title: MDS.U5

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U5


title: MDS.U59

status: Public on Aug 01 2009

type: genomic

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U59

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: MDS primary specimens

label_protocol: Affymetrix standard protocol

extract_protocol: As per PUREGENE DNA extracting kit

tag: disease

value: Myelodysplastic syndromes (MDS)

tag: who classification


title: MDS.U61

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U61


title: MDS.U56

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U56


title: MDS.U48

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U48


title: MDS.U46

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U46


title: MDS.U51

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U51

value: MDS–unclassified


title: MDS.U54

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U54


title: MDS.U60

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U60


title: MDS.U49

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U49


title: MDS.U47

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U47


title: MDS.U58

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U58


title: MDS.U41

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U41


title: MDS.U44

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U44


title: MDS.U42

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U42


title: MDS.U45

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U45


title: MDS.U43

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U43

value: RCMD


title: MDS.U40

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U40


title: MDS.U37

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U37


title: MDS.U35

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U35


title: MDS.U38

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U38


title: MDS.U3

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U3


title: MDS.U34

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U34


title: MDS.U32

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U32


title: MDS.U33

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U33


title: MDS.U23

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U23


title: MDS.U50

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U50


title: MDS.U22

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U22


title: MDS.U29

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U29


title: MDS.U31

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U31


title: MDS.U25

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U25


title: MDS.U1

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U1


title: MDS.U14

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U14


title: MDS.U2

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U2


title: MDS.U19

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U19


title: MDS.U26

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U26


title: MDS.U27

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U27


title: MDS.U20

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U20


title: MDS.U15

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U15


title: MDS.U16

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U16


title: MDS.U12

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U12


title: MDS.U11

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U11

value: RARS


title: MDS.U125

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U125


title: MDS.U28

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U28


title: MDS.U18

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U18


title: MDS.U10

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U10


title: MDS.U17

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U17


title: MDS.U57

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U57


title: MDS.U124

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U124

value: 5q– syndrome


title: High calcium, Colon mucosa, HLAB27, repl 18

status: Public on Jul 17 2009

type: RNA

city: Ede

first: Marloes

last: Schepens

address: P.O. Box 20

country: Netherlands

institute: NIZO food research

description: Rat Colon Mucosa

hyb_protocol: Hybridization was performed by preparing a 2x cRNA target solution containing 825 ng Cy5-labeled cRNA of an individual rat, 825 ng Cy3-labeled pool cRNA, and 11 ?L 10x Blocking agent in a total volume of 52.8 ?L. Fragmentation buffer (2.2 ?L) was added and this was incubated at 65°C for 30 min. Fragmentation was stopped by the addition of 55 ?L 2x GEx hybridization buffer HI-RPM, after which samples were hybridized on 4x 44K rat whole genome Agilent arrays (G4131F) for 17 hours at 65°C in hybridization chambers in a hybridization oven rotating at 10 rpm. After hybridization the arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned with an Agilent G2565B microarray scanner on the basis of integrating both the low and high intensity scans per array, in order to obtain a larger linear range for spot fluorescence quantification according to the manufacturer’s protocol.

data_processing: Signal intensities for each spot were quantified using Feature Extraction 9.5 (Agilent Technologies). Median density values and background values of each spot were extracted for both the experimental samples (Cy5) and the reference samples (Cy3). Data was exported into GeneMaths XT 1.60 (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. We discarded spots with an average intensity, over all arrays, of Cy5 lower than 2-fold above average background. Then, the Cy5 intensities were normalized as described before (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

molecule: total RNA

organism: Rattus norvegicus

source_name: Colon mucosa, HLAB27, repl 18

label_protocol: Amplification and labeling of colonic mucosal samples of individual transgenic rats was performed following the Agilent procedures for whole genome microarray technology (Agilent Technologies, Palo Alto, CA), unless stated otherwise. Briefly, of each animal, 1 ?g total RNA was reverse transcribed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Each cDNA sample was split in two fractions which were subsequently used for linear RNA amplification and labeled with Cy5 and Cy3, respectively, using half the amounts as indicated by the manufacturer. The labeled cRNA samples were purified using Rneasy columns (Qiagen).

extract_protocol: Total RNA was isolated from the colon homogenates using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Total RNA was purified using Rneasy columns (Qiagen, Venlo, The Netherlands).

treatment_protocol: Colon scrapings were homogenized in liquid N2 using a mortar and pestle cooled with liquid N2.

tag: HLA-B27/?2-microglobulin transgenic rats on an inbred Fisher 344 background, Gender

value: Female, Age:8-10 weeks, Tissue:Colon Mucosa.

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.


title: High calcium, Colon mucosa, HLAB27, repl 2

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 2


title: High calcium, Colon mucosa, HLAB27, repl 14

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 14


title: MDS.U107

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U107

value: AML


title: Low calcium, Colon mucosa, HLAB27, repl 16

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 16


title: High calcium, Colon mucosa, HLAB27, repl 17

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 17


title: High calcium, Colon mucosa, HLAB27, repl 13

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 13


title: Low calcium, Colon mucosa, HLAB27, repl 15

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 15


title: High calcium, Colon mucosa, HLAB27, repl 10

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 10


title: MDS.U138

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U138


title: High calcium, Colon mucosa, HLAB27, repl 9

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 9


title: MDS.U149

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U149


title: Low calcium, Colon mucosa, HLAB27, repl 7

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 7


title: Low calcium, Colon mucosa, HLAB27, repl 6

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 6


title: MDS.U141

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U141


title: Low calcium, Colon mucosa, HLAB27, repl 5

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 5


title: MDS.U148

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U148


title: MDS.U150

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U150


title: MDS.U133

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U133


title: Low calcium, Colon mucosa, HLAB27, repl 4

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 4


title: MDS.U146

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U146


title: MDS.U142

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U142


title: MDS.U134

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U134


title: High calcium, Colon mucosa, HLAB27, repl 3

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 3


title: MDS.U135

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U135


title: Low calcium, Colon mucosa, HLAB27, repl 1

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 1


title: H4K16Ac

status: Public on Jul 01 2009

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description:
This sample contains two replicates
Reference: Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae.
Reference: Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae.

hyb_protocol: Hybridization was performed as affymetrix protocol. Samples were hybridized for 16 hours at 42oC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)

data_processing: We used affymetrix tiling array software(TAS) V1.1 to analyze our data. The raw cel data were imported into TAS as two analysis treatment groups -- our IP or nucleosome sample and genomic background control. We use two side test, bandwidth is 70 for nucleosome and 150 for H4K16ac. Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar or CHP format signal files.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: H4K16Ac in wild type strain

label_protocol: DNA was labeled with biotin-N6-dATP using terminal transferase TdT (Roche, 400U/ul)

growth_protocol: Cells in YP + 2% glucose were collected in log phase

extract_protocol: Extraction was performed as previously described (yuan et al. 2005,Liu et al. 2005). For nucleosome position,  we digested chromatin with Mnase to get mono nucleosome, then we purified mononucleosome from gel. For H4K16ac, we used antibody from abcam(ab61240) as the normal ChIP-chip  study.

