title: FY834-10% vs FY834-0%

status: Public on Nov 29 2008

city: Osaka

first: Thai

middle: Nho

last: Dinh

state: Osaka

address: 2-1 Yamadaoka, Suita

department: Biotechnology

institute: Osaka University

description: The preparation of fluorescent-dye-labeled cDNA targets, hybridization, and washing were carried out as described in instruction manuals supplied by the manufacturer of the DNA microarray

hyb_protocol: Hybridized for 16 h at 65 degrees C

scan_protocol: The fluorescent signal intensities of Cy3 and Cy5 on the DNA microarray were acquired using Genepix pro ver. 3.0 software (Molecular Devices, CA, USA).

data_processing: The signal was normalized by the locally weighted linear regression (Lowess) method. The data analysis was performed using Matlab ver. 2006b (Mathworks Inc., USA) and Microsoft Excel (Microsoft, USA)

molecule: polyA RNA

label_protocol: Fluorescent-dye-labeled cDNA targets were prepared from purified mRNA (1.5 μg) using Superscript II RNaseH− reverse transcriptase (Invitrogen Co., USA) and fluorescent-dye-labeled nucleotide, Cy3-dCTP (Amersham Biosciences Inc., UK).

growth_protocol: Yeast cells were precultured in 5 ml of yeast YPD medium at 30 degrees C for 24 h. Then, for the main culture, the precultured yeast cells were cultivated aerobically at 30 degrees C in a 500 ml Sakaguchi flask containing 100 ml of YPD medium adding 10% (v/v) ethanol at the beginning of the main culture. Cells were harvested in the logarithmic growth phase for RNA extraction.

extract_protocol: Total RNA was extracted by the hot phenol method and mRNA was obtained using an Oligo dT30 <Super> mRNA purification kit from total RNA (Takara Bio Inc.)

treatment_protocol: 10% ethanol

tag: Yeast cells were precultured in 5 ml of YPD medium at 30 degrees C for 24 h. Then, for the main culture, the precultured yeast cells were cultivated aerobically at 30 degrees C in a 500 ml Sakaguchi flask containing 100 ml of YPD medium. Cells were harvested in the logarithmic growth phase for RNA extraction.

label_protocol: Fluorescent-dye-labeled cDNA targets were prepared from purified mRNA (1.5 μg) using Superscript II RNaseH− reverse transcriptase (Invitrogen Co., USA) and fluorescent-dye-labeled nucleotide, Cy5-dCTP (Amersham Biosciences Inc., UK).

treatment_protocol: Untreated

tag: strain FY834


title: Ethanol-adapted-10% vs Control-0%

type: RNA

country: Japan

organism: Saccharomyces cerevisiae

tag: The ethanol adapted strain A1, original from FY834

growth_protocol: Yeast cells were precultured in 5 ml of YPD medium at 30 degrees C for 24 h. Then, for the main culture, the precultured yeast cells were cultivated aerobically at 30 degrees C in a 500 ml Sakaguchi flask containing 100 ml of YPD medium. Cells were harvested in the logarithmic growth phase for RNA extraction.


title: wild-type, biological rep 3

status: Public on Dec 01 2008

city: Cambridge

first: Sebastian

last: Hoersch

state: MA

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

country: USA

institute: Massachusetts Institute of Technology

description:
Gene expression data from stage L1-L2 wild type nematodes
A7028_WT_3

hyb_protocol: Following fragmentation, 18 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 7G.

data_processing: Raw data (CEL files) processing and normalization was performed using the Bioconductor (http://www.bioconductor.org/ ) packages ‘affy’ and ‘gcrma’ to generate the dataset of GC-RMA expression measures.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: L1-L2 stage nematodes, wild type

label_protocol: Biotinylated cRNA was prepared according to the standard (one-cycle) Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix, P/N 702232 Rev. 2).

growth_protocol: Worms were maintained on nematode growth medium plates seeded with OP50 bacteria.

extract_protocol: Tri Reagent (MRC) was used for total RNA preparation from frozen worms resulting in 5-30 microgram RNA per sample. The quality of RNA samples was confirmed by BioRad Bioanalyzer.

treatment_protocol: Nematodes were synchronized at L1 stage by hypochlorite treatment of gravid hermaphrodites and hatching their eggs overnight in liquid culture without food. Resulting populations were cultured on OP50 bacteria for 6-7h and collected for RNA preparations.

