title: NA0100-000_NspI

description: SNP data from proband in simplex family


title: NA0099-000_NspI

status: Public on Dec 20 2007

type: genomic

city: Toronto

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: SNP data from proband in multiplex family

hyb_protocol: Following fragmentation, 90 ug of genomic DNA were hybridized for 16 hr at 49C on either the GeneChip® Mapping NspI or StyI chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed using GCOS software. Genotypes were analyzed with GTYPE using Affymetrix defaults.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblast or blood

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol from 90 ug PCR product (GeneChip® Mapping 500K Assay Manual, 2005, Affymetrix).

growth_protocol: Not Applicable

extract_protocol: DNA was extracted from blood or lymphoblast using a standard phenol/chloroform method. 500ng of genomic DNA was used for subsequent PCR complexity reduction (GeneChip® Mapping 500K Assay Manual, 2005, Affymetrix)

treatment_protocol: Not Applicable

tag: Family ID

tag: DNA ID

tag: Gender

value: M

tag: Family Type

value: MPX

tag: Individual Type

value: proband


title: SK0059-003_StyI

description: SNP data from trio simplex family

value: SPX


title: SK0062-003_StyI

description: SNP data from proband in simplex family

value: F


title: NA0097-000_NspI

description: SNP data from proband with abnormal karyotype

value: CHR


title: SK0064-003_StyI

description: SNP data from proband in simplex family


title: SK0058-003_StyI


title: NA0096-000_NspI

description: SNP data from proband in simplex family


title: SK0054-001_StyI

description: SNP data from trio multiplex family

value: parents


title: SK0057-002_StyI

description: SNP data from trio simplex family


title: SK0057-001_StyI

description: SNP data from trio simplex family


title: SK0059-002_StyI

description: SNP data from trio simplex family


title: SK0054-002_StyI

description: SNP data from trio multiplex family


title: SK0070-003_StyI


title: SK0059-001_StyI

description: SNP data from trio simplex family


title: NA0098-000_NspI

description: SNP data from proband in simplex family


title: SK0054-004_StyI

description: SNP data from trio multiplex family


title: NA0093-101_NspI

description: SNP data from trio simplex family


title: SK0049-002_StyI

description: SNP data from trio multiplex family


title: NA0093-000_NspI

description: SNP data from trio simplex family


title: SK0051-001_StyI

description: SNP data from trio multiplex family


title: SK0051-003_StyI

description: SNP data from trio multiplex family


title: NA0090-000_NspI

description: SNP data from proband in simplex family


title: SK0049-004_StyI

description: SNP data from trio multiplex family


title: SK0051-002_StyI

description: SNP data from trio multiplex family


title: SK0049-001_StyI

description: SNP data from trio multiplex family


title: SK0055-003_StyI


title: NA0095-000_NspI

description: SNP data from proband in simplex family


title: SK0048-001_StyI

description: SNP data from trio multiplex family


title: NA0093-100_NspI

description: SNP data from trio simplex family


title: SK0040-003_StyI


title: NA0089-000_NspI

description: SNP data from proband in simplex family


title: SK0045-002_StyI

description: SNP data from trio multiplex family


title: SK0036-003_StyI

description: SNP data from trio simplex family


title: NA0086-000_NspI

description: SNP data from proband in simplex family


title: SK0036-001_StyI

description: SNP data from trio simplex family


title: SK0045-001_StyI

description: SNP data from trio multiplex family


title: SK0027-002_StyI

description: SNP data from trio simplex family


title: SK0048-002_StyI

description: SNP data from trio multiplex family


title: SK0036-002_StyI

description: SNP data from trio simplex family


title: SK0023-003_StyI

description: SNP data from proband in simplex family


title: SK0027-001_StyI

description: SNP data from trio simplex family


title: NA0082-000_NspI


title: NA0076-000_NspI

description: SNP data from proband in simplex family


title: NA0083-100_NspI

description: SNP data from trio simplex family


title: SK0025-002_StyI

description: SNP data from trio multiplex family


title: SK0024-003_StyI

description: SNP data from proband in simplex family


title: SK0021-008_StyI


title: SK0026-003_StyI

description: SNP data from proband in simplex family


title: SK0025-001_StyI

description: SNP data from trio multiplex family


title: NA0083-101_NspI

description: SNP data from trio simplex family


title: NA0078-000_NspI


title: SK0012-003_StyI

description: SNP data from proband in simplex family


title: SK0010-001_StyI

description: SNP data from trio multiplex family


title: SK0014-003_StyI

description: SNP data from proband in simplex family


title: NA0080-000_NspI

description: SNP data from proband in simplex family


title: NA0074-000_NspI

description: SNP data from proband in simplex family


title: NA0083-000_NspI

description: SNP data from trio simplex family


title: SK0009-001_StyI

description: SNP data from trio multiplex family


title: NA0073-000_NspI

description: SNP data from proband in simplex family


title: SK0009-004_StyI

description: SNP data from trio multiplex family


title: SK0010-002_StyI

description: SNP data from trio multiplex family


title: NA0069-000_NspI

description: SNP data from proband in simplex family


title: SK0004-003_StyI

description: SNP data from trio simplex family


title: SK0009-002_StyI

description: SNP data from trio multiplex family


title: NA0070-000_NspI

description: SNP data from proband in simplex family


title: SK0004-002_StyI

description: SNP data from trio simplex family


title: SK0006-002_StyI

description: SNP data from trio multiplex family


title: SK0006-001_StyI

description: SNP data from trio multiplex family


title: NA0172-000_StyI

description: SNP data from proband in simplex family


title: NA0147-000_StyI

description: SNP data from proband in simplex family


title: NA0133-000_StyI

description: SNP data from proband in simplex family


title: NA0138-000_StyI

description: SNP data from proband in simplex family


title: NA0071-000_NspI

description: SNP data from proband in simplex family


title: NA0066-000_NspI

description: SNP data from proband in simplex family


title: NA0122-100_StyI

description: SNP data from trio simplex family


title: NA0129-000_StyI

description: SNP data from proband in simplex family


title: NA0140-000_StyI

description: SNP data from proband in simplex family


title: NA0148-000_StyI

description: SNP data from proband in simplex family


title: NA0065-000_NspI

description: SNP data from proband in simplex family


title: NA0067-000_NspI

description: SNP data from proband in simplex family


title: NA0064-000_NspI

description: SNP data from proband in simplex family


title: NA0134-000_StyI

description: SNP data from proband in simplex family


title: NA0122-101_StyI

description: SNP data from trio simplex family


title: NA0116-000_StyI


title: NA0063-000_NspI

description: SNP data from trio simplex family


title: NA0152-000_StyI

description: SNP data from proband in simplex family


title: SK0004-001_StyI

description: SNP data from trio simplex family


title: NA0063-101_NspI

description: SNP data from trio simplex family


title: NA0145-000_StyI

description: SNP data from proband in simplex family


title: NA0117-000_StyI

description: SNP data from proband in simplex family


title: NA0063-100_NspI

description: SNP data from trio simplex family


title: NA0114-000_StyI

description: SNP data from proband in simplex family


title: NA0122-000_StyI

description: SNP data from trio simplex family


title: NA0115-000_StyI

description: SNP data from proband in simplex family


title: NA0112-000_StyI

description: SNP data from proband in simplex family


title: NA0061-000_NspI

description: SNP data from proband in simplex family


title: NA0068-000_NspI

description: SNP data from proband in simplex family


title: NA0060-000_NspI

description: SNP data from proband in simplex family


title: NA0108-000_StyI


title: NA0105-000_StyI

description: SNP data from proband in simplex family


title: NA0111-000_StyI

description: SNP data from proband in simplex family


title: NA0056-000_NspI

description: SNP data from proband in simplex family


title: NA0055-000_NspI

description: SNP data from proband in simplex family


title: NA0097-000_StyI


title: NA0096-000_StyI

description: SNP data from proband in simplex family


title: NA0090-000_StyI

description: SNP data from proband in simplex family


title: NA0093-101_StyI

description: SNP data from trio simplex family


title: NA0057-000_NspI

description: SNP data from proband in simplex family


title: NA0100-000_StyI

description: SNP data from proband in simplex family


title: NA0052-100_NspI

description: SNP data from trio simplex family


title: NA0093-000_StyI

description: SNP data from trio simplex family


title: NA0095-000_StyI

description: SNP data from proband in simplex family


title: NA0106-000_StyI

description: SNP data from proband in simplex family


title: NA0052-101_NspI

description: SNP data from trio simplex family


title: NA0086-000_StyI

description: SNP data from proband in simplex family


title: NA0109-000_StyI

description: SNP data from proband in simplex family


title: NA0098-000_StyI

description: SNP data from proband in simplex family


title: NA0110-000_StyI

description: SNP data from proband in simplex family


title: NA0050-000_NspI

description: SNP data from proband in simplex family


title: NA0083-101_StyI

description: SNP data from trio simplex family


title: NA0051-000_NspI

description: SNP data from proband in simplex family


title: NA0083-100_StyI

description: SNP data from trio simplex family


title: NA0058-000_NspI

description: SNP data from proband in simplex family


title: NA0052-000_NspI

description: SNP data from trio simplex family


title: NA0049-000_NspI


title: NA0083-000_StyI

description: SNP data from trio simplex family


title: NA0078-000_StyI


title: NA0082-000_StyI


title: NA0080-000_StyI

description: SNP data from proband in simplex family


title: NA0067-000_StyI

description: SNP data from proband in simplex family


title: NA0089-000_StyI

description: SNP data from proband in simplex family


title: NA0044-000_NspI

description: SNP data from proband in simplex family


title: NA0074-000_StyI

description: SNP data from proband in simplex family


title: NA0069-000_StyI

description: SNP data from proband in simplex family


title: NA0065-000_StyI

description: SNP data from proband in simplex family


title: NA0043-000_NspI

description: SNP data from proband in simplex family


title: NA0048-000_NspI

description: SNP data from proband in simplex family


title: NA0071-000_StyI

description: SNP data from proband in simplex family


title: NA0045-000_NspI

description: SNP data from proband in simplex family


title: NA0064-000_StyI

description: SNP data from proband in simplex family


title: NA0041-000_NspI

description: SNP data from proband in simplex family


title: NA0076-000_StyI

description: SNP data from proband in simplex family


title: NA0113-000_StyI

description: SNP data from proband in simplex family


title: NA0068-000_StyI

description: SNP data from proband in simplex family


title: NA0070-000_StyI

description: SNP data from proband in simplex family


title: NA0042-000_NspI

description: SNP data from proband in simplex family


title: NA0073-000_StyI

description: SNP data from proband in simplex family


title: NA0063-101_StyI

description: SNP data from trio simplex family


title: NA0047-000_NspI

description: SNP data from proband in simplex family


title: NA0099-000_StyI


title: NA0058-000_StyI

description: SNP data from proband in simplex family


title: NA0061-000_StyI

description: SNP data from proband in simplex family


title: NA0053-000_NspI

description: SNP data from proband in simplex family


title: NA0063-100_StyI

description: SNP data from trio simplex family


title: NA0057-000_StyI

description: SNP data from proband in simplex family


title: NA0056-000_StyI

description: SNP data from proband in simplex family


title: NA0039-101_NspI

description: SNP data from trio family where proband has abnormal karyotype


title: NA0060-000_StyI

description: SNP data from proband in simplex family


title: NA0039-100_NspI


title: NA0093-100_StyI

description: SNP data from trio simplex family


title: NA0055-000_StyI

description: SNP data from proband in simplex family


title: NA0053-000_StyI

description: SNP data from proband in simplex family


title: NA0063-000_StyI

description: SNP data from trio simplex family


title: NA0049-000_StyI


title: NA0051-000_StyI

description: SNP data from proband in simplex family


title: NA0032-000_NspI

description: SNP data from proband in simplex family


title: NA0030-000_NspI

description: SNP data from proband in simplex family


title: NA0052-100_StyI

description: SNP data from trio simplex family


title: NA0052-101_StyI

description: SNP data from trio simplex family


title: NA0052-000_StyI

description: SNP data from trio simplex family


title: NA0028-000_NspI

description: SNP data from proband in simplex family


title: NA0066-000_StyI

description: SNP data from proband in simplex family


title: NA0025-000_NspI

description: SNP data from proband in simplex family


title: NA0047-000_StyI

description: SNP data from proband in simplex family


title: NA0031-000_NspI

description: SNP data from proband in simplex family


title: NA0044-000_StyI

description: SNP data from proband in simplex family


title: NA0037-000_NspI

description: SNP data from proband in simplex family


title: NA0041-000_StyI

description: SNP data from proband in simplex family


title: NA0048-000_StyI

description: SNP data from proband in simplex family


title: NA0039-101_StyI


title: NA0027-000_NspI


title: NA0045-000_StyI

description: SNP data from proband in simplex family


title: NA0037-000_StyI

description: SNP data from proband in simplex family


title: NA0023-100_NspI

description: SNP data from trio simplex family


title: NA0039-100_StyI


title: NA0032-000_StyI

description: SNP data from proband in simplex family


title: NA0043-000_StyI

description: SNP data from proband in simplex family


title: NA0023-101_NspI

description: SNP data from trio simplex family


title: NA0019-000_NspI

description: SNP data from proband in simplex family


title: NA0042-000_StyI

description: SNP data from proband in simplex family


title: NA0023-000_NspI

description: SNP data from trio simplex family


title: NA0028-000_StyI

description: SNP data from proband in simplex family


title: NA0031-000_StyI

description: SNP data from proband in simplex family


title: NA0050-000_StyI

description: SNP data from proband in simplex family


title: NA0027-000_StyI


title: NA0023-101_StyI

description: SNP data from trio simplex family


title: NA0030-000_StyI

description: SNP data from proband in simplex family


title: NA0018-000_NspI

description: SNP data from proband in simplex family


title: NA0025-000_StyI

description: SNP data from proband in simplex family


title: NA0016-101_NspI

description: SNP data from trio simplex family


title: NA0016-100_NspI

description: SNP data from trio simplex family


title: NA0016-101_StyI

description: SNP data from trio simplex family


title: NA0023-100_StyI

description: SNP data from trio simplex family


title: NA0019-000_StyI

description: SNP data from proband in simplex family


title: NA0018-000_StyI

description: SNP data from proband in simplex family


title: NA0008-100_NspI


title: NA0008-101_NspI


title: NA0016-100_StyI

description: SNP data from trio simplex family


title: NA0016-000_StyI

description: SNP data from trio simplex family


title: NA0008-100_StyI


title: NA0007-000_StyI

description: SNP data from proband in simplex family


title: NA0023-000_StyI

description: SNP data from trio simplex family


title: NA0005-100_StyI


title: NA0008-101_StyI


title: NA0005-000_StyI


title: NA0016-000_NspI

description: SNP data from trio simplex family


title: NA0005-101_NspI


title: NA0005-101_StyI


title: NA0007-000_NspI

description: SNP data from proband in simplex family


title: NA0005-000_NspI


title: Embryo 72 h; Seed germination; Rep 2

type: RNA

city: Potsdam

first: Björn

last: Usadel

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description: Gene expression data from germinationg barley embryo 72h after imbibition

hyb_protocol: 10 µg labeled, fragmented cRNA was then hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

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.

label: Probe synthesis, labelling and hybridisation were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the UCI MicroArray Core Facility, Irvine, Ca.]

molecule: total RNA

organism: Hordeum vulgare

source_name: Barley Embryos from germinating seeds, 72h imbibed

label_protocol: The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.

growth_protocol: Seeds were germinated on a moist filter paper in Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) with 16 h light (17oC; 337-377 mmol m-2 s-1 light intensity measured by Sky Quantium light sensor) and 8 h darkness (12oC), 80% humidity.

extract_protocol: PURESCRIPT® RNA isolation kits (Gentra Systems, Inc., Minneapolis, MN) , followed by Rneasy spincolumn cleanup

treatment_protocol: endosperm+aleurone (e/a) and embryo+scutellum (em)  fractions were dissected from germinating seeds 0, 24, 48 and 72 after imbibition

tag: Genotype

value: Barke cultivar

tag: Age

value: 72h after imbibition


title: NA0004-000_StyI

description: SNP data from proband in simplex family


title: Embryo 72 h; Seed germination; Rep 1


title: NA0005-100_NspI


title: NA0003-000_StyI

description: SNP data from proband in simplex family


title: NA0004-000_NspI

description: SNP data from proband in simplex family


title: NA0001-100_StyI

description: SNP data from trio simplex family


title: Embryo 48 h; Seed germination; Rep 2

description: Gene expression data from germinationg barley embryo 48h after imbibition

source_name: Barley Embryos from germinating seeds, 48h imbibed

value: 48h after imbibition


title: NA0002-000_NspI

description: SNP data from proband in simplex family


title: NA0001-000_StyI

description: SNP data from trio simplex family


title: MM1086-004_StyI


title: NA0001-101_NspI

description: SNP data from trio simplex family


title: NA0001-101_StyI

description: SNP data from trio simplex family


title: Embryo 48 h; Seed germination; Rep 1


title: MM1094-004_StyI


title: NA0001-100_NspI

description: SNP data from trio simplex family


title: NA0003-000_NspI

description: SNP data from proband in simplex family


title: MM1084-003_StyI


title: MM0320-003_StyI


title: NA0001-000_NspI

description: SNP data from trio simplex family


title: Embryo 24 h; Seed germination; Rep 2

description: Gene expression data from germinationg barley embryo 24h after imbibition

source_name: Barley Embryos from germinating seeds, 0h imbibed

value: 24h after imbibition


title: Embryo 24 h; Seed germination; Rep 1

source_name: Barley Embryos from germinating seeds, 24h imbibed


title: MM0321-004_StyI


title: MM0733-003_StyI


title: MM0703-003_StyI

description: SNP data from proband in simplex family


title: MM1094-004_NspI


title: NA0002-000_StyI

description: SNP data from proband in simplex family


title: MM0711-003_StyI


title: MM0319-003_StyI


title: MM0323-004_StyI


title: MM1086-004_NspI


title: MM0309-003_StyI


title: MM0307-002_StyI

description: SNP data from trio multiplex family


title: Embryo 25DAF; Seed development; Rep 2

description: Gene expression data from barley embryo 25 DAF

source_name: Barley Embryo 25DAF

growth_protocol: Barley plants were cultivated in growth chambers at 20oC/18°C under a 16 h light/8 h dark cycle until seed set. The developmental stage of a caryopsis was determined from the mid-region of the ear and assigned as 4, 8, 16 and 25 days after flowering (DAF).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by Rneasy spincolumn cleanup

treatment_protocol: From the early stages of developing caryopsis, the maternal tissues, i.e. mostly pericarp (p), and the filial endosperm/embryo fraction as embryo sac (es) were separated by manual dissection as described by Sreenivasulu et al. (2002). At later stages 16 and 25 DAF endosperm+aleurone (e/a) and embryo+scutellum (em) fractions were prepared.