tag: antibody from abcam(ab61240)

source_name: input

tag: input


title: Low calcium, Colon mucosa, HLAB27, repl 8

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 8

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.


title: MDS.U144

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U144

source_name: MDS primary specimens


title: Low calcium, Colon mucosa, HLAB27, repl 11

description: Rat Colon Mucosa

source_name: Colon mucosa, HLAB27, repl 11


title: MDS.U77

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U77


title: nucleosome position

data_processing: We used affymetrix tiling array software(TAS) V1.1 to analyze our data. The raw cel data were imported into TAS as two analysis treatment group -- our IP or nucleosome sample and genomic background control. We use two side test, bandwidth is 70 for nucleosome and 150 for H4K16ac. Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar or CHP format signal files.

source_name: nucleosome position of wild type budding yeast strain

tag: purified mononucleosome from gel

source_name: genomic background control

tag: control


title: MDS.U143

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U143


title: MDS.U139

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U139


title: Tet-CarD vs Control (Replicates 1, 2, and 3)

city: New York

first: Christina

middle: Leigh

last: Stallings

state: NY

department: Immunology

country: USA

institute: Sloan Kettering Institute

description: Biological replicates 1, 2 and 3

hyb_protocol: Slides were cross-linked in a Stratalinker (Stratagene), using the “auto-link” function at 3000ujoulesx100. Prior to hybridization, slides were pre-hybridized for 2 hours at room temperature in 0.2% SDS then   rinsed in filtered water (10 sec)  then in 70%.EtOH (5sec). Slides were dried by centrifugation at 1000rpm for 3 min. Labeled cDNA was mixed to 500ul of Ambion SlideHyb#3 hybridization buffer (cat# AM8863). Hybridization mix was spin at 15,000xg for 5 min, denatured at 98C for 2 min and kept at 70C until loading onto the slide. Hybridization was performed in the Agilent hybridization chambers and oven for 18hrs, at 50C, rotation setting at 7.  At the end of hybridization, slides were disassembled  in 0.2xSSC/0.1%SDS, washed for 15 min at RT in  0.2xSSC/0.1%SDS, then 15min at RT in 0.1xSSC  and dried by centrifugation at 1000rpm for 3 min.

scan_protocol: Arrays were scanned using an Axon 4200AL scanner (Axon Instruments Inc) using the “autoscanning” function.

data_processing: Images were analyzed using GenePix Pro 6.0 (Axon Instruments Inc) for background subtraction and processing. GeneSpring software (v. 7.3.1) was used for analysis

organism: Mycolicibacterium smegmatis

source_name: CarD depletion (mgm1703)

label_protocol: 10 ug of RNA was reversed transcribed with Stratagene Fairplay kit and the cDNA was coupled to either Cy5 (mgm1703) or Cy3 (mgm1701) dyes

growth_protocol: Mycobacterium smegmatis strains mgm1701 (control) and mgm1703 (Tet-CarD) were diluted in nutrient rich media containing hygromycin and kanamycin to an OD600 of 0.05 and grown for 13 hours shaking at 37 degrees

extract_protocol: Total RNA was extracted using Trizol and bead beating

tag: strain

source_name: control (mgm1701)


title: MDS.U137

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U137


title: MDS.U145

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U145

value: RA–RARS


title: MDS.U147

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U147


title: MDS.U136

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
MDS.U136


title: 8404 PSY 2

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

department: Microbiology

country: Switzerland

institute: ETH Zürich

description: B. japonicum ecfG mutant strain grown grown aerobically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com). Normalized signal values from the arrays were then processed using Genespring GX 7.3 (Agilent Technologies,CA, USA). Only those probe sets that were called "present" or "marginal" in two of the three replicates were considered for further analysis. The experiment was normalized with the default settings for Affymetrix arrays, i.e., first data transformation to set measurements of below 0.01 to 0.01 followed by a per-chip normalization to the 50th percentile and a per-gene normalization to median. For statistical comparisons, the student t-test with a P value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2 when comparing the different strains.

organism: Bradyrhizobium japonicum

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix).   The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: B. japonicum cells were grown aerobically to mid-exponential phase (OD600 0.5 to 0.7) in PSY medium. For microarray experiments with carbon-starved cells, cultures were pre-grown and further incubated for 24 h in minimal medium lacking a carbon source . For harvesting, cultures were rapidly transferred to cold tubes containing one tenth of the culture volume of “stop solution” (10% Tris-HCl-buffered phenol [pH 8] in ethanol), centrifuged for 5 min (10,800 × g; 4°C), the supernatant was decanted, and cells were frozen in liquid nitrogen and stored at −80°C.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 4-to–20% acrylamide gradient gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada).

tag: genotype


title: 8402 MM starvation 3

description: B. japonicum phyR mutant strain under carbon sterved conditions


title: 8404 PSY 3

source_name: B. japonicum ecfG mutant strain grown grown aerobically


title: 8402 PSY 3

description: B. japonicum phyR mutant strain grown grown aerobically


title: 110spc4 MM starvation 2

description: B. japonicum wild type strain under carbon starved conditions


title: 8402 PSY 2

source_name: B. japonicum phyR mutant strain grown grown aerobically


title: 110spc4 MM starvation 1

source_name: B. japonicum wild type strain under carbon starved conditions


title: 8404 MM starvation 3

description: B. japonicum ecfG mutant strain under carbon starved conditions


title: 8402 MM starvation 2

source_name: B. japonicum phyR mutant strain under carbon sterved conditions


title: 8404 PSY 1


title: 110spc4 MM starvation 3


title: 8404 MM starvation 1

source_name: B. japonicum ecfG mutant strain under carbon starved conditions


title: 8402 MM starvation 1

description: B. japonicum phyR mutant strain under carbon starved conditions


title: 8404 MM starvation 2


title: 110spc4 PSY 3

description: B. japonicum wild-type strain grown aerobically


title: 110spc4 PSY 2

source_name: B. japonicum wild-type strain grown aerobically


title: 110spc4 PSY 1


title: White matter control 3

status: Public on Jun 15 2009

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

country: Italy

institute: Università Cattolica del Sacro Cuore di Roma

description: Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.

hyb_protocol: Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.

scan_protocol: Arrays were read with the geneChip Affymetrix 3000 7G scanner.

data_processing: Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.

source_name: human white matter

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

extract_protocol: RNA was extracted from frozen biopsies. Samples were homogenized in 1ml guanidine isothiocyanate solution.  RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.

tag: White matter control biopsies were retrieved from patients operated on for deep intracerebral cavernomas.