tag: strain

value: wild type Bristol strain N2


title: rde-4 mutant, biological rep 1

description:
Gene expression data from stage L1-L2 rde-4 mutant nematodes
A7035_rde-4_1

source_name: L1-L2 stage nematodes, rde-4 mutant


title: zfp-1 mutant, biological rep 2, technical rep 2

description:
Gene expression data from stage L1-L2  zfp-1 mutant nematodes
A7034_zfp-1_3

source_name: L1-L2 stage nematodes, zfp-1 mutant


title: Individual 2, single round, day 2, Cy3

status: Public on Nov 21 2008

city: Miami

first: Cinda

middle: P

last: Scott

state: FL

address: 4600 Rickenbacker Cswy

department: Marine Biology and Fisheries

institute: University of Miami

description: Individual 2, single round, day 2, Cy3

hyb_protocol: Dye labeled aRNA aliquots for each hybridization (30 pmol each of Cy3 and Cy5) were vacuum dried together and resuspended in 15ul hybridization buffer (final concentration of each labeled sample = 2 pmol/ul).  Hybridization buffer consisted of 5X SSPE, 1% SDS, 50% formamide, 1mg/ml polyA, 1mg/ml sheared herring sperm carrier DNA, and 1mg/ml BSA.  Slides were washed in sodium borohydride solution in order to reduce autofluorescence.  Following rinsing, slides were boiled for 2 minutes and spin-dried in a centrifuge at 800 rpm for 3 minutes.  Samples (15ul) were heated to 90ºC for 2 minutes, quick cooled to 42ºC, applied to the slide (hybridization zone area was 350mm2), and covered with a cover slip.  Slides were placed in an airtight chamber humidified with paper soaked in 5X SSPE and incubated 24-48 hours at 42ºC.

scan_protocol: The microarray slides were scanned using ScanArray Express.  The raw TIFF-image data was quantified using Imagene (v5).  Genes with a fluorescence signal greater than 60,000 or less than the Ctenophore negative controls were eliminated from the analysis.

data_processing: Values were sum normalized and then subject to global loess analysis using SAS JMP genomics v6.0.2.

organism: Fundulus heteroclitus

source_name: Individual 2, single round, day 2

label_protocol: RNA was converted into amino allyl labeled RNA (aRNA) using the Ambion Amino Allyl MessageAmp II aRNA Amplification kit.  This method converts poly-A RNA into cDNA with a T7 RNA polymerase binding site and T7 is used to synthesize many new strands of RNA (in vitro transcription) .  During the in vitro transcription of aRNA, an amino allyl UTP (aaUTP) is incorporated into the elongating strand.  aaUTP incorporation allows for the coupling of Cy3 or Cy5 dyes (GE biosciences) onto aRNA for microarray hybridization.

growth_protocol: Fish were acclimated to laboratory conditions prior to sacrifice for hearts for approximately 6 months

extract_protocol: Total RNA was isolated from using 4.5M guanidinium thiocyanate, 2% N-lauroylsarcosine, 50mM EDTA, 25mM Tris-HCl, 0.1M beta-Mercaptoethanol and .2% Antifoam A.  The extracted RNA was further purified using a Qiagen RNeasy Mini kit in accordance with the manufacturer’s protocols.  The quantity and quality of the RNA was determined using a spectrophotometer.

tag: Tissue

value: cardiac


title: Individual 2, single round, day 1, Cy3

description: Individual 2, single round day 1, Cy3

source_name: Individual 2, single round day 1


title: Individual 1, double round, day 1, Cy3

description: Individual 1, double round, day 1, Cy3

source_name: Individual 1, double round, day 1


title: Individual 2, double round, day 3, Cy5

description: Individual 2, double round, day 3, Cy5

source_name: Individual 2, double round, day 3


title: zfp-1 mutant, biological rep 2, technical rep 1

description:
Gene expression data from stage L1-L2 zfp-1 mutant nematodes
A7033_zfp-1_2


title: Individual 1, double round, day 3, Cy5

description: Individual 1, double round, day 3, Cy5

source_name: Individual 1, double round, day 3


title: wild-type, biological rep 2

description:
Gene expression data from stage L1-L2 wild type nematodes
A7027_WT_2