tag: Age:


title: MM0307-001_StyI

description: SNP data from trio multiplex family


title: MM0307-003_StyI

description: SNP data from trio multiplex family


title: Embryo 25DAF; Seed development; Rep 1


title: MM0733-003_NspI


title: MM1084-003_NspI


title: MM0306-004_StyI

description: SNP data from proband in simplex family


title: MM0310-005_StyI


title: Embryo 16DAF; Seed development; Rep 2

description: Gene expression data from barley embryo 16 DAF

source_name: Barley Embryo 16DAF


title: Embryo 0 h; Seed germination; Rep 2

description: Gene expression data from germinationg barley embryo 0h after imbibition

value: 0h after imbibition


title: Embryo 0 h; Seed germination; Rep 1


title: Embryo 16DAF; Seed development; Rep 1


title: Endosperm 72 h; Seed germination; Rep 2

description: Gene expression data from germinationg barley endosperm 72h after imbibition

source_name: Barley Enodsperm from germinating seeds, 72h imbibed


title: MM0318-003_StyI


title: MM0305-001_StyI

description: SNP data from trio multiplex family


title: MM0321-004_NspI


title: MM0323-004_NspI


title: MM0305-002_StyI

description: SNP data from trio multiplex family


title: Endosperm 72 h; Seed germination; Rep 1


title: MM0703-003_NspI

description: SNP data from proband in simplex family


title: Endosperm 48 h; Seed germination; Rep 2

description: Gene expression data from germinationg barley endosperm 48h after imbibition

source_name: Barley Enodsperm from germinating seeds, 48h imbibed


title: MM0303-002_StyI

description: SNP data from trio multiplex family


title: MM0303-003_StyI

description: SNP data from trio multiplex family


title: MM0304-004_StyI


title: MM0711-003_NspI


title: MM0299-003_StyI


title: MM0320-003_NspI


title: MM0298-004_StyI


title: Endosperm 48 h; Seed germination; Rep 1


title: MM0318-003_NspI


title: MM0303-001_StyI

description: SNP data from trio multiplex family


title: MM0295-003_StyI


title: Endosperm 24 h; Seed germination; Rep 1

description: Gene expression data from germinationg barley endosperm 24h after imbibition

source_name: Barley Enodsperm from germinating seeds, 24h imbibed


title: MM0319-003_NspI


title: MM0297-003_StyI


title: MM0289-003_StyI


title: MM0305-003_StyI

description: SNP data from trio multiplex family


title: Endosperm 0 h; Seed germination Rep 2

description: Gene expression data from germinationg barley endosperm 0h after imbibition

