroke blood sample


title: genomic DNA from blood 9610361002_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104045_R06C02

description: stroke blood sample


title: genomic DNA from blood 9611518002_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104045_R04C02

description: stroke blood sample


title: genomic DNA from blood 9534104044_R05C02

description: stroke blood sample


title: genomic DNA from blood 9534104045_R01C02

description: stroke blood sample


title: genomic DNA from blood 9534104044_R02C02

description: stroke blood sample


title: genomic DNA from blood 9534104045_R03C02

description: stroke blood sample


title: genomic DNA from blood 9534104045_R03C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R04C02

description: stroke blood sample


title: genomic DNA from blood 9534104045_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R06C02

description: stroke blood sample


title: genomic DNA from blood 9534104045_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R03C02

description: stroke blood sample


title: genomic DNA from blood 9534104043_R05C02

description: stroke blood sample


title: genomic DNA from blood 9534104044_R03C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R06C02

description: stroke blood sample


title: genomic DNA from blood 9534104044_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R04C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R05C01

description: stroke blood sample


title: genomic DNA from blood 9534104045_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104044_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R01C02

description: stroke blood sample


title: genomic DNA from blood 9534104043_R03C02

description: stroke blood sample


title: genomic DNA from blood 9534104043_R05C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R03C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R04C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R02C02

description: stroke blood sample


title: genomic DNA from blood 9534104043_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R04C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R04C02

description: stroke blood sample


title: genomic DNA from blood 9534104003_R01C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R05C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R06C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R01C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104004_R03C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R06C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R04C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R05C01

description: stroke blood sample


title: genomic DNA from blood 9534104004_R05C01

description: stroke blood sample


title: genomic DNA from blood 9534104003_R05C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104043_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R04C02

description: stroke blood sample


title: genomic DNA from blood 9534104001_R03C02

description: stroke blood sample


title: genomic DNA from blood 9534104001_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R01C02

description: stroke blood sample


title: genomic DNA from blood 9534104001_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R06C02

description: stroke blood sample


title: genomic DNA from blood 9534104003_R02C02

description: stroke blood sample


title: genomic DNA from blood 9534104004_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R02C01

description: stroke blood sample


title: genomic DNA from blood 9534104004_R03C02

description: stroke blood sample


title: genomic DNA from blood 9534104001_R02C02

description: stroke blood sample


title: genomic DNA from blood 9534104001_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774108_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R06C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774108_R05C01

description: stroke blood sample


title: genomic DNA from blood 9534104003_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774099_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774108_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774108_R01C01

description: stroke blood sample


title: genomic DNA from blood 9534104001_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774099_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774099_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774098_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774098_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774099_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774098_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774108_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774096_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774096_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774089_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774096_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774089_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774099_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774098_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774089_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774089_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774087_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774089_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774087_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774087_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774089_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774087_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774085_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R06C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774085_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774085_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774085_R02C02

description: stroke blood sample


title: genomic DNA from blood 9533774085_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774085_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774086_R03C02

description: stroke blood sample


title: genomic DNA from blood 9533774086_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774085_R01C02

description: stroke blood sample


title: genomic DNA from blood 9533774087_R05C02

description: stroke blood sample


title: genomic DNA from blood 9533774085_R05C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R02C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R04C02

description: stroke blood sample


title: minKGFP_low_rep4

type: RNA

city: Chicago

first: David

last: Arnolds

state: IL

address: 920 E 57th St

department: Pediatrics

country: USA

institute: University of Chicago

hyb_protocol: 3.26 ug of AlexaFluor-3 labeled sample in a volume of 24 uL was added to 6 uL of 10x blocking agent (Agilent) and 30 uL of 2x hybridization buffer (Agilent) for a final volume of 60 uL.  55 uL was added to a Tecan HS 4800 Pro chamber and hybridized to Agilent G4122F mouse whole genome microarrays using a standard 17 hour 65C gene expression hybridization.

scan_protocol: Slides were scanned after washing on the Agilent Technologies Scanner G2505C using one color settings for 4 x 44k arrays at a resolution of 5 microns per pixel.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid 014868_D_F_20090416).

molecule: total RNA

organism: Mus musculus

source_name: E10.5 minKGFP low chamber mycocardium

label_protocol: 5 ng of total RNA from each sample was amplified with the NuGen WT Ovation Pico kit according to the manufacturer's instructions.  2 ug of amplified product was subsequently labeled with AlexaFluor-3 using the BioPrime Total Labeling Kit (Invitrogen) according to the manufacturer's instructions.

growth_protocol: Hearts from E10.5 minKGFP transgenic embryos were isolated and digested to single cells with pancreatin and collagenase.  Cells were FACS sorted into minKGFP high and minKGFP low groups on the basis of fluoresence intensity.

extract_protocol: Cells were sorted directly into Trizol LS (Invitrogen), and RNA was extracted according to the manufacturer's instructions.

tag: transgenic line

value: minKGFP

tag: Stage


title: genomic DNA from blood 9533774085_R01C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R06C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R03C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R02C02

description: stroke blood sample


title: minKGFP_high_rep4

source_name: E10.5 minKGFP high conduction system cells


title: genomic DNA from blood 9533774087_R04C02

description: stroke blood sample


title: genomic DNA from blood 9533774070_R05C02

description: stroke blood sample


title: minKGFP_low_rep3


title: genomic DNA from blood 9422492042_R03C01

description: stroke blood sample


title: minKGFP_high_rep3


title: minKGFP_high_rep2


title: minKGFP_low_rep2


title: minKGFP_high_rep1


title: genomic DNA from blood 9533774070_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774070_R01C02

description: stroke blood sample


title: genomic DNA from blood 9513149117_R02C01

description: stroke blood sample


title: genomic DNA from blood 9513149117_R01C01

description: stroke blood sample


title: minKGFP_low_rep1


title: genomic DNA from blood 9513149117_R01C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R06C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R06C01

description: stroke blood sample


title: Patient 12 - Lesional skin-1

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

country: France

institute: GALDERMA R & D

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with GEA model: The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data.  Mansourian R1, Mutch DM, Antille N, Aubert J, Fogel P, Le Goff JM, Moulin J, Petrov A, Rytz A, Voegel JJ, Roberts MA.(2004) Bioinformatics Oxford Journals

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

extract_protocol: RNeasy (Qiagen) RNA extraction was performed according to the manufacturer's instructions.

tag: tissue

value: face biopsy

tag: cell type

value: melasma


title: Patient 12 - Lesional skin-2


title: genomic DNA from blood 9422492042_R05C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R02C02

description: stroke blood sample


title: Patient 12 - Non lesional skin-2

value: normal


title: genomic DNA from blood 9422492042_R03C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R04C01

description: stroke blood sample


title: Patient 12 - Non lesional skin-1


title: genomic DNA from blood 9422492042_R04C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R05C01

