title: UASMC - mAdbID:93259

description: mAdb experiment ID: 93259

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.2;; 3.62 Temperature: 29.62

source_name: UASMC

value: Umbilical artery smooth muscle cells


title: H9-EB-day7 - replicate 1 - mAdbID:93543

status: Public on Apr 17 2009

type: RNA

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 93543

hyb_protocol: Sample Hybridization Protocol Other: The samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.19 Temperature: 28.34

data_processing:
miRNA Data Processing
Calculation Method: The signal intensities were exported by R-based package mArray; the background-substracted intensities were normalized by variance stabilization normalization (VSN)and imported into BRRArray Tools.

molecule: total RNA

organism: Homo sapiens

source_name: EBV-infected lymphcytes

label_protocol:
Cy3 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

extract_protocol:
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

tag: Cell type

value: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)

source_name: WA09 (H9) - differentiation day 7

label_protocol:
Cy5 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

treatment_protocol:
Treatment time: day 7
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 7 days in maintenance medium without bFGF. The medium was changed every three days.

tag: Cell line

value: Human embryonic stem cell line


title: NHA - mAdbID:93264

description: mAdb experiment ID: 93264

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.74 Temperature: 29.74

source_name: NHA

tag: Tissue

value: brain

value: Normal human astrocytes


title: H9-EB-day10 - replicate 1 - mAdbID:93535

description: mAdb experiment ID: 93535

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.1 Temperature: 29.38

source_name: WA09 (H9) - differentiation day 10

treatment_protocol:
Treatment time: day 10
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 10 days in maintenance medium without bFGF. The medium was changed every three days.


title: Human osteoblast sample 648 repl 1

status: Public on Apr 16 2009

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

country: Canada

institute: McGill University and Genome Quebec Innovation Centre

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using variance-stabilizing transformation and robust spline normalization

label: Biotin

source_name: Primary human osteoblasts

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

growth_protocol: The cells were grown in medium containing α-MEM supplemented with 2 mmol/l L-Glutamine, 100U/mL penicillin, 100mg/mL streptomycin and 10% fetal bovine serum at 37°C with 5% CO2. At 70-80% confluence, the cells were passaged and sub-cultured in 6-well plates (100,000 cells/well) for 12 days after which the cells were harvested and stored at -70°C until RNA extraction.

extract_protocol: RNA was extracted from cell lysates resuspended in 600µl RLT lysis buffer using the RNeasy® Mini Kit. High RNA quality was confirmed for all samples using the Agilent 2100 BioAnalyzer and the concentrations were determined using Nanodrop ND-1000.

tag: tissue

value: Trabecular bone

tag: gender

value: male


title: Human osteoblast sample 646 repl 1

value: female


title: Human osteoblast sample 646 repl 2


title: Round1 A2780 vs parental A2780

type: genomic

city: Bloomington

first: Meng

last: Li

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

country: USA

institute: Indiana University

description: Differential methylation hybridization between Round1 and parental A2780

hyb_protocol: Followed Agilent protocol.

scan_protocol: Scanned on Axon GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were processed using R program.

molecule: genomic DNA

source_name: parental A2780

label_protocol: Labeled the fluorophores Cy3 (parental A2780) or Cy5 (A2780 following various “rounds” of cisplatin treatment) following Agilent protocols

growth_protocol: Cells were maintained in RPMI 1640 media with 2 mM L-glutamine, 50 U/ml penicillin, 50 mg/ml streptomycin, and 10% fetal bovine serum, at 30o C

extract_protocol: Genomic DNA was isolated from parental (drug-sensitive) A2780, Round1, Round3, and Round5 cells using Qiagen DNeasy purification kits (Valencia, CA)

tag: cell line

source_name: Round1 A2780


title: Round3 A2780 vs parental A2780

description: Differential methylation hybridization between Round3 and parental A2780

source_name: Round3 A2780


title: Round5 A2780 vs parental A2780

description: Differential methylation hybridization between Round5 and parental A2780

source_name: Round5 A2780


title: Human osteoblast sample 648 repl 2


title: Human osteoblast sample 645 repl 2


title: Human osteoblast sample 644 repl 1


title: Human osteoblast sample 634 repl 1


title: Human osteoblast sample 644 repl 2


title: Human osteoblast sample 643 repl 2


title: Human osteoblast sample 633 repl 1


title: Human osteoblast sample 633 repl 2


title: Human osteoblast sample 642 repl 2


title: Human osteoblast sample 622 repl 1


title: Human osteoblast sample 630 repl 2


title: Human osteoblast sample 645 repl 1


title: Human osteoblast sample 625 repl 1

description: 2nd replicate failed


title: Human osteoblast sample 629 repl 2


title: Human osteoblast sample 623 repl 2


title: Human osteoblast sample 643 repl 1


title: Human osteoblast sample 621 repl 2


title: Human osteoblast sample 623 repl 1


title: Human osteoblast sample 642 repl 1


title: Human osteoblast sample 619 repl 1


title: Human osteoblast sample 629 repl 1


title: Human osteoblast sample 618 repl 2


title: Human osteoblast sample 621 repl 1


title: Human osteoblast sample 620 repl 1


title: Human osteoblast sample 618 repl 1


title: Human osteoblast sample 619 repl 2


title: Human osteoblast sample 622 repl 2


title: Human osteoblast sample 615 repl 2


title: Human osteoblast sample 616 repl 1


title: Human osteoblast sample 616 repl 2


title: Human osteoblast sample 634 repl 2


title: Human osteoblast sample 630 repl 1


title: Human osteoblast sample 617 repl 1


title: Human osteoblast sample 613 repl 1


title: Human osteoblast sample 612 repl 2


title: Human osteoblast sample 614 repl 1


title: Human osteoblast sample 620 repl 2


title: Human osteoblast sample 612 repl 1


title: Human osteoblast sample 613 repl 2


title: Human osteoblast sample 609 repl 1


title: Human osteoblast sample 608 repl 1


title: Human osteoblast sample 611 repl 1


title: Human osteoblast sample 615 repl 1


title: Human osteoblast sample 617 repl 2


title: Human osteoblast sample 611 repl 2


title: Human osteoblast sample 609 repl 2


title: Human osteoblast sample 614 repl 2


title: Human osteoblast sample 608 repl 2


title: Human osteoblast sample 606 repl 1


title: Human osteoblast sample 606 repl 2


title: Human osteoblast sample 607 repl 2


title: Human osteoblast sample 605 repl 2


title: Human osteoblast sample 607 repl 1


title: Human osteoblast sample 603 repl 2


title: Human osteoblast sample 600 repl 2


title: Human osteoblast sample 602 repl 1


title: Human osteoblast sample 603 repl 1


title: Human osteoblast sample 601 repl 2


title: Human osteoblast sample 602 repl 2


title: Human osteoblast sample 598 repl 1


title: Human osteoblast sample 595 repl 2


title: Human osteoblast sample 598 repl 2


title: Human osteoblast sample 595 repl 1


title: Human osteoblast sample 600 repl 1


title: Human osteoblast sample 594 repl 2


title: Human osteoblast sample 597 repl 1


title: Human osteoblast sample 597 repl 2


title: Human osteoblast sample 594 repl 1


title: Human osteoblast sample 596 repl 2


title: Human osteoblast sample 593 repl 2


title: Human osteoblast sample 596 repl 1


title: Human osteoblast sample 601 repl 1


title: Human osteoblast sample 605 repl 1


title: Human osteoblast sample 592 repl 1


title: Human osteoblast sample 593 repl 1


title: Human osteoblast sample 592 repl 2


title: Human osteoblast sample 591 repl 1


title: Human osteoblast sample 589 repl 2


title: Human osteoblast sample 590 repl 1


title: Human osteoblast sample 589 repl 1


title: Human osteoblast sample 588 repl 2


title: Human osteoblast sample 591 repl 2


title: Human osteoblast sample 588 repl 1


title: Human osteoblast sample 587 repl 2


title: Human osteoblast sample 583 repl 2


title: Human osteoblast sample 585 repl 1


title: Human osteoblast sample 586 repl 2


title: Human osteoblast sample 587 repl 1


title: Human osteoblast sample 585 repl 2


title: Human osteoblast sample 583 repl 1


title: Human osteoblast sample 580 repl 2


title: Human osteoblast sample 582 repl 2


title: Human osteoblast sample 582 repl 1


title: Human osteoblast sample 581 repl 2


title: Human osteoblast sample 577 repl 2


title: Human osteoblast sample 578 repl 1


title: Human osteoblast sample 576 repl 2


title: Human osteoblast sample 581 repl 1


title: Human osteoblast sample 579 repl 2


title: Human osteoblast sample 578 repl 2


title: Human osteoblast sample 579 repl 1


title: Human osteoblast sample 575 repl 1


title: Human osteoblast sample 573 repl 2


title: Human osteoblast sample 576 repl 1


title: Human osteoblast sample 573 repl 1


title: Human osteoblast sample 572 repl 2


title: Human osteoblast sample 570 repl 2


title: Human osteoblast sample 570 repl 1


title: Human osteoblast sample 572 repl 1


title: Human osteoblast sample 567 repl 2


title: Human osteoblast sample 586 repl 1


title: Human osteoblast sample 567 repl 1


title: Human osteoblast sample 566 repl 1


title: Human osteoblast sample 557 repl 2


title: Human osteoblast sample 566 repl 2


title: Human osteoblast sample 580 repl 1


title: Human osteoblast sample 565 repl 2


title: Human osteoblast sample 554 repl 1


title: Human osteoblast sample 557 repl 1


title: Human osteoblast sample 554 repl 2


title: Human osteoblast sample 577 repl 1


title: Human osteoblast sample 553 repl 2


title: Human osteoblast sample 553 repl 1


title: Human osteoblast sample 555 repl 2


title: Human osteoblast sample 548 repl 1


title: Human osteoblast sample 555 repl 1


title: Human osteoblast sample 565 repl 1


title: Human osteoblast sample 551 repl 1


title: Human osteoblast sample 546 repl 1


title: Human osteoblast sample 546 repl 2


title: Human osteoblast sample 548 repl 2


title: Human osteoblast sample 544 repl 2


title: Human osteoblast sample 551 repl 2


title: Human osteoblast sample 550 repl 1


title: Human osteoblast sample 550 repl 2


title: Human osteoblast sample 543 repl 2


title: Human osteoblast sample 544 repl 1


title: Human osteoblast sample 575 repl 2


title: Human osteoblast sample 590 repl 2


title: Human osteoblast sample 540 repl 2


title: Human osteoblast sample 543 repl 1


title: Human osteoblast sample 529 repl 2


title: Human osteoblast sample 540 repl 1


title: Human osteoblast sample 531 repl 1


title: Human osteoblast sample 536 repl 1

description: 2nd replicate failed


title: Human osteoblast sample 531 repl 2


title: Connective tissue

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

description: Connective tissue tissue of pufferfish

hyb_protocol: Hybridizations were carried out as described by Zhang et al., 2004 (PMID: 15588312)

scan_protocol: Arrays were scanned on an Axon 4000A scanner and images quatified using GenePix

data_processing: Data was processed as described by Zhang et al., 2004 (PMID: 15588312) and dye-swapped replicates were averaged.