source_name: Barley Enodsperm from germinating seeds, 0h imbibed


title: MM0302-005_StyI

description: SNP data from proband in simplex family


title: Endosperm 0 h; Seed germination; Rep 1


title: MM0300-003_StyI


title: MM0286-003_StyI


title: MM0307-002_NspI

description: SNP data from trio multiplex family


title: Endosperm 24 h; Seed germination; Rep 2


title: MM0307-003_NspI

description: SNP data from trio multiplex family


title: MM0277-004_StyI


title: MM0296-003_StyI


title: MM0278-002_StyI

description: SNP data from trio simplex family


title: Endosperm 25DAF; Seed development; Rep 1

description: Gene expression data from barley endosperm 25 DAF

source_name: Barley Endosperm 25DAF


title: MM0309-003_NspI


title: MM0278-001_StyI

description: SNP data from trio simplex family


title: MM0307-001_NspI

description: SNP data from trio multiplex family


title: MM0273-004_StyI


title: MM0272-003_StyI


title: MM0305-003_NspI

description: SNP data from trio multiplex family


title: MM0265-003_StyI


title: MM0244-003_StyI

description: SNP data from trio multiplex family


title: MM0263-004_StyI


title: Endosperm 25DAF; Seed development; Rep 2


title: MM0269-004_StyI


title: MM0262-003_StyI


title: Endosperm 8DAF; Seed development; Rep 1

description: Gene expression data from barley endosperm 8DAF

source_name: Barley Endosperm 8DAF


title: MM0306-004_NspI

description: SNP data from proband in simplex family


title: Endosperm 8DAF; Seed development; Rep 2


title: MM0244-002_StyI

description: SNP data from trio multiplex family


title: MM0304-004_NspI


title: MM0305-001_NspI

description: SNP data from trio multiplex family


title: MM0240-003_StyI


title: MM0244-001_StyI

description: SNP data from trio multiplex family


title: MM0256-004_StyI


title: MM0305-002_NspI

description: SNP data from trio multiplex family


title: MM0238-003_StyI


title: MM0303-001_NspI

description: SNP data from trio multiplex family


title: MM0236-004_StyI


title: Endosperm 16DAF; Seed development; Rep 1

description: Gene expression data from barley endosperm 16 DAF

source_name: Barley Endosperm 16DAF


title: MM0241-004_StyI


title: Endosperm 4DAF; Seed development; Rep 2

description: Gene expression data from barley endosperm 4DAF

source_name: Barley Endosperm 4DAF


title: MM0226-003_StyI

description: SNP data from proband in multiplex family


title: MM0310-005_NspI


title: MM0303-003_NspI

description: SNP data from trio multiplex family


title: MM0303-002_NspI

description: SNP data from trio multiplex family


title: Endosperm 4DAF; Seed development; Rep 1


title: MM0302-005_NspI

description: SNP data from proband in simplex family


title: Endosperm 16DAF; Seed development; Rep 2


title: MM0225-001_StyI

description: SNP data from trio multiplex family


title: MM0225-002_StyI

description: SNP data from trio multiplex family


title: Pericarp 4DAF; seed development; Rep 2

description: Gene expression data from barley Pericarp 4DAF

source_name: Barley Pericarp 4DAF


title: Pericarp 4DAF; seed development; Rep 1


title: Pericarp 8DAF; seed development; Rep 1

description: Gene expression data from barley Pericarp 8DAF

source_name: Barley Pericarp 8DAF


title: MM0223-003_StyI

source_name: lymphoblast or blood


title: MM0274-003_StyI


title: MM0278-003_StyI

description: SNP data from trio simplex family


title: MM0215-004_StyI


title: Pericarp 8DAF; seed development; Rep 2


title: MM0270-003_StyI


title: MM0220-003_StyI


title: MM0218-004_StyI


title: MM0300-003_NspI


title: MM0299-003_NspI


title: MM0298-004_NspI


title: MM0297-003_NspI


title: MM0219-003_StyI


title: MM0214-003_StyI


title: MM0208-004_StyI


title: MM0212-004_StyI


title: MM0210-004_StyI

description: SNP data from trio multiplex family


title: MM0295-003_NspI


title: MM0210-001_StyI

description: SNP data from trio multiplex family


title: MM0202-003_StyI


title: MM0289-003_NspI


title: MM0176-003_StyI


title: MM0286-003_NspI


title: MM0197-003_StyI


title: MM0185-003_StyI


title: MM0210-002_StyI

description: SNP data from trio multiplex family


title: MM0171-001_StyI

description: SNP data from trio multiplex family


title: MM0278-003_NspI

description: SNP data from trio simplex family


title: MM0171-002_StyI

description: SNP data from trio multiplex family


title: MM0278-002_NspI

description: SNP data from trio simplex family


title: MM0152-003_StyI

description: SNP data from proband in simplex family


title: MM0171-004_StyI

description: SNP data from trio multiplex family


title: MM0278-001_NspI

description: SNP data from trio simplex family


title: MM0136-003_StyI


title: MM0153-003_StyI


title: MM0154-003_StyI


title: MM0277-004_NspI


title: MM0142-003_StyI


title: MM0135-003_StyI


title: MM0274-003_NspI


title: MM0149-003_StyI


title: MM0143-004_StyI


title: MM0272-003_NspI


title: MM0129-004_StyI


title: MM0122-003_StyI

description: SNP data from trio multiplex family


title: MM0122-001_StyI

description: SNP data from trio multiplex family


title: MM0270-003_NspI


title: MM0269-004_NspI


title: MM0126-003_StyI


title: MM0273-004_NspI


title: MM0119-003_StyI


title: MM0122-002_StyI

description: SNP data from trio multiplex family


title: MM0296-003_NspI


title: MM0116-004_StyI


title: MM0109-003_StyI

description: SNP data from trio simplex family


title: MM0103-003_StyI


title: MM0117-003_StyI


title: MM0262-003_NspI


title: MM0228-004_StyI


title: MM0102-003_StyI

description: SNP data from trio multiplex family


title: MM0109-001_StyI

description: SNP data from trio simplex family


title: MM0265-003_NspI


title: MM0112-005_StyI


title: MM0244-003_NspI

description: SNP data from trio multiplex family


title: MM0263-004_NspI


title: MM0108-003_StyI


title: MM0256-004_NspI


title: MM0109-002_StyI

description: SNP data from trio simplex family


title: MM0088-003_StyI


title: MM0102-002_StyI

description: SNP data from trio multiplex family


title: MM0225-004_StyI

description: SNP data from trio multiplex family


title: MM0102-001_StyI

description: SNP data from trio multiplex family


title: MM0063-003_StyI


title: MM0132-004_StyI


title: MM0064-003_StyI


title: MM0244-002_NspI

description: SNP data from trio multiplex family


title: MM0068-003_StyI


title: MM0057-003_StyI


title: MM0081-003_StyI


title: MM0241-004_NspI


title: MM0236-004_NspI


title: MM0020-004_StyI


title: MM0087-003_StyI


title: MM0019-003_StyI


title: MM0238-003_NspI


title: MM0013-003_StyI

description: SNP data from trio multiplex family


title: MM0022-003_StyI


title: MM0014-003_StyI


title: MM0010-005_StyI


title: MM0018-003_StyI


title: MM0011-003_StyI


title: MM0225-004_NspI

description: SNP data from trio multiplex family


title: MM0013-002_StyI

description: SNP data from trio multiplex family


title: MM0240-003_NspI


title: MM0013-001_StyI

description: SNP data from trio multiplex family


title: MM0007-003_StyI


title: MM0225-001_NspI

description: SNP data from trio multiplex family


title: MM0226-003_NspI


title: MM0228-004_NspI


title: MM0214-003_NspI


title: MM0225-002_NspI

description: SNP data from trio multiplex family


title: MM0003-003_StyI


title: MM0219-003_NspI


title: MM0223-003_NspI


title: MM0004-004_StyI


title: MM0154-003_NspI


title: MM0006-003_StyI


title: MM0208-004_NspI


title: MM0215-004_NspI


title: MM0210-004_NspI

description: SNP data from trio multiplex family


title: MM0244-001_NspI

description: SNP data from trio multiplex family


title: MM0210-001_NspI

description: SNP data from trio multiplex family


title: MM0171-004_NspI

description: SNP data from trio multiplex family


title: MM0143-004_NspI


title: MM0218-004_NspI


title: MM0136-003_NspI


title: MM0142-003_NspI


title: MM0153-003_NspI


title: MM0197-003_NspI


title: MM0212-004_NspI


title: MM0152-003_NspI

description: SNP data from proband in simplex family


title: MM0220-003_NspI


title: MM0171-001_NspI

description: SNP data from trio multiplex family


title: MM0149-003_NspI


title: MM0129-004_NspI


title: MM0126-003_NspI


title: MM0135-003_NspI


title: MM0122-003_NspI

description: SNP data from trio multiplex family


title: MM0185-003_NspI


title: MM0122-002_NspI

description: SNP data from trio multiplex family


title: MM0117-003_NspI


title: MM0109-003_NspI

description: SNP data from trio simplex family


title: MM0112-005_NspI


title: MM0109-002_NspI

description: SNP data from trio simplex family


title: MM0176-003_NspI


title: MM0103-003_NspI


title: MM0122-001_NspI

description: SNP data from trio multiplex family


title: MM0108-003_NspI


title: MM0171-002_NspI

description: SNP data from trio multiplex family


title: MM0119-003_NspI


title: SK0284-003_StyI

description: SNP data from trio simplex family


title: MM0109-001_NspI

description: SNP data from trio simplex family


title: MM0102-002_NspI

description: SNP data from trio multiplex family


title: MM0102-003_NspI

description: SNP data from trio multiplex family


title: MM0102-001_NspI

description: SNP data from trio multiplex family


title: MM0081-003_NspI


title: MM0202-003_NspI


title: SK0279-003_StyI

description: SNP data from trio multiplex family


title: MM0088-003_NspI


title: SK0267-003_StyI

description: SNP data from proband in simplex family


title: SK0274-003_StyI

description: SNP data from trio multiplex family


title: MM0068-003_NspI


title: MM0210-002_NspI

description: SNP data from trio multiplex family


title: SK0275-003_StyI