description: stroke blood sample


title: genomic DNA from blood 9422492042_R02C01

description: stroke blood sample


title: genomic DNA from blood 9513149117_R03C02

description: stroke blood sample


title: genomic DNA from blood 9422491083_R06C02

description: stroke blood sample


title: Patient 11 - Lesional skin-1


title: Patient 11 - Lesional skin-2


title: genomic DNA from blood 9422491083_R06C01

description: stroke blood sample


title: genomic DNA from blood 9422491083_R05C02

description: stroke blood sample


title: Patient 11 - Non lesional skin-2


title: Patient 11 - Non lesional skin-1


title: genomic DNA from blood 9422491083_R04C02

description: stroke blood sample


title: Patient 10 - Lesional skin-2


title: genomic DNA from blood 9422491083_R04C01

description: stroke blood sample


title: genomic DNA from blood 9533774085_R04C01

description: stroke blood sample


title: genomic DNA from blood 9422491083_R05C01

description: stroke blood sample


title: genomic DNA from blood 9422492042_R01C01

description: stroke blood sample


title: Patient 10 - Lesional skin-1


title: Patient 10 - Non lesional skin-2


title: genomic DNA from blood 9422491059_R06C01

description: stroke blood sample


title: genomic DNA from blood 9422491083_R03C02

description: stroke blood sample


title: genomic DNA from blood 9422492042_R01C02

description: stroke blood sample


title: Patient 9 - Lesional skin-2


title: genomic DNA from blood 9422491083_R02C01

description: stroke blood sample


title: Patient 9 - Lesional skin-1


title: genomic DNA from blood 9422491083_R01C02

description: stroke blood sample


title: genomic DNA from blood 9422491083_R02C02

description: stroke blood sample


title: Patient 10 - Non lesional skin-1


title: genomic DNA from blood 9422491083_R01C01

description: stroke blood sample


title: Patient 9 - Non lesional skin-2


title: genomic DNA from blood 9422491083_R03C01

description: stroke blood sample


title: genomic DNA from blood 9422491059_R04C02

description: stroke blood sample


title: Patient 7 - Lesional skin-2

description: Patient 7 rejected; no normalized data


title: Patient 8 - Lesional skin-1


title: genomic DNA from blood 9422491059_R04C01

description: stroke blood sample


title: genomic DNA from blood 9422491059_R05C01

description: stroke blood sample


title: genomic DNA from blood 9422491059_R03C01

description: stroke blood sample


title: Patient 9 - Non lesional skin-1


title: Patient 8 - Non lesional skin-1


title: genomic DNA from blood 9422491059_R01C02

description: stroke blood sample


title: Patient 8 - Non lesional skin-2


title: genomic DNA from blood 9422491059_R02C02

description: stroke blood sample


title: genomic DNA from blood 9422491058_R05C02

description: stroke blood sample


title: genomic DNA from blood 9422491058_R05C01

description: stroke blood sample


title: genomic DNA from blood 9422491059_R05C02

description: stroke blood sample


title: Patient 7 - Lesional skin-1

description: Patient 7 rejected; no normalized data


title: genomic DNA from blood 9422491058_R06C02

description: stroke blood sample


title: Patient 8 - Lesional skin-2


title: Patient 6 - Lesional skin-2


title: Patient 7 - Non lesional skin-2

description: Patient 7 rejected; no normalized data


title: genomic DNA from blood 9533774085_R03C01

description: stroke blood sample


title: Patient 6 - Lesional skin-1


title: genomic DNA from blood 9422491058_R04C01

description: stroke blood sample


title: Patient 6 - Non lesional skin-2


title: genomic DNA from blood 9422491058_R06C01

description: stroke blood sample


title: Patient 6 - Non lesional skin-1


title: genomic DNA from blood 9422491058_R02C01

description: stroke blood sample


title: genomic DNA from blood 9422491058_R03C02

description: stroke blood sample


title: genomic DNA from blood 9422491058_R01C01

description: stroke blood sample


title: genomic DNA from blood 9422491042_R06C02

description: stroke blood sample


title: Patient 7 - Non lesional skin-1

description: Patient 7 rejected; no normalized data


title: genomic DNA from blood 9422491042_R06C01

description: stroke blood sample


title: genomic DNA from blood 9422491058_R02C02

description: stroke blood sample


title: Patient 5 - Lesional skin-1


title: Patient 5 - Non lesional skin-2


title: Patient 5 - Lesional skin-2


title: genomic DNA from blood 9422491058_R01C02

description: stroke blood sample


title: Patient 5 - Non lesional skin-1


title: genomic DNA from blood 9422491042_R05C01

description: stroke blood sample


title: DEN-NA TA G0

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

institute: INSERM

description: SAMPLE 82

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with GenomeStudio Illumina Software.

label: Biotin

source_name: human adipose tissue, 0 days

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: subcutaneous adipose tissue

tag: treatment

tag: time point

value: 0 days

tag: subject id

value: DEN-NA


title: genomic DNA from blood 9422491042_R04C02

description: stroke blood sample


title: Patient 4 - Lesional skin-2


title: DEN-NA TA 1A

description: SAMPLE 81

source_name: human adipose tissue, 1 year

value: bariatric surgery

value: 1 year


title: Patient 4 - Lesional skin-1


title: ANT-LA TA G0

description: SAMPLE 84

value: ANT-LA


title: genomic DNA from blood 9422491042_R04C01

description: stroke blood sample


title: ANT-LA TA 1A

description: SAMPLE 83


title: genomic DNA from blood 9422491042_R05C02

description: stroke blood sample


title: BER-MA TA G0

description: SAMPLE 80

value: BER-MA


title: Patient 4 - Non lesional skin-2


title: Patient 4 - Non lesional skin-1


title: BER-MA TA 1A

description: SAMPLE 79


title: OUZ-CO G0

description: SAMPLE 78

value: OUZ-CO


title: genomic DNA from blood 9422491042_R03C01

description: stroke blood sample

value: blood

value: stroke


title: genomic DNA from blood 9422491042_R03C02

description: stroke blood sample

value: Male

value: cardio emobolic


title: genomic DNA from blood 9422491058_R03C01

description: stroke blood sample

value: Female


title: Patient 3 - Lesional skin-1


title: genomic DNA from blood 9422491042_R02C02

description: stroke blood sample


title: OUZ-CO G1A

description: SAMPLE 77


title: Patient 3 - Non lesional skin-1


title: Patient 3 - Non lesional skin-2


title: genomic DNA from blood 9422491042_R01C02

description: stroke blood sample


title: Patient 3 - Lesional skin-2


title: Patient 2 - Lesional skin-2


title: genomic DNA from blood 9422491019_R06C01

description: stroke blood sample

value: lacunar


title: RAB-JE G0

description: SAMPLE 76

value: RAB-JE


title: SAU-FL G0

description: SAMPLE 74

value: SAU-FL


title: SAU-FL G1A

description: SAMPLE 73


title: Patient 2 - Non lesional skin-2

value: face biopsy

value: normal


title: Patient 2 - Lesional skin-1

value: melasma


title: RAB-JE G1A

description: SAMPLE 75

value: subcutaneous adipose tissue


title: BAL-MA G0

description: SAMPLE 71

value: 0 days

value: BAL-MA


title: BAL-MA G1A

description: SAMPLE 72

value: bariatric surgery

value: 1 year


title: genomic DNA from blood 9422491042_R01C01

description: stroke blood sample


title: genomic DNA from blood 9422491019_R05C01

description: stroke blood sample


title: Patient 2 - Non lesional skin-1


title: Patient 1 - Lesional skin-1


title: LAR-JU G0

description: SAMPLE 69

value: LAR-JU


title: genomic DNA from blood 9422491042_R02C01

description: stroke blood sample

value: blood


title: BAG-MU G1A

description: SAMPLE 68

value: BAG-MU


title: Patient 1 - Lesional skin-2


title: Patient 1 - Non lesional skin-2


title: Patient 1 - Non lesional skin-1


title: genomic DNA from blood 9422491019_R03C01

description: stroke blood sample

value: Large-artery atherosclerosis

value: stroke


title: BAG-MU G0

description: SAMPLE 67


title: genomic DNA from blood 9422491019_R03C02

description: stroke blood sample

value: Male

value: cardio emobolic


title: genomic DNA from blood 9422491019_R04C01

description: stroke blood sample

value: Female


title: LAR-JU G1A

description: SAMPLE 70


title: genomic DNA from blood 9422491019_R06C02

description: stroke blood sample

value: lacunar


title: genomic DNA from blood 9422491019_R04C02

description: stroke blood sample


title: MAR-SA 40226 G0

description: SAMPLE 65


title: genomic DNA from blood 9422491019_R02C02

description: stroke blood sample


title: genomic DNA from blood 9422491019_R02C01

description: stroke blood sample


title: genomic DNA from blood 9422491058_R04C02

description: stroke blood sample


title: OPA-TA TA G0

description: SAMPLE 63

value: OPA-TA


title: genomic DNA from blood 9422491012_R06C02

description: stroke blood sample


title: PAP-EU TA 1A

description: SAMPLE 61

value: PAP-EU


title: PAP-EU TA G0

description: SAMPLE 62


title: HER-FA G1A

description: SAMPLE 59

value: HER-FA


title: genomic DNA from blood 9422491012_R05C01

description: stroke blood sample


title: OPA-TA TA 1A

description: SAMPLE 64

value: subcutaneous adipose tissue


title: HER-FA G0

description: SAMPLE 60

value: 0 days


title: FUL-RO G0

description: SAMPLE 58

value: FUL-RO


title: FUL-RO G1A

description: SAMPLE 57

value: bariatric surgery


title: genomic DNA from blood 9422491019_R01C02

description: stroke blood sample


title: PIG-AN G0

description: SAMPLE 56

value: PIG-AN


title: genomic DNA from blood 9422491019_R01C01

description: stroke blood sample


title: KAP-EV G0

description: SAMPLE 54

value: KAP-EV


title: genomic DNA from blood 9422491012_R05C02

description: stroke blood sample

value: blood


title: KAP-EV G1A

description: SAMPLE 53

value: 1 year


title: ALL-GH G1A

description: SAMPLE 51

value: ALL-GH


title: CHA-CA G1A

description: SAMPLE 50

value: CHA-CA


title: CHA-CA G0

description: SAMPLE 49


title: PIG-AN G1A

description: SAMPLE 55


title: genomic DNA from blood 9422491012_R04C01

description: stroke blood sample

value: Male

value: stroke


title: genomic DNA from blood 9403904130_R06C02

description: stroke blood sample

value: Large-artery atherosclerosis


title: genomic DNA from blood 9422491012_R01C02

description: stroke blood sample


title: ALL-GH G0

description: SAMPLE 52


title: genomic DNA from blood 9422491012_R06C01

description: stroke blood sample

value: lacunar


title: genomic DNA from blood 9422491012_R02C01

description: stroke blood sample

value: cardio emobolic


title: CHA-VE G1A

description: SAMPLE 48

value: CHA-VE


title: genomic DNA from blood 9422491012_R02C02

description: stroke blood sample


title: genomic DNA from blood 9403904130_R04C01

description: stroke blood sample

value: Female


title: CHA-VE G0

description: SAMPLE 47

value: subcutaneous adipose tissue


title: MAR-SA 40124 G0

description: SAMPLE 45

value: 0 days


title: MAR-SA 40124 G1A

description: SAMPLE 46


title: genomic DNA from blood 9403904130_R03C02

description: stroke blood sample


title: genomic DNA from blood 9422491012_R01C01

description: stroke blood sample


title: genomic DNA from blood 9422491012_R03C01

description: stroke blood sample


title: SI.66.r2

type: mixed

city: León

first: Alma

middle: María

last: Botas

state: León

address: Campus de Vegazana

institute: Área de Microbiología. Facultad de Ciencias Biológicas y Ambientales. Universidad de León