title: 8402 PSY 1


title: White matter control 2


title: slide 44 - fadrozole

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

description:
Sexually mature female goldfish were exposed (waterborne) to fadrozole (50 µg/L) or untreated water (control). Animals were anaesthetized in MS222, and telcephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #44

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS and GPA methods.

organism: Carassius auratus

source_name: control

extract_protocol: RNeasy Mini Plus kit (Qiagen)

tag: Sexually mature female adult goldfish; telencephalon tissue

source_name: fadrozole 50ug/L


title: slide 22 - fadrozole

description:
Sexually mature female goldfish were exposed (waterborne) to fadrozole (50 µg/L) or untreated water (control). Animals were anaesthetized in MS222, and telcephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #22

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)


title: slide 4 - fadrozole

description:
Sexually mature female goldfish were exposed (waterborne) to fadrozole (50 µg/L) or untreated water (control). Animals were anaesthetized in MS222, and telcephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #4


title: slide 33 - fadrozole

description:
Sexually mature female goldfish were exposed (waterborne) to fadrozole (50 µg/L) or untreated water (control). Animals were anaesthetized in MS222, and telcephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #33


title: White matter control 1


title: GBM surrounding tissue 3R

source_name: GBM surrounding tissue

extract_protocol: RNA was extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution.  RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.

tag: GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border. This is a biological replicate of GBM surrounding tissue 3, harvested independently.


title: GBM surrounding tissue 4

tag: GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.


title: GBM surrounding tissue 5


title: GBM surrounding tissue 3


title: GBM surrounding tissue 4R

tag: GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border. This sample is a biological replicate of GBM surrounding tissue sample 4, harvested independently.


title: Core sample 1

source_name: Human glioblastoma tumor mass

extract_protocol: RNA was extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution.  RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.

tag: Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.


title: Core sample 2


title: Core sample 3


title: Core sample 4


title: blood_MP_4_rep4

status: Public on Jun 01 2009

city: Morgantown

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description: Rats from Charles River Laboratories, Wilmington, MA

hyb_protocol: All procedures for array hybridization were done at the Vanderbilt Microarray Shared Resources (Vanderbilt University, Nashville, TN). Stated briefly, the cRNA samples meeting the ABI criteria in terms of quantity and size of targets produced were fragmented and then hybridized to the rat genome microarray for 16 hours, 100 RPM and 55oC. The hybridized arrays were washed and incubated with the Anti-Dig-AP antibody for 20 minutes. The arrays were washed and incubated with the Chemiluminescence Enhancing Solution (Applied Biosystems, Foster City, CA), washed, and incubated with the substrate for chemiluminescence reaction.

scan_protocol: All procedures for chemiluminescence detection were done at the Vanderbilt Microarray Shared Resources (Vanderbilt University, Nashville, TN) using Applied Biosystems’ AB1700 Chemiluminescent Microarray Analyzer following the procedures established by Applied Biosystems (Foster City, CA). To encompass the entire array, the analyzer images the microarray in two positions. In each position, the camera captures a series of four images. The images from each position are processed independently and the results from both positions are combined into a single output Feature Table. For each position, the inputs to the algorithm are: a default 25-second chemiluminescent CL image, a fixed 5-second short chemiluminescent image, a fixed 25-second long fluorescent image, and a fixed 25-second long spectral correction image.

data_processing: All procedures for image analysis were done at the Vanderbilt Microarray Shared Resources (Vanderbilt University, Nashville, TN) following procedures established by Applied Biosystems (Foster City, CA). Microarray data was analyzed using the ABarray package written in Bioconductor for R (http://www.bioconductor.org/packages/1.9/bioc/html/ABarray.html). Raw data was processed for quality control by evaluating signal distribution ranges, MA plots, and CV plots for variation among hybridization replicates. Data was transformed into log base 2 units and underwent a quantile normalization procedure and these data were analyzed for differential expression using ANOVA and subsequent t-tests. Only genes with a signal to noise ratio greater than 3, and a quality flag value less than 5000 were included in the analysis.

label: digoxygenin

source_name: blood, methyl parathion, 4 hours

label_protocol: All procedures for target labeling were done at the Vanderbilt Microarray Shared Resources (Vanderbilt University, Nashville, TN) using Applied Biosystems’ Chemiluminescence Kit following the procedures established by Applied Biosystems (Foster City, CA). Stated briefly, one microgram total RNA was reverse transcribed to synthesize double stranded cDNA using the NanoAmp RT-IVT Probe Labeling Kit (Applied Biosystems, Foster City, CA). The cDNA samples were purified and in vitro transcribed to generate digoxygenin (DIG) labeled cRNA. Subsequently, the cRNA samples were purified and quantitated using UV-spectrophotometry and assessed for quality on a Bioanalyzer (Agilent Technologies, Palo Alto, CA).

growth_protocol: Rats were housed in the animal facility at the National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV. The animals were kept under controlled lighting (12-hour light-dark cycle), temperature (72o + 5o F), and humidity (50 + 20%) with free access to food and water.

extract_protocol: At time intervals of 4, 12, 24, and 168 hours following administration of the chemicals, four rats each were sacrificed using a head-only, focused microwave irradiation (power level of 3 kilowatts for 1.5 seconds) using a microwave applicator (Muromachi Kikai, Inc, Tokyo, Japan, Model TMW 4012C, 10 kilowatts). Blood was collected immediately from the heart and placed into Vacutainer tubes (Becton Dickinson and Company, Franklin Lakes, NJ). Total RNA, with significantly depleted globin mRNA, was isolated from the leukocytes collected from the unclotted blood samples using the LeukoLOCKTM Total RNA Isolation System (Ambion, Inc, Austin, TX).

treatment_protocol: The rats were randomly assigned to the various control and treatment groups and were administered intraperitoneally a single dose of AP (1200 mg/kg b.w., Sigma Chemical Company, St. Louis, MO) or MP (15 mg/kg b.w., Supelco, Bellefonte, PA) prepared as homogeneous suspensions in vegetable oil. The control rats received an equivalent volume of vegetable oil used as the vehicle to prepare the chemicals.

tag: Strain

value: CDF Fisher 344

tag: Gender

value: male

tag: Age

value: approximately 4 months old

tag: Tissue

value: blood


title: GBM surrounding tissue 2


title: blood_MP_4_rep1


title: blood_MP_24_rep3

source_name: blood, methyl parathion, 24 hours


title: blood_MP_4_rep2


title: pre-miR-196a-T1

status: Public on Jun 08 2009

city: New Haven

first: Aaron

middle: Ezra

last: Hoffman

state: CT

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

description: All protocols performed by an Agilent-certified service provider

hyb_protocol: Agilent's Gene Expression Hybridization Kit followed by Agilent's Gene Expression Wash Buffer Kit

scan_protocol: Agilent’s Microarray Scanner with SureScan technology

data_processing: Agilent Feature Extraction Software, data were analyzed using the Rosetta Luminator gene expression data analysis system. Value = log10(intensity2/intensity1).