description: SNP data from trio simplex family


title: SK0268-003_StyI

description: SNP data from proband in simplex family


title: SK0280-003_StyI

description: SNP data from proband in simplex family


title: MM0087-003_NspI


title: MM0064-003_NspI


title: MM0063-003_NspI


title: MM0057-003_NspI


title: MM0132-004_NspI


title: SK0260-003_StyI

description: SNP data from trio multiplex family


title: SK0282-003_StyI

description: SNP data from trio simplex family


title: SK0252-003_StyI

description: SNP data from trio multiplex family


title: MM0019-003_NspI


title: SK0262-003_StyI

description: SNP data from trio simplex family


title: MM0020-004_NspI


title: SK0249-003_StyI

description: SNP data from trio simplex family


title: MM0022-003_NspI


title: MM0011-003_NspI


title: SK0237-004_StyI

description: SNP data from proband in simplex family


title: MM0007-003_NspI


title: MM0014-003_NspI


title: MM0013-001_NspI

description: SNP data from trio multiplex family


title: SK0261-003_StyI

description: SNP data from trio simplex family


title: MM0013-003_NspI

description: SNP data from trio multiplex family


title: SK0254-003_StyI

description: SNP data from proband in simplex family


title: SK0230-003_StyI

description: SNP data from trio simplex family


title: MM0013-002_NspI

description: SNP data from trio multiplex family


title: MM0010-005_NspI


title: SK0228-003_StyI

description: SNP data from proband in simplex family


title: MM0116-004_NspI


title: SK0231-003_StyI

description: SNP data from trio multiplex family


title: SK0224-004_StyI

description: SNP data from trio multiplex family


title: MM0006-003_NspI


title: SK0215-006_StyI

description: SNP data from trio family where proband has abnormal karyotype


title: SK0232-003_StyI

description: SNP data from trio multiplex family


title: SK0251-004_StyI

description: SNP data from proband in simplex family


title: MM0004-004_NspI


title: MM0003-003_NspI


title: SK0210-004_StyI

description: SNP data from trio multiplex family


title: SK0211-003_StyI

description: SNP data from proband with abnormal karyotype


title: SK0203-004_StyI

description: SNP data from trio multiplex family


title: SK0209-003_StyI

description: SNP data from proband in simplex family


title: SK0214-003_StyI

description: SNP data from trio simplex family


title: SK0200-004_StyI

description: SNP data from trio simplex family


title: SK0202-003_StyI

description: SNP data from trio multiplex family


title: SK0206-004_StyI

description: SNP data from trio multiplex family


title: SK0222-003_StyI

description: SNP data from trio simplex family


title: MM0018-003_NspI


title: SK0196-005_StyI

description: SNP data from trio simplex family


title: SK0195-003_StyI


title: SK0199-004_StyI

description: SNP data from proband in simplex family


title: SK0279-003_NspI

description: SNP data from trio multiplex family


title: SK0282-003_NspI

description: SNP data from trio simplex family


title: SK0284-003_NspI

description: SNP data from trio simplex family


title: SK0193-003_StyI

description: SNP data from proband in simplex family


title: SK0191-003_StyI

description: SNP data from trio multiplex family


title: SK0275-003_NspI

description: SNP data from trio simplex family


title: SK0182-003_StyI


title: SK0185-004_StyI


title: SK0181-004_StyI


title: SK0274-003_NspI

description: SNP data from trio multiplex family


title: SK0280-003_NspI

description: SNP data from proband in simplex family


title: SK0262-003_NspI

description: SNP data from trio simplex family


title: SK0190-003_StyI

description: SNP data from trio simplex family


title: SK0268-003_NspI

description: SNP data from proband in simplex family


title: SK0178-003_StyI


title: SK0171-004_StyI

description: SNP data from trio multiplex family


title: SK0175-003_StyI

description: SNP data from trio simplex family


title: SK0263-003_StyI

description: SNP data from proband in simplex family


title: SK0263-003_NspI

description: SNP data from proband in simplex family


title: SK0186-004_StyI

description: SNP data from trio simplex family


title: SK0172-005_StyI

description: SNP data from trio simplex family


title: SK0261-003_NspI

description: SNP data from trio simplex family


title: SK0267-003_NspI

description: SNP data from proband in simplex family


title: SK0251-004_NspI

description: SNP data from proband in simplex family


title: SK0260-003_NspI

description: SNP data from trio multiplex family


title: SK0254-003_NspI

description: SNP data from proband in simplex family


title: SK0162-004_StyI

description: SNP data from trio simplex family


title: SK0252-003_NspI

description: SNP data from trio multiplex family


title: SK0169-004_StyI

description: SNP data from trio multiplex family


title: SK0155-003_StyI

description: SNP data from trio simplex family


title: SK0230-003_NspI

description: SNP data from trio simplex family


title: SK0237-004_NspI

description: SNP data from proband in simplex family


title: SK0249-003_NspI

description: SNP data from trio simplex family


title: SK0160-003_StyI

description: SNP data from trio multiplex family


title: SK0158-003_StyI

description: SNP data from trio multiplex family


title: SK0161-003_StyI

description: SNP data from trio multiplex family


title: SK0222-003_NspI

description: SNP data from trio simplex family


title: SK0232-003_NspI

description: SNP data from trio multiplex family


title: SK0214-003_NspI

description: SNP data from trio simplex family


title: SK0215-006_NspI


title: SK0228-003_NspI

description: SNP data from proband in simplex family


title: SK0211-003_NspI


title: SK0224-004_NspI

description: SNP data from trio multiplex family


title: SK0206-004_NspI

description: SNP data from trio multiplex family


title: SK0231-003_NspI

description: SNP data from trio multiplex family


title: SK0209-003_NspI

description: SNP data from proband in simplex family


title: SK0141-003_StyI

description: SNP data from trio multiplex family


title: SK0200-004_NspI

description: SNP data from trio simplex family


title: SK0199-004_NspI

description: SNP data from proband in simplex family


title: SK0139-003_StyI


title: SK0210-004_NspI

description: SNP data from trio multiplex family


title: SK0202-003_NspI

description: SNP data from trio multiplex family


title: SK0196-005_NspI

description: SNP data from trio simplex family


title: SK0136-003_StyI


title: SK0195-003_NspI


title: SK0203-004_NspI

description: SNP data from trio multiplex family


title: SK0133-003_StyI


title: SK0153-004_StyI

description: SNP data from trio multiplex family


title: SK0130-003_StyI

description: SNP data from trio multiplex family


title: SK0191-003_NspI

description: SNP data from trio multiplex family


title: SK0175-003_NspI

description: SNP data from trio simplex family


title: SK0178-003_NspI


title: SK0185-004_NspI


title: SK0193-003_NspI

description: SNP data from proband in simplex family


title: SK0186-004_NspI

description: SNP data from trio simplex family


title: SK0120-003_StyI

description: SNP data from proband in simplex family


title: SK0190-003_NspI

description: SNP data from trio simplex family


title: SK0182-003_NspI


title: SK0122-003_StyI

description: SNP data from proband in simplex family


title: SK0172-005_NspI

description: SNP data from trio simplex family


title: SK0169-004_NspI

description: SNP data from trio multiplex family


title: SK0126-003_StyI


title: SK0162-004_NspI

description: SNP data from trio simplex family


title: SK0107-003_StyI

description: SNP data from proband in simplex family


title: SK0106-003_StyI

description: SNP data from proband in simplex family


title: SK0113-003_StyI

description: SNP data from trio simplex family


title: SK0108-004_StyI

description: SNP data from proband in simplex family


title: SK0161-003_NspI

description: SNP data from trio multiplex family


title: SK0171-004_NspI

description: SNP data from trio multiplex family


title: SK0141-003_NspI

description: SNP data from trio multiplex family


title: SK0155-003_NspI

description: SNP data from trio simplex family


title: SK0139-003_NspI


title: SK0158-003_NspI

description: SNP data from trio multiplex family


title: SK0105-003_StyI


title: SK0104-003_StyI


title: SK0160-003_NspI

description: SNP data from trio multiplex family


title: SK0153-004_NspI

description: SNP data from trio multiplex family


title: SK0181-004_NspI


title: SK0136-003_NspI


title: SK0126-003_NspI


title: SK0102-004_StyI

description: SNP data from proband in simplex family


title: SK0096-004_StyI

description: SNP data from proband in simplex family


title: SK0133-003_NspI


title: SK0107-003_NspI

description: SNP data from proband in simplex family


title: War1-C_replicate_2

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

description: no comments

hyb_protocol: Hybridization to whole-genome cDNA microarrays (Ontario Cancer Institute, Toronto, Canada; www.microarrays.ca) was done in DigEasyHyb (Roche, Mannheim, Germany) solution at 37°C overnight with 70 µg of salmon sperm DNA/ml as a carrier. Microarrays were washed three times in 1x SSC-0.1% SDS at 50°C, followed by a 1-minute wash in 1x SSC at room temperature. Glass slides were spun dry for 5 minutes at 500 rpm in a tabletop centrifuge

scan_protocol: Scanned on an Axon 4000B scanner (Molecular Devices), and analyzed and normalized using Gene Pix Pro4.1 software (Axon). DNA microarrays and protocols were obtained from the Ontario Cancer Institute.