description: S. coelicolorM145_66hours_Replicate2

hyb_protocol: Hybridization mixes (100 µl) were applied to the microarray surface following the manufacturer’s instructions, and hybridized at 55°C for 67 hours. The slide was washed in 50 ml of Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature and then in 50 ml of Wash Buffer 2 preheated to 37°C for 1 min, both with horizontal agitation (85 rpm). The slide was then briefly immersed in the Agilent Stabilization and Drying Solution prior to measuring fluorescence

scan_protocol: Fluorescence was measured with an Agilent DNA Microarray Scanner G2565BA using the extended dynamic mode.

data_processing:
Quantification of fluorescence intensities was performed using the FeatureExtraction software (v9.5.1, Agilent). Fluorescence intensities were processed and normalized using the limma package in the R environment (R Core Team, 2012). For each spot on the microarray, net fluorescence intensities were calculated subtracting the median of background pixels values from the mean of foreground pixels. When the intensity value was negative or lower than the background standard deviation, the standard deviation of the background pixels was used as the surrogate intensity, while S. coelicolor genomic DNA labeled with Cy5 was used as the common reference. Quality weights were estimated for the non-control spots (43 798) of each array. These weights were used for the normalization and linear models statistics.
For each gene, the normalized Mg values were calculated as the average among 3 biological replicates of the binary logarithms of the Cy3-cDNA signal divided by the Cy5-gDNA signal. Probe values were previously averaged if more than one probe for a gene were present (mean of 4.6 probes per gene in the arrays). For each culture time, comparisons between the Mg values of the mutant and the parental strain were the base of the statistical results.

organism: Streptomyces coelicolor

source_name: S. coelicolor M145 total RNA, 66 hours

label_protocol: Genomic DNA from S. coelicolor M145, used as the common reference, was labeled with Cy5-dCTP (GE Healthcare Life Sciences) using the BioPrime Array CGH Genomic Labeling Module (Invitrogen) and purified with the MinElute kit. RNA was labeled with Cy3. Labeling efficiencies were quantified with a NanoDrop ND-1000 spectrophotometer. Mixtures of Cy3-cDNA (825 ng)/Cy5-gDNA (20 pmol of Cy5) were prepared in 110 µl of hybridization buffer (1 M NaCl, 100 mM MES, pH 6.5, 20% formamide, 20 mM EDTA, 1% Triton X-100).

growth_protocol: S. coelicolor cultures were inoculated using 108 spores in 100 ml defined MG medium with 2.5 mM phosphate.The cultures were grown in tripplicated 500 ml baffled flasks containing 100 ml of medium at 30ºC and 300 rpm. Samples from 3 biological replicates were taken at 32, 42, 49, 56 and 66 hours.

extract_protocol: Total RNA was obtained combining lysozyme digestion and mechanical disruption in FastPrep (MP Biomedical) with glass beads, prior to phenol extraction and purification with the RNeasy Mini Kit (Qiagen).

tag: strain

value: Streptomyces coelicolor M145

tag: phenotype

value: Wild type

source_name: S. coelicolor M145 total DNA (common reference)