source_name: Empty Vector 1

label_protocol: mRNA converted to Cyanine 3-labeled cRNA using Agilent's Quick Amp Labeling Kit

extract_protocol: Qiagen RNeasy mini kit with on-column DNAse digestion

tag: cell line

value: MCF7 cells

tag: reference

value: transfected with an empty vector (Negative Control)

tag: replicate

label_protocol: mRNA converted to Cyanine 5-labeled cRNA using Agilent's Quick Amp Labeling Kit

tag: test

value: transfected with a vector expressing pre-miR-196a-T


title: blood_MP_24_rep1


title: pre-miR-196a-C1

value: transfected with a vector expressing pre-miR-196a-C


title: blood_MP_168_rep3

source_name: blood, methyl parathion, 168 hours


title: pre-miR-196a-T2

source_name: Empty Vector 2

value: transfected with an empty vector (Negative control)


title: pre-miR-196a-C2


title: blood_MP_4_rep3


title: slide 14 - fadrozole

description:
Sexually mature female goldfish were exposed (waterborne) to fadrozole (50 µg/L) or untreated water (control). Animals were anaesthetized in MS222, and telcephalon tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #14


title: blood_MP_24_rep2


title: Core sample 5


title: blood_MP_12_rep4

source_name: blood, methyl parathion, 12 hours


title: blood_MP_168_rep2


title: blood_MP_12_rep3


title: blood_MP_0_rep4

source_name: blood, control


title: blood_MP_12_rep2


title: blood_MP_12_rep1


title: blood_AP_4_rep3

source_name: blood, acetaminophen, 4 hours


title: blood_MP_0_rep1


title: blood_AP_4_rep2


title: blood_MP_24_rep4


title: blood_AP_24_rep4

source_name: blood, acetaminophen, 24 hours


title: blood_MP_0_rep2


title: blood_AP_24_rep1


title: blood_MP_0_rep3


title: blood_AP_24_rep2


title: blood_AP_168_rep1

source_name: blood, acetaminophen, 168 hours


title: blood_AP_24_rep3


title: blood_AP_12_rep3

source_name: blood, acetaminophen, 12 hours


title: blood_MP_168_rep1


title: blood_AP_4_rep1


title: blood_AP_168_rep2


title: blood_AP_168_rep3


title: blood_AP_12_rep2


title: blood_AP_12_rep4


title: blood_AP_0_rep3


title: blood_AP_12_rep1


title: blood_AP_0_rep2


title: PMA-1h1-rep

city: Seoul

first: Jin-Kyung

last: Limb

address: 11-1 Daehyun-dong, Seodaemun-gu,

department: Molecular life science

country: South Korea

institute: Ewha Womans University

description: Gene expression data from erythroleukemic cells cultured with PMA for 1 hour.

hyb_protocol: standard Illumina microarray protocol

scan_protocol: standard Illumina microarray protocol

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio (Gene Expression Module v3.1)

source_name: human erythroleukemic cells

label_protocol: 100 nanoram of total RNA was reverse transcribed with Anchor Oligo-dT

growth_protocol: K562 cells were maintained in RPMI 1640 medium: 10% (v/v) heat-inactivated fetal bovine serum, 1% penicillin-streptomycin mixtures (Gibco BRL.), 5% CO2 at 37℃. All experiments using K562 cells employed mid-log phase cells at a density of 1.0 x 105 cells/ml. For the experiment, exponentially growing K562 cells were collected (1,200 x rpm, 5 min) and resuspended in fresh culture medium.

extract_protocol: K562 cells were collected by centrifugation, and washed with phosphate buffered saline (PBS). Total RNA was isolated using RNeasy Mini Kit (Quiagen) according to manufacturer’s protocol.

treatment_protocol: K562 cells were cultured in media containing 20 nM phorbol 12-myristate 13-acetate (PMA) (Sigma Chemical Co., St. Louis, MO) in a time dependent manner.

tag: human chronic myelogenous leukemia cell line, K562


title: PMA-6h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 6 hours(replication).


title: PMA-0.5h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 0.5h.


title: PMA-3h1

description: Gene expression data from erythroleukemic cells cultured with PMA for 3 hour.


title: PMA-48h1

description: Gene expression data from erythroleukemic cells cultured with PMA during 48 hours.


title: no-PMA1-rep

description: Gene expression data from erythroleukemic cells cultured without PMA


title: PMA-12h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 12 hours(replication).


title: PMA-24h1

description: Gene expression data from erythroleukemic cells cultured with PMA during 24 hours.


title: PMA-1h1


title: PMA-0.5h1

description: Gene expression data from erythroleukemic cells cultured with PMA.


title: PMA-12h1

description: Gene expression data from erythroleukemic cells cultured with PMA during 12 hours.


title: GBM surrounding tissue 1

description: Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.


title: PMA-24h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 24 hours(replication).


title: blood_AP_0_rep1

tag: strain

tag: gender

tag: age

tag: tissue


title: PMA-3h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 3 hours(replication).


title: PMA-6h1

description: Gene expression data from erythroleukemic cells cultured with PMA for 6 hour.


title: PMA-48h1-rep

description: Gene expression data from erythroleukemic cells cultured with PMA for 48 hours(replication).


title: no-PMA1

description: Gene expression data from erythroleukemic cells cultured without PMA.


title: blood_AP_0_rep4

description: Rats from Charles River Laboratories, Wilmington, MA


title: blood_AP_4_rep4


title: Peripheral blood from patient N2044

city: Rockville

first: Robert

middle: J

last: Clifford

state: MD

address: 2115 E Jefferson

department: CCR

institute: NCI

description: Hybridized to 250K_Sty

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were washed and stained in the Genechip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.  Chips were scanned with the Affymetrix GeneChip Scanner 3000 using GeneChipOperating System 1.4

data_processing: *.CHP files were generated using Affymetrix Power Tools version 1.85 gtype-probeset-genotype program.

source_name: patient N2044

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from micro-dissected tumor using the protocol from Puregene DNA Purification Tissue Kit (Gentra Systems, Inc., Minneapolis, MN).  DNA from whole blood was extracted and purified using the standard phenol/chloroform method.