data_processing: Normalization to set sum of all Median of ratios to one. Flagged features and control spots removed.

organism: Saccharomyces cerevisiae

label_protocol: RNA concentration was measured at 260 nm in TE pH 7. 20 µg of total RNA were used for cDNA synthesis with 200 U of Superscript II reverse transcriptase (Invitrogen, Carlsbad, Calif.) with either Cy3-dCTP or Cy5-dCTP. Labeled cDNAs were pooled, and RNA hydrolyzed for 20 minutes in 50mM NaOH at 65°C, followed by neutralization with acetic acid.

growth_protocol: Growth on rich medium in batch culture in rich medium with 2% Raffinose until OD600 reached 0.8; cells were harvested 1h after addition of 2% Galactose.

extract_protocol: RNA extraction by the hot-Phenol method.

treatment_protocol: Cells were grown at 30°C in batch culture, harvested by centrifugation and pellts whashed with sterile water and frozen at -80° until RNA extraction.

tag: Yeast strain W303-1A with Gal1 promoter driven WAR1-K762R gene

tag: Yeast strain W303-1A with Gal1 promoter driven War1


title: SK0108-004_NspI

description: SNP data from proband in simplex family


title: SK0130-003_NspI

description: SNP data from trio multiplex family


title: SK0122-003_NspI

description: SNP data from proband in simplex family


title: SK0095-003_StyI


title: War1-C_replicate_3

description: no comments

hyb_protocol: Hybridization to whole-genome cDNA microarrays (Ontario Cancer Institute, Toronto, Canada; www.microarrays.ca) was done in DigEasyHyb (Roche, Mannheim, Germany) solution at 37°C overnight with 70 µg of salmon sperm DNA/ml as a carrier. Microarrays were washed three times in 1x SSC-0.1% SDS at 50°C, followed by a 1-minute wash in 1x SSC at room temperature. Glass slides were spun dry for 5 minutes at 500 rpm in a tabletop centrifuge,


title: War1-C_replicate_1

description: no comments

treatment_protocol: Yeast strain W303-1A with Gal1 promoter driven WAR1-K762R gene


title: SK0092-003_StyI

description: SNP data from trio multiplex family


title: SK0113-003_NspI

description: SNP data from trio simplex family


title: SK0105-003_NspI


title: SK0096-004_NspI

description: SNP data from proband in simplex family


title: Human TB106 SC1-6 50KXba

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

country: Japan

institute: RIKEN

description: Bulk genomic DNA from lymphoblastoid cell, CMK11-5 cell line, and postmortem brains, as well as their single cells were analyzed.

hyb_protocol: Arrays were washed with Affymetrix fluidics station 450.

scan_protocol: Arrays were scanned using the Gene Chip Scanner 3000.

data_processing: CEL files were generated using GCOSv1.4 and SNP calls generated using GTYPEv 4.1.

source_name: Lymphoblastoid cells

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

extract_protocol: Standarad DNA extraction protocol. DNA quantity was assessed with a Nanodrop Spectrophotometer.

tag: EB-virus induced cell line, establised from Japanese female. Single-cell whole-genome amplified.


title: SK0095-003_NspI


title: SK0120-003_NspI

description: SNP data from proband in simplex family


title: SK0094-005_NspI


title: SK0087-008_StyI


title: SK0094-005_StyI


title: SK0090-003_StyI

description: SNP data from trio simplex family


title: Human TB106 SC1-1 50KXba


title: SK0102-004_NspI

description: SNP data from proband in simplex family


title: Human TB106 SC46 50KXba


title: SK0089-004_StyI


title: SK0104-003_NspI


title: Human TB106 SC34 50KXba


title: SK0073-003_StyI


title: SK0089-004_NspI


title: Human TB106 SC40 50KXba


title: Human TC106 SC45 50KXba


title: SK0090-003_NspI

description: SNP data from trio simplex family


title: SK0061-003_StyI


title: Human TB106 SC32 50KXba


title: Human TB106 SC42 50KXba


title: SK0057-003_StyI

description: SNP data from trio simplex family


title: SK0047-003_StyI

description: SNP data from proband in simplex family


title: SK0106-003_NspI

description: SNP data from proband in simplex family


title: SK0044-003_StyI


title: Human TB106 SC41 50KXba


title: SK0087-008_NspI


title: SK0048-003_StyI

description: SNP data from trio multiplex family


title: Human CMK11-5 SC13 50KXba

source_name: CMK11-5 cell line

tag: CMK11-5 cell line, established from a patient with Down syndrome


title: SK0061-003_NspI


title: SK0048-003_NspI

description: SNP data from trio multiplex family


title: SK0043-003_StyI


title: Human CMK11-5 SC17 50KXba


title: SK0027-003_StyI

description: SNP data from trio simplex family


title: SK0073-003_NspI


title: SK0045-003_NspI

description: SNP data from trio multiplex family


title: SK0057-003_NspI

description: SNP data from trio simplex family


title: SK0044-003_NspI


title: Human CMK86 50KXba

source_name: CMK86 cell line

tag: CMK86 cell line, established from a patient with Down syndrome


title: SK0031-003_StyI


title: Human CMK11-5 SC04 50KXba


title: SK0025-003_StyI

description: SNP data from trio multiplex family


title: OL33

status: Public on Dec 19 2007

city: Bologna

first: Luca

last: Morandi

address: Via Altura 3

department: Oncology Dept

country: Italy

institute: University of Bologna

description:
Fluorescent
intensities on scanned images were quantified by the feature extraction
software 7.5, and LogRatio data were available for further statistical
analysis.

hyb_protocol: 0.75 ug of labeled test and reference cRNA were fragmented and hybridized at 60 C for 17 hours. The washing steps were done following the SSC protocol (version 3.0, Agilent)

scan_protocol: After  hybridization and washes, the slides were  scanned with a confocal laser scanner (Agilent G2565BA).

data_processing:
The
scan data were analysed with Agilent Feature Extraction Software, which
performs spots localization (Find Spot Algorithm), outlier pixels
rejection based on the Interquartile Range method (Cookie Cutter
Algorithm), flagging of saturated features (a feature is considered
saturated when more than 50% of its pixels had an intensity above
65502). Loess normalization and between array scale normalization were
performed using the “LIMMA” package of Bioconductor
(www.bioconductor.org).

source_name: low grade brain tumor pool

label_protocol:
The labeled cRNA was generated by in vitro transcription with the use of T7
RNA polymerase (low RNA input fluorescent linear amplification kit
Agilent cod. 5184-3523).

extract_protocol: Protect RNAeasy Mini kit protocol (Qiagen)

treatment_protocol:
Fresh frozen biopsies in liquid nitrogen and put them at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio= 1.66

tag: pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.51

tag: Fresh frozen biopsy from right frontal oligodendroglioma (recurrence of a primary oligodendroglioma resected on 05/12/1993) of a 41 years old women. Overall Survival (months)


title: SK0045-003_StyI

description: SNP data from trio multiplex family


title: Human TB106 50KXba

source_name: lymphoblastoid cells

tag: EB-virus induced cell line, establised from Japanese female.


title: SK0027-003_NspI

description: SNP data from trio simplex family


title: Human CMK11-5 50KXba


title: SK0092-003_NspI

description: SNP data from trio multiplex family


title: OL31

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.50

tag: Fresh frozen biopsy from right frontal oligodendroglioma of a 60 years old men. Alive, surgical resection


title: OL30

tag: Fresh frozen biopsy from oligodendroglioma of a 60 years old women. Alive, surgical resection


title: Human TB106 SC27 50KXba


title: SK0043-003_NspI

tag: Family ID

tag: DNA ID


title: SK0047-003_NspI

description: SNP data from proband in simplex family

tag: Gender

tag: Family Type


title: Human TB106 WGA 50KXba

tag: EB-virus induced cell line, establised from Japanese female. Whole-genome amplified.


title: PA32

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.54

tag: Fresh frozen biopsy from a pilocytic astrocytoma of a 3 years old child. Alive, surgical resection


title: SK0015-003_StyI

tag: Individual Type


title: SK0010-003_StyI

description: SNP data from trio multiplex family


title: SK0031-003_NspI


title: OL29

tag: Fresh frozen biopsy from right frontal oligodendroglioma of a 32 years old men. Overall Survival (months)


title: SK0015-003_NspI


title: FA34

tag: Fresh frozen biopsy from right frontal glioblastoma of a 68 years old women. OS (months)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.45

tag: Fresh frozen biopsy from parietal fibrillary astrocytoma  of a 34 years old women. OS (months)


title: SK0010-003_NspI

description: SNP data from trio multiplex family


title: SK0006-003_StyI

description: SNP data from trio multiplex family


title: PA28

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.67

tag: Fresh frozen biopsy from a pilocytic astrocytoma  of a 26 years old women. Alive

value: surgical resection:06/30/1991


title: NA0008-0000_StyI


title: SK0002-003_StyI


title: SK0025-003_NspI

description: SNP data from trio multiplex family


title: GL35

data_processing:
The
scan data were analysed with Agilent Feature Extraction Software, which
performs spots localization (Find Spot Algorhythm), outlier pixels
rejection based on the Interquartile Range method (Cookie Cutter
Algorhythm), flagging of saturated features (a feature is considered
saturated when more than 50% of its pixels had an intensity above
65502). Loess normalization and between array scale normalization were
performed using the “LIMMA” package of Bioconductor
(www.bioconductor.org).