title: VEB-AU TA 1A

description: SAMPLE 44

value: bariatric surgery

value: VEB-AU


title: VEB-AU TA G0

description: SAMPLE 43


title: genomic DNA from blood 9403904130_R05C02

description: stroke blood sample

value: blood


title: genomic DNA from blood 9403904130_R02C01

description: stroke blood sample


title: SI.66.r3

description: S. coelicolorM145_66hours_Replicate3


title: genomic DNA from blood 9403904130_R02C02

description: stroke blood sample


title: genomic DNA from blood 9403904130_R05C01

description: stroke blood sample


title: BOS CH TA 1A

description: SAMPLE 41

value: 1 year

value: BOS


title: SI.66.r1

description: S. coelicolorM145_66hours_Replicate1


title: BOS CA TA G0

description: SAMPLE 42


title: MAR-SA 40226 G1A

description: SAMPLE 66


title: genomic DNA from blood 9403904130_R03C01

description: stroke blood sample


title: SI.56.r3

description: S. coelicolorM145_56hours_Replicate3

source_name: S. coelicolor M145 total RNA, 56 hours


title: FLE-NA TA G0

description: SAMPLE 40

value: FLE-NA


title: genomic DNA from blood 9403904130_R01C01

description: stroke blood sample


title: genomic DNA from blood 9403904085_R06C02

description: stroke blood sample

value: Male


title: SI.56.r1

description: S. coelicolorM145_56hours_Replicate1


title: SI.49.r3

description: S. coelicolorM145_49hours_Replicate3

source_name: S. coelicolor M145 total RNA, 49 hours


title: FLE-NA TA 1A

description: SAMPLE 39


title: genomic DNA from blood 9403904085_R05C02

description: stroke blood sample

value: stroke


title: genomic DNA from blood 9403904085_R06C01

description: stroke blood sample


title: genomic DNA from blood 9403904130_R06C01

description: stroke blood sample

value: Large-artery atherosclerosis


title: genomic DNA from blood 9422491012_R03C02

description: stroke blood sample


title: genomic DNA from blood 9403904085_R03C02

description: stroke blood sample


title: genomic DNA from blood 9403904085_R05C01

description: stroke blood sample

value: lacunar


title: HUE-MI TA 1A

description: SAMPLE 35

value: HUE-MI


title: HOF-NA G1A

description: SAMPLE 37

value: HOF-NA


title: HOF-NA G0

description: SAMPLE 38


title: TEI-MA TA 1A

description: SAMPLE 34

value: TEI-MA


title: genomic DNA from blood 9403904085_R04C01

description: stroke blood sample

value: cardio emobolic


title: genomic DNA from blood 9403904085_R02C02

description: stroke blood sample


title: genomic DNA from blood 9403904085_R03C01

description: stroke blood sample

value: Female


title: SI.42.r2

description: S. coelicolorM145_42hours_Replicate2

source_name: S. coelicolor M145 total RNA, 42 hours

value: Streptomyces coelicolor M145


title: TEI-MA TA G0

description: SAMPLE 33

value: subcutaneous adipose tissue

value: 0 days


title: HUE-MI TA G0

description: SAMPLE 36


title: genomic DNA from blood 9403904085_R02C01

description: stroke blood sample


title: SI.42.r1

description: S. coelicolorM145_42hours_Replicate1

value: Wild type


title: DEA-SI G0

description: SAMPLE 31

value: DEA-SI


title: SI.56.r2

description: S. coelicolorM145_56hours_Replicate2


title: SI.32.r3

description: S. coelicolorM145_32hours_Replicate3

source_name: S. coelicolor M145 total RNA, 32 hours


title: DEA-SI G1A

description: SAMPLE 32

value: bariatric surgery

value: 1 year


title: SI.49.r1

description: S. coelicolorM145_49hours_Replicate1


title: THI-ND G0

description: SAMPLE 29

value: THI-ND


title: THI-ND G1A

description: SAMPLE 30


title: SI.32.r2

description: S. coelicolorM145_32hours_Replicate2


title: genomic DNA from blood 9403904094_R06C02

description: stroke blood sample

value: Male

value: blood


title: MU.66.r3

description: S. coelicolor∆argR_66hours_Replicate3

source_name: S. coelicolor ∆argR total RNA, 66 hours

value: Streptomyces coelicolor ∆argR

value: Mutant without argR gene


title: SI.32.r1

description: S. coelicolorM145_32hours_Replicate1


title: SI.42.r3

description: S. coelicolorM145_42hours_Replicate3


title: FAG-GA G1A

description: SAMPLE 28

value: FAG-GA


title: FAG-GA G0

description: SAMPLE 27


title: SI.49.r2

description: S. coelicolorM145_49hours_Replicate2


title: genomic DNA from blood 9403904094_R05C02

description: stroke blood sample

value: lacunar

value: stroke


title: genomic DNA from blood 9403904085_R04C02

description: stroke blood sample

value: cardio emobolic


title: MU.66.r2

description: S. coelicolor∆argR_66hours_Replicate2


title: genomic DNA from blood 9403904130_R01C02

description: stroke blood sample

value: Female

value: Large-artery atherosclerosis


title: genomic DNA from blood 9403904085_R01C01

description: stroke blood sample


title: MU.56.r3

description: S. coelicolor∆argR_56hours_Replicate3

source_name: S. coelicolor ∆argR total RNA, 56 hours

value: Streptomyces coelicolor M145


title: genomic DNA from blood 9403904085_R01C02

description: stroke blood sample


title: genomic DNA from blood 9403904094_R05C01

description: stroke blood sample


title: LAR-MA TA 1A

description: SAMPLE 24

value: subcutaneous adipose tissue

value: LAR-MA


title: MON-CA G1A

description: SAMPLE 26

value: MON-CA


title: MON-CA G0

description: SAMPLE 25

value: 0 days


title: MU.66.r1

description: S. coelicolor∆argR_66hours_Replicate1

value: Wild type


title: genomic DNA from blood 9403904094_R04C02

description: stroke blood sample


title: MU.56.r1

description: S. coelicolor∆argR_56hours_Replicate1


title: MU.56.r2

description: S. coelicolor∆argR_56hours_Replicate2


title: LAR-MA TA G0

description: SAMPLE 23


title: genomic DNA from blood 9403904094_R02C02

description: stroke blood sample


title: genomic DNA from blood 9403904094_R03C02

description: stroke blood sample


title: genomic DNA from blood 9403904094_R06C01

description: stroke blood sample


title: PIQ EL TA 1A

description: SAMPLE 21

value: bariatric surgery

value: 1 year

value: PIQ


title: PIQ EL TA G0

description: SAMPLE 22


title: MU.49.r2

description: S. coelicolor∆argR_49hours_Replicate2

source_name: S. coelicolor ∆argR total RNA, 49 hours

value: Streptomyces coelicolor ∆argR


title: MU.49.r3

description: S. coelicolor∆argR_49hours_Replicate3

value: Mutant without argR gene


title: genomic DNA from blood 9403904094_R03C01

description: stroke blood sample

value: blood


title: MU.49.r1

description: S. coelicolor∆argR_49hours_Replicate1


title: POU-VI TA G0

description: SAMPLE 20

value: POU-VI


title: genomic DNA from blood 9403904094_R02C01

description: stroke blood sample

value: Male

value: lacunar

value: stroke


title: genomic DNA from blood 9403904094_R01C01

description: stroke blood sample

value: Large-artery atherosclerosis


title: MU.42.r3

description: S. coelicolor∆argR_42hours_Replicate3

source_name: S. coelicolor ∆argR total RNA, 42 hours

value: Streptomyces coelicolor M145


title: MER-AR G0

description: SAMPLE 18

value: subcutaneous adipose tissue

value: MER-AR


title: genomic DNA from blood 9403904087_R06C01

description: stroke blood sample


title: MU.42.r1

description: S. coelicolor∆argR_42hours_Replicate1


title: POU-VI TA 1A

description: SAMPLE 19


title: MU.42.r2

description: S. coelicolor∆argR_42hours_Replicate2


title: MU.32.r3

description: S. coelicolor∆argR_32hours_Replicate3

source_name: S. coelicolor ∆argR total RNA, 32 hours


title: DEL-CH G0

description: SAMPLE 16

value: DEL-CH


title: MER-AR G1A

description: SAMPLE 17


title: MU.32.r2

description: S. coelicolor∆argR_32hours_Replicate2


title: MU.32.r1

description: S. coelicolor∆argR_32hours_Replicate1


title: EKU-AU TA G0

description: SAMPLE 13

value: 0 days

value: EKU-AU


title: EKU-AU TA 1A

description: SAMPLE 14

value: bariatric surgery


title: genomic DNA from blood 9403904087_R04C02

description: stroke blood sample

source_name: blood

value: cardio emobolic


title: MAR-PA TA 1A

description: SAMPLE 12

value: 1 year

value: MAR-PA


title: genomic DNA from blood 9403904087_R05C02

description: stroke blood sample

value: Female


title: genomic DNA from blood 9403904087_R06C02

description: stroke blood sample

value: blood


title: DEH-CA TA 1A

description: SAMPLE 10

value: DEH-CA


title: MAR-PA TA G0

description: SAMPLE 11


title: spnE-_2-4h_rep6

city: MONTPELLIER

first: Simonelig

last: Martine

address: 141, rue de la Cardonille

department: Genetics and Development

institute: Institut de Genetique Humaine - CNRS

hyb_protocol: Samples were hybridized to Nimblegen Drosophila melanogaster 12 x 135 K microarrays

scan_protocol: Microarrays were scanned in Cy3 and Cy5 channels at 1 µm resolution using Innoscan900 scanner (Innopsys) and variable photomultiplier tube (PMT) settings to obtain maximal signal intensities. Nimblescan v2.5 software (Roche Nimblegen) was used for feature extraction

data_processing: The data were normalized using the VSN (Variance Stabilizing Normalization) method. Differentially expressed probes were identified using LIMMA and FDR (False Discovery Rate) set to 0.1%.

organism: Drosophila melanogaster

source_name: 2-4h spn-Ehls-03987/spn-E1 embryos

label_protocol: Experimental samples were labelled with Cy5 and the common reference sample (made by pooling equimolar amounts of RNA from all 18 experimental samples) was labelled with Cy3.

extract_protocol: RNA was prepared with Trizol (Invitrogen) from 0-2 h and 2-4 h-embryos from wild-type, aubHN2/aubQC42 or spn-Ehls-03987/spn-E1 females crossed with wild-type males.

tag: developmental stage

value: embryos 2-4h

tag: allele

source_name: equimolar mix of all 18 samples

value: pooled all stages


title: genomic DNA from blood 9403904087_R02C01

description: stroke blood sample

value: stroke


title: DEH-CA TA G0

description: SAMPLE 9


title: spnE-_2-4h_rep5


title: genomic DNA from blood 9403904087_R03C02

description: stroke blood sample

value: Large-artery atherosclerosis


title: genomic DNA from blood 9403904067_R05C02

description: stroke blood sample


title: DEL-CH G1A

description: SAMPLE 15


title: genomic DNA from blood 9403904087_R01C02

description: stroke blood sample

value: Male

value: lacunar


title: genomic DNA from blood 9403904087_R02C02

description: stroke blood sample


title: WIN-KA G0

description: SAMPLE 7

value: subcutaneous adipose tissue

value: WIN-KA


title: spnE-_2-4h_rep4


title: COI-SA TA 1A

description: SAMPLE 6

value: COI-SA


title: genomic DNA from blood 9403904087_R03C01

description: stroke blood sample


title: spnE-_2-4h_rep2


title: spnE-_0-2h_rep6

source_name: 0-2h spn-Ehls-03987/spn-E1 embryos

value: embryos 0-2h


title: genomic DNA from blood 9403904087_R01C01

description: stroke blood sample


title: COI-SA TA G0

description: SAMPLE 5

source_name: human adipose tissue, 0 days

value: 0 days


title: WIN-KA G1A

description: SAMPLE 8

source_name: human adipose tissue, 1 year

value: bariatric surgery


title: spnE-_0-2h_rep5


title: spnE-_0-2h_rep4


title: spnE-_2-4h_rep1


title: DUC-AG G1A

description: SAMPLE 4

value: 1 year

value: DUC-AG


title: genomic DNA from blood 9403904067_R06C02

description: stroke blood sample

value: Female

value: cardio emobolic


title: genomic DNA from blood 9403904067_R02C01

description: stroke blood sample

value: blood


title: genomic DNA from blood 9403904067_R04C01

description: stroke blood sample


title: COR-AD G1A

description: SAMPLE 2

value: COR-AD


title: genomic DNA from blood 9403904067_R06C01

description: stroke blood sample


title: DUC-AG G0

description: SAMPLE 3


title: spnE-_0-2h_rep3

value: pooled all stages


title: COR-AD G0

description: SAMPLE 1


title: KI-M97

city: Atlanta

first: Viren

last: Patel

state: GA

address: 101 Woodruff Circle

department: EICC

institute: Emory University School of Medicine

description: KI

hyb_protocol: Independent hybridizations (3 for SCA17 KI vs. WT) of synthesized cRNAs were performed on the Gene Expression 8 Affymetrix Mouse Gene1.0ST by Emory University Integrated Genomics Core.