title: alg-1 mutant, biological rep 2

description:
Gene expression data from stage L1-L2 alg-1 mutant nematodes
A7030_alg-1_2

source_name: L1-L2 stage nematodes, alg-1 mutant


title: alg-1 mutant, biological rep 1

description:
Gene expression data from stage L1-L2 alg-1 mutant nematodes
A7029_alg-1_1


title: GM12878_sample9

status: Public on Sep 16 2008

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Stanford-Myers

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

organism: Homo sapiens

source_name: GM12878, Stanford

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol or RNEasy protocol

treatment_protocol: cells were supplied as frozen pellets, pellets in trizol, pellets in RNA later or pellets in RLT buffer

tag: Coriell cell line repository identifier

tag: cell pellet in RLT


title: GM12878_sample8

description: Uwash-Stamatoyannopoulos

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: GM12878, Uwash

tag: cell pellet in RNA later


title: alg-1 mutant, biological rep 3

description:
Gene expression data from stage L1-L2 alg-1 mutant nematodes
A7031_alg-1_3


title: wild-type, biological rep 1

description:
Gene expression data from stage L1-L2 wild type nematodes
A7026_WT_1


title: Individual 1, single round, day 2, Cy3

description: Individual 1, single round, day 2, Cy3

source_name: Individual 1, single round, day 2


title: GM12878_sample7

description: Broad-Bernstein

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays

source_name: GM12878, Broad

tag: cell pellet in Trizol


title: Individual 1, single round, day 2, Cy5

description: Individual 1, single round, day 2, Cy5


title: GM12878_sample4

description: Duke-Crawford

source_name: GM12878, Duke


title: GM12878_sample5

description: Duke-Crawford


title: K562_sample11

description: Stanford-Myers

source_name: K562, Stanford

tag: K562 (ATCC)


title: Individual 2, double round, day 2, Cy5

description: Individual 2, double round, day 2, Cy5

source_name: Individual 2, double round, day 2


title: K562_sample9

description: Broad-Bernstein

source_name: K562, Broad


title: GM12878_sample2

description: Ualbany-Tenenbaum

source_name: GM12878, UAlbany


title: GM12878_sample1

description: Ualbany-Tenenbaum


title: GM12878_sample3

description: Ualbany-Tenenbaum


title: K562_sample10

description: Uwash-Stamatoyannopoulos

source_name: K562, Uwash


title: Xenopus laevis Brain, biological replicate 3

status: Public on Sep 03 2008

city: Hamilton

first: Frederic

last: Chain

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description: 1 of 3 biological replicates of gene expression data from adult brain.

hyb_protocol: Hybridization to Affymetrix Xenopus laevis Genome expression array followed the manufacturer's (Affymetrix) protocol.

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

data_processing:
Data were RMA normalized using RMA Express and a probemask (based on perfect match probes for X.laevis and X.borealis).
Normalization of 3 biological replicates were performed with 3 biological replicates of X.laevis testis

organism: Xenopus laevis

source_name: Xenopus laevis, Adult male hindbrain (dorsal tegmental area of the medulla to the end of n.IX-X)

label_protocol: Two micrograms of total RNA was used to prepare biotin labeled cRNA probes following the manufacturer’s (Affymetrix) protocol.

extract_protocol: Total RNA was isolated using TRIzol® Reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol and purified with RNeasy Mini Kit (Qiagen).

treatment_protocol: Animal was immersed in MS222 and tissue was immediately extracted

tag: Adult male Xenopus laevis


title: Xenopus laevis Brain, biological replicate 2


title: K562_sample8

description: Yale-Snyder

source_name: K562, Yale


title: K562_sample7

description: Affymetrix-Gingeras

source_name: K562, Affymetrix


title: K562_sample5

description: Duke-Crawford

source_name: K562, Duke


title: K562_sample6

description: Duke-Crawford


title: zfp-1 mutant, biological rep 1

description:
Gene expression data from stage L1-L2 zfp-1 mutant nematodes
A7032_zfp-1_1

source_name: L1-L2 stage nematodes, zfp-1 mutant


title: K562_sample1

description: Ualbany-Tenenbaum

source_name: K562, UAlbany


title: K562_sample3

description: Ualbany-Tenenbaum


title: K562_sample4

description: Duke-Crawford


title: K562_sample2

description: Ualbany-Tenenbaum


title: Xenopus laevis Brain, biological replicate 1


title: Xenopus borealis Brain, biological rep 3

description: 1 of 3 biological replicates of gene expression data from adult male brain