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.44

tag: Fresh frozen biopsy from left frontal glioblastoma of a 50 years old men. Overall Survival (months)


title: SK0002-003_NspI


title: GL38

tag: pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=2.18

tag: Fresh frozen biopsy from right frontal glioblastoma of a 67 years old men. OS (months)


title: GL25

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.33

tag: Fresh frozen biopsy from right parietal glioblastoma of a 61 years old men. Overall Survival (months)


title: GL36

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=2.14

tag: Fresh frozen biopsy from temporal glioblastoma of a 69 years old women. Overall Survival (months)


title: PA23

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=2.26

tag: Fresh frozen biopsy from  pilocytic astrocytoma of a 39 years old women. Alive (surgical resection


title: FA24

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.47

tag: Fresh frozen biopsy from a fibrillary astrocytoma  of a 29 years old men. Alive

value: (surgical resection:06/01/1991)


title: GL37

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.58

tag: Fresh frozen biopsy from right temporal glioblastoma of a 66 years old women. OS (months)


title: GL26

tag: Fresh frozen biopsy from right frontal glioblastoma of a 34 years old women. Overall Survival (months)


title: NA0008-0000_NspI

treatment_protocol: Not Applicable

tag: Family ID

tag: DNA ID

tag: Gender

tag: Family Type


title: NA0039-000_NspI

tag: Individual Type


title: GL42

description: Fluorescent intensities on scanned images were quantified by the feature extraction software 7.5, and LogRatio data were available for further statistical analysis.

hyb_protocol: 0.75 ug of labeled test and reference cRNA were fragmented and hybridized at 60 C for 17 hours. The washing steps were done following the SSC protocol (Agilent version 3.0)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.66

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.51

tag: Fresh frozen biopsy from right temporal-insular glioblastoma of a 57 years old men. Overall Survival (months)


title: GL46

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.29

tag: Fresh frozen biopsy from left frontal glioblastoma (focal necrosis) of a 79 years old women. Alive, surgical resection


title: GL19

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.08

tag: Fresh frozen biopsy from frontal-temporal glioblastoma of a 59 years old men. OS (months)


title: SK0006-003_NspI

description: SNP data from trio multiplex family


title: GL47

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.30

tag: Fresh frozen biopsy from left parietal glioblastoma of a 73 years old men. Overall Survival (months)


title: GL44

treatment_protocol:
Fresh frozen biopsies in liquid nitrogen and put them at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio= 1.66

tag: pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.56

tag: Fresh frozen biopsy from right frontal glioblastoma of a 53 years old men. Overall Survival (months)


title: GL20

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio= 1.66

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.02

tag: Fresh frozen biopsy from right frontal glioblastoma of a 57 years old men. Overall Survival (months)


title: GL17

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.34

tag: Fresh frozen biopsy from left frontal glioblastoma of a 67 years old women. Overall Survival (months)


title: GL27

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.46

tag: Fresh frozen biopsy from left frontal glioblastoma of a 53 years old men. OS (months)

value: not available:lost during follow-up


title: GL18

tag: Fresh frozen biopsy from left frontal glioblastoma of a 53 years old women. Overall Survival (months)


title: GL16

tag: Fresh frozen biopsy from right temporal glioblastoma of a 35 years old women. OS (months)


title: ACK11_10

city: Durham

first: Bryan

last: Cullen

state: NC

address: CARL Bldg 427, Research Drive

country: USA

institute: Duke University Medical Center

description: Arrays were printed at the Duke Microarray Facility using the Genomics Solutions OmniGrid 300 Arrayer. The arrays contain the Human Operon v3.0.2 arrays (Oligo Source) that possess 34,602 unique optimized 70-mers.

hyb_protocol: Sample and reference cDNA were pooled, purified with QIAquick Purification Columns (Qiagen), mixed with hybridization buffer (50% formamide, 5 SSC, and 0.1% SDS), COT-1 DNA, and poly-deoxyadenylic acid to limit nonspecific binding, and heated to 95º C for 2 minutes. This mixture was pipetted onto a microarray slide, and hybridized overnight at 42º C on the MAUI hybridization system (BioMicro Systems). The array was then washed at increasing stringencies before scanning. All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

scan_protocol: Arrays were scanned on a GenePix 4000B microarray scanner (Axon Instruments). All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

data_processing: All arrays were subject to background subtraction followed by loess normalization within each array and scale normalization across all arrays using the arrayMagic package in R (Buness A., Huber W., Steiner K., Sueltmann H., Poustka A. arrayMagic: two-colour cDNA microarray quality control and preprocessing. Bioinformatics 2005 21, 554–556). KNN impute package in GenePattern (Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500) was used to impute missing data if a probe had intensity values for at least half the samples. Otherwise the probes were excluded from analysis. Replicate probes were collapsed to one probe corresponding to the median value of all the replicates.

source_name: Stably Transduced B-Cell Line

label_protocol: Total RNA (10 µg) from each sample and the reference (Universal Human Reference RNA, Stratagene) were hybridized to oligo (dT) primers at 65º C and then incubated at 42º C for 2 hours in the presence of reverse transcriptase, Cy5- or Cy3-dUTP and Cy5- or Cy3-dCTP, and a deoxynucleotide mix. In all cases, BJAB derived RNA samples were labeled with Cy5 and reference samples were labeled with Cy3. NaOH was used to destroy residual RNA. All protocols are available in greater detail on the Duke Microarray Facility Web site (http://microarray.genome.duke.edu/services/spotted-arrays/protocols).

extract_protocol: total RNA was prepared using TRIzol reagent as instructed and 10µg of RNA was used per reaction. RNA quality was ascertained using an Agilent 2100 bioanalyzer (Agilent technologies).

tag: BJAB cells stably transduced with lentiviral vector pNL-SIN-CMV-AcGFP/miR-K12-11


title: GL10

data_processing: The scan data were analysed with Agilent Feature Extraction Software, which performs spots localization (Find Spot Algorhythm), outlier pixels rejection based on the Interquartile Range method (Cookie Cutter Algorhythm), flagging of  saturated features (a feature is considered saturated when more than 50% of its pixels had an intensity above 65502). Loess normalization and between array scale normalization  were performed using the “LIMMA” package of Bioconductor (www.bioconductor.org).

label_protocol: The labeled cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (low RNA input fluorescent linear amplification kit Agilent cod. 5184-3523).

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S:1.66

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.49

tag: Fresh frozen biopsy from right frontal glioblastoma of a 67 years old men. OS (months):1.6


title: ACK11_4

source_name: Universal Human Reference RNA, Stratagene


title: C_jejuni_strain_RM4278_rep2

city: Albany

first: Craig

middle: T

last: Parker

state: CA

address: 800 Buchanan St

department: PSM

institute: USDA ARS

description: Intensity ratios of DNA (channel 1) divided by DNA (channel 2) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Labeled reference and sample DNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Axon GenePix4000B, 10nm resolution. GenePix software. Optimize intensities manually.

data_processing: Data normalization was performed in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

organism: Campylobacter jejuni

source_name: Campylobacter jejuni strain NCTC 11168/RM1221

label_protocol: Labeling protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

extract_protocol: Genomic DNA isolated using protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

tag: DNA labelled with Cy5-dUTP and laser scanned at 635nm with background subtracted from feature signal

source_name: Campylobacter jejuni strain RM4278

tag: DNA labelled with Cy3-dUTP and laser scanned at 532nm with background subtracted from feature signal


title: C_jejuni_strain_RM3207_rep1

source_name: Campylobacter jejuni strain RM3207


title: ACGFP_8

tag: BJAB cells stably transduced with lentiviral vector pNL-SIN-CMV-AcGFP

tag: Universal Human Reference RNA, Stratagene


title: NA0039-000_StyI

tag: Family ID

tag: DNA ID

tag: Gender

tag: Family Type

tag: Individual Type


title: ACK11_6


title: ACGFP_9


title: ACK11_5


title: GL15

tag: pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.18

tag: Fresh frozen biopsy from temporal glioblastoma of a 59 years old women. Overall Survival (months)


title: GL9

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.57

tag: Fresh frozen biopsy from right temporal glioblastoma of a 33 years old men. Overall Survival (months):18.6


title: GL12

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.60

tag: Fresh frozen biopsy from right parietal glioblastoma of a73 years old men. OS (months)


title: C_jejuni_strain_RM4278_rep1


title: C_jejuni_strain_RM4275_rep2

source_name: Campylobacter jejuni strain RM4275


title: C_jejuni_strain_RM4275_rep1


title: ACGFP_7


title: ACGFP_10


title: PA22

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.88

tag: Fresh frozen biopsy from a pilocytic astrocytoma   of a 20 years old men. Alive, surgical resection


title: C_jejuni_strain_RM3198_rep1

source_name: Campylobacter jejuni strain RM3198


title: C_jejuni_strain_RM4274_rep2

source_name: Campylobacter jejuni strain RM4274


title: GL7

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.24

tag: Fresh frozen biopsy from right frontal-parietal glioblastoma of a 54 years old women. OS (months)


title: GL6

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.27

tag: Fresh frozen biopsy from left parietal glioblastoma of a 71 years old women. Overall Survival (months)


title: Cbh1_1_WT

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, Cbh1-FLAG ChIP(chromatin immunoprecipitation)-on-chip replicate 1