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

data_processing:
Raw data obtained via the GCOS software (Affymetrix) were subjected to background adjustment and normalization with RMAExpress, using all chips at the same time. RMA-normalized values were averaged across hybridizations. Log2-scaled RMA results were analyzed to calculate ANOVA two-sided P-values. Natural-scaled results from RMAExpress were used to calculate log ratios. Specifically, the mutant TBP group RMA average was divided by the normal TBP group RMA average, and the base-2 logarithm (Log2) of this value constituted the log ratio.
To combine the P-value and log ratio calculations and weight each with the same importance, we used the following method for selecting significantly changed probes from RMA and ANOVA values. First, we ascertained the number of probe sets that met the threshold P-value (< 0.01). Second, the absolute value of log ratios was taken, and a cutoff set so that the same number of probe sets was obtained based on ranked log ratios as was obtained based on ranked P-values. Finally, the probe sets that fulfilled thresholds for both P-value and log ratio were selected as significantly changed.

source_name: Mouse muscle

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cerebellum and muscle tissues were collected from WT and SCA17 KI mice, and homogenized by Wheaton Dounce tissue grinders

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) and further purified with RNeasy columns (Qiagen) following manufacturers’ instructions. RNA was isolated from 3 3-month-old mice of each genotype (SCA17 KI and WT).

value: muscle


title: spnE-_0-2h_rep2


title: spnE-_2-4h_rep3

value: embryos 2-4h


title: genomic DNA from blood 9403904067_R04C02

description: stroke blood sample

value: stroke


title: genomic DNA from blood 9403904067_R05C01

description: stroke blood sample

value: Male

value: lacunar


title: genomic DNA from blood 9403904067_R01C02

description: stroke blood sample


title: genomic DNA from blood 9403904067_R02C02

description: stroke blood sample


title: spnE-_0-2h_rep1


title: WT-M96

description: WT


title: genomic DNA from blood 9403904067_R03C01

description: stroke blood sample

value: Large-artery atherosclerosis


title: genomic DNA from blood 9403904043_R05C02

description: stroke blood sample


title: aub-_2-4h_rep6

source_name: 2-4h aubHN2/aubQC42  embryos


title: aub-_2-4h_rep4


title: aub-_2-4h_rep5


title: genomic DNA from blood 9403904067_R01C01

description: stroke blood sample


title: KI-M94

description: KI


title: genomic DNA from blood 9403904087_R05C01

description: stroke blood sample


title: KI-C97

description: KI

source_name: Mouse cerebellum

value: cerebellum


title: WT-C96

description: WT


title: genomic DNA from blood 9403904043_R05C01

description: stroke blood sample


title: genomic DNA from blood 9403904043_R04C01

description: stroke blood sample


title: genomic DNA from blood 9403904043_R03C02

description: stroke blood sample


title: aub-_2-4h_rep1


title: genomic DNA from blood 9403904043_R02C01

description: stroke blood sample


title: WT-C95

description: WT


title: aub-_2-4h_rep3


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt and LPS, replicate 3

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

country: Germany

institute: German Cancer Research Center

description: gene expression data from bone marrow-derived dendritic cells cultured in the presence of 450 mOsm NaCl and LPS

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with R/Bioncoductor, using RMA (oligo package) as normalization method with default settings. Control probes and probes without gene symbol were removed.

source_name: bone marrow-derived dendritic cells

label_protocol: cDNA was fragmented and biotin-labeled using Nugen Encore Biotin Module (Nugen Technologies Inc.).

growth_protocol: Dendritic cells were generated from bone marrows of C57BL/6 mice in a medium supplemented with 10 ng/ml GM-CSF, under standard cell culture conditions

extract_protocol: Total RNA was isolated using the Rneasy Mini Kit (Qiagen)

treatment_protocol: The dendritic cells were developed in either normosmolar (290 mOsm/L) or hyperosmolar (450 mOsm/L) medium. The hyperosmolarity was achieved by adding NaCl from day 3 of the culture. The cells were collected on day 7, plated for another 6 hours (without LPS stimulation or stimulated by 10 ng/mL LPS) and used for analysis.

tag: mouseid

tag: condition

value: 450 mOsm salt with LPS

value: bone marrow-derived dendritic cells


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt and LPS, replicate 4


title: KI-C94

description: KI


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt and LPS, replicate 2


title: genomic DNA from blood 9403904041_R06C01

description: stroke blood sample

tag: stroke subtype

tag: disease state


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt and LPS, replicate 1


title: aub-_0-2h_rep5

source_name: 0-2h aubHN2/aubQC42  embryos

value: embryos 0-2h


title: genomic DNA from blood 9403904043_R01C01

description: stroke blood sample

tag: gender

tag: sample type


title: WT-M95

description: WT


title: aub-_0-2h_rep3


title: aub-_0-2h_rep2


title: aub-_0-2h_rep4


title: aub-_2-4h_rep2


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt, replicate 4

description: gene expression data from bone marrow-derived dendritic cells cultured in the presence of 450 mOsm NaCl

value: 450 mOsm salt without LPS


title: aub-_0-2h_rep6


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt, replicate 3


title: aub-_0-2h_rep1


title: w1118_2-4h_rep4

source_name: 2-4h w1118 embryos

value: control :w1118


title: genomic DNA from blood 9403904041_R05C01

description: stroke blood sample

value: Female


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt, replicate 1


title: Bone marrow-derived dendritic cells cultured in Medium containing 450 mOsm salt, replicate 2


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt and LPS, replicate 3

description: gene expression data from bone marrow-derived dendritic cells cultured in the presence of 290 mOsm NaCl and LPS

value: 290 mOsm salt with LPS


title: genomic DNA from blood 9403904041_R04C02

description: stroke blood sample

value: blood


title: w1118_2-4h_rep6


title: genomic DNA from blood 9403904041_R05C02

description: stroke blood sample


title: w1118_2-4h_rep3


title: w1118_2-4h_rep2


title: w1118_2-4h_rep5


title: genomic DNA from blood 9403904041_R03C02

description: stroke blood sample


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt and LPS, replicate 4


title: genomic DNA from blood 9403904041_R03C01

description: stroke blood sample

value: cardio emobolic


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt and LPS, replicate 2


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt and LPS, replicate 1


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt, replicate 4

description: gene expression data from bone marrow-derived dendritic cells cultured in the presence of 290 mOsm NaCl

value: 290 mOsm salt without LPS


title: genomic DNA from blood 9403904041_R01C02

description: stroke blood sample


title: w1118_2-4h_rep1

value: pooled all stages


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt, replicate 3


title: genomic DNA from blood 9403904043_R01C02

description: stroke blood sample


title: genomic DNA from blood 9403904025_R06C02

description: stroke blood sample


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt, replicate 2


title: w1118_0-2h_rep5

source_name: 0-2h w1118 embryos


title: w1118_0-2h_rep6


title: genomic DNA from blood 9403904041_R04C01

description: stroke blood sample


title: genomic DNA from blood 9403904041_R06C02

description: stroke blood sample


title: MDA-MVAC51

status: Public on Aug 18 2015

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

hyb_protocol: Standard Illumina whole genome DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization in the R language environment was used to normalize the data

source_name: Bladder

label_protocol: Standard Illuminal whole genome DASL method

extract_protocol: Total RNA from FFPE was extracted by High Pure miRNA Isolation Kit (Roche). Quality control was performed by NanoDrop ND-1000.

value: bladder cancer

value: adjuvant MVAC

tag: arm

value: Adj (Surg First)

tag: survival (months)

value: Uncensored

value: Bladder


title: genomic DNA from blood 9403904025_R06C01

description: stroke blood sample

value: lacunar

value: stroke


title: w1118_0-2h_rep2


title: MDA-MVAC50

tag: tissue


title: w1118_0-2h_rep4


title: genomic DNA from blood 9403904041_R02C02

description: stroke blood sample

value: Large-artery atherosclerosis


title: w1118_0-2h_rep1

value: embryos 0-2h


title: genomic DNA from blood 9403904025_R05C01

description: stroke blood sample

value: Male


title: MDA-MVAC49


title: MDA-MVAC46


title: MDA-MVAC48


title: Bone marrow-derived dendritic cells cultured in Medium containing 290 mOsm salt, replicate 1

tag: cell type

value: bone marrow-derived dendritic cells


title: genomic DNA from blood 9403904025_R04C02

description: stroke blood sample

value: Female


title: w1118_0-2h_rep3

value: control :w1118


title: MDA-MVAC45

tag: treatment

value: Censored


title: genomic DNA from blood 9403904025_R05C02

description: stroke blood sample

value: blood


title: MDA-MVAC38


title: MDA-MVAC37


title: MDA-MVAC43


title: MDA-MVAC36


title: MDA-MVAC47


title: MDA-MVAC41


title: MDA-MVAC40


title: genomic DNA from blood 9403904025_R03C01

description: stroke blood sample


title: MDA-MVAC42


title: MDA-MVAC35

source_name: Bladder and ureter

value: Bladder and ureter


title: MDA-MVAC39


title: genomic DNA from blood 9403904025_R03C02

description: stroke blood sample


title: MDA-MVAC33


title: genomic DNA from blood 9403904025_R01C02

description: stroke blood sample


title: genomic DNA from blood 9403904025_R04C01

description: stroke blood sample


title: MDA-MVAC32


title: genomic DNA from blood 9403904025_R01C01

description: stroke blood sample


title: genomic DNA from blood 9403904025_R02C01

description: stroke blood sample


title: MDA-MVAC30


title: MDA-MVAC29


title: MDA-MVAC31


title: MDA-MVAC25


title: MDA-MVAC20

value: NAC-MVAC

value: Pre (Pre OP chemo)