label: Cy5 or Cy3

molecule: polyA RNA

organism: Tetraodon nigroviridis

source_name: Connective tissue tissue of pufferfish

label_protocol: cDNA labelling procedures were done as described by Zhang et al., 2004 (PMID: 15588312)

extract_protocol: mRNA extraction and cDNA synthesis were done as described by Zhang et al., 2004 (PMID: 15588312)

tag: Connective tissue


title: Human osteoblast sample 526 repl 1


title: Human osteoblast sample 526 repl 2


title: Human osteoblast sample 528 repl 1


title: Human osteoblast sample 529 repl 1


title: Human osteoblast sample 525 repl 1


title: Stomach

description: Stomach tissue of pufferfish

source_name: Stomach tissue of pufferfish

tag: Stomach


title: Swimbladder

description: Swimbladder tissue of pufferfish

source_name: Swimbladder tissue of pufferfish

tag: Swimbladder


title: Red muscle

description: Red muscle tissue of pufferfish

source_name: Red muscle tissue of pufferfish

tag: Red muscle


title: Spleen

description: Spleen tissue of pufferfish

source_name: Spleen tissue of pufferfish

tag: Spleen


title: Human osteoblast sample 528 repl 2


title: Liver

description: Liver tissue of pufferfish

source_name: Liver tissue of pufferfish

tag: Liver


title: Human osteoblast sample 525 repl 2


title: Human osteoblast sample 524 repl 2


title: Ovary

description: Ovary tissue of pufferfish

source_name: Ovary tissue of pufferfish

tag: Ovary


title: White muscle

description: White muscle tissue of pufferfish

source_name: White muscle tissue of pufferfish

tag: White muscle


title: Skin

description: Skin tissue of pufferfish

source_name: Skin tissue of pufferfish

tag: Skin


title: Human osteoblast sample 524 repl 1


title: Kidney

description: Kidney tissue of pufferfish

source_name: Kidney tissue of pufferfish

tag: Kidney


title: Intestine

description: Intestine tissue of pufferfish

source_name: Intestine tissue of pufferfish

tag: Intestine


title: Gallbladder

description: Gallbladder tissue of pufferfish

source_name: Gallbladder tissue of pufferfish

tag: Gallbladder


title: Human osteoblast sample 522 repl 1

source_name: Primary human osteoblasts


title: Heart

description: Heart tissue of pufferfish

source_name: Heart tissue of pufferfish

tag: Heart


title: Gill

description: Gill tissue of pufferfish

source_name: Gill tissue of pufferfish

tag: Gill


title: Eye

description: Eye tissue of pufferfish

source_name: Eye tissue of pufferfish

tag: Eye


title: Human osteoblast sample 522 repl 2

tag: tissue

tag: gender


title: Human osteoblast sample 523 repl 1


title: Human osteoblast sample 521 repl 2


title: 20dpa vs 10dpa replicate 3b

city: East Lansing

first: Jeffrey

middle: R

last: Landgraf

state: MI

address: 612 Wilson Rd.

department: RTSF

institute: Michigan State University

hyb_protocol: Corning UltraGAPS slide were prehybed according to the manufaturers instructions. Labeled cDNAs were hybridized in Ambion Slidehyb#1 buffer overnight at 52C. Stringency washed were according to the Corning protocol.

scan_protocol: Slides were scanned using an Affymetrix 428 Array Scanner. Images quantified using Axon GenePix 3.0 software.

data_processing: Array normalization and statistical analysis were performed using the “limma: Linear Models for Microarray Data” library module (version 2.2.0) of the R statistical package (version 2.2.0).  Slide intensity data was normalized using the global loess method. The least squares method was used for the linear model fit utilizing the Benjamini and Hochberg method to control the false discovery rate.

organism: Gossypium hirsutum

source_name: 20dpa cotton fiber

label_protocol: 10 µg of total RNA was mixed with 3 µl of oligo dT(23)V (2ug/ul) DNA primer, incubated at 70°C for 10 min then put on ice. Reversed transcription was carried out at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 25 µM each dATP, dCTP, dGTP,  8 µM dTTP, and 17 µM aminoallyl dUTP. After purification of cDNA, the approriate NHS-ester Cy dye (Amersham/Pharmacia) was attached by incubation in 0.1M Sodium carbonte buffer (pH 9.0).

growth_protocol: Analyses performed on greenhouse grown G. hirsutum cv. DeltaPine90

extract_protocol: Fiber tissue was ground under liquid nitrogen and treated with proteinase K in hot borate extraction buffer (0.2 M Borax (Sodium-borate decahydrate); 30 mM EGTA; 1% (w/v) SDS; 1% (w/v) Sodium Deoxylic acid). RNA ultimately collected by LiCl precipitation.

tag: 20dpa cotton fiber

source_name: 10dpa cotton fiber

tag: 10dpa cotton fiber


title: Human osteoblast sample 521 repl 1


title: 10dpa vs 20dpa replicate 3a


title: Testis

description: Testis tissue of frog

organism: Xenopus tropicalis

source_name: Testis tissue of frog

tag: Testis


title: Calvaria

description: Calvaria tissue of pufferfish

source_name: Calvaria tissue of pufferfish

tag: Calvaria


title: Human osteoblast sample 518 repl 2


title: Fin

description: Fin tissue of pufferfish

source_name: Fin tissue of pufferfish

tag: Fin


title: Human osteoblast sample 519 repl 1


title: 20dpa vs 6dpa replicate 3b

source_name: 6dpa cotton fiber

tag: 6dpa cotton fiber


title: Human osteoblast sample 519 repl 2


title: Brain

description: Brain tissue of pufferfish

source_name: Brain tissue of pufferfish

tag: Brain


title: Testis

description: Testis tissue of pufferfish

source_name: Testis tissue of pufferfish


title: Human osteoblast sample 518 repl 1


title: Stomach

description: Stomach tissue of frog

source_name: Stomach tissue of frog

tag: Stomach


title: Beak (fused teeth)

description: Beak tissue of pufferfish

source_name: Beak tissue of pufferfish

tag: Beak


title: Spleen

description: Spleen tissue of frog

source_name: Spleen tissue of frog

tag: Spleen


title: Human osteoblast sample 517 repl 2


title: Small intestine

description: Small intestine tissue of frog

source_name: Small intestine tissue of frog

tag: Small intestine


title: 6dpa vs 20dpa replicate 3a


title: 20dpa vs 24dpa replicate 3b

source_name: 24dpa cotton fiber

tag: 24dpa cotton fiber


title: 20dpa vs 24dpa replicate 2b


title: Skin

description: Skin tissue of frog

source_name: Skin tissue of frog

tag: Skin


title: Muscle

description: Muscle tissue of frog

source_name: Muscle tissue of frog

tag: Muscle


title: Human osteoblast sample 517 repl 1

source_name: Primary human osteoblasts


title: Heart

description: Heart tissue of frog

source_name: Heart tissue of frog

tag: Heart


title: 24dpa vs 20dpa replicate 3a

source_name: 20dpa cotton fiber


title: Liver

description: Liver tissue of frog

source_name: Liver tissue of frog

tag: Liver


title: Human osteoblast sample 515 repl 1

tag: tissue

tag: gender


title: Oviduct

description: Oviduct tissue of frog

source_name: Oviduct tissue of frog

tag: Oviduct


title: Lung

description: Lung tissue of frog

source_name: Lung tissue of frog

tag: Lung


title: Kidney

description: Kidney tissue of frog

source_name: Kidney tissue of frog

tag: Kidney


title: Large intestine

description: Large intestine tissue of frog

source_name: Large intestine tissue of frog

tag: Large intestine


title: Femur

description: Femur tissue of frog

source_name: Femur tissue of frog

tag: Femur


title: Ovary

description: Ovary tissue of frog

source_name: Ovary tissue of frog

tag: Ovary


title: 24dpa vs 20dpa replicate 2a

tag: 20dpa cotton fiber


title: Human osteoblast sample 516 repl 1


title: Human osteoblast sample 516 repl 2


title: Gallbladder

description: Gallbladder tissue of frog

source_name: Gallbladder tissue of frog

tag: Gallbladder


title: 20dpa vs 24dpa replicate 1b


title: Fat body

description: Fat body tissue of frog

source_name: Fat body tissue of frog

tag: Fat body


title: Eye

description: Eye tissue of frog

source_name: Eye tissue of frog

tag: Eye


title: Human osteoblast sample 515 repl 2


title: Esophagus

description: Esophagus tissue of frog

source_name: Esophagus tissue of frog

tag: Esophagus


title: Human osteoblast sample 523 repl 2


title: 10dpa vs 20dpa replicate 2b

source_name: 10dpa cotton fiber

tag: 10dpa cotton fiber


title: Human osteoblast sample 514 repl 1


title: Human osteoblast sample 514 repl 2


title: 20dpa vs 10dpa replicate 2a


title: 20dpa vs 10dpa replicate 1b


title: 20dpa vs 6dpa replicate 2a

source_name: 6dpa cotton fiber

tag: 6dpa cotton fiber


title: 20dpa vs 6dpa replicate 1b


title: 6dpa vs 20dpa replicate 2b


title: Brain

description: Brain tissue of frog

source_name: Brain tissue of frog

tag: Brain


title: Human osteoblast sample 513 repl 1

source_name: Primary human osteoblasts


title: Human osteoblast sample 509 repl 2


title: Cartilage

description: Cartilage tissue of frog

source_name: Cartilage tissue of frog

tag: Cartilage


title: 6dpa vs 20dpa replicate 1a

source_name: 20dpa cotton fiber


title: 24dpa vs 20dpa replicate 1a

source_name: 24dpa cotton fiber

tag: 24dpa cotton fiber


title: Human osteoblast sample 511 repl 2

tag: tissue

tag: gender


title: Human osteoblast sample 511 repl 1


title: Human osteoblast sample 509 repl 1


title: 10dpa vs 20dpa replicate 1a


title: Human osteoblast sample 513 repl 2


title: Human osteoblast sample 508 repl 2


title: Human osteoblast sample 508 repl 1


title: Human osteoblast sample 507 repl 1

description: 2nd replicate failed


title: Human osteoblast sample 506 repl 1


title: Human osteoblast sample 506 repl 2


title: Yap6 0 min post salt induction replicate 1

city: Woodbridge

first: Can

last: Bruce

state: CT

address: 5 Chestnut Lane

institute: Sciomix

description:
S.cerevisiae Yap6::13myc (0 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 88155