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformadehyde at 18C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

tag: Chromatin DNA not enriched for Cbh1-FLAG

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

tag: Chromatin DNA enriched for Cbh1-FLAG


title: GL5

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.09

tag: Fresh frozen biopsy from right frontal glioblastoma of a 43 years old men. OS (months)


title: C_jejuni_strain_RM4274_rep1

tag: DNA labelled with Cy5-dUTP and laser scanned at 635nm with background subtracted from feature signal

tag: DNA labelled with Cy3-dUTP and laser scanned at 532nm with background subtracted from feature signal


title: C_jejuni_strain_RM4270_rep2

source_name: Campylobacter jejuni strain RM4270


title: PA21

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio=1.99

tag: Fresh frozen biopsy from a pilocytic astrocytoma  of a 7 years old child. Alive

value: surgical resection 23/09/1996


title: C_jejuni_strain_RM4269_rep2

source_name: Campylobacter jejuni strain RM4269


title: GL1

hyb_protocol: 0.75 ug of labeled test and reference cRNA were fragmented and hybridized at 60 C for 17 hours. The washing steps were done following the SSC protocol (version 3.0)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S ratio: 1.66

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent): 28S/18S: 1.38

tag: Fresh frozen biopsy from right frontal glioblastoma of a 68 years old women. OS (months)

value: 0.5. Died for thromboembolism


title: GL4

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.29

tag: Fresh frozen biopsy from left cerebellar of  a 40 years old men. Overall Survival (months)


title: GL8

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.61

tag: Fresh frozen biopsy from  frontal glioblastoma of a 30 years old men. Overall Survival (months)


title: BOEC, not_at_risk 9

status: Public on Dec 18 2007

city: Minneapolis

first: Robert

middle: P.

last: Hebbel

state: MN

address: MMC 480, 420 Delaware St. SE

department: Medicine

institute: University of Minnesota

description: BOEC (blood outgrowth endothelial cells) from 20 subjects with sickle cell anemia shown to be either at-risk or not-at-risk for ischemic stroke

hyb_protocol: After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing,

scan_protocol: An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual

data_processing: For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays).

source_name: BOEC, not_at_risk 9

label_protocol: We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.

growth_protocol: We obtained citrated fresh peripheral blood (50-100 ml) from each donor. For donors outside the Minneapolis metropolitan area, blood was shipped by same-day express delivery in Saf-T-Pak cartons that had been pre-equilibrated to room temperature. Samples were processed immediately upon arrival at the University of Minnesota. Blood buffy coat mononuclear cells were prepared and cultured on rat collagen I, in presence of endothelial cell growth factors, as previous described in detail 15,16. All samples were handled identically

extract_protocol: We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).

treatment_protocol: BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.

tag: At Risk

tag: Age

tag: Sex

value: M


title: D.m.Third_instar_larval_midgut_normal_12h_rep1

city: Urbana

first: Hongmei

last: LI

state: IL

address: 505 S. Goodwin Ave

department: Entomology

institute: University of Illinois at Urbana-Champaign

description: Gene expression data from the third instar Drosophila larval midgut

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 2500A

data_processing: The data were analyzed with GCOS software (Affymetrix, Santa Clara, CA).

organism: Drosophila melanogaster

source_name: Third instar larval midgut, normal, 12 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Temp: 24°C Humid:60% Light/Dark cycle: 14:10

extract_protocol: Total RNA was isolated by using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen Inc., Valencia, CA) following the manufacturers’ protocol.

treatment_protocol: Midguts were dissected out in 214 mM NaCl solution, and then transferred to RNAlater® (Ambion Inc., Austin, TX). After dissecting, fifty midguts were pooled in the RNAlater and immediately frozen in liquid nitrogen, then transferred to -80°C. Fifty midguts represented a single replicate for each microarray experiment. Three biological replicates were performed, with one biological replicate per oligoarray for a total of three oligoarrays.

tag: Strain

value: W1118 Age:Third instar, 120 hours

tag: Tissue

value: midgut


title: GL3

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S:1.66

tag: pool of 4 oligodendrogliomas(OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (RNA 6000 Nano LabChip® kit, Agilent): ratio 28S/18S: 1.3

tag: Fresh frozen biopsy from right temporal glioblastoma of a 69 years old men. OS (months)


title: D.m.Third_instar_larval_midgut_normal_12h_rep3


title: Macaca fascicularis testis 1

city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

institute: National Institute of Biomedical Innovation

description: Three-year-old male Macaca fascicularis testis, duplicate 1.

hyb_protocol: Hybridization was performed using the Affymetrix protocol (49 Format Array).

scan_protocol: GeneChip was scanned using an Affymetrix GeneChip scanner.

data_processing: Data were analyzed GeneChip Operating Software 1.4.

label: Biotin

organism: Macaca fascicularis

source_name: Testis

label_protocol: One cycle target labeling (Affymetrix)

extract_protocol: Total RNA was extracted using TRIZOL.

tag: Macaca fascicularis testis, 3-year-old male


title: Macaca fascicularis testis 2

description: Three-year-old male Macaca fascicularis testis, duplicate 2.


title: BOEC, not_at_risk 6

source_name: BOEC, not_at_risk 6


title: BOEC, not_at_risk 7

source_name: BOEC, not_at_risk 7


title: BOEC, at_risk 1

source_name: BOEC, at_risk 1


title: GL2

source_name: pool of low grade brain tumors

treatment_protocol:
Fresh frozen in liquid nitrogen and put at -80. After thawing, RNA Later treatment before tissue homogenization.
Total RNA was measured by Bioanalyzer 2100 (Agilent).

tag: pool of 4 oligodendrogliomas (OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytoma (FA)

tag: Fresh frozen biopsy from a left frontal glioblastoma of a 77 years old women


title: C_jejuni_strain_RM4270_rep1

source_name: Campylobacter jejuni strain NCTC 11168/RM1221


title: Macaca fascicularis liver 2

description: Three-year-old male Macaca fascicularis liver, duplicate 2.

source_name: Liver

tag: Macaca fascicularis liver, 3-year-old male


title: Abp1_2_WT

description: Schizosaccharomyces pombe cells, Abp1-FLAG ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Abp1-FLAG

tag: Chromatin DNA enriched for Abp1-FLAG


title: Macaca fascicularis liver 1

description: Three-year-old male Macaca fascicularis liver, duplicate 1.


title: Cbh1_2_WT

description: Schizosaccharomyces pombe cells, Cbh1-FLAG ChIP(chromatin immunoprecipitation)-on-chip replicate 2

tag: Chromatin DNA not enriched for Cbh1-FLAG

tag: Chromatin DNA enriched for Cbh1-FLAG


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin 4D-N

city: Seoul

first: Su

last: Hong

department: Life Science Institute

country: South Korea

institute: Macrogen Inc.

description: In order to determine how Noggin may induce cardiac differentiation, we compared differentially expressed genes during Noggin treatment of ES cells using microarray analysis

hyb_protocol: Beads individually manufactured and QC’d with full length OligatorTM oligos Bead type = unique IllumiCodeTM

scan_protocol: GenePix

data_processing:
Quantile normalization
1. developed for affymetrix probeset arrays
2. uses the whole datasetm no particular distribution assumed
3. makes the distribution of probe intensities for each array in a set of arrays the same
4. reduction of variance slightly better than Lowess

organism: Mus musculus

source_name: Mock treated 4 day

label_protocol:
1.50 base gene-specific Probe linked to 23 base Address
2.Hybridized to labeled nucleic acid made from total RNA
3.Each bead coated with same probe oligo (100,000’s copies)
4.~30 copies of each bead type per array
5.RNA isolation > RT cDNA synthesis > IVT biotinylated cRNA > Hyb SA-Cy3

extract_protocol: Trizol extraction of total RNA

tag: Cell

value: J1 ES cell

tag: Treatment

value: Noggin treat for 3days with LIF


title: BOEC, not_at_risk 8

source_name: BOEC, not_at_risk 8

tag: At Risk

value: F


title: Abp1_1_WT

description: Schizosaccharomyces pombe cells, Abp1-FLAG ChIP(chromatin immunoprecipitation)-on-chip replicate 1


title: D.m.Third_instar_larval_midgut_normal_12h_rep2


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin D2-N

source_name: Mock treated 2 day


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin D4-P

source_name: Noggin treated 4 day


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin D2-P

source_name: Noggin treated 2 day


title: Macaca fascicularis cerebellum 1

description: Three-year-old male Macaca fascicularis cerebellum, duplicate 1.

source_name: Cerebellum

tag: Macaca fascicularis cerebellum, 3-year-old male


title: Macaca fascicularis brain 2

description: Three-year-old male Macaca fascicularis brain, duplicate 2.

source_name: Brain

tag: Macaca fascicularis brain, 3-year-old male


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin D0-N

source_name: Mock treated 0 day


title: C_jejuni_strain_RM4269_rep1

tag: DNA labelled with Cy5-dUTP and laser scanned at 635nm with background subtracted from feature signal

source_name: Campylobacter jejuni strain RM4269

label_protocol: Labeling protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135

tag: DNA labelled with Cy3-dUTP and laser scanned at 532nm with background subtracted from feature signal


title: Macaca fascicularis cerebellum 2

description: Three-year-old male Macaca fascicularis cerebellum, duplicate 2.


title: H37Rv 4hrs after infection in macrophage vs. H37Rv grown in 7H9 media biological replicate 6 (A 4hrs)

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

hyb_protocol: Slides were blocked prior to hybridization using BSA The purified cDNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).  The probes were covered by a flat 22x22mm coverslip (Corning) and hybridized in sealed hybridization chambers (Genemachines) for sixteen hours in a 50°C water bath.

scan_protocol: The slides were scanned using an Axon 4000B scanner

data_processing: The images were processed using GenePix 5.1 and resulting text files were exported to Microsoft Excel

organism: Mycobacterium tuberculosis

source_name: H37Rv grown in 7H9 media

label_protocol: Total RNA was reversed transcribed into cDNA using Superscript II RT in the presence of Cyanine-3 or Cyanine-5 dUTP (PerkinElmer) by a modification of the procedure described by Voskuil et. al. (Voskuil et. al, 2003).  This was accomplished using a reaction mix with a final concentration of 0.17ug/ul random hexamers (IDT), 0.96x first strand buffer (Invitrogen), 9.6mM DTT (Invitrogen), 0.44mM dATP, dCTP and dGTP (Invitrogen), 0.02mM dTTP (Invitrogen), 0.06mM Cyanine 3 or 5 dUTP (PerkinElmer) and 9.4units Superscript II (Invitrogen).  The combination of reaction mix and total RNA was incubated for ten minutes at 25°C followed by ninety minutes at 42°C.  The labeled cDNA probes were then purified and concentrated using a Microcon YM10 filter (Millipore) and TE buffer pH 8.0 (Ambion).  Slides were blocked prior to hybridization using BSA The purified cDNA probes were added to the arrays together with a hybridization solution mix resulting in a final concentration of 0.5ug/ul tRNA (Invitrogen), 2.0X SSC (Ambion), 0.25% Formamide (Sigma) and 0.1% SDS (Ambion).