title: MDA-MVAC28

value: bladder cancer

value: adjuvant MVAC


title: MDA-MVAC26

value: Adj (Surg First)

value: Uncensored


title: genomic DNA from blood 9403904025_R02C02

description: stroke blood sample

value: lacunar


title: MDA-MVAC17

value: Bladder


title: MDA-MVAC24


title: MDA-MVAC11


title: MDA-MVAC15


title: MDA-MVAC10


title: MDA-MVAC22


title: MDA-MVAC14


title: MDA-MVAC7


title: MDA-MVAC12


title: MDA-MVAC8


title: MDA-MVAC19


title: MDA-MVAC18


title: MDA-MVAC13


title: MDA-MVAC9


title: MDA-MVAC1


title: MDA-MVAC23


title: MDA-MVAC5


title: MDA-MVAC4


title: MDA-MVAC6


title: MDA_FFPE122

data_processing: Quantile normalization in the Linear Models for Microarray Data (LIMMA) package in the R language environment was used to normalize the data

label: whole genome DASL

source_name: BLADDER

tag: sample procured

value: surgery

value: DDMVAC and bevacizumab

tag: pretreatment sample record-pair


title: MDA-MVAC3


title: MDA_FFPE124


title: MDA_FFPE129


title: MDA_FFPE127


title: MDA_FFPE123


title: MDA_FFPE126


title: MDA-MVAC2


title: MDA_FFPE121


title: MDA_FFPE119


title: MDA_FFPE116

source_name: UTUC


title: MDA_FFPE114


title: MDA_FFPE118


title: MDA_FFPE125


title: MDA_FFPE120


title: MDA_FFPE113


title: MDA_FFPE115


title: MDA_FFPE111


title: MDA_FFPE117


title: MDA_FFPE112


title: MDA_FFPE110


title: MDA_FFPE109


title: MDA_FFPE106

tag: survival

tag: Cause of death

value: ANED

tag: os censor

value: TUR

tag: subtype (tur) 1-basal;2-p53 like;3-luminal

tag: age at registration

tag: ps at registration

tag: cystectomy

value: Yes

tag: cstage

tag: lvi

tag: pstage


title: MDA_FFPE97


title: MDA_FFPE101

value: Upper tract


title: MDA_FFPE103

value: Censored

value: Ta N0


title: MDA_FFPE93

value: DOD

value: No

tag: comments

value: Developed lung cancer during treatment, count as pstage 4 treatment failure.


title: MDA_FFPE107


title: MDA_FFPE96


title: MDA_FFPE92


title: MDA_FFPE108


title: MDA_FFPE102

value: HG upper tract


title: MDA_FFPE95


title: MDA_FFPE99


title: MDA_FFPE104


title: MDA_FFPE94


title: MDA_FFPE91


title: MDA_FFPE90


title: MDA_FFPE105


title: MDA_FFPE86


title: MDA_FFPE98


title: MDA_FFPE100


title: MDA_FFPE89


title: MDA_FFPE85


title: MDA-MVAC34

tag: disease state

value: bladder cancer

value: adjuvant MVAC

tag: arm

tag: survival (months)


title: MDA_FFPE87

tag: treatment


title: GSM1173982

source_name: URETHRA

tag: sample procured


title: MDA_FFPE84


title: GSM1173983

value: Uncensored


title: GSM1173977


title: GSM1173976


title: GSM1173979


title: JVM2_shp53_1

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Cell line JVM2, TP53 knockdown by shRNA, untreated, replicate 1

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Cells were cultured in RPMI 1640 containing 15% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: Stable forms of JVM2 were created by transduction with retroviruses encoding either TP53-specific shRNA (nucleotides 611-629, Genbank NM000546) or scrambled shRNA, followed by selection of transduced cells. In triplicate cultures, cells of both types (control and TP53 knockdown) were either left untreated or treated with KPT-185 (100 nM for 18 hours). Cultures were harvested individually for gene expression profiling.

tag: cell line

tag: transduction

value: TP53 knockdown by shRNA

value: untreated


title: GSM1173978

tag: survival

tag: Cause of death


title: GSM1173981

tag: os censor

tag: subtype (tur) 1-basal;2-p53 like;3-luminal


title: JVM2_shp53_KPT185_1

source_name: Cell line JVM2, TP53 knockdown by shRNA, treated with KPT-185, replicate 1

value: treated with KPT-185


title: Edited FXS Mature Neurons

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: iPS cells-derived neurons, CGG repeat deleted Fragile X clone 52

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit

tag: material

value: Cell line

tag: gender

value: Male


title: JVM2_shp53_3

source_name: Cell line JVM2, TP53 knockdown by shRNA, untreated, replicate 3


title: JVM2_shp53_2

source_name: Cell line JVM2, TP53 knockdown by shRNA, untreated, replicate 2


title: JVM22_shC_KPT185_3

source_name: Cell line JVM2, scrambled shRNA control, treated with KPT-185, replicate 3

value: scrambled shRNA


title: JVM22_shC_KPT185_2

source_name: Cell line JVM2, scrambled shRNA control, treated with KPT-185, replicate 2


title: GSM1173974

value: TUR

tag: age at registration

tag: ps at registration

tag: cystectomy

value: Yes

tag: cstage


title: JVM22_shC_KPT185_1

source_name: Cell line JVM2, scrambled shRNA control, treated with KPT-185, replicate 1


title: JVM2_shp53_KPT185_3

source_name: Cell line JVM2, TP53 knockdown by shRNA, treated with KPT-185, replicate 3


title: FXS Mature Neurons

source_name: iPS cells-derived neurons, Fragile X clone 52


title: rat at C3, biological rep2

city: Wuhan

first: Jiang

last: Hongyang

state: Hubei

address: No. 1095 Jie Fang Avenue

country: China

institute: Tongji Hospital, Huazhong University of Science and Technology

description: Gene expression data from rats which were supplied with tap water for 2 weeks.

hyb_protocol: The labled RNA were hybridized for 16 hr at 60 rpm at 48C on Affymetrix miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data files were analyzed by using Affymetrix Expression Console with the default miRNA array settings. Raw data were processed and normalized on basis of organism rat using RMA-DABG algorithm.

organism: Rattus norvegicus

source_name: Rats which were supplied with tap water for 2 weeks.

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit(Affymetrix, Santa Clara, CA, USA).

growth_protocol: all rats were acclimated at 23℃ on a 12 h light/dark cycle before initiation of experiments in the SPF level animal house.

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

treatment_protocol: experimental (T) group for the gene and protein expression studies and control (C) group. Rats in T group were provided free access to drinking water containing 1% (vol/vol) ethylene glycol and 0.5% ammonium chloride for a period of 2 weeks in order to induce hyperoxaluria, while the rats in C group were supplied with tap water for 2 weeks.

tag: tissue

value: kidney


title: GSM1173975

value: ANED

value: Censored

tag: lvi

tag: pstage


title: MDA-MVAC16

tag: disease state

tag: treatment

value: NAC-MVAC

tag: arm

value: Pre (Pre OP chemo)

tag: survival (months)

value: Bladder


title: GSM1173972

tag: survival

tag: sample procured


title: JVM2_shC_3

source_name: Cell line JVM2, scrambled shRNA control, untreated, replicate 3

tag: cell line

tag: transduction


title: JVM2_shC_2

source_name: Cell line JVM2, scrambled shRNA control, untreated, replicate 2


title: GSM1173973

tag: Cause of death

value: DOD

tag: os censor

tag: subtype (tur) 1-basal;2-p53 like;3-luminal


title: MDA_FFPE88

tag: age at registration

tag: ps at registration


title: JVM2_shC_1

source_name: Cell line JVM2, scrambled shRNA control, untreated, replicate 1


title: MDA-MVAC27

source_name: Bladder

value: bladder cancer

value: adjuvant MVAC

value: Adj (Surg First)


title: GSM1173971

source_name: BLADDER

tag: cystectomy

tag: cstage


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 3 replicate 1

status: Public on Aug 17 2015

city: Pittsburgh

first: Luis

middle: A

last: Ortiz

state: PA

address: 100 Technology Drive Room 557

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: miRNA expression microarrays of exosome from human MSC

hyb_protocol: The entire sample of Cy3-labelled cRNA was heated at 100°C for 5 minutes in a reaction volume of 10x Agilent blocking agent and 2× Hi-RPM Hybridization Buffer following the manufacturers instructions. On completion of the reaction the mixture was hybridized to Agilent Human miRNA Microarray Kit8x15K V3 (G4470C) for at 55°C for 20 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Tiff 20 bit, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (miRNA_107_Sep09_patch and Grid: 021827_D_F_20091031 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  miRNA expression data was normalized using Genespring 12.6 and performing quantile normalization with no baseline geometric transformation.  The file "Normalized_data.txt" contains the normalized signal intensity and is available on the series record.