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: Samples were scanned and with each channel (635 (ch1) and 532 (ch2)) normalized separately according to Nimblegen protocols. log(2) ratios were calculated from these normalized 635 and 532 signals, with Random control spots removed during processing.

organism: Saccharomyces cerevisiae

source_name: Yap6::13myc, 0 min post salt induction

label_protocol: Klenow random priming (Borneman et al Genes Dev 2006)

growth_protocol: Cells grown overnight to mid exponential phase (OD 600=0.6) at 30°C in liquid minimal medium (SD; 2% glucose, 00.5% 38mM ammonium sulphate, 0.17% yeast nitrogen base, 5 mM uracil), then treated with 0.6M NaCl (generated using a 5 M stock solution) at 30°C. Samples were then harvested by vacuum filtration.

extract_protocol: Chromatin immunoprecipitation (Borneman et al Genes Dev 2006)

tag: strain

value: BY4741 containing Yap6 with C-terminal 13myc

tag: time

value: 0 min post salt treatment

tag: biological replicate

source_name: BY4741 control strain

growth_protocol: Cells grown overnight to mid exponential phase (OD 600=0.6) at 30°C in liquid minimal medium (SD; 2% glucose, 0.5% 38mM aammonium sulphate, 0.17% yeast nitrogen base, 5 mM uracil), then treated with 0.6M NaCl (generated using a 5 M stock solution) at 30°C. Samples were then harvested by vacuum filtration.


title: Yap6 30 min post salt induction replicate 3

description:
S.cerevisiae Yap6::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 94830

source_name: Yap6::13myc, 30 min post salt induction

value: 30 min post salt treatment


title: Yap4 45 min post salt induction replicate 2

description:
S.cerevisiae Yap4::13myc (45 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 43894

source_name: Yap4::13myc, 45 min post salt induction

value: BY4741 containing Yap4 with C-terminal 13myc

value: 45 min post salt treatment


title: Yap6 30 min post salt induction replicate 1

description:
S.cerevisiae Yap6::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 104435


title: Yap4 5 min post salt induction replicate 3

description:
S.cerevisiae Yap4::13myc (5 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 70446

source_name: Yap4::13myc, 5 min post salt induction

value: 5 min post salt treatment


title: Yap4 45 min post salt induction replicate 1

description:
S.cerevisiae Yap4::13myc (45 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 36633


title: Yap6 0 min post salt induction replicate 2

description:
S.cerevisiae Yap6::13myc (0 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 88163


title: Yap4 45 min post salt induction replicate 3

description:
S.cerevisiae Yap4::13myc (45 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 43901


title: Yap4 30 min post salt induction replicate 2

description:
S.cerevisiae Yap4::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 43897

source_name: Yap4::13myc, 30 min post salt induction


title: Yap4 15 min post salt induction replicate 3

description:
S.cerevisiae Yap4::13myc (15 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 88154

source_name: Yap4::13myc, 15 min post salt induction

value: 15 min post salt treatment


title: Yap4 30 min post salt induction replicate 3

description:
S.cerevisiae Yap4::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 58378


title: Yap6 30 min post salt induction replicate 2

description:
S.cerevisiae Yap6::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 94829


title: Yap4 15 min post salt induction replicate 1

description:
S.cerevisiae Yap4::13myc (15 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 88143


title: Thymus

description: Thymus tissue of chicken

organism: Gallus gallus

source_name: Thymus tissue of chicken

tag: Thymus


title: Yap4 30 min post salt induction replicate 1

description:
S.cerevisiae Yap4::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 36537


title: Yap4 15 min post salt induction replicate 2

description:
S.cerevisiae Yap4::13myc (15 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 88153


title: Yap4 0 min post salt induction replicate 1

description:
S.cerevisiae Yap4::13myc (0 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 70449

source_name: Yap4::13myc, 0 min post salt induction


title: Testis

description: Testis tissue of chicken

source_name: Testis tissue of chicken

tag: Testis


title: Yap4 5 min post salt induction replicate 2

description:
S.cerevisiae Yap4::13myc (5 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 64866


title: Yap4 0 min post salt induction replicate 3

description:
S.cerevisiae Yap4::13myc (0 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 73323


title: Yap4 5 min post salt induction replicate 1

description:
S.cerevisiae Yap4::13myc (5 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 61072


title: Yap4 0 min post salt induction replicate 2

description:
S.cerevisiae Yap4::13myc (0 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 71757


title: Yap6 0 min post salt induction replicate 3

description:
S.cerevisiae Yap6::13myc (0 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 88164


title: Spleen

description: Spleen tissue of chicken

source_name: Spleen tissue of chicken

tag: Spleen


title: Stomach

description: Stomach tissue of chicken

source_name: Stomach tissue of chicken

tag: Stomach


title: Skin

description: Skin tissue of chicken

source_name: Skin tissue of chicken

tag: Skin


title: Smp1 30 min post salt induction replicate 3

description:
S.cerevisiae Smp1::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 68568

source_name: Smp1::13myc, 30 min post salt induction

value: BY4741 containing Smp1 with C-terminal 13myc


title: Oviduct

description: Oviduct tissue of chicken

source_name: Oviduct tissue of chicken

tag: Oviduct


title: pleomorphic xanthoastrocytoma 1

city: London

first: Tim

last: Forshew

address: 4 Newark Street

department: Centre for Neuroscience

country: United Kingdom

institute: Queen Mary's School of Medicine and Dentistry

description: Hybridized to 250K_Nsp

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

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

data_processing: CHP files generated by Affymetrix GTYPE using the DM algorithm.

source_name: pleomorphic xanthoastrocytoma

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: DNA was extracted from fresh frozen tissue using the QIAamp DNA mini kit (Qiagen, Crawley, UK).

tag: pathology

value: pleomorphic xanthoastrocytoma

tag: site

value: cerebral cortex

tag: age

value: 6 yrs

value: F


title: Ovary

description: Ovary tissue of chicken

source_name: Ovary tissue of chicken

tag: Ovary


title: pilocytic astrocytoma 7

description: Hybridized to 250K_Nsp

source_name: pilocytic astrocytoma

value: pilocytic astrocytoma

value: cerebellum

value: 13 yrs

value: M


title: Muscle

description: Muscle tissue of chicken

source_name: Muscle tissue of chicken

tag: Muscle


title: pilomyxoid astrocytoma 1

description: Hybridized to 250K_Nsp

source_name: pilomyxoid astrocytoma

value: pilomyxoid astrocytoma

value: diencephalon

value: 1 yrs


title: pilomyxoid glioma 2

description: Hybridized to 250K_Nsp

source_name: pilomyxoid glioma

value: pilomyxoid glioma

value: 7 yrs


title: Smp1 30 min post salt induction replicate 1

description:
S.cerevisiae Smp1::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 66614

value: 30 min post salt treatment

source_name: BY4741 control strain


title: Lung

description: Lung tissue of chicken

source_name: Lung tissue of chicken

tag: Lung


title: pilocytic astrocytoma 4

description: Hybridized to 250K_Nsp

value: 2 yrs


title: Sko1 45 min post salt induction replicate 2

description:
S.cerevisiae Sko1::13myc (45 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 129109

source_name: Sko1::13myc, 45 min post salt induction

value: BY4741 containing Sko1 with C-terminal 13myc

value: 45 min post salt treatment


title: Sko1 30 min post salt induction replicate 3

description:
S.cerevisiae Sko1::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 61347

source_name: Sko1::13myc, 30 min post salt induction


title: Liver

description: Liver tissue of chicken

source_name: Liver tissue of chicken

tag: Liver


title: Sko1 30 min post salt induction replicate 2

description:
S.cerevisiae Sko1::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 60768


title: Sko1 30 min post salt induction replicate 1

description:
S.cerevisiae Sko1::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 60639


title: Sko1 15 min post salt induction replicate 3

description:
S.cerevisiae Sko1::13myc (15 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 130242

source_name: Sko1::13myc, 15 min post salt induction

value: 15 min post salt treatment


title: Sko1 15 min post salt induction replicate 2

description:
S.cerevisiae Sko1::13myc (15 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 129114


title: pilocytic astrocytoma 20

description: Hybridized to 250K_Nsp

value: 4 yrs

tag: gender


title: pilocytic astrocytoma 3

description: Hybridized to 250K_Nsp


title: Sko1 5 min post salt induction replicate 2

description:
S.cerevisiae Sko1::13myc (5 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 124302

source_name: Sko1::13myc, 5 min post salt induction

tag: strain

value: 5 min post salt treatment


title: Sko1 5 min post salt induction replicate 1

description:
S.cerevisiae Sko1::13myc (5 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 123433

tag: time


title: Smp1 30 min post salt induction replicate 2

description:
S.cerevisiae Smp1::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 66620

value: BY4741 containing Smp1 with C-terminal 13myc

tag: biological replicate


title: Sko1 0 min post salt induction replicate 3

description:
S.cerevisiae Sko1::13myc (0 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 89452

source_name: Sko1::13myc, 0 min post salt induction

value: 0 min post salt treatment


title: Kidney

description: Kidney tissue of chicken

source_name: Kidney tissue of chicken

tag: Kidney


title: Sko1 15 min post salt induction replicate 1

description:
S.cerevisiae Sko1::13myc (15 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 129106


title: Sko1 45 min post salt induction replicate 1

description:
S.cerevisiae Sko1::13myc (45 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 124088


title: Sko1 45 min post salt induction replicate 3

description:
S.cerevisiae Sko1::13myc (45 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 130240


title: pilocytic astrocytoma 29

description: Hybridized to 250K_Nsp

value: pilocytic astrocytoma

value: cerebellum

value: 19 yrs


title: pilocytic astrocytoma 22

description: Hybridized to 250K_Nsp

value: 6 yrs

value: F


title: Abf1_Reb1_degron-degron_ON-culture_D

status: Public on May 01 2009

first: Hiten

last: Madhani

state: CA

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: No further information

hyb_protocol: arrays were blocked with a SDS/BSA solution and each probe was hybridized 1:1 using Agilent hybridization buffer; hybes were allowed to proceed at 65 degrees for at least 12 hours

scan_protocol: Scanned with a GenePix 4000B at 5 or 10 uM, depending on the size of print tips used to print array

data_processing: Median background subtracted first, then each print block normalized using a loess algorithm

source_name: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::REB1,  pMET3::UB14::abf1(M1R), Reb1:dT7 inserted into PRM1

label_protocol: DNA was linear amplified by first T-tailing with TdT, then adapting a T7 promoter (using complementary A tails), followed by IVT using a mix of aaUTP:UTP to generate aminoallyl-RNA probe that could be labeled with either Cy3 or Cy5 dye

growth_protocol: Cells that were growing in synthetic complete media lacking methionine and cysteine at 30 degrees were spiked with 2% galactose for 30 minutes and collected by centrifugation at room temperature, then added to rich (YPA) media supplemented with 2% galactose and prewarmed at 37 degrees.  After 5 hours of growth at 37 degrees, cells were collected.