value: peripheral blood


title: Peripheral blood from patient N1710

description: Hybridized to 250K_Sty

source_name: patient N1710


title: Peripheral blood from patient N1563

description: Hybridized to 250K_Sty

source_name: patient N1563


title: Peripheral blood from patient N1227

description: Hybridized to 250K_Sty

source_name: patient N1227


title: Peripheral blood from patient N0096

description: Hybridized to 250K_Sty

source_name: patient N0096


title: Peripheral blood from patient N0478

description: Hybridized to 250K_Sty

source_name: patient N0478


title: Peripheral blood from patient N1539

description: Hybridized to 250K_Sty

source_name: patient N1539


title: Peripheral blood from patient N0178

description: Hybridized to 250K_Sty

source_name: patient N0178


title: Peripheral blood from patient N1499

description: Hybridized to 250K_Sty

source_name: patient N1499


title: Peripheral blood from patient N0588

description: Hybridized to 250K_Sty

source_name: patient N0588


title: Peripheral blood from patient N1423

description: Hybridized to 250K_Sty

source_name: patient N1423


title: Peripheral blood from patient E1796

description: Hybridized to 250K_Sty

source_name: patient E1796


title: Peripheral blood from patient N1305

description: Hybridized to 250K_Sty

source_name: patient N1305


title: Peripheral blood from patient N2055

description: Hybridized to 250K_Sty

source_name: patient N2055


title: Peripheral blood from patient N0261

description: Hybridized to 250K_Sty

source_name: patient N0261


title: Peripheral blood from patient N0941

description: Hybridized to 250K_Sty

source_name: patient N0941


title: Peripheral blood from patient N0912

description: Hybridized to 250K_Sty

source_name: patient N0912


title: Peripheral blood from patient N0510

description: Hybridized to 250K_Sty

source_name: patient N0510


title: Peripheral blood from patient N0405

description: Hybridized to 250K_Sty

source_name: patient N0405


title: Peripheral blood from patient E1782

description: Hybridized to 250K_Sty

source_name: patient E1782


title: Peripheral blood from patient N0459

description: Hybridized to 250K_Sty

source_name: patient N0459


title: Peripheral blood from patient N0299

description: Hybridized to 250K_Sty

source_name: patient N0299


title: Peripheral blood from patient N0103

description: Hybridized to 250K_Sty

source_name: patient N0103


title: Peripheral blood from patient N1100

description: Hybridized to 250K_Sty

source_name: patient N1100


title: Peripheral blood from patient E1756

description: Hybridized to 250K_Sty

source_name: patient E1756


title: Peripheral blood from patient E1709

description: Hybridized to 250K_Sty

source_name: patient E1709


title: Peripheral blood from patient E1629

description: Hybridized to 250K_Sty

source_name: patient E1629


title: Peripheral blood from patient E2644

description: Hybridized to 250K_Sty

source_name: patient E2644


title: Peripheral blood from patient E1614

description: Hybridized to 250K_Sty

source_name: patient E1614


title: Peripheral blood from patient E1610

description: Hybridized to 250K_Sty

source_name: patient E1610


title: Peripheral blood from patient E1635

description: Hybridized to 250K_Sty

source_name: patient E1635


title: Peripheral blood from patient E1589

description: Hybridized to 250K_Sty

source_name: patient E1589


title: Peripheral blood from patient E1573

description: Hybridized to 250K_Sty

source_name: patient E1573


title: Peripheral blood from patient E1575

description: Hybridized to 250K_Sty

source_name: patient E1575


title: Peripheral blood from patient E1566

description: Hybridized to 250K_Sty

source_name: patient E1566


title: Peripheral blood from patient E1578

description: Hybridized to 250K_Sty

source_name: patient E1578


title: Peripheral blood from patient E1576

description: Hybridized to 250K_Sty

source_name: patient E1576


title: Peripheral blood from patient E1510

description: Hybridized to 250K_Sty

source_name: patient E1510


title: Peripheral blood from patient E1556

description: Hybridized to 250K_Sty

source_name: patient E1556


title: Peripheral blood from patient E1520

description: Hybridized to 250K_Sty

source_name: patient E1520


title: Peripheral blood from patient E1558

description: Hybridized to 250K_Sty

source_name: patient E1558


title: Peripheral blood from patient E1603

description: Hybridized to 250K_Sty

source_name: patient E1603


title: Peripheral blood from patient E1584

description: Hybridized to 250K_Sty

source_name: patient E1584


title: Peripheral blood from patient E1517

description: Hybridized to 250K_Sty

source_name: patient E1517


title: Peripheral blood from patient E1535

description: Hybridized to 250K_Sty

source_name: patient E1535


title: Peripheral blood from patient E1521

description: Hybridized to 250K_Sty

source_name: patient E1521


title: Peripheral blood from patient L207_012

description: Hybridized to 250K_Sty

source_name: patient L207_012


title: Peripheral blood from patient L206_005

description: Hybridized to 250K_Sty

source_name: patient L206_005


title: Peripheral blood from patient L203_003

description: Hybridized to 250K_Sty

source_name: patient L203_003


title: Peripheral blood from patient L208_005

description: Hybridized to 250K_Sty

source_name: patient L208_005


title: Peripheral blood from patient E1551

description: Hybridized to 250K_Sty

source_name: patient E1551


title: Peripheral blood from patient E1546

description: Hybridized to 250K_Sty

source_name: patient E1546


title: Peripheral blood from patient E1572

description: Hybridized to 250K_Sty

source_name: patient E1572


title: Peripheral blood from patient E1542

description: Hybridized to 250K_Sty

source_name: patient E1542


title: Peripheral blood from patient E1532

description: Hybridized to 250K_Sty

source_name: patient E1532


title: Peripheral blood from patient E1507

description: Hybridized to 250K_Sty

source_name: patient E1507


title: Peripheral blood from patient L201_008

description: Hybridized to 250K_Sty

source_name: patient L201_008


title: Peripheral blood from patient L196_009

description: Hybridized to 250K_Sty

source_name: patient L196_009


title: Peripheral blood from patient L186_007

description: Hybridized to 250K_Sty

source_name: patient L186_007


title: Peripheral blood from patient L188_006

description: Hybridized to 250K_Sty

source_name: patient L188_006


title: Peripheral blood from patient L199_006

description: Hybridized to 250K_Sty

source_name: patient L199_006


title: Peripheral blood from patient L191_006

description: Hybridized to 250K_Sty

source_name: patient L191_006


title: Peripheral blood from patient N2055

description: Hybridized to 250K_Nsp

source_name: patient N2055


title: Peripheral blood from patient L178_004

description: Hybridized to 250K_Sty

source_name: patient L178_004


title: Peripheral blood from patient L172_011

description: Hybridized to 250K_Sty

source_name: patient L172_011


title: Peripheral blood from patient L170_004

description: Hybridized to 250K_Sty

source_name: patient L170_004


title: Peripheral blood from patient N2044

description: Hybridized to 250K_Nsp

source_name: patient N2044


title: Peripheral blood from patient L166_009

description: Hybridized to 250K_Sty