source_name: Human MSC from which exosomes were derived

label_protocol: Labeling reactions were performed for each sample using Agilent miRNA Complete Labeling and Hyb Kit Agilent (5190-0456, Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 100 nanograms of total RNA, an initial cDNA strand was Dephosphorylated using a Phosphatase Treatment, this Dephosphorylated RNA was then reverse transcribed and labeled using Cy3 dye by a reverse transcriptase enzyme. After the cRNA was obtained a purification/desalting step was performed using Micro Bio-Spin P-6 Gel Column Bio-Rad (732-6221, Qiagen, Valencia, CA) followed by a drying of the sample according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit.

growth_protocol: MSCs were expanded in multilayer tissue culture plates (Millipore) in medium depleted of serum derived- microvesicles/exosomes by overnight ultracentrifugation at 100,000 g or in serum reduced mesenchymal stem cell medium (Invitrogen) supplemented with bovine serum albumin (Sigma-Aldrich).   Condition medium from 10 x106 MSCs was collected every 24 h and subjected to successive centrifugations at 300 g and 2000 g (10 min. each) to remove cells.  The cell-free supernatant was then centrifuged at 10,000 g for 30 min to remove cell debris and 100,000 g (Beckman Coulter Optima L-90K ultracentrifuge) 4°C for 90 minutes.  The 10,000 and 100,000 g pellets were washed and re suspended in 100 µl of PBS.

extract_protocol: Total RNA was extracted and purified using the miRNeasy Mini Kit (217004, Qiagen, Valencia, CA) under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol.After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

tag: cell type

value: Human Mesenchymal Stem Cell

tag: rna source

value: cell line (control)


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 2 replicate 3


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 2 replicate 2


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 1 replicate 3


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 2 replicate 1


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 1 replicate 2


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 1 replicate 1


title: Exosome from cell line sample 3 replicate 2

source_name: Exosome from human MSC

value: exosome


title: Exosome from cell line sample 2 replicate 2


title: JVM2_shp53_KPT185_2

source_name: Cell line JVM2, TP53 knockdown by shRNA, treated with KPT-185, replicate 2

value: TP53 knockdown by shRNA

value: treated with KPT-185


title: Exosome from cell line sample 2 replicate 1


title: Exosome from cell line sample 1 replicate 3


title: Exosome from cell line sample 3 replicate 1


title: Exosome from cell line sample 2 replicate 3


title: GSM1173969

value: Uncensored

value: TUR

tag: lvi

tag: pstage


title: Exosome from cell line sample 1 replicate 2


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 3 replicate 2


title: rat at T2, biological rep1

description: Gene expression data from rats which were provided free access to drinking water containing 1% (vol/vol) ethylene glycol and 0.5% ammonium chloride for a period of 2 weeks.

source_name: Rats which were provided free access to drinking water containing 1% (vol/vol) ethylene glycol and 0.5% ammonium chloride for a period of 2 weeks

tag: tissue

value: kidney


title: Human Mesencyhmal Stem Cells (which exosomes were derived from) sample 3 replicate 3


title: Exosome from cell line sample 1 replicate 1


title: GSM1173970

tag: treatment

value: Yes


title: MDA_FFPE128

value: surgery

value: DDMVAC and bevacizumab

tag: pretreatment sample record-pair


title: GSM1173968

tag: survival

tag: sample procured


title: Exosome from cell line sample 3 replicate 3


title: rat at T1, biological rep1


title: rat at T3, biological rep1


title: DGM-10170_M0_sm

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker


title: DGM-10342_M0_sm

value: nonsmoker


title: DN3 replicate 1

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

hyb_protocol: Following fragmentation, 2.5ug/ul cDNA were hybrizied at 16 hours at 45 C on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Affymetrix Expression Console with default analysis setting.

source_name: Thymus

label_protocol: Biotinylated cDNA were prepared using Encore Biotin Mudule (Nugene) kit from 5.5 ug RNA according to the manufacture's instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA were amplified by the Nugene PicaV2 kit.


title: NK, replicate2

source_name: Bone Marrow

value: NK


title: DN3 replicate 2


title: ETP  replicate 1

value: ETP


title: rat at C2, biological rep2


title: DGM-12730_sm


title: ETP replicate 2


title: Term 10 (T10)

city: Amsterdam

first: Febilla

last: Fernando

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Academic Medical Center

description:
Term sample
SAMPLE 22

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: standard Illumina Protocol

data_processing: The quality control was performed using the  array quality metrics and ChAMP R packages. 2 samples were excluded due to failed quality control. BMIQ normalization was performed  on 22 samples and differential methylated values were calculated on M values (limma package). The non_normalized.txt contains unmethylated and methylated signal intensities (for all 24 samples).

source_name: term_umbilical cord blood DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from Umbilical Cord Blood was isolated by Gentra Autopure LS98TM system (Gentra Systems)

tag: gender

value: Female

tag: gestational_age (days)

tag: oxytocin

value: No

tag: initiation of labor

value: Spontaneous contractions

value: Umbilical cord blood


title: Term 7 (T7)

description:
Term sample
SAMPLE 19

value: Male


title: Term 12 (T12)

description:
Term sample
SAMPLE 24


title: Term 8 (T8)

description:
Term sample
SAMPLE 20

value: Spontaneous ruptureof membranes


title: CLP, replicate 1

value: CLP


title: NK, replicate1


title: CLP, replicate 2


title: EILP

value: EILP


title: Term 6 (T6)

description:
Term sample
SAMPLE 18


title: PNB-028-2

city: Memphis

first: Ramesh

last: Narayanan

state: Tennessee

address: 19 S. Manassas, Room 120

department: Medicine

institute: University of Tennessee Health Science Center

hyb_protocol: Standard

scan_protocol: Affymetrix scan protocol

data_processing: Affymetrix console

source_name: PNB-028- treated MAC-16 colon cancer xenograft tumors

label_protocol: Affymetrix standard protocol

extract_protocol: Qiaquik RNA extraction kit

treatment_protocol: All xenograft animal protocols were approved by The University of Tennessee Animal Care and Use Research Committee. MAC-16 cells were harvested, counted under microscope using trypan blue exclusion, and a suspension in growth medium was prepared. The cell suspension (5 million cells/mouse) was implanted subcutaneously in NSG mice. Once the tumors reached 100-200 mm3, the animals were randomized within the respective cell line and treated orally at 50 mg/kg/day. PNB-028 was dissolved in 20% DMSO+80% PEG-300 and administered by oral gavage. Body weight and tumor volumes were measured thrice weekly. Animals were sacrificed (6 hrs after the last dose) when tumors reached 1500 mm3 or when the animals lost over 20% body weight. Tumors were excised, weighed, and stored for further analysis (two parts snap frozen and stored at -80°C and one part stored in formalin for histology). RNA was isolated from MAC-16 tumors (n=3/group) using Qiagen RNAeasy kit. RNA was quantified using nanodrop and diluted to equal concentrations of 100 ng/µl. RNA quality was determined using Agilent Bioanalyzer and RNA samples with RNA Integrity Number (RIN) greater than 7 were used for microarray experiments (ST 2.0 mouse array from Affymetrix). Results from microarray studies were analyzed using Affymetrix software (Transcriptome Analysis Console (TAC)). Pathways differentially regulated by PNB-028 were identified using Ingenuity Pathway Analysis software.

tag: cell line

value: colon cancer


title: Preterm 6 (PT6)

description:
Preterm sample
SAMPLE 6

source_name: preterm_umbilical cord blood DNA


title: rat at C1, biological rep2

value: kidney


title: flt3- CMP, replicate 2

value: flt3- CMP


title: Preterm 8 (PT8)

description:
Preterm sample
SAMPLE 8


title: Preterm 12 (PT12)

description:
Preterm sample
SAMPLE 12


title: Preterm 10 (PT10)

description:
Preterm sample
SAMPLE 10


title: Preterm 3 (PT3)

description:
Preterm sample
SAMPLE 3

value: Yes


title: Term 9 (T9)

description:
Term sample
SAMPLE 21


title: Preterm 4 (PT4)

description:
Preterm sample
SAMPLE 4


title: Preterm 7 (PT7)

description:
Preterm sample
SAMPLE 7


title: Term 2 (T2)

description:
Term sample
SAMPLE 14


title: flt3- CMP, replicate 1


title: Term 11 (T11)

description:
Term sample
SAMPLE 23


title: flt3+ CMP, replicate2

value: flt3+ CMP


title: Term 5 (T5)

description:
Term sample
SAMPLE 17


title: Preterm 5 (PT5)

description:
Preterm sample
SAMPLE 5


title: PNB-028-3


title: Term 1 (T1)

description:
Term sample
SAMPLE 13


title: Term 3 (T3)

description:
Term sample
SAMPLE 15


title: LMPP, replicate 2

value: LMPP


title: flt3+ CMP, replicate1


title: LMPP, replicate 1


title: PNB-028-1


title: Vehicle-3

source_name: vehicle- treated MAC-16 colon cancer xenograft tumors


title: Preterm 2 (PT2)

description:
Preterm sample
SAMPLE 2


title: Preterm 11 (PT11)

description:
Preterm sample
SAMPLE 11


title: Preterm 1 (PT1)

description:
Preterm sample
SAMPLE 1


title: Adipocyte_wax_10d_rep1

city: Taiwan, R.O.C.