data_processing:
Data were RMA normalized using RMA Express and a probemask (based on perfect match probes for X.laevis and X.borealis).
Normalization of 3 biological replicates were performed with 3 biological replicates of X.borealis testis

organism: Xenopus borealis

source_name: Xenopus borealis male Adult hindbrain (dorsal tegmental area of the medulla to the end of n.IX-X)

tag: Adult male Xenopus borealis (Kenya)


title: 2 min light stimulated male head at -30 min vs. 2 min light stimulated female head at -30 min rep 2

status: Public on Nov 13 2008

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Agilent

hyb_protocol: Agilent

scan_protocol: AXON

data_processing: GENEPIX

organism: Anopheles gambiae

label_protocol: Agilent

extract_protocol: QIAGEN

treatment_protocol: dark

tag: Adult male head

treatment_protocol: 2 hr light

tag: Adult female head


title: Xenopus borealis Brain, biological rep 1

description: 1 of 3 biological replicates of gene expression data from adult male brain.

source_name: X.borealis male, Adult hindbrain (dorsal tegmental area of the medulla to the end of n.IX-X)


title: GM12878_sample6

description: Duke-Crawford


title: Xenopus borealis Brain, biological rep 2

source_name: Xenopus borealis male, Adult hindbrain (dorsal tegmental area of the medulla to the end of n.IX-X)


title: X1736925551_A

status: Public on Mar 31 2008

city: Paris

first: Julien

last: Laffaire

address: 10 rue Vauquelin

country: France

institute: ESPCI - CNRS UMR 7637

description: Illumina provides one expression value per gene corresponding to the mean of at least 20 beads on the microarray. Genes were considered to be expressed if their detection p-value (provided by Illumina) was less than 0.01.

hyb_protocol: Hybridization was performed by Integragen (Evry - France) following Illumina's instructions.

scan_protocol: Scan was performed by Integragen (Evry - France) following Illumina's instructions with standard scan factors.

data_processing: Filtered data were processed under R software for normalization by the mean and  Student t-test.

organism: Mus musculus

source_name: EGL P0 Ts1Cje

label_protocol: 50ng of total RNA was labeled using TotalPrep RNA Amplification kit from Ambion following the manufacturer's instructions.

extract_protocol: Total RNA was extracted from frozen individual dissected cerebellar external granular layer and treated with DNAse using RNeasy Minikit (Qiagen) in accordance with the manufacturer's protocol. RNA quality and quantity were then checked on the Agilent 2100 Bioanalyzer with RNA 6000 NanoChips (Agilent Technologies).

tag: Strain

value: B6EiC3SnF1/J A/a

tag: Genotype

tag: Stage

value: dissected External Granular Layer


title: X1736925556_D

source_name: EGL P0 euploid

value: euploid


title: X1736925556_E


title: X1736925551_B


title: X1736925551_D

source_name: Cerebellum P0 euploid


title: X1736925556_C


title: X1736925538_E


title: X1736925551_F


title: X1736925551_E


title: X1736925538_A


title: X1736925556_F


title: X1736925551_C


title: X1736925556_B


title: X1736925538_C


title: X1736925538_D


title: X1736925538_F


title: X1736925556_A


title: X1736925538_B


title: CMT-U229 vs CMT-U335 rep 5

status: Public on Sep 01 2007

city: Utrecht

first: Nagesha

middle: A S

last: Rao

state: Utrecht

department: Veterinary sciences

country: Netherlands

institute: Utrecht University

description: Biological replicate of 5 out of 5

hyb_protocol: Microarray slides were washed for 1 min in 2x SSC containing 0.05% Sodium dodecyl sulphate (SDS) at room temperature (RT), incubated in 0.25% sodium borohydride and 0.25% SDS in 2x SSC for 30 min at 420C  and then rinsed 5 times in double distilled water at RT.  Slides were incubated for 45 minutes at 420C in pre-warmed pre-hybridization buffer (2X) consisting of 10xSSC, 25% formamide, 0.1% SDS and 1% BSA. Slides were washed 5 times in water followed by 5 times in isopropanol at RT and air dried. To 40 µl containing 2.5 µg of each Cy3 and Cy5 labeled RNA 40 µl hybridization buffer was added consisting of 50% formamide, 0.2% SDS and 200 µg/ml sheared herring sperm DNA. The mixture was heated at 95°C for 5 min, centrifuged for 2 min at 12,000xg and hybridized to the slides at 420C for 16 hours using hybridization chambers (Corning Life Sciences) in a water bath. After hybridization, slides were washed three times: first a low-stringency wash for 4 min at RT in 1xSSC and 0.2% SDS, next a high-stringency wash in 0.1% SDS and 0.2% SDS for 4 min and finally 2 washes in 0.1xSSC at room temperature. Slides were blown dry using compressed nitrogen.