extract_protocol: culture was crosslinked with 1% formaldehyde for 15 minutes at growth temperature and quenched with 0.125M glycine for 5 minutes at room temperature.  Spheroplasts were prepared by digestion with Zymolyase 100T, followed by chromatin digestion with MNase in a buffer containing NP-40 for permeabilization

tag: formaldehyde-crosslinked chromatin digested with MNase to >90% mononucleosomal-sized DNA

source_name: reference DNA obtained from strain isogenic for features being probed

growth_protocol: Culture containing reference DNA isogenic to mononucleosome DNA source was grown in rich media to log phase (OD=1.0) prior to harvesting for purification of genomic DNA

extract_protocol: pure genomic DNA was purified using a Qiagen 100T column as specified by the manufacturer

tag: purified genomic DNA digested with MNase to ~200bp


title: Sko1 5 min post salt induction replicate 3

description:
S.cerevisiae Sko1::13myc (5 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 124833


title: Sko1 0 min post salt induction replicate 2

description:
S.cerevisiae Sko1::13myc (0 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 88378


title: Heart

description: Heart tissue of chicken

source_name: Heart tissue of chicken

tag: Heart


title: Gallbladder

description: Gallbladder tissue of chicken

source_name: Gallbladder tissue of chicken

tag: Gallbladder


title: Gizzard

description: Gizzard tissue of chicken

source_name: Gizzard tissue of chicken

tag: Gizzard


title: Sko1 0 min post salt induction replicate 1

description:
S.cerevisiae Sko1::13myc (0 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 81225


title: Skn7 30 min post salt induction replicate 1

description:
S.cerevisiae Skn7::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 47695

source_name: Skn7::13myc, 30 min post salt induction

value: BY4741 containing Skn7 with C-terminal 13myc


title: Skn7 30 min post salt induction replicate 3

description:
S.cerevisiae Skn7::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 88157


title: Intestine

description: Intestine tissue of chicken

source_name: Intestine tissue of chicken

tag: Intestine


title: pilocytic astrocytoma 18

description: Hybridized to 250K_Nsp

source_name: pilocytic astrocytoma

tag: pathology

tag: site

value: 3 yrs

value: M


title: pilocytic astrocytoma 26

description: Hybridized to 250K_Nsp

tag: age


title: Femur with bone marrow

description: Femur with bone marrow tissue of chicken

tag: Femur with bone marrow


title: pilocytic astrocytoma 17

description: Hybridized to 250K_Nsp


title: Eye

description: Eye tissue of chicken

source_name: Eye tissue of chicken

tag: Eye


title: Skn7 30 min post salt induction replicate 2

description:
S.cerevisiae Skn7::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 47892

value: 30 min post salt treatment

source_name: BY4741 control strain


title: Cerebral cortex

description: Cerebral cortex tissue of chicken

source_name: Cerebral cortex tissue of chicken

tag: Cerebral cortex


title: Msn4 30 min post salt induction replicate 3

description:
S.cerevisiae Msn4::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 73324

source_name: Msn4::13myc, 30 min post salt induction

value: BY4741 containing Msn4 with C-terminal 13myc


title: Msn4 30 min post salt induction replicate 2

description:
S.cerevisiae Msn4::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 71765


title: Cerebellum

description: Cerebellum tissue of chicken

source_name: Cerebellum tissue of chicken

tag: Cerebellum


title: pilocytic astrocytoma 14

description: Hybridized to 250K_Nsp

value: 10 yrs

tag: gender


title: Msn4 0 min post salt induction replicate 1

description:
S.cerevisiae Msn4::13myc (0 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 90750

source_name: Msn4::13myc, 0 min post salt induction

tag: strain

tag: time


title: pilocytic astrocytoma 16

description: Hybridized to 250K_Nsp


title: Msn4 0 min post salt induction replicate 3

description:
S.cerevisiae Msn4::13myc (0 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 94834

tag: biological replicate


title: Msn2 0 min post salt induction replicate 3

description:
S.cerevisiae Msn2::13myc (0 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 88165

source_name: Msn2::13myc, 0 min post salt induction

value: BY4741 containing Msn2 with C-terminal 13myc


title: Bursa of Fabricius

description: Bursa of Fabricius tissue of chicken

source_name: Bursa of Fabricius tissue of chicken

tag: Bursa of Fabricius


title: Msn2 30 min post salt induction replicate 1

description:
S.cerevisiae Msn2::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 100228

source_name: Msn2::13myc, 30 min post salt induction


title: pilocytic astrocytoma 11

description: Hybridized to 250K_Nsp

value: 14 yrs


title: Msn2 30 min post salt induction replicate 3

description:
S.cerevisiae Msn2::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 104737


title: day 5 donor 3

status: Public on Apr 15 2009

city: Los Angeles

first: Sara

middle: Tajyar

last: Hashimi

address: 657 Charles E Young Dr. East

department: MIMG

institute: UCLA

description: miRNA expression profiling of stage specific monocyte derived dendritic cell differentiation.

hyb_protocol: Hybridization was done by Asuragen full service processing according to manufacturer's protocol.

scan_protocol: Scanning was done by Asuragen full service processing according to manufacturer's protocol.

data_processing: Values were normalized using Variance Stabilization Normalization (VSN).

source_name: monocyte derived dendritic cells (MDDC)

label_protocol: Labeling was done according to manufacturer's protocol (Ambion/Applied Biosystems). Labeling was done by Asuragen microarray full service.

extract_protocol: total RNA was extracted according to manufacturers protocol (ambion miRVana total miRNA isolation kit).  Then miRNA was extracted by Asuragen using a flash PAGE fractionator.

tag: time point

value: day 5

tag: cell type

value: monocyte derived dendritic cells

tag: donor


title: day 5 donor 2


title: Msn4 30 min post salt induction replicate 1

description:
S.cerevisiae Msn4::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 71613


title: Msn2 30 min post salt induction replicate 2

description:
S.cerevisiae Msn2::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 104658


title: day 5 donor 1


title: Msn4 0 min post salt induction replicate 2

description:
S.cerevisiae Msn4::13myc (0 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 94833


title: Msn2 0 min post salt induction replicate 2

description:
S.cerevisiae Msn2::13myc (0 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 87931


title: day 3 donor 3

value: day 3


title: day 3 donor 2


title: Msn2 0 min post salt induction replicate 1

description:
S.cerevisiae Msn2::13myc (0 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 81371

value: 0 min post salt treatment


title: day 3 donor 1


title: Msn1 30 min post salt induction replicate 1

description:
S.cerevisiae Msn1::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 100345

source_name: Msn1::13myc, 30 min post salt induction

value: BY4741 containing Msn1 with C-terminal 13myc


title: day 1 donor 2

value: day 1


title: day 1 donor 3


title: day 0 donor 3

value: day 0


title: Msn1 30 min post salt induction replicate 2

description:
S.cerevisiae Msn1::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 104662


title: pilocytic astrocytoma 13

description: Hybridized to 250K_Nsp

value: pilocytic astrocytoma

value: cerebellum


title: day 1 donor 1


title: day 0 donor 1


title: diffuse astrocytoma 9

description: Hybridized to 250K_Nsp

source_name: diffuse astrocytoma

value: diffuse astrocytoma

value: cerebral cortex

value: 9 yrs

value: F


title: Msn1 30 min post salt induction replicate 3

description:
S.cerevisiae Msn1::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 94831

value: 30 min post salt treatment


title: Hot1 30 min post salt induction replicate 2

description:
S.cerevisiae Hot1::13myc (30 min post salt induction) biological replicate 2.
Slide number used for this hybridization: 100352

source_name: Hot1::13myc, 30 min post salt induction

value: BY4741 containing Hot1 with C-terminal 13myc


title: MDT-MB-79_Hind

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: See label protocol above

scan_protocol: See label protocol above

data_processing: Affymetrix CEL files were extracted using the Affymetrix Data Transfer Tool (Version 1.1.0). For SNP genotyping, the BRLMM Analysis Tool (Version 1.0) was employed for individual array platforms using default parameters. Copy number and loss of heterozygosity (LOH) analyses were performed using dChip 2006. Arrays were normalized by invariant set normalization and signal intensities computed using PM/MM model-based expression. Raw copy number data was computed using 100 normal control samples as a reference (provided by SWS) and inferred copy numbers were predicted using the Hidden Markov Model (HMM).

label: biotin

source_name: genomic DNA from fresh-frozen tissue

label_protocol: MB samples were processed and hybridized to Affymetrix SNP arrays at The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children. Genomic DNA samples isolated from primary medulloblastomas and cell lines were genotyped using the Affymetrix 50K Hind 240 and 50K Xba 240, or the 250K Nsp and 250K Sty GeneChip Mapping arrays as directed by the manufacturer. Briefly, 250ng of DNA was digested with HindIII, XbaI, NspI, or StyI (NEB), adapter-ligated and PCR amplified using a single primer with AmpliTaq Gold (Applied Biosystems). Amplified PCR products were pooled, concentrated, and fragmented with DNAase I. Products were subsequently labeled, denatured, and hybridized overnight to the respective arrays. Arrays were washed using an Affymetrix fluidics station and scanned using the GeneChip Scanner 3000. CEL files were generated using the Affymetrix GeneChip Operating Software (GCOS) 3.0.