first: chihchiang

last: chen

address: No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan 11217, R.O.C

department: Dermatology Department

country: Taiwan

institute: Taipei Veterans General Hospital

description:
Adipocyte gene expression at 10 days after plucking.
CCC-120503-7

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis
Nnormalization software is used to quantify signal and background intensity for each feature.

source_name: adipose cell, wax, 10d, replicate 1

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: RNA was prepared using the TRI Reagent BD (Sigma-Aldrich, Inc.) following the manufacturer's recommendations.The protocol includes differential lysis of adipose cells and isolates total RNA. RNA was quantified using a ASP-3700-Micro-volume spectrophotometer (ACTGene, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: We used female C57 BL/6 mice at 7–8 weeks of age with all hair follicles of the back skin in telogen. Conventional club hair plucking was performed with the wax dressing method. Treament samples were taken immediately after shaveing, and 12 hours after plucking, at 1, 2, 4, 6, 10 and 50 days. And isolated of adipose cells from the treament samples.

value: adipose cell

value: female

tag: age

value: 11 weeks


title: Adipocyte_wax_6d_rep1

description:
Adipocyte gene expression at 6 days after plucking.
CCC-120503-6

source_name: adipose cell, wax, 6d, replicate 1


title: Adipocyte_wax_4d_rep1

description:
Adipocyte gene expression at 4 days after plucking.
CCC-120503-5

source_name: adipose cell, wax, 4d, replicate 1

value: 10 weeks


title: Hnf1b-Mut-Biological rep 1

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

institute: University of Texas Southwestern

description: Gene expression data from kidney cells

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

data_processing: Raw data were processed with the Expression Console (Affymetrix) for RMA summarization and Quantile normalization.

source_name: Mouse Intermedullary collecting duct cells

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

growth_protocol: Cells were cultired in a 6 well plates for 72 hours

extract_protocol: RNA extraction was perfomred using miRNeasy kit (Qiagin) according to manufacturer protocol

treatment_protocol: Domiannt negative Hnf1b was induced for 48 hoyurs by adding mifeprin (mut)  or Ethanol (control) to the cells.

value: kidney cells

tag: agent

value: mifeprin

tag: genotype/variation

value: mutant


title: HSC, replicate 2

tag: cell type

value: HSC


title: Adipocyte_wax_50d_rep1

description:
Adipocyte gene expression at 50 days after plucking.
CCC-120503-8

source_name: adipose cell, wax, 50d, replicate 1

value: 17 weeks


title: Adipocyte_wax_2d_rep1

description:
Adipocyte gene expression at 2 days after plucking.
CCC-120503-4

source_name: adipose cell, wax,2d, replicate 1


title: Adipocyte_wax_1d_rep1

description:
Adipocyte gene expression at 1 day after plucking.
CCC-120503-3

source_name: adipose cell, wax, 1d, replicate 1


title: Hnf1b-WT-Biological rep 3

description: Gene expression data from kidney cells

value: Ethanol (control)

value: wild-type


title: Validation_Control_03

status: Public on Aug 16 2015

city: Fukuoka

first: Satohiro

last: Masuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmacy

country: Japan

institute: Kyushu University Hospital

description: Control103; Normal kidney total RNA in validation set, replicate3

hyb_protocol: 1.0 ug of cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The signals were normalized with each median.

source_name: validation set_normal kidney

label_protocol: Cyanine-3-labeled complementary (c) RNA was generated with Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the Spectrophotometer.

extract_protocol: Total RNA was isolated from biopsy specimens using an RNeasy micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified using a spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: study set

value: validation set

tag: sample type

value: Normal kidney total RNA

tag: disease status

value: normal kidney


title: Hnf1b-WT-Biological rep 2

description: Gene expression data from kidney cells


title: Validation_CKD_05

description: #105; Renal biopsy specimens #105 in validation set

source_name: validation set_renal biopsy specimen

value: Renal biopsy specimens

tag: specimen id

tag: tissue

value: kidney

value: chronic kidney disease (CKD)


title: Hnf1b-Mut-Biological rep 3

description: Gene expression data from kidney cells


title: Validation_CKD_04

description: #104; Renal biopsy specimens #104 in validation set


title: Vehicle-1

value: colon cancer


title: Hnf1b-WT-Biological rep 1

description: Gene expression data from kidney cells


title: Validation_CKD_03

description: #103; Renal biopsy specimens #103 in validation set


title: HSC, replicate 1


title: Adipocyte_shave_control_rep1

description:
Adipocyte gene expression immediately after shaveing.
CCC-120503-1

source_name: adipose cell , shave, control, replicate 1

value: adipose cell

value: female


title: Validation_CKD_01

description: #101; Renal biopsy specimens #101 in validation set


title: Validation_Control_01

description: Control101; Normal kidney total RNA in validation set, replicate1


title: Validation_CKD_02

description: #102; Renal biopsy specimens #102 in validation set


title: Adipocyte_wax_12hr_rep1

description:
Adipocyte gene expression at 12 hours after plucking.
CCC-120503-2

source_name: adipose cell, wax, 12hr, replicate 1

value: 10 weeks


title: Hnf1b-Mut-Biological rep 2

description: Gene expression data from kidney cells

value: kidney cells


title: Discovery_Control_03

description: Control3; Normal kidney total RNA in discovery set, replicate3

source_name: discovery set_normal kidney

value: discovery set


title: Discovery_Control_05

description: Control5; Normal kidney total RNA in discovery set, replicate5


title: Vehicle-2


title: Discovery_Control_04

description: Control4; Normal kidney total RNA in discovery set, replicate4


title: Discovery_Control_01

description: Control1; Normal kidney total RNA in discovery set, replicate1


title: Discovery_CKD_47

description: #47; Renal biopsy specimens #47 in discovery set

source_name: discovery set_renal biopsy specimen


title: Discovery_CKD_49

description: #49; Renal biopsy specimens #49 in discovery set


title: Discovery_CKD_46

description: #46; Renal biopsy specimens #46 in discovery set


title: Discovery_Control_02

description: Control2; Normal kidney total RNA in discovery set, replicate2


title: Discovery_CKD_48

description: #48; Renal biopsy specimens #48 in discovery set


title: Discovery_CKD_42

description: #42; Renal biopsy specimens #42 in discovery set


title: Discovery_CKD_45

description: #45; Renal biopsy specimens #45 in discovery set


title: Discovery_CKD_40

description: #40; Renal biopsy specimens #40 in discovery set


title: Discovery_CKD_43

description: #43; Renal biopsy specimens #43 in discovery set


title: Discovery_CKD_37

description: #37; Renal biopsy specimens #37 in discovery set


title: Discovery_CKD_41

description: #41; Renal biopsy specimens #41 in discovery set


title: Discovery_CKD_36

description: #36; Renal biopsy specimens #36 in discovery set


title: Validation_Control_02

description: Control102; Normal kidney total RNA in validation set, replicate2


title: Discovery_CKD_33

description: #33; Renal biopsy specimens #33 in discovery set


title: Discovery_CKD_30

description: #30; Renal biopsy specimens #30 in discovery set


title: Discovery_CKD_44

description: #44; Renal biopsy specimens #44 in discovery set


title: Discovery_CKD_32

description: #32; Renal biopsy specimens #32 in discovery set


title: Discovery_CKD_28

description: #28; Renal biopsy specimens #28 in discovery set


title: Discovery_CKD_27

description: #27; Renal biopsy specimens #27 in discovery set


title: Discovery_CKD_38

description: #38; Renal biopsy specimens #38 in discovery set


title: Discovery_CKD_34

description: #34; Renal biopsy specimens #34 in discovery set


title: Discovery_CKD_26

description: #26; Renal biopsy specimens #26 in discovery set


title: Discovery_CKD_39

description: #39; Renal biopsy specimens #39 in discovery set


title: Discovery_CKD_22

description: #22; Renal biopsy specimens #22 in discovery set


title: Discovery_CKD_31

description: #31; Renal biopsy specimens #31 in discovery set


title: Discovery_CKD_21

description: #21; Renal biopsy specimens #21 in discovery set


title: Discovery_CKD_35

description: #35; Renal biopsy specimens #35 in discovery set


title: Discovery_CKD_29

description: #29; Renal biopsy specimens #29 in discovery set


title: Discovery_CKD_24

description: #24; Renal biopsy specimens #24 in discovery set


title: Discovery_CKD_20

description: #20; Renal biopsy specimens #20 in discovery set


title: Discovery_CKD_19

description: #19; Renal biopsy specimens #19 in discovery set


title: Discovery_CKD_18

description: #18; Renal biopsy specimens #18 in discovery set


title: Discovery_CKD_17

description: #17; Renal biopsy specimens #17 in discovery set