source_name: patient L166_009


title: Peripheral blood from patient L163_010

description: Hybridized to 250K_Sty

source_name: patient L163_010


title: Peripheral blood from patient L165_004

description: Hybridized to 250K_Sty

source_name: patient L165_004


title: Peripheral blood from patient L161_012

description: Hybridized to 250K_Sty

source_name: patient L161_012


title: Peripheral blood from patient N1563

description: Hybridized to 250K_Nsp

source_name: patient N1563


title: Peripheral blood from patient N1499

description: Hybridized to 250K_Nsp

source_name: patient N1499


title: Peripheral blood from patient L162_011

description: Hybridized to 250K_Sty

source_name: patient L162_011


title: Peripheral blood from patient L157_012

description: Hybridized to 250K_Sty

source_name: patient L157_012


title: Peripheral blood from patient L155_010

description: Hybridized to 250K_Sty

source_name: patient L155_010


title: Peripheral blood from patient L158_011

description: Hybridized to 250K_Sty

source_name: patient L158_011


title: Peripheral blood from patient L076_012

description: Hybridized to 250K_Sty

source_name: patient L076_012


title: Peripheral blood from patient L154_012

description: Hybridized to 250K_Sty

source_name: patient L154_012


title: Peripheral blood from patient N1539

description: Hybridized to 250K_Nsp

source_name: patient N1539


title: Peripheral blood from patient N1710

description: Hybridized to 250K_Nsp

source_name: patient N1710


title: Peripheral blood from patient L073_011

description: Hybridized to 250K_Sty

source_name: patient L073_011


title: Peripheral blood from patient L152_011

description: Hybridized to 250K_Sty

source_name: patient L152_011


title: Peripheral blood from patient N1423

description: Hybridized to 250K_Nsp

source_name: patient N1423


title: Peripheral blood from patient N1305

description: Hybridized to 250K_Nsp

source_name: patient N1305


title: Peripheral blood from patient L065_003

description: Hybridized to 250K_Sty

source_name: patient L065_003


title: Peripheral blood from patient L072_003

description: Hybridized to 250K_Sty

source_name: patient L072_003


title: Peripheral blood from patient L070_011

description: Hybridized to 250K_Sty

source_name: patient L070_011


title: Peripheral blood from patient L062_008

description: Hybridized to 250K_Sty

source_name: patient L062_008


title: Peripheral blood from patient L066_009

description: Hybridized to 250K_Sty

source_name: patient L066_009


title: Peripheral blood from patient L061_009

description: Hybridized to 250K_Sty

source_name: patient L061_009


title: Peripheral blood from patient N1227

description: Hybridized to 250K_Nsp

source_name: patient N1227


title: Peripheral blood from patient L060_008

description: Hybridized to 250K_Sty

source_name: patient L060_008


title: Peripheral blood from patient N1100

description: Hybridized to 250K_Nsp

source_name: patient N1100


title: Peripheral blood from patient L058_007

description: Hybridized to 250K_Sty

source_name: patient L058_007


title: Peripheral blood from patient L047_008

description: Hybridized to 250K_Sty

source_name: patient L047_008


title: Peripheral blood from patient N0941

description: Hybridized to 250K_Nsp

source_name: patient N0941


title: Peripheral blood from patient N0588

description: Hybridized to 250K_Nsp

source_name: patient N0588


title: Peripheral blood from patient L048_011

description: Hybridized to 250K_Sty

source_name: patient L048_011


title: Peripheral blood from patient L049_003

description: Hybridized to 250K_Sty

source_name: patient L049_003


title: Peripheral blood from patient L043_004

description: Hybridized to 250K_Sty

source_name: patient L043_004


title: Peripheral blood from patient L041_007

description: Hybridized to 250K_Sty

source_name: patient L041_007


title: Peripheral blood from patient L035_010

description: Hybridized to 250K_Sty

source_name: patient L035_010


title: Peripheral blood from patient N0510

description: Hybridized to 250K_Nsp

source_name: patient N0510


title: Peripheral blood from patient N0912

description: Hybridized to 250K_Nsp

source_name: patient N0912


title: Peripheral blood from patient N0478

description: Hybridized to 250K_Nsp

source_name: patient N0478


title: Peripheral blood from patient L034_003

description: Hybridized to 250K_Sty

source_name: patient L034_003


title: Peripheral blood from patient L019_007

description: Hybridized to 250K_Sty

source_name: patient L019_007


title: Peripheral blood from patient L038_004

description: Hybridized to 250K_Sty

source_name: patient L038_004


title: Peripheral blood from patient L009_008

description: Hybridized to 250K_Sty

source_name: patient L009_008


title: Peripheral blood from patient N0405

description: Hybridized to 250K_Nsp

source_name: patient N0405


title: Peripheral blood from patient L014_003

description: Hybridized to 250K_Sty

source_name: patient L014_003


title: Peripheral blood from patient L012_005

description: Hybridized to 250K_Sty

source_name: patient L012_005


title: Peripheral blood from patient L018_017

description: Hybridized to 250K_Sty

source_name: patient L018_017


title: Peripheral blood from patient L021_003

description: Hybridized to 250K_Sty

source_name: patient L021_003


title: Peripheral blood from patient L005_003

description: Hybridized to 250K_Sty

source_name: patient L005_003


title: Peripheral blood from patient N0178

description: Hybridized to 250K_Nsp

source_name: patient N0178


title: Peripheral blood from patient N0459

description: Hybridized to 250K_Nsp

source_name: patient N0459


title: Esophageal squamous cell carcinoma from patient E1796

description: Hybridized to 250K_Sty

source_name: patient E1796

value: esophageal squamous cell carcinoma tumor


title: Peripheral blood from patient N0261

description: Hybridized to 250K_Nsp

source_name: patient N0261


title: Peripheral blood from patient L002_014

description: Hybridized to 250K_Sty

source_name: patient L002_014


title: Esophageal squamous cell carcinoma from patient E1782

description: Hybridized to 250K_Sty

source_name: patient E1782


title: Peripheral blood from patient L017_013

description: Hybridized to 250K_Sty

source_name: patient L017_013


title: Esophageal squamous cell carcinoma from patient E1709

description: Hybridized to 250K_Sty

source_name: patient E1709


title: Peripheral blood from patient N0096

description: Hybridized to 250K_Nsp

source_name: patient N0096


title: Esophageal squamous cell carcinoma from patient E1635

description: Hybridized to 250K_Sty

source_name: patient E1635


title: Peripheral blood from patient E1796

description: Hybridized to 250K_Nsp


title: Esophageal squamous cell carcinoma from patient E2644

description: Hybridized to 250K_Sty

source_name: patient E2644


title: Esophageal squamous cell carcinoma from patient E1629

description: Hybridized to 250K_Sty

source_name: patient E1629


title: Esophageal squamous cell carcinoma from patient E1756

description: Hybridized to 250K_Sty

source_name: patient E1756


title: Peripheral blood from patient E2644

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient N0299

description: Hybridized to 250K_Nsp

source_name: patient N0299


title: Peripheral blood from patient N0103