growth_protocol: All media and reagents for culturing mammalian cells lines were purchased from Wisent. Medulloblastoma cell lines ONS76, UW228, and MED8A were grown as a monolayer in DMEM supplemented with 10% FBS. DAOY and D283 cell lines were grown as monolayers in AMEM with 10% FBS. The RES256 cell line was grown adherent in DMEM/F12 media supplemented with 2% FBS. D425, D458, and D556 were grown as suspension cultures in IMEM with 20% FBS, 10mM HEPES, and 0.225% Sodium Bicarbonate. MHH-MED-1 and D341 were grown in suspension in DMEM and AMEM with 10% FBS, respectively

extract_protocol: Fresh-frozen medulloblastoma specimens were stored at -80°C prior to being processed for extraction of nucleic acid. Tissue samples were pulverized under liquid nitrogen using a mortar and pestle.  For genomic DNA isolation, approximately 25-50mg of crushed tissue was subjected to digestion using SDS/Proteinase K (Roche) for 3 hours at 50°C. Homogenates were extracted 3 times with buffer-saturated phenol (Invitrogen) prior to precipitation of DNA with two volumes of anhydrous ethanol and 10% (vol/vol) 10M ammonium acetate.  Precipitated DNA was washed 3 times with 70% ethanol and re-suspended in reduced EDTA-TE (10mM Tris, 0.1mM EDTA; pH=8.0). Samples were quantitated by Nanodrop and integrity of isolated DNA was assessed by agarose gel electrophoresis prior to submission for SNP array.

tag: Age

tag: Gender

value: M

tag: Histology

value: Classic


title: pilocytic astrocytoma 10

description: Hybridized to 250K_Nsp

tag: pathology

tag: site

value: 19 yrs


title: MDT-MB-80_Hind


title: MDT-MB-78_Hind

value: Large Cell/Anaplastic


title: MDT-MB-74_Hind

value: Desmoplastic


title: MDT-MB-76_Hind


title: MDT-MB-77_Hind


title: Hot1 30 min post salt induction replicate 1

description:
S.cerevisiae Hot1::13myc (30 min post salt induction) biological replicate 1.
Slide number used for this hybridization: 100238


title: MDT-MB-72_Hind

value: Meduloblastoma with extensive neuronal differentiation


title: MDT-MB-73_Hind


title: diffuse astrocytoma 8

description: Hybridized to 250K_Nsp

tag: age

value: 15 yrs


title: MDT-MB-75_Hind


title: MDT-MB-68_Hind


title: MDT-MB-70_Hind


title: MDT-MB-71_Hind


title: MDT-MB-66_Hind


title: MDT-MB-69_Hind


title: MDT-MB-59_Hind


title: MDT-MB-63_Hind


title: MDT-MB-67_Hind


title: MDT-MB-61_Hind


title: MDT-MB-64_Hind


title: MDT-MB-65_Hind


title: MDT-MB-60_Hind


title: MDT-MB-62_Hind


title: CONTROL A

description: Hybridized to 250K_Nsp

source_name: Normal blood

value: Normal

value: Blood

value: 20 yrs


title: diffuse astrocytoma 2

description: Hybridized to 250K_Nsp


title: Hot1 30 min post salt induction replicate 3

description:
S.cerevisiae Hot1::13myc (30 min post salt induction) biological replicate 3.
Slide number used for this hybridization: 104670


title: MDT-MB-57_Hind


title: CyaC O2 lim, rep2

city: Richland

first: Alexander

last: Beliaev

state: WA

address: 902 Battelle Blvd.

institute: Pacific Northwest National Laboratory

description: Gene expression data from ΔcyaC S. oneidensis MR-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a high-density Shewanella custom microarray manufactured by Affymetrix. The arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned using the Affymetrix 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. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Shewanella oneidensis MR-1

source_name: Cells from oxygen-limited chemostat culture

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

growth_protocol: Cells were at 30oC under O2-limited conditions in chemostats using 6-l Bioflow 3000 (New Brunswick Scientific, Edison, NJ) bioreactors containing 3 l of minimal medium (pH 7.0) supplemented with 90 mM D,L-lactate

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

treatment_protocol: 50-ml aliquots from oxygen-limited chemostats were centrifuged at 10,000 x g for 5 min (4oC) and flash frozen in liquid nitrogen prior to total RNA extraction.

tag: genotype

value: ΔcyaC deletion mutant


title: MDT-MB-56_Hind


title: CyaC O2 lim, rep1


title: MDT-MB-58_Hind


title: diffuse astrocytoma 7

description: Hybridized to 250K_Nsp

value: diffuse astrocytoma

value: 5 yrs


title: MDT-MB-55_Hind


title: MDT-MB-54_Hind


title: CONTROL B

description: Hybridized to 250K_Nsp


title: WT O2 lim, rep2

description: Gene expression data from wild-type S. oneidensis MR-1

value: Wild type strain


title: CRP O2 lim, rep1

description: Gene expression data from Δcrp S. oneidensis MR-1

value: Δcrp deletion mutant


title: MDT-MB-52_Hind

value: F


title: MDT-MB-53_Hind


title: MDT-MB-51_Hind


title: day 0 donor 2

value: day 0

value: monocyte derived dendritic cells


title: CRP O2 lim, rep2


title: WT O2 lim, rep1


title: MDT-MB-49_Hind

value: M

value: Classic


title: Genomic DNA isolated from C57BL6/J mice at E17.5, chr11 to chrY, biol rep2

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: Methylated DNA enriched by the MCAM method. Biological replicate 2 of 2.

hyb_protocol: Followed Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US23502362 Images were quantified using Agilent Feature Extraction Software (version 9.1.1.1).

data_processing: Agilent Feature Extraction Software (9.1.1.1) was used for background subtraction and normalization, default normalization procedure.

organism: Mus musculus

label_protocol: Followed Agilent protocol

growth_protocol: C57BL6/J mice (Jackson Laboratories, Bar Harbor, ME) were used. For collection of fetal liver samples, timing of coitus was determined by observation of vaginal plugs; the morning a plug was observed was considered 0.5 days post coitum. At 17.5 days post coitum (E17.5), pregnant females were killed by CO2 asphyxiation, and fetal liver collected. P21 liver was collected directly after removing mice from their dams in the morning.

extract_protocol: Genomic DNA was extracted using a standard phenol–chloroform method

tag: tissue

value: liver


title: MDT-MB-47_Hind


title: MDT-MB-45_Hind


title: MDT-MB-41_Hind

value: Desmoplastic


title: MDT-MB-46_Hind


title: Genomic DNA isolated from C57BL6/J mice at E17.5, chr11 to chrY, biol rep1

description: Methylated DNA enriched by the MCAM method. Biological replicate 1 of 2