scan_protocol: Slides were scanned using an Agilent G2565AA DNA microarray scanner (100% laser power, 30% photomultiplier tube)

data_processing: Image analysis was carried out using Imagene 5.0 software (Biodiscovery Inc). Data were normalized based on Lowess print-tip normalization by using the gene spots to calculate the Lowess line for each sub grid and then applying the these lines to all spots.

organism: Canis lupus familiaris

source_name: Cell line CMT-U229

label_protocol: Total RNA was isolated from cells which were grown to near confluence and is used for cRNA synthesis. About 2 µg total RNA was reverse transcribed using Superscript II reverse transcriptase and T7 promoter coupled poly T primers (5' GGCCAGTGAATTGTAATACGACTCACCTATAGGGAGG CGGT). After second strand synthesis, cDNA products were purified using QIAquick PCR Purification Kit and transcribed using the T7 Megascript kit (Ambion) using a UTP to 5-(3-aminoallyl)-UTP ratio of 1/3.5. The RNeasy mini kit (Qiagen) was used to clean the resulting cRNA. Three µg cRNA  was coupled to Cy3 or Cy5 fluorophores. Labeled cRNA was cleaned using ChromaSpin-30 columns and cRNA samples with specific activity of 2-5% dye-labeled nucleosides were used for microarray hybridization

extract_protocol: Total RNA was isolated using Qiagen RNA isolation (mini) kit and DNAse treatment kit

tag: Passage no.19

source_name: Cell line CMT-U335

label_protocol: Identical to the protocol used for samle labelling for ch1


title: CMT-U229 vs CMT-U335 rep 4

description: Biological replicate of 4 out of 5

tag: Passage no.17

tag: Passage no.22


title: CMT-U229 vs CMT-U335 rep 3

description: Biological replicate of 3 out of 5

tag: Passage no.7

tag: Passage no.20


title: A30395

status: Public on Jan 31 2007

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

institute: Veridex, LLC

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: bone marrow from AML patient

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated from bone marrow of AML patients using Qiagen Rneasy Kit.