growth_protocol: The Mtb strains H37Rv was used for all the experiments.  Bacterial stocks were maintained at -80?C in 7H9ADCTW (Middlebrook 7H9 (Difco) supplemented with 1x ADC [0•5% bovine serum albumin, fraction V (Boehringer Manheim), 0•2% glucose and 0•085% NaCl], 0•2% glycerol and 0•1% Tween 80).   Aliquots of bacteria were thawed and cultured in solid media 7H10 ADCTW.   For preparation of liquid cultures bacteria growing in 7H10 agar plates were resuspended in 7H9ADCTW media at an OD: 0.05.  Liquid cultures were grown in plastic roller bottles in a roller apparatus until OD 0.2.

extract_protocol: Mtb RNA from in vitro cultures:  Bacterial cell pellets were resuspended in 1 ml TRI reagent  (Molecular Research Center,OH) and immediately transferred to a 2ml screw cap microcentrifuge tube with o-rings containing 0.5ml zirconia beads (0.1mm diameter, Biospec Products, Inc., OH).  Samples were disrupted by two 1-min pulses in a BeadBeater, keeping the samples on ice for 2 minutes in between the pulses.  The liquid was removed from the beads, incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quiagen).  The eluted RNA was kept at -80°C until further use.

tag: strain H37Rv

tag: Time

value: Control exponentially growing H37Rv in 7H9 media

source_name: H37Rv 4hrs after infection in macrophage (THP1)

extract_protocol: Macrophages infected with Mtb were lysed with 20 ml per 175 cm2 flask of guanidinium thiocyanate -based buffer (25 mM sodium citrate/4 M guanidine thiocyanate/0.5% N-lauryl sarcosine/0.125 M mercaptoethanol, 0.5% Tween 80, pH 7.0) and eukaryotic DNA was sheared by homogenization of the samples for 5 min with a Vertis homogenizer  (Vertis).  Samples were spin down for 30 min at 4,000xg and bacterial pellets were washed with 10 ml of guanidinium thiocyanate -based buffer and spin down for 15 min at 4,000xg.  Bacterial cell pellets were resuspended in 1 ml TRI reagent  (Molecular Research Center,OH) and immediately transferred to a 2ml screw cap microcentrifuge tube with o-rings containing 0.5ml zirconia beads (0.1mm diameter, Biospec Products, Inc., OH).  Samples were disrupted by two 1-min pulses in a BeadBeater, keeping the samples on ice for 2 minutes in between the pulses.  The liquid was removed from the beads, incubated at room temperature for 10 min and centrifugated for 10 min at 12,000g.  The supernatant was transferred to a clean tube, 100µl BCP Reagent (Molecular Research Center) was added to 1ml samples in TRI, and then the tubes were shaken vigorously for 15 sec, incubated 10 min at room temperature and then centrifuged for 15 min at 12,000xg.  The supernatant was recovered and precipitated with 600µl isopropanol.  After washing with 75% ethanol the RNA was resuspended in 30-100µl of DEPC-treated H2O and then treated with RNAse-free DNAse (Ambion) for 30min at 37°c. After DNAse treatment samples were further purified using Rneasy columns (Quiagen).  The eluted RNA was kept at -80°C until further use.

treatment_protocol: Ten 175cm2 flasks were seeded with 100 ml of 106 THP-1 cells/ml.  THP-1 cells were differentiated with 40 nMolar PMA (phorbol myristate acetate) overnight at 37°C, 5%CO2 and 95% humidity.  Mtb cultures were grown exponentially in the usual 7H9ADCTW to an OD of 0.2 for the infection.  An appropriate volume of this culture was resuspended in RPMI with 20% FCS to obtain a bacterial suspension of 2x106 cfu/ml.  One hundred milliliters of bacterial suspension were added to each flask (MOI: 2). Macrophages and bacteria were incubated for 2 h.  After incubation macrophages were washed with warm PBS and 100ml of RPMI +20% FCS were added to each flask.   Infections were followed for 4 hours and cells from five flasks were processed  for bacterial RNA extraction.

value: 4hrs after infection


title: Macaca fascicularis brain 1

description: Three-year-old male Macaca fascicularis brain, duplicate 1.


title: E6_nRBCs_2

status: Public on Dec 17 2007

city: Kobe

first: Brendan

last: McIntyre

state: Hyogo

address: 2-2-3 /minatojima-minamimachi

institute: Kobe RIKEN Center for Developmental Biology

description: Blood was extracted from embryonic hearts at E4 and E6 and non-red blood was separated by density gradient centrifugation

hyb_protocol: Standard Affymetrix Expression Array

scan_protocol: Standard Affymetrix Expression Array

data_processing: Standard Affymetrix Expression Array

organism: Gallus gallus

source_name: Fractionated non-red blood cells from E6 chicken

label_protocol: 2 cycle labeling

extract_protocol: Qiagen RNEasy

tag: Primary Cells


title: Macrogen Stem Cell-Mouse-6-v1.0-Noggin D0-P

source_name: Noggin treated 0 day


title: 4 Hour Recovery 2

status: Public on Dec 14 2007

city: Portland

first: Brad

last: Buckley

state: OR

address: 1719 SW 10th Ave

department: Biology

institute: Portland State University

description: Tb_gill_4 h recovery_individual_2

hyb_protocol: cDNAs were coupled to a monoreactive fluorescent dye (either Cy3 or Cy5; Amersham) and hybridized to the microarray for 15 h at 65˚C; lowering hybridization temperature can increase detection of features with low sequence homology, so the use of a single, high hybridization temperature were used to reduce non-specific binding of probe to the arrays. Control or heat shocked samples from a given species were labeled with Cy5 dye, and were competitively hybridized against a reference sample of total RNA from the same species that was labeled with Cy3 dye.

scan_protocol: Slides were scanned on an Axon Pro 4.0 scanner

data_processing: GeneSpring software was used to convert raw data values into ratios of Cy5 to Cy3. These ratios were Lowess normalized and then each value was normalized to the average of the three control slides.

organism: Trematomus bernacchii

source_name: Tb 4-h Recovery 2

label_protocol: Samples were converted to cDNA and labeled with either a Cy3 or Cy5 dye.

growth_protocol: Fish were maintained in recirculating aquaria at room temperature and fed trout pellets.

treatment_protocol: Fish were either maintained at a control temperature of -1.8C or subjected to either 4 hours of exposure to 4C, 4 hours of 4C and 2 h recovery at -1.8C, or 4 hours at 4C and 4 h recovery at -1.8C.

tag: Gill tissue

source_name: Reference gill tissue


title: 4 Hour Recovery 3

description: Tb_gill_4 h recovery_individual_3

source_name: Tb 4-h Recovery 3


title: E4_nRBC_2

source_name: Fractionated non-red blood cells from E4 chicken


title: E6_Heart

source_name: E6 whole heart

tag: Heart Tissue


title: 2 Hour Recovery 1

description: Tb_gill_2 h recovery_individual_1

source_name: Tb 2-h Recovery 1


title: 4 Hour Heat Shock 3

source_name: Tb 4-h Heat Shock 3


title: 2 Hour Recovery 2

description: Tb_gill_2 h recovery_individual_2

source_name: Tb 2-h Recovery 2


title: E6_nRBCs


title: E4 RBC

source_name: red blood cells from E4 chicken


title: 4 Hour Recovery 1

description: Tb_gill_4 h recovery_individual_1

source_name: Tb 4-h Recovery 1


title: 2 Hour Recovery 3

description: Tb_gill_2 h recovery_individual_3

source_name: Tb 2-h Recovery 3


title: 4 Hour Heat Shock 2

source_name: Tb 4-h Heat Shock 2


title: 4 Hour Heat Shock 1

source_name: Tb 4-h Heat Shock 1


title: Tb Control 3

source_name: Tb control 3


title: E6_RBC_2

source_name: red blood cells from E6 chicken


title: E6_RBC


title: E4_RBC_2


title: E4 nRBC


title: Tb Control 2

source_name: Tb control 2


title: Gm Control 3

organism: Gillichthys mirabilis

source_name: Gm control

treatment_protocol: Fish were either maintained at a control temperature of 18C or subjected to 4 hours of exposure to 32C.


title: Gm Control 2


title: 2-27-07 Mn-B T0

city: Omaha

first: Paul

middle: M

last: Dunman

state: NE

address: 986495 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: Biological Replicate to 2-27-07 Mn-A T0

hyb_protocol: Affymetrix Antisense Prokaryotic

scan_protocol: Affymetrix Antisense Prokaryotic

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: S. aureus strain Newman, mid-log grown in RPMI lacking Mn

label_protocol: Affymetrix Antisense Prokaryotic

extract_protocol: Qiagen RNeasy Mini Prep


title: Heat Shock 2

source_name: Gm 4-h Heat Shock

source_name: Reference gill tissue


title: 2-27-07 Zn-B T0

description: Biological Replicate to 2-27-07 Zn-A T0

source_name: S. aureus strain Newman, mid-log grown in RPMI lacking Zn


title: Heat Shock 3


title: 2-27-07 Zn-A T0

tag: S. aureus strain Newman, mid-log grown in RPMI lacking Zn


title: 2-27-07 Calprotectin A T0

source_name: S. aureus strain Newman, mid log Calprotectin treated RPMI medium


title: 2-22-07 WT-B T0

description: Biological Replicate of WT-A T0

source_name: S. aureus strain Newman, mid-log grown in RPMI medium + metals