title: Genomic DNA isolated from C57BL6/J mice at P21, chr11 to chrY, biol rep2


title: MDT-MB-48_Hind


title: Genomic DNA isolated from C57BL6/J mice at P21, chr11 to chrY, biol rep1


title: MDT-MB-44_Hind


title: MDT-MB-40_Hind


title: MDT-MB-39_Hind


title: MDT-MB-225_Sty


title: MDT-MB-224_Sty

value: Large Cell/Anaplastic


title: MDT-MB-42_Hind


title: MDT-MB-228_Sty


title: MDT-MB-229_Sty


title: MDT-MB-43_Hind


title: MDT-MB-37_Hind


title: MDT-MB-36_Hind


title: MDT-MB-34_Hind


title: MDT-MB-221_Sty


title: MDT-MB-38_Hind


title: MDT-MB-222_Sty


title: MDT-MB-50_Hind


title: MDT-MB-223_Sty


title: RES256_Sty

source_name: genomic DNA from cell lysate


title: MDT-MB-35_Hind


title: MDT-MB-32_Hind


title: MDT-MB-31_Hind


title: MDT-MB-220_Sty


title: MDT-MB-215_Sty


title: MDT-MB-226_Sty


title: MDT-MB-216_Sty


title: MDT-MB-29_Hind


title: MDT-MB-26_Hind


title: MDT-MB-30_Hind


title: MDT-MB-28_Hind


title: MDT-MB-217_Sty


title: MDT-MB-219_Sty


title: MDT-MB-24_Hind


title: MDT-MB-25_Hind


title: MDT-MB-23_Hind


title: MDT-MB-22_Hind


title: MDT-MB-27_Hind


title: MDT-MB-21_Hind


title: MDT-MB-211_Sty


title: MDT-MB-209_Sty


title: MDT-MB-210_Sty


title: MDT-MB-208_Sty


title: MDT-MB-19_Hind


title: MDT-MB-212_Sty


title: MDT-MB-203_Sty


title: MDT-MB-20_Hind


title: MDT-MB-213_Sty


title: MDT-MB-207_Sty


title: MDT-MB-206_Sty


title: MDT-MB-201_Sty


title: MDT-MB-18_Hind


title: MDT-MB-202_Sty


title: MDT-MB-17_Hind


title: MDT-MB-214_Sty

value: Meduloblastoma with extensive neuronal differentiation


title: MDT-MB-14_Hind


title: MDT-MB-12_Hind


title: MDT-MB-16_Hind


title: MDT-MB-15_Hind


title: MDT-MB-197_Sty


title: MDT-MB-198_Sty


title: MDT-MB-200_Sty


title: MDT-MB-199_Sty


title: MDT-MB-10_Hind


title: MDT-MB-196_Sty


title: MDT-MB-11_Hind


title: MDT-MB-205_Sty


title: MDT-MB-193_Sty


title: MDT-MB-195_Sty


title: MDT-MB-9_Hind


title: MDT-MB-13_Hind


title: MDT-MB-194_Sty


title: MDT-MB-2_Hind


title: MDT-MB-191_Sty


title: MDT-MB-190_Sty


title: MDT-MB-8_Hind


title: MDT-MB-6_Hind


title: MDT-MB-1_Hind


title: MDT-MB-3_Hind


title: MDT-MB-189_Sty


title: UW228_Hind


title: MDT-MB-4_Hind


title: MDT-MB-187_Sty


title: MDT-MB-7_Hind


title: MDT-MB-5_Hind


title: MDT-MB-188_Sty


title: MDT-MB-185_Sty


title: MDT-MB-186_Sty


title: MDT-MB-183_Sty


title: MHH-MED1_Hind


title: MDT-MB-184_Sty


title: MDT-MB-181_Sty


title: MED8A_Hind


title: D556_Hind


title: D458_Hind


title: MDT-MB-182_Sty


title: D425_Hind


title: D341_Hind


title: MDT-MB-192_Sty


title: MDT-MB-80_Xba


title: DAOY_Hind


title: MDT-MB-177_Sty


title: MDT-MB-176_Sty


title: MDT-MB-78_Xba


title: MDT-MB-179_Sty


title: MDT-MB-173_Sty


title: MDT-MB-77_Xba


title: MDT-MB-79_Xba


title: D283_Hind


title: MDT-MB-76_Xba


title: ONS76_Hind


title: MDT-MB-180_Sty


title: MDT-MB-168_Sty


title: MDT-MB-73_Xba


title: MDT-MB-178_Sty


title: MDT-MB-172_Sty


title: MDT-MB-74_Xba


title: MDT-MB-72_Xba


title: MDT-MB-169_Sty


title: MDT-MB-175_Sty


title: MDT-MB-164_Sty


title: MDT-MB-174_Sty


title: MDT-MB-69_Xba


title: MDT-MB-170_Sty


title: MDT-MB-165_Sty


title: MDT-MB-70_Xba


title: MDT-MB-71_Xba


title: MDT-MB-68_Xba


title: MDT-MB-65_Xba


title: MDT-MB-64_Xba


title: MDT-MB-63_Xba


title: MDT-MB-67_Xba


title: MDT-MB-160_Sty


title: MDT-MB-166_Sty


title: MDT-MB-66_Xba


title: MDT-MB-62_Xba


title: MDT-MB-61_Xba


title: MDT-MB-161_Sty


title: MDT-MB-60_Xba


title: MDT-MB-163_Sty


title: MDT-MB-157_Sty


title: MDT-MB-162_Sty


title: MDT-MB-151_Sty


title: MDT-MB-59_Xba


title: MDT-MB-154_Sty


title: MDT-MB-155_Sty


title: MDT-MB-54_Xba


title: MDT-MB-56_Xba


title: MDT-MB-150_Sty


title: MDT-MB-58_Xba


title: MDT-MB-153_Sty


title: MDT-MB-75_Xba


title: MDT-MB-57_Xba


title: MDT-MB-148_Sty


title: MDT-MB-55_Xba


title: MDT-MB-152_Sty


title: MDT-MB-52_Xba


title: MDT-MB-158_Sty


title: MDT-MB-53_Xba


title: MDT-MB-146_Sty


title: MDT-MB-149_Sty


title: MDT-MB-145_Sty


title: MDT-MB-51_Xba


title: MDT-MB-50_Xba


title: MDT-MB-144_Sty


title: MDT-MB-147_Sty


title: MDT-MB-167_Sty


title: MDT-MB-49_Xba


title: MDT-MB-47_Xba


title: MDT-MB-48_Xba


title: MDT-MB-45_Xba


title: MDT-MB-142_Sty


title: RES256_Nsp


title: MDT-MB-44_Xba


title: MDT-MB-137_Sty


title: MDT-MB-140_Sty


title: MDT-MB-46_Xba


title: MDT-MB-156_Sty


title: MDT-MB-43_Xba


title: MDT-MB-139_Sty


title: MDT-MB-141_Sty


title: MDT-MB-228_Nsp


title: MDT-MB-133_Sty


title: MDT-MB-225_Nsp


title: MDT-MB-136_Sty


title: MDT-MB-226_Nsp


title: MDT-MB-135_Sty


title: MDT-MB-223_Nsp


title: MDT-MB-134_Sty


title: MDT-MB-42_Xba


title: MDT-MB-41_Xba


title: MDT-MB-229_Nsp


title: MDT-MB-40_Xba


title: MDT-MB-222_Nsp


title: MDT-MB-224_Nsp


title: MDT-MB-138_Sty


title: MDT-MB-132_Sty


title: MDT-MB-220_Nsp


title: MDT-MB-39_Xba


title: MDT-MB-219_Nsp


title: MDT-MB-38_Xba


title: MDT-MB-130_Sty


title: MDT-MB-221_Nsp


title: MDT-MB-215_Nsp


title: MDT-MB-129_Sty


title: MDT-MB-213_Nsp


title: MDT-MB-131_Sty


title: MDT-MB-36_Xba


title: MDT-MB-128_Sty


title: MDT-MB-212_Nsp


title: MDT-MB-37_Xba


title: MDT-MB-126_Sty


title: MDT-MB-217_Nsp


title: MDT-MB-208_Nsp


title: MDT-MB-210_Nsp


title: MDT-MB-211_Nsp


title: MDT-MB-207_Nsp


title: MDT-MB-34_Xba


title: MDT-MB-206_Nsp


title: MDT-MB-216_Nsp


title: MDT-MB-127_Sty


title: MDT-MB-123_Sty


title: MDT-MB-32_Xba


title: MDT-MB-124_Sty


title: MDT-MB-209_Nsp


title: MDT-MB-31_Xba


title: MDT-MB-203_Nsp


title: MDT-MB-35_Xba


title: MDT-MB-122_Sty


title: MDT-MB-125_Sty


title: MDT-MB-205_Nsp


title: MDT-MB-199_Nsp


title: MDT-MB-30_Xba


title: MDT-MB-198_Nsp


title: MDT-MB-28_Xba


title: MDT-MB-29_Xba


title: MDT-MB-214_Nsp


title: MDT-MB-197_Nsp


title: MDT-MB-202_Nsp


title: MDT-MB-196_Nsp


title: MDT-MB-121_Sty


title: MDT-MB-26_Xba


title: MDT-MB-117_Sty


title: MDT-MB-195_Nsp


title: MDT-MB-118_Sty


title: MDT-MB-27_Xba


title: MDT-MB-25_Xba


title: MDT-MB-194_Nsp


title: MDT-MB-193_Nsp


title: MDT-MB-200_Nsp


title: MDT-MB-189_Nsp


title: MDT-MB-191_Nsp


title: MDT-MB-192_Nsp


title: MDT-MB-187_Nsp


title: MDT-MB-190_Nsp


title: MDT-MB-186_Nsp


title: MDT-MB-201_Nsp


title: MDT-MB-23_Xba


title: MDT-MB-184_Nsp


title: MDT-MB-188_Nsp


title: MDT-MB-116_Sty


title: MDT-MB-22_Xba


title: MDT-MB-21_Xba


title: MDT-MB-113_Sty


title: MDT-MB-119_Sty


title: MDT-MB-115_Sty


title: MDT-MB-185_Nsp


title: MDT-MB-112_Sty


title: MDT-MB-20_Xba


title: MDT-MB-183_Nsp


title: MDT-MB-19_Xba


title: MDT-MB-176_Nsp


title: MDT-MB-18_Xba


title: MDT-MB-111_Sty


title: MDT-MB-178_Nsp


title: MDT-MB-179_Nsp


title: MDT-MB-110_Sty


title: MDT-MB-180_Nsp


title: MDT-MB-181_Nsp


title: MDT-MB-177_Nsp


title: MDT-MB-173_Nsp


title: MDT-MB-182_Nsp


title: MDT-MB-24_Xba


title: MDT-MB-174_Nsp


title: MDT-MB-16_Xba


title: MDT-MB-175_Nsp


title: MDT-MB-17_Xba


title: MDT-MB-109_Sty


title: MDT-MB-172_Nsp


title: MDT-MB-107_Sty


title: MDT-MB-14_Xba


title: MDT-MB-15_Xba


title: MDT-MB-114_Sty


title: MDT-MB-169_Nsp


title: MDT-MB-170_Nsp


title: MDT-MB-168_Nsp


title: MDT-MB-106_Sty


title: MDT-MB-165_Nsp


title: MDT-MB-103_Sty


title: MDT-MB-13_Xba


title: MDT-MB-164_Nsp


title: MDT-MB-105_Sty


title: MDT-MB-12_Xba


title: MDT-MB-100_Sty


title: MDT-MB-108_Sty


title: MDT-MB-102_Sty


title: MDT-MB-166_Nsp


title: MDT-MB-167_Nsp


title: MDT-MB-10_Xba


title: MDT-MB-160_Nsp


title: MDT-MB-162_Nsp


title: MDT-MB-158_Nsp


title: MDT-MB-161_Nsp


title: MDT-MB-101_Sty


title: MDT-MB-156_Nsp


title: MDT-MB-163_Nsp


title: MDT-MB-9_Xba


title: MDT-MB-8_Xba


title: MDT-MB-157_Nsp


title: MDT-MB-155_Nsp


title: MDT-MB-154_Nsp


title: MDT-MB-152_Nsp


title: MDT-MB-150_Nsp


title: MDT-MB-6_Xba


title: MDT-MB-11_Xba


title: MDT-MB-7_Xba


title: MDT-MB-5_Xba


title: MDT-MB-149_Nsp


title: MDT-MB-151_Nsp


title: MDT-MB-4_Xba


title: MDT-MB-148_Nsp


title: MDT-MB-153_Nsp


title: MDT-MB-145_Nsp


title: UW228_Xba


title: MED8A_Xba


title: MDT-MB-1_Xba


title: ONS76_Xba


title: MDT-MB-146_Nsp


title: MDT-MB-3_Xba


title: MHH-MED1_Xba


title: DAOY_Xba


title: MDT-MB-147_Nsp


title: MDT-MB-2_Xba


title: D556_Xba


title: MDT-MB-142_Nsp


title: MDT-MB-137_Nsp


title: MDT-MB-138_Nsp


title: D458_Xba


title: Pilocytic Astrocytoma, Case no. 65 (chr7 tiling-path)

city: Cambridge

first: David

middle: T W

last: Jones

address: Box 231, Level 3 Lab Block, Addenbrooke's Hospital

department: Pathology

institute: University of Cambridge

description: Log2 tumour/reference intensity ratios for analysis of copy number variations

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45µg of Cot1 DNA and ethanol precipitated. The precipitated DNA was dissolved in 30µl of hybridisation buffer, incubated at 37˚C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humidified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37˚C for 48 hours under a coverslip. The arrays were then washed successively in 1x PBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42˚C for 30 min once, 1x PBS/0.05% Tween20 at room temperature for 15min and 1x PBS for 5min twice.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of the 5Mb-clones in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.