tag: AML class

value: REFRACTORY

tag: Sex

value: MALE

tag: Age

tag: Best Response

value: No response

tag: Survival time


title: P114 vs CMT-U229 rep 4

description: Biological replicate of 4 out of 5

source_name: Cell line P114

tag: Passage no.6


title: A30377

value: RELAPSED


title: A30378

value: FEMALE


title: A30354


title: A30363


title: A30376


title: P114 vs CMT-U335 rep 2

description: Biological replicate of 2 out of 5

tag: Passage no.3


title: P114 vs CMT-U229 rep 2

description: Biological replicate of 2out of 5

tag: Passage no.5


title: CMT-U229 vs CMT-U335 rep 2

description: Biological replicate of 2 out of 5


title: A30359


title: P114 vs CMT-U335 rep 5

description: Biological replicate of 5out of 5


title: A30381


title: A30349


title: CMT-U229 vs CMT-U335 rep 1

description: Biological replicate of 1 out of 5


title: P114 vs CMT-U335 rep 1

description: Biological replicate of 1 out of 5


title: A30311


title: P114 vs CMT-U335 rep 4

description: Biological replicate of 4 out of 5


title: P114 vs CMT-U229 rep 1

description: Biological replicate of 1 out of 5


title: P114 vs CMT-U229 rep 5

description: Biological replicate of 5 out of 5


title: P114 vs CMT-U229 rep 3

description: Biological replicate of 3 out of 5


title: A30306


title: P114 vs CMT-U335 rep 3

description: Biological replicate of 3 out of 5


title: A30304


title: A30308


title: A30247


title: A30248


title: A30178


title: A30190


title: A30245


title: A30179


title: A30191


title: A30244


title: A30119


title: A30176


title: A30180


title: A30153


title: A30302


title: A30183


title: A30113


title: A30096


title: A30091


title: A30111


title: A30300


title: A30182


title: A30112


title: A30092


title: A30090


title: A30007


title: A30063


title: A30047


title: A30060


title: A30008


title: A30055


title: A30057


title: A30355

value: Hematologic improvement


title: A30364


title: A30360


title: A30379

value: Stable disease


title: A30380


title: A30235

value: Complete response


title: A30177


title: A30353


title: A30059


title: A30053


title: A30095


title: A30011

value: PR


title: A30246


title: A30009


title: P21CN3

status: Public on Oct 15 2005

city: Seattle

first: Julie

last: Harris

state: WA

department: Otolaryngology-HNS

institute: University of Washington

description: P21 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 3 replicates.

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

data_processing: GCOS

label: Affymetrix biotin cRNA

source_name: Cochlear nucleus

label_protocol: Standard Affymetrix Procedures

extract_protocol: Qiagen RNeasy

value: C57Bl6/J Cochlear nucleus tissue from P21


title: genomic F5

status: Public on Jul 29 2004

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
F5 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA

molecule: genomic DNA

source_name: Yeast genomic DNA


title: P21CN2


title: genomic F6

description:
F6 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA


title: genomic F4

description:
F4 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA


title: genomic F1

description:
F1 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA


title: A30192


title: mRNA3-t5

description:
Total RNA isolated from culture of BQS252 yeast strain 850 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F5 filter.
Keywords = yeast

source_name: 850 min after shift to galactose medium


title: genomic F3

description:
F3 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA


title: P7CN2

description: P7 cochlear nuclei pooled from 5 pups for one replicate hybridization.

value: C57bl6/J Cochlear nucleus tissue from P7


title: genomic F2

description:
F2 filter hybridization with labeled yeast genomic DNA. DNA labelling by random priming procedure and 33P-dCTP.
Keywords = yeast
Keywords = DNA


title: P14CN2

description: P14 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 2 replicates.

value: C57Bl6/J Cochlear nucleus tissue from P14


title: mRNA3-t2

description:
Total RNA isolated from culture of BQS252 yeast strain 120 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F1 filter.
Keywords = yeast

source_name: 120 min after shift to galactose medium


title: mRNA3-t1

description:
Total RNA isolated from culture of BQS252 yeast strain 5 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F6 filter.
Keywords = yeast

source_name: 5 min after shift to galactose medium


title: P14CN1

value: C57Bl6/J Cochlear nucleus from P14


title: mRNA3-t3

description:
Total RNA isolated from culture of BQS252 yeast strain 360 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F2 filter.
Keywords = yeast

source_name: 360 min after shift to galactose medium


title: mRNA3-t0

description:
Total RNA isolated from a YPD exponentially growing culture of BQS252 yeast strain. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F4 filter.
Keywords = yeast

source_name: YPD exponentially growing yeast strain


title: P7CN1

hyb_protocol: standard affymetrix procedures

scan_protocol: standard affymetrix procedures

label_protocol: Standard affymetrix procedures

extract_protocol: Qiagen RNAeasy

value: C57bl/6J, Cochlear nucleus, age P7


title: mRNA3-t4

description:
Total RNA isolated from culture of BQS252 yeast strain 450 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F3 filter.
Keywords = yeast

source_name: 450 min after shift to galactose medium


title: mRNA2-t3

description:
Total RNA isolated from culture of BQS252 yeast strain 360 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F6 filter.
Keywords = yeast


title: mRNA2-t4

description:
Total RNA isolated from culture of BQS252 yeast strain 450 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F2 filter.
Keywords = yeast


title: mRNA2-t5

description:
Total RNA isolated from culture of BQS252 yeast strain 850 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F1 filter.
Keywords = yeast


title: mRNA2-t2

description:
Total RNA isolated from culture of BQS252 yeast strain 120 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F4 filter.
Keywords = yeast


title: P21CN1

description: P21 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 2 replicates.