description: Hybridized to 250K_Nsp

source_name: patient N0103


title: Esophageal squamous cell carcinoma from patient E1610

description: Hybridized to 250K_Sty

source_name: patient E1610


title: Peripheral blood from patient E1782

description: Hybridized to 250K_Nsp


title: Esophageal squamous cell carcinoma from patient E1603

description: Hybridized to 250K_Sty

source_name: patient E1603


title: Esophageal squamous cell carcinoma from patient E1614

description: Hybridized to 250K_Sty

source_name: patient E1614


title: Esophageal squamous cell carcinoma from patient E1584

description: Hybridized to 250K_Sty

source_name: patient E1584


title: Esophageal squamous cell carcinoma from patient E1589

description: Hybridized to 250K_Sty

source_name: patient E1589


title: Esophageal squamous cell carcinoma from patient E1575

description: Hybridized to 250K_Sty

source_name: patient E1575


title: Peripheral blood from patient E1756

description: Hybridized to 250K_Nsp


title: Esophageal squamous cell carcinoma from patient E1578

description: Hybridized to 250K_Sty

source_name: patient E1578


title: Esophageal squamous cell carcinoma from patient E1558

description: Hybridized to 250K_Sty

source_name: patient E1558


title: Peripheral blood from patient E1635

description: Hybridized to 250K_Nsp


title: Esophageal squamous cell carcinoma from patient E1576

description: Hybridized to 250K_Sty

source_name: patient E1576


title: Peripheral blood from patient E1709

description: Hybridized to 250K_Nsp

source_name: patient E1709


title: Esophageal squamous cell carcinoma from patient E1573

description: Hybridized to 250K_Sty

source_name: patient E1573


title: Peripheral blood from patient E1614

description: Hybridized to 250K_Nsp


title: Esophageal squamous cell carcinoma from patient E1556

description: Hybridized to 250K_Sty

source_name: patient E1556


title: Esophageal squamous cell carcinoma from patient E1546

description: Hybridized to 250K_Sty

source_name: patient E1546


title: Peripheral blood from patient E1629

description: Hybridized to 250K_Nsp

source_name: patient E1629


title: Esophageal squamous cell carcinoma from patient E1572

description: Hybridized to 250K_Sty

source_name: patient E1572


title: Esophageal squamous cell carcinoma from patient E1566

description: Hybridized to 250K_Sty

source_name: patient E1566


title: Esophageal squamous cell carcinoma from patient E1542

description: Hybridized to 250K_Sty

source_name: patient E1542


title: Peripheral blood from patient E1610

description: Hybridized to 250K_Nsp

source_name: patient E1610


title: Esophageal squamous cell carcinoma from patient E1551

description: Hybridized to 250K_Sty

source_name: patient E1551


title: Esophageal squamous cell carcinoma from patient E1521

description: Hybridized to 250K_Sty

source_name: patient E1521


title: Peripheral blood from patient E1603

description: Hybridized to 250K_Nsp

source_name: patient E1603


title: Peripheral blood from patient E1589

description: Hybridized to 250K_Nsp

source_name: patient E1589


title: Esophageal squamous cell carcinoma from patient E1532

description: Hybridized to 250K_Sty

source_name: patient E1532


title: Esophageal squamous cell carcinoma from patient E1535

description: Hybridized to 250K_Sty

source_name: patient E1535


title: Peripheral blood from patient E1584

description: Hybridized to 250K_Nsp

source_name: patient E1584


title: Esophageal squamous cell carcinoma from patient E1517

description: Hybridized to 250K_Sty

source_name: patient E1517


title: Esophageal squamous cell carcinoma from patient E1520

description: Hybridized to 250K_Sty

source_name: patient E1520


title: Esophageal squamous cell carcinoma from patient E1510

description: Hybridized to 250K_Sty

source_name: patient E1510


title: Peripheral blood from patient E1578

description: Hybridized to 250K_Nsp

source_name: patient E1578


title: Esophageal squamous cell carcinoma from patient E1507

description: Hybridized to 250K_Sty

source_name: patient E1507


title: Peripheral blood from patient E1576

description: Hybridized to 250K_Nsp

source_name: patient E1576


title: Peripheral blood from patient E1566

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient E1532

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient E1572

description: Hybridized to 250K_Nsp

source_name: patient E1572


title: Peripheral blood from patient E1573

description: Hybridized to 250K_Nsp

source_name: patient E1573


title: Peripheral blood from patient E1558

description: Hybridized to 250K_Nsp

source_name: patient E1558


title: Peripheral blood from patient E1575

description: Hybridized to 250K_Nsp

source_name: patient E1575


title: Peripheral blood from patient E1551

description: Hybridized to 250K_Nsp

source_name: patient E1551


title: Peripheral blood from patient E1542

description: Hybridized to 250K_Nsp

source_name: patient E1542


title: Peripheral blood from patient E1546

description: Hybridized to 250K_Nsp

source_name: patient E1546


title: Peripheral blood from patient E1535

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient E1521

description: Hybridized to 250K_Nsp

source_name: patient E1521


title: Peripheral blood from patient L208_005

description: Hybridized to 250K_Nsp

source_name: patient L208_005


title: Peripheral blood from patient E1507

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient E1510

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient L203_003

description: Hybridized to 250K_Nsp

source_name: patient L203_003


title: Peripheral blood from patient E1517

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient L201_008

description: Hybridized to 250K_Nsp

source_name: patient L201_008


title: Peripheral blood from patient E1520

description: Hybridized to 250K_Nsp


title: Peripheral blood from patient L207_012

description: Hybridized to 250K_Nsp

source_name: patient L207_012


title: Peripheral blood from patient L206_005

description: Hybridized to 250K_Nsp

source_name: patient L206_005


title: Peripheral blood from patient L199_006

description: Hybridized to 250K_Nsp

source_name: patient L199_006


title: Peripheral blood from patient L191_006

description: Hybridized to 250K_Nsp

source_name: patient L191_006


title: Peripheral blood from patient L186_007

description: Hybridized to 250K_Nsp

source_name: patient L186_007


title: Peripheral blood from patient L196_009

description: Hybridized to 250K_Nsp

source_name: patient L196_009


title: Peripheral blood from patient L170_004

description: Hybridized to 250K_Nsp

source_name: patient L170_004


title: Peripheral blood from patient L178_004

description: Hybridized to 250K_Nsp

source_name: patient L178_004


title: FFPE97 - mAdbID:86612

status: Public on Mar 11 2010

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: 86612

hyb_protocol: microRNA Hybridization Protocol Other: Resuspend Cy3 and Cy5 labeled miR in 10ul and combine them together (20ul total) and add the following reagents: 1ul 50x Denhardt’s blocking solution ,1ul poly dA (8ug/), 1ul yeast tRNA (4mg/ml), 10ul Human Cot I DNA (10mg/ml), 3ul 20X SSC and 1ul 10% SDS. Heat sample at 70C for 3min and immediately hybridize after spin at 10,000g for 30 sec. Start hybridization at RT over night in the dark.