source_name: Primary tumour sample

label_protocol: 400ng of genomic DNA was labelled with a Bioprime labelling kit (Invitrogen)

extract_protocol: Proteinase K digestion followed by phenol:chloroform extraction

tag: Female

tag: Location

value: Brain stem

source_name: Mixed normal blood from 20 individuals (reference)

label_protocol: 400ng of tumour and reference genomic DNA were labelled with Cy5-dCTP and Cy3-dCTP (GE Healthcare), respectively, using BioPrime kit (Invitrogen) according to the manufacturer’s instruction, except that custom-prepared dNTP (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM) was used. After overnight incubation at 37°C, the labelled DNA were purified using a G-50 spin column (GE Healthcare).

tag: Male


title: MDT-MB-136_Nsp


title: Pilocytic Astrocytoma, Case no. 67 (chr7 tiling-path)


title: MDT-MB-135_Nsp


title: Pilocytic Astrocytoma, Case no. 68 (chr7 tiling-path)


title: MDT-MB-141_Nsp


title: MDT-MB-140_Nsp


title: MDT-MB-134_Nsp


title: D425_Xba


title: MDT-MB-139_Nsp


title: Pilocytic Astrocytoma, Case no. 60 (chr7 tiling-path)

value: Cerebellum


title: MDT-MB-144_Nsp


title: MDT-MB-132_Nsp


title: MDT-MB-133_Nsp


title: ZR751_emetine_10h

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

description: Cells treated with emetine for 10 hours.

hyb_protocol: 15 micrograms of fragmented cRNA from each sample was used for hybridizations. The arrays were stained with phycoerythrin-streptavidin and the signal intensity was amplified by treatment with a biotin-conjugated anti-streptavidin antibody, followed by a second staining using phycoerythrin-streptavidin.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Data from all samples was preprocessed using the dCHIP program (Li and Wong, PNAS, Vol. 98, 31-38, 2001)

label_protocol: Biotinylated cRNA was prepared from 3 micrograms of total RNA per sample according to manufacturers (Affymetrix) instructions.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit according to manufacturers instructions.

treatment_protocol: Parallel cell cultures were grown to 70-80% confluence in 175 cm2 flasks. Half of the cultures were treated with 100 micrograms ml-1 of emetine dihydrochloride hydrate. The other half of cultures were left as untreated controls. Both treated and untreated cultures were incubated at 37C for 10 h.

tag: cell line

value: ZR751 breast cancer cell line

tag: treatment

value: emetine

tag: time


title: WS1_emetine_10h

value: WS1 non-malignant cell line


title: D283_Xba


title: MDT-MB-130_Nsp


title: MDT-MB-129_Nsp


title: Pilocytic Astrocytoma, Case no. 57 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 51 (chr7 tiling-path)


title: ZR751_untreated

description: Untreated control cells in regular growth medium

value: untreated (control)


title: Pilocytic Astrocytoma, Case no. 52 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 50 (chr7 tiling-path)

value: Child

value: 4th ventricle


title: MDT-MB-128_Nsp


title: MDT-MB-127_Nsp

value: F


title: Pilocytic Astrocytoma, Case no. 49 (chr7 tiling-path)


title: MDT-MB-126_Nsp


title: Pilocytic Astrocytoma, Case no. 48 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 47 (chr7 tiling-path)


title: T47D_emetine_10h

value: T47D breast cancer cell line


title: WS1_untreated


title: Pilocytic Astrocytoma, Case no. 45 (chr7 tiling-path)


title: T47D_untreated


title: MDA-MB-468_untreated

value: MDA-MB-468 breast cancer cell line


title: MDA-MB-231_untreated

value: MDA-MB-231 breast cancer cell line


title: MDA-MB-231_emetine_10h


title: MDT-MB-121_Nsp

value: M

value: Classic


title: MDT-MB-119_Nsp


title: MDT-MB-124_Nsp

value: Desmoplastic


title: MDT-MB-125_Nsp


title: MDT-MB-122_Nsp


title: MDT-MB-123_Nsp


title: Pilocytic Astrocytoma, Case no. 42 (chr7 tiling-path)

value: Left frontal lobe


title: Pilocytic Astrocytoma, Case no. 43 (chr7 tiling-path)

value: Optic nerve


title: MDT-MB-131_Nsp

value: Large Cell/Anaplastic


title: Pilocytic Astrocytoma, Case no. 41 (chr7 tiling-path)


title: MCF7_untreated

value: MCF7 breast cancer cell line


title: D341_Xba


title: MCF7_emetine_10h


title: MDA-MB-468_emetine_10h


title: IMR-90_emetine_10h

value: IMR-90 non-malignant cell line


title: Pilocytic Astrocytoma, Case no. 44 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 39 (chr7 tiling-path)

value: Cerebellum


title: Pilocytic Astrocytoma, Case no. 40 (chr7 tiling-path)


title: IMR-90_untreated


title: MDT-MB-115_Nsp


title: MDT-MB-116_Nsp


title: HMEC_emetine_10h

source_name: HMEC

value: HMEC non-malignant cell line

value: emetine


title: HMEC_untreated

value: untreated (control)


title: Pilocytic Astrocytoma, Case no. 33 (chr7 tiling-path)

value: 3rd ventricle


title: Pilocytic Astrocytoma, Case no. 32 (chr7 tiling-path)


title: MDT-MB-118_Nsp


title: MDT-MB-114_Nsp

value: F


title: BT474_untreated

value: BT474 breast cancer cell line


title: BT474_emetine_10h


title: Pilocytic Astrocytoma, Case no. 35 (chr7 tiling-path)

value: Adult


title: Pilocytic Astrocytoma, Case no. 30 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 29 (chr7 tiling-path)


title: MDT-MB-117_Nsp


title: MDT-MB-112_Nsp


title: MDT-MB-111_Nsp


title: Pilocytic Astrocytoma, Case no. 28 (chr7 tiling-path)

value: Right temporal lobe


title: Saos-2-His273, 6 hours treatment, rep 3

city: Stockholm

first: Jeremy

last: Lambert

country: Sweden

institute: Karolinska Institutet

description: Microsoft Excel program was used to merge the overlapping significant genes from the settings. Annotations from Affymetrix for significant genes were checked in NCBI public database and pathway analysis were used by Ingenuity.

hyb_protocol: Fifteen micrograms of the resulting biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320) to probe sets on an Affymetrix Genechip Rice Genome Array.

scan_protocol: The chip was washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400, followed by scanning on a GeneChip Scanner 3000 (Affymetrix, Inc.).

data_processing: The results were quantified, and normalized using MAS5.0. The genes with probe set signal lower than 50 on the repeated arrays were considered as non-expression and filtered out. The cutoff value of expression fold change was set as 2.0 that was commonly used for microarray analysis to further increase the stringency. GeneSpring software from Agilent was used for the filtration and pathway analysis.

source_name: Saos-2 osteosarcoma, p53-His273, 6 hours treatment

label_protocol: Biotin labeled cRNA was produced according to Affymetrix protocol

extract_protocol: RNA was extracted using RNeasy Mini Kit (Qiagen, Sweden) according to manufacturer’s instructions

tag: mutation

value: 6 hours treatment with Prima

value: osteosarcoma


title: Pilocytic Astrocytoma, Case no. 27 (chr7 tiling-path)


title: Saos-2-His273, 12 hours treatment, rep 2

source_name: Saos-2 osteosarcoma, p53-His273, 12 hours treatment

value: 12 hours treatment with Prima

tag: cell type


title: MDT-MB-108_Nsp

value: Desmoplastic


title: MDT-MB-110_Nsp


title: Saos-2-His273, 6 hours treatment, rep 1


title: MDT-MB-106_Nsp

value: M


title: MDT-MB-109_Nsp

value: Classic


title: Pilocytic Astrocytoma, Case no. 24 (chr7 tiling-path)

value: 4th ventricle


title: MDT-MB-105_Nsp


title: Pilocytic Astrocytoma, Case no. 23 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 25 (chr7 tiling-path)

value: Optic nerve


title: Pilocytic Astrocytoma, Case no. 37 (chr7 tiling-path)

value: Cerebellum


title: Saos-2-His273, untreated, rep 3

source_name: Saos-2 osteosarcoma, p53-His273, untreated

value: untreated


title: Pilocytic Astrocytoma, Case no. 18 (chr7 tiling-path)

value: Pineal region


title: Pilocytic Astrocytoma, Case no. 14 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 19 (chr7 tiling-path)


title: Saos-2-His273, untreated, rep 2


title: Pilocytic Astrocytoma, Case no. 20 (chr7 tiling-path)


title: MDT-MB-113_Nsp


title: Saos-2-His273, untreated, rep 1


title: Pilocytic Astrocytoma, Case no. 12 (chr7 tiling-path)


title: MDT-MB-101_Nsp


title: Saos-2-His273, 12 hours treatment, rep 3


title: MDT-MB-102_Nsp

value: Large Cell/Anaplastic


title: Saos-2-His273, 6 hours treatment, rep 2


title: Pilocytic Astrocytoma, Case no. 10 (chr7 tiling-path)


title: Saos-2-His273, 12 hours treatment, rep 1


title: Pilocytic Astrocytoma, Case no. 15 (chr7 tiling-path)


title: MDT-MB-103_Nsp


title: Pilocytic Astrocytoma, Case no. 8 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 9 (chr7 tiling-path)

value: Hypothalamus


title: Pilocytic Astrocytoma, Case no. 2 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 5 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 7 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 16 (chr7 tiling-path)


title: Pilocytic Astrocytoma, Case no. 1 (chr7 tiling-path)


title: Genomic DNA isolated from C57BL6/J mice at E17.5, chr1 to chr10, biol rep2

tag: strain

value: liver


title: Pilocytic Astrocytoma, Case no. 3 (chr7 tiling-path)

tag: Age


title: MDT-MB-100_Nsp

tag: Gender

value: F


title: Genomic DNA isolated from C57BL6/J mice at P21, chr1 to chr10, biol rep1


title: Genomic DNA isolated from C57BL6/J mice at E17.5, chr1 to chr10, biol rep1


title: synchronized L4 fasted

city: Seoul

first: Hyunsun

last: Jo

address: San 56-1, Sillim-Dong, Kwanak-Gu

country: South Korea

institute: Seoul National University

description: Gene expression data from 6 hours fasted worms.