title: mRNA2-t1

description:
Total RNA isolated from culture of BQS252 yeast strain 5 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F3 filter.
Keywords = yeast


title: mRNA2-t0

description:
Total RNA isolated from a YPD exponentially growing culture of BQS252 yeast strain. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F5 filter.
Keywords = yeast


title: mRNA1-t4

description:
Total RNA isolated from culture of BQS252 yeast strain 450 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F5 filter.
Keywords = yeast


title: mRNA1-t1

description:
Total RNA isolated from culture of BQS252 yeast strain 5 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F2 filter.
Keywords = yeast


title: mRNA1-t5

description:
Total RNA isolated from culture of BQS252 yeast strain 850 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F6 filter.
Keywords = yeast


title: P7CN3

description: P7 cochlear nuclei pooled from 5 pups for one replicate hybridization out of 3 replicates.

value: C57Bl6/J Cochlear nucleus tissue from P7


title: mRNA1-t2

description:
Total RNA isolated from culture of BQS252 yeast strain 120 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F3 filter.
Keywords = yeast


title: mRNA1-t3

description:
Total RNA isolated from culture of BQS252 yeast strain 360 min after shift to YPGal. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F4 filter.
Keywords = yeast


title: GRO2-t5

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 850 min after shift to YPGal. Hibridization on F1 filter.


title: GRO3-t0

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a YPD exponentially growing culture of BQS252 yeast strain. Hibridization on F4 filter.


title: GRO3-t1

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 5 min after shift to YPGal. Hibridization on F6 filter.


title: mRNA1-t0

description:
Total RNA isolated from a YPD exponentially growing culture of BQS252 yeast strain. cDNA labelling using random decamers and 33P-dCTP. Hibridization on F1 filter.
Keywords = yeast


title: GRO2-t0

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a YPD exponentially growing culture of BQS252 yeast strain. Hibridization on F5 filter.


title: GRO3-t5

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 850 min after shift to YPGal. Hibridization on F5 filter.


title: GRO3-t3

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 360 min after shift to YPGal. Hibridization on F2 filter.


title: GRO2-t3

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 360 min after shift to YPGal. Hibridization on F6 filter.


title: GRO2-t2

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 120 min after shift to YPGal. Hibridization on F4 filter.


title: GRO1-t4

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 450 min after shift to YPGal. Hibridization on F5 filter.


title: GRO1-t3


title: GRO3-t2

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 120 min after shift to YPGal. Hibridization on F1 filter.


title: GRO1-t2

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 120 min after shift to YPGal. Hibridization on F3 filter.


title: GRO1-t5

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 850 min after shift to YPGal. Hibridization on F6 filter.


title: GRO1-t1

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 5 min after shift to YPGal. Hibridization on F2 filter.


title: GRO2-t4

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 450 min after shift to YPGal. Hibridization on F2 filter.


title: GRO1-t0

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a YPD exponentially growing culture of BQS252 yeast strain. Hibridization on F1 filter.


title: GRO3-t4

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 450 min after shift to YPGal. Hibridization on F3 filter.


title: GRO2-t1

description: Total RNA, in vivo labeled by run-on (GRO) using 33P-UTP, isolated from a culture of BQS252 yeast strain 5 min after shift to YPGal. Hibridization on F3 filter.


title: Medium control replicate 3 - SCAT

status: Public on Dec 15 2008

city: Lausanne

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

country: Switzerland

institute: University of Lausanne

description: Biological replicate 3 of 4 for MC group (SCAT)

hyb_protocol: Cy5-labeled RNA from adipose tissue and Cy3-labeled mouse universal reference of total RNA were hybridized on the M17K spotted array according published protocols (de Fourmestraux, J Biol Chem, 2004)

scan_protocol: Scanned on a Scanarray 4000 scanner. Tiff image analysis was done using the software ImaGene 4 (from BioDiscovery) in order to extract spot intensity signal for Cy3 and Cy5 channels.

data_processing: Print Tip Lowess normalized data obtained from log2 of processed Red signal/processed Green signal. The sma (Statistical Microarray Analysis) package from the statistical R software was used.

source_name: subcutaneous adipose tissue, under high fat diet with medium body weight treated with the vehicle

label_protocol: Indirect labeling of amplified RNA with Cy3 or Cy5 fluorascent dye according to published protocols (de Fourmestraux, J Biol Chem, 2004)

growth_protocol: Six-week-old C57BL/6J male mice (Janvier, France) were fed a normal chow (NC; 12% fat, 28% protein, and 60% carbohydrate) or a high fat diet (HFD; 72% fat, 28% protein, and <1% carbohydrate) for 7 months. Their body weight and tolerance to intraperitoneal

extract_protocol: RNA from each sample was extracted as described in the protocol of peqGOLD TriFast (from peqLab). RNA quality was checked before and after amplification with a bioanalyzer 2100 (Agilent). RNA was amplified with MessageAmpTM kit (Ambion) according the manu

treatment_protocol: Each mouse was further treated with vehicle (0.1% Tween 80 (Fluka) in H2O) or rimonabant (10 mg.kg-1.day-1) administrated daily by gavage for 1 month. Vehicle or rimonabant treatments were randomly assigned in each group of NC and HFD mice. The body weigh

tag: C57Bl/6J mouse

source_name: Mouse universal reference total RNA (DB Biosciences, ref: 636657)

tag: Commercial RNA


title: Normal chow treated replicate 4 - VAT

description: Biological replicate 4 of 5 for NCT group (VAT)

source_name: visceral adipose tissue of normal chow fed-mouse treated with rimonabant


title: not3_exponential phase_rep2

status: Public on Dec 10 2008

city: Geneva

first: Martine

last: Collart

address: Rue Michel-Servet 1, Centre Médical Universitaire

department: Microbiology and Molecular Medicine

institute: University of Geneva

description: not3, exponential phase, rep2

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: scan analyzed by Affymetrix MicroArraySuite, MicroDB and DataMiningTool

source_name: not3 null strain, exponential phase

label_protocol: standard Affymetrix procedure

growth_protocol: Cells were grown in glucose rich medium to exponential phase and collected, or in glucose rich medium to glucose depletion and collected 30 min after glucose depletion.

extract_protocol: acid phenol method

tag: MATa gcn4Δ ura3-52 trp1Δ1 leu2::PET56 gal2 not3::KanMX4


title: CC-P20_tumor

status: Public on Dec 03 2008

city: Durham

first: Chaitanya

middle: R

last: Acharya

state: NC

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

institute: Duke University

description: Array Print: Hs-OperonV2-vB2.2

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42Ã¸C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100Ã¸C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42Ã¸C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42Ã¸C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Slides were scanned on an Axon scanner using GenePixPro (3.0) software. Spot quality was assessed according to criteria in GenePixPro (3.0) software. Background subtraction and normalization was performed upon data extraction from the CIT/NIH-microarray database, mAdb (http://nciarray.nci.nih.gov/).

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

label_protocol: Cy3 and Cy5 Labeling protocols - generic

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

tag: Tissue

value: Colon

tag: age

tag: no recurrence

source_name: Control


title: A12_CD34_C

city: Amsterdam

first: Stephan

middle: Henrik

last: Schirmer

address: Meibergdreef 9

department: Cardiology

institute: Academic Medical Center

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted using Illumina's BeadStudio software. From 13 controls and 18 patients we analyzed CD14+ monocyte, CD4+ T-cell, LPS-stimulated monocytes and macrophage samples, in total 130 arrays (including 6 technical replicates). From the CD34+ cell samples, only 23 passed quality control and were analyzed by array, giving a grand total of 153 arrays. Normalization and statistical analysis of the bead summary data from the arrays was carried out using the limma package14 and in-house scripts in R/Bioconductor. Bead summary intensities were log2-transformed and then normalized using quantile normalization. To find differentially expressed genes, we performed a linear model analysis. Technical replicates were handled by estimating a common value for the intra-replicate correlation and including it in the linear model. Differential expression between the treatments of interest was assessed using a moderated t-test. This test is similar to a standard t-test for each probe except that the standard errors are moderated across genes to ensure more stable inference for each gene. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

source_name: stem cells

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Using immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA), CD14+ monocytes, CD4+ T-cells and CD34+ stem cells were positively isolated for direct cell lysis, while negatively isolated monocytes were split into two fractions for stimulation with 10 ng/ml lipopolysaccharide (LPS) for 3h, or for 20h cell culture towards macrophages.

extract_protocol: Positively isolated monocytes, T-cells and stem cells as well as cultured stimulated monocytes and macrophages were lysed and total RNA was isolated (Absolutely RNA Microprep Kit, Stratagene, La Jolla, CA).

tag: control

tag: patient ID_REF


title: A36_T_P

scan_protocol: According to beadchip array manufacturer's protocol

source_name: T cells

tag: patient