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Caenorhabditis elegans

source_name: Synchronized L4 worms, fed

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

growth_protocol: N2 was grown at 20℃ on NGM plates

treatment_protocol: Synchronized worms were cultured on either NGM plates containing OP50 bacteria or NGM plates only

value: Whole-worm extract

value: Bristol strain N2

value: Larval stage 4

source_name: Synchronized L4 worms, fasted


title: MDA-MB-468 genomic DNA

description: no additional information

hyb_protocol: Labelled tumor and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using the G2565 scanner from Agilent Technologies. Signal intensities were quantified using the Feature Extraction software version 7.5.1 from Agilent.

data_processing: Agilent Feature Extraction Software (v 7.5.1) was used for spot quality filtering and normalization.

source_name: healthy female donors

label_protocol: Six micrograms of digested and purified tumour and reference DNA was labelled with Cy5-dUTP and Cy3-dUTP, respectively, in a random priming reaction using BioPrime DNA Labelling System.

growth_protocol: Cell cultures were grown to 70-80% confluence in 175 cm2 flasks according to distributor's instructions (ATCC).

extract_protocol: Genomic DNA was extracted from untreated cells using the NucleoSpin Tissue kit with the protocol for cultured cells.

tag: sample type

value: reference (pooled genomic DNA)

tag: gender

value: female

source_name: breast cancer cell line MDA-MB-468

value: test

value: MDA-MB-468 breast cancer cell line


title: ZR751 genomic DNA

description: no additional information

source_name: breast cancer cell line ZR751

value: ZR751 breast cancer cell line


title: T47D genomic DNA

description: no additional information

source_name: breast cancer cell line T47D

value: T47D breast cancer cell line


title: MDA-MB-231 genomic DNA

description: no additional information

source_name: breast cancer cell line MDA-MB-231

value: MDA-MB-231 breast cancer cell line


title: MCF7 genomic DNA

description: no additional information

source_name: breast cancer cell line MCF7

value: MCF7 breast cancer cell line


title: BT474 genomic DNA

description: no additional information

source_name: breast cancer cell line BT474

value: BT474 breast cancer cell line


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10989

status: Public on Apr 14 2009

city: Seattle

first: Dan

last: Tenenbaum

institute: Institute for Systems Biology

description: Cells incubated under entrainment conditions

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details. The arrays are 75th percentile normalized between channels on each array. Taking ratios to the common reference RNA serves as a means of normalization to compare across arrays.

organism: Halobacterium salinarum

source_name: Halobacterium salinarum

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: od

source_name: Halobacterium standard reference sample

tag: sample

value: standard Halobacterium standard reference sample

tag: media

value: CM


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10987

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10968


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10995


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10984


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10988


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10992


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10986


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10994


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10969


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10985


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10983


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10990


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10982


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10993


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10966


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10991


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10967


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10965


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10964


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10962


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10961


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10905


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10958


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10904


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10963


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10899


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10900


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10901


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10960


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10892


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10898


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10896


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10893


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10897


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10895


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10914


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10894


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10915


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10912


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10917


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10902


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10911


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10916


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10903


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10909


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10913


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10910


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10908


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10906


title: Genomic DNA isolated from C57BL6/J mice at P21, chr1 to chr10, biol rep2

tag: age

tag: tissue


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10888


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10884


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10959


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10885


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10886


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10883


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10882


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10879


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10873


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10881


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10868


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10887


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10875


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10876


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10877


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10907


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10869


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10867


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10878


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10872


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10880


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10857


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10863


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10871


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10862


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10870


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10865


title: MDT-MB-107_Nsp

source_name: genomic DNA from fresh-frozen tissue

value: M

tag: Histology

value: Classic


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10889


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10864


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10855


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10854


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10851


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10852


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10850


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10848


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10853


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10849


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10847


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10838


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10843


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10845


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10840


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10846


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10841


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11357


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10837


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10839


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10834


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10832


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11355


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11349


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11352


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10833


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11350


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10842


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11356


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11353


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11347


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11345


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11351


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10836


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11346


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10475


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10477


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10479


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10478


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10474


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10473


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11336


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10476


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10844


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10472


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11354


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11344


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11348


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11335


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11337


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11332


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11339


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11333


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11329


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11326


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11328


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11330


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11331


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11327


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11324


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11334


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11338


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10132


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10130


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 11325


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10126


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10128


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10125


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10133


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10122


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10121


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10127


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10120


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10123


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10117


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10119


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10124


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10131


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10116


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10106


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10104


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10103


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10102


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10100


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10118


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10098


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10105


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10101


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10097


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10099


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10093


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10092


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10094


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10091


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10076


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10095


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10078


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10077


title: Halobacterium salinarum at OD=0.65, t=3870 min., Array 07350


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 07374


title: Halobacterium salinarum at OD=0.55, t=3360 min., Array 07373


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10096


title: Halobacterium salinarum at OD=0.61, t=3600 min., Array 07433


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 07435


title: Halobacterium salinarum at OD=0.65, t=3870 min., Array 07434


title: Halobacterium salinarum at OD=0.61, t=3600 min., Array 07349


title: Halobacterium salinarum at OD=0.55, t=3360 min., Array 07432


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10079


title: Halobacterium salinarum at OD=0.61, t=2400 min., Array 07344


title: Halobacterium salinarum at OD=0.65, t=2880 min., Array 07430


title: Halobacterium salinarum at OD=0.65, t=2880 min., Array 07371


title: Halobacterium salinarum at OD=0.61, t=2640 min., Array 07345


title: Halobacterium salinarum at OD=0.59, t=3120 min., Array 07431


title: Halobacterium salinarum at OD=0.59, t=3120 min., Array 07372


title: Halobacterium salinarum at OD=0.63, t=2160 min., Array 07343


title: Halobacterium salinarum at OD=0.61, t=2640 min., Array 07307


title: Halobacterium salinarum at OD=0.63, t=2160 min., Array 07305


title: Halobacterium salinarum at OD=0.61, t=1920 min., Array 07342


title: Halobacterium salinarum at OD=0.54, t=1680 min., Array 07341


title: Halobacterium salinarum at OD=0.61, t=1920 min., Array 07304


title: Halobacterium salinarum at OD=0.61, t=2400 min., Array 07306


title: Halobacterium salinarum at OD=0.54, t=1680 min., Array 07267


title: Halobacterium salinarum at OD=0.57, t=1440 min., Array 07340


title: Halobacterium salinarum at OD=0.57, t=1440 min., Array 07266


title: Halobacterium salinarum at OD=0.61, t=960 min., Array 07367


title: Halobacterium salinarum at OD=0.66, t=4110 min., Array 10129


title: Rat SSC GDNF 8hr Replacement Rep3

city: Philadelphia

first: Jonathan

middle: A

last: Schmidt

state: PA

address: 3850 Baltimore Avenue

institute: University of Pennsylvania

description: Rat SSC GDNF 8hr Replacement Rep3

hyb_protocol: The cDNA products were fragmented, heated, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays.  Each sample (n=15) was hybridized to its own array.  Microarrays were then washed and stained with streptavidin-phycoerythrin and a confocal scanner was used to collect the fluorescence signals after excitation at 570 nm.

scan_protocol: The average signal from two sequential scans was calculated for each microarray.  For initial data analysis, Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes.  The default values were provided by Affymetrix and were applied to all analysis parameters.  For each probe, border pixels were removed, and the average intensity of pixels within the 75th percentile was computed.  The average of the lowest 2% of probe intensities in each of 16 microarray sectors was used as background and subtracted from all features in that sector.  Probe pairs were scored as positive or negative for detection of the specific sequence by comparing signals from the perfect match and mismatch probe features.  The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call.

data_processing: For microarray analysis, Affymetrix probe level data (.cel files) were imported into ArrayAssist (v3.4, Stratagene, La Jolla, CA) and probeset signal values were calculated using the GCRMA algorithm.  The newly generated probeset signal values were exported into GeneSpring (Agilent).  Within GeneSpring, the probeset list was filtered such that only those probes that were flagged as present in at least 2 of the 15 data sets were utilized for further analysis.  The filtered data set (21935 probesets) was imported into Partek Genomics Suite (v6.3, Partek Inc., St. Louis, MO) where it was Log2 transformed.  In order to generate a list of genes significantly regulated by GDNF, the transformed data was analyzed using ANOVA, and only those genes with a p-value less than 0.05 were considered further (7948 probe sets).  This analysis generated a list of genes that was used as a means to prioritize genes for further conformation using functional experimentation.  To identify candidate genes, the list was scrutinized by only considering genes that had at least a 2-fold change in signal values between the control and the GDNF withdrawal samples (137 probe sets).  Finally, genes that were positively regulated by GDNF and subsequently recovered at least 2-fold in expression after GDNF replacement were evaluated for further analysis (61 probe sets).

organism: Rattus norvegicus

source_name: Rat SSC GDNF 8hr Replacement

label_protocol: 5mg of cRNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter.  Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Rat Spermatogonial Stem Cells were cultured in serum free media in the presence of GDNF.  After 1 month of culture, which included self-renewal expansion, treatments were applied.

extract_protocol: Trizol + RNeasy Column

treatment_protocol: Cultured rat SSCs were subjected to 1 of 5 treatments.  Each treatment was replicated 3 times with independent cultures.  Treatments 1: Contol + GDNF, 2: 18 hr GDNF withdrawal, 3: 18 hr GDNF withdrawal followed by 2 hr GDNF replacement, 4: 18 hr GDNF withdrawal followed by 4 hr GDNF replacement, 5: 18 hr GDNF withdrawal followed by 8 hr GDNF replacement.

value: Cultured spermatogonial stem cells


title: Rat SSC GDNF 8hr Replacement Rep2

description: Rat SSC GDNF 8hr Replacement Rep2


title: Rat SSC GDNF 4hr Replacement Rep3

description: Rat SSC GDNF 4hr Replacement Rep3

source_name: Rat SSC GDNF 4hr Replacement


title: Rat SSC GDNF 4hr Replacement Rep2

description: Rat SSC GDNF 4hr Replacement Rep2


title: MEF Med23-/- (KO) cells 20% serum stimulated Set 1

city: Berkeley

first: Michael

middle: Andrew

last: Balamotis

address: 1 Cycotron Rd. Bld. 84

department: Life Sciences

institute: Lawrence Berkeley National Lab

hyb_protocol: UCLA Microarray Core

scan_protocol: UCLA Microarray Core

source_name: Mouse Med23 -/- embryonic fibroblasts (E11) passaged through crisis, cultured

label_protocol: UCLA Microarray Core

extract_protocol: Trizol and Qiagen column purification

treatment_protocol: Starved 16 h in 0.5% FBS DMEM and then stimulated with 20% FBS for 30 minutes, then total RNA harvested (see below). First replicate.