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.2;; 5.12 Temperature: 28.43

data_processing:
BRB-ArrayTools Data Processing Protocol
Calculation Method: Included duplicate spots per each miR, whose intensity was averaged. A spot with signal intensity <100 in both channels was filtered out. If the signal intensity was <100 in one channel only, it was set to 100 in computing the log-ratio value. A spot size smaller than 25 pixels was also filtered out. The normalization method used is ratio median over entire array method.

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV Control Sample

label_protocol:
Cy3 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy3 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated from 20um sections from FFPE tissue blocks using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX USA). Small RNA was enriched and purified by flashPAGE Fractionator (Ambion, Austin, TX USA) according to the manufacturer’s instruction.

value: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell line

tag: cell type

value: lymphoblastoid

label_protocol:
Cy5 Labeling Protocol
Other: Small RNA, equivalent to 10 ug of the total RNA from FFPE and EBV reference samples, was labeled with Cy5 using mirVana™ miRNA Labeling Kit (Ambion, Austin, TX USA).

value: Lung

tag: disease state

value: None Small Cell Carcinoma

tag: clinical info

value: Final pathology diagnosis:Squamous Cell Carcinoma

value: Histology of male smoker:male squamous smoker


title: Peripheral blood from patient L165_004

description: Hybridized to 250K_Nsp

source_name: patient L165_004


title: Peripheral blood from patient L166_009

description: Hybridized to 250K_Nsp

source_name: patient L166_009


title: Peripheral blood from patient L162_011

description: Hybridized to 250K_Nsp

source_name: patient L162_011


title: Peripheral blood from patient E1556

description: Hybridized to 250K_Nsp

source_name: patient E1556


title: Peripheral blood from patient L172_011

description: Hybridized to 250K_Nsp

source_name: patient L172_011


title: Peripheral blood from patient L158_011

description: Hybridized to 250K_Nsp

source_name: patient L158_011


title: Peripheral blood from patient L163_010

description: Hybridized to 250K_Nsp

source_name: patient L163_010


title: Peripheral blood from patient L157_012

description: Hybridized to 250K_Nsp

source_name: patient L157_012


title: Peripheral blood from patient L155_010

description: Hybridized to 250K_Nsp

source_name: patient L155_010


title: Peripheral blood from patient L161_012

description: Hybridized to 250K_Nsp

source_name: patient L161_012


title: Peripheral blood from patient L076_012

description: Hybridized to 250K_Nsp

source_name: patient L076_012


title: Peripheral blood from patient L072_003

description: Hybridized to 250K_Nsp

source_name: patient L072_003


title: Peripheral blood from patient L073_011

description: Hybridized to 250K_Nsp

source_name: patient L073_011


title: Peripheral blood from patient L154_012

description: Hybridized to 250K_Nsp

source_name: patient L154_012


title: Peripheral blood from patient L066_009

description: Hybridized to 250K_Nsp

source_name: patient L066_009


title: Peripheral blood from patient L070_011

description: Hybridized to 250K_Nsp

source_name: patient L070_011


title: Peripheral blood from patient L062_008

description: Hybridized to 250K_Nsp

source_name: patient L062_008


title: Peripheral blood from patient L061_009

description: Hybridized to 250K_Nsp

source_name: patient L061_009


title: Peripheral blood from patient L065_003

description: Hybridized to 250K_Nsp

source_name: patient L065_003


title: Peripheral blood from patient L060_008

description: Hybridized to 250K_Nsp

source_name: patient L060_008


title: Peripheral blood from patient L047_008

description: Hybridized to 250K_Nsp

source_name: patient L047_008


title: Peripheral blood from patient L152_011

description: Hybridized to 250K_Nsp

source_name: patient L152_011


title: Liver_Obese_DM_poorly-controlled_rep4

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description: Gene expression from liver of obese subject with diabetes, poorly-controlled

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Human Genome U133A array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G2500.

data_processing: Data were analyzed using Affymetrix GCOS v.1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

source_name: liver

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

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

value: Female

tag: body mass index (kg/m2)

tag: hemoglobin a1c

tag: fasting glucose

tag: fasting insulin

tag: si

tag: sg

tag: cholesterol

tag: triglycerides

tag: hdl


title: Liver_Obese_DM_poorly-controlled_rep3

value: Male


title: Peripheral blood from patient L048_011

description: Hybridized to 250K_Nsp

source_name: patient L048_011


title: Peripheral blood from patient L058_007

description: Hybridized to 250K_Nsp

source_name: patient L058_007


title: Peripheral blood from patient L188_006

description: Hybridized to 250K_Nsp

source_name: patient L188_006


title: Peripheral blood from patient L049_003

description: Hybridized to 250K_Nsp

source_name: patient L049_003


title: Peripheral blood from patient L038_004

description: Hybridized to 250K_Nsp

source_name: patient L038_004


title: Peripheral blood from patient L043_004

description: Hybridized to 250K_Nsp

source_name: patient L043_004


title: Liver_Obese_DM_poorly-controlled_rep1


title: Peripheral blood from patient L014_003

description: Hybridized to 250K_Nsp

source_name: patient L014_003


title: Peripheral blood from patient L034_003

description: Hybridized to 250K_Nsp

source_name: patient L034_003


title: Liver_Obese_DM_poorly-controlled_rep2


title: Liver_Obese_DM_well-controlled_rep5

description: Gene expression from liver of obese subject with diabetes, well-controlled


title: Peripheral blood from patient L021_003

description: Hybridized to 250K_Nsp

source_name: patient L021_003


title: Liver_Obese_DM_well-controlled_rep4


title: Peripheral blood from patient L012_005

description: Hybridized to 250K_Nsp

source_name: patient L012_005


title: Peripheral blood from patient L009_008

description: Hybridized to 250K_Nsp

source_name: patient L009_008


title: Peripheral blood from patient L019_007

description: Hybridized to 250K_Nsp

source_name: patient L019_007


title: D1 T48_TCL

status: Public on Jan 08 2010

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: Xray (Biotique Systems)

source_name: T-lymphocytes at time 48

label_protocol: Whole Transcript sense target labeling

growth_protocol: T and B Cells in RPMI-1640 ( See study Design)

extract_protocol: Total RNA was extracted using the Mirvana kit

treatment_protocol: CD3/28 and anti-CD40 + rIL2, rIL10

tag: Purified T cells from healthy human donor


title: Liver_Obese_DM_well-controlled_rep2


title: Peripheral blood from patient L035_010

description: Hybridized to 250K_Nsp

source_name: patient L035_010


title: Peripheral blood from patient L018_017

description: Hybridized to 250K_Nsp

source_name: patient L018_017


title: Peripheral blood from patient L017_013

description: Hybridized to 250K_Nsp

source_name: patient L017_013


title: Liver_Obese_DM_well-controlled_rep3

source_name: liver


title: Peripheral blood from patient L005_003

description: Hybridized to 250K_Nsp

source_name: patient L005_003


title: Liver_Obese_noDM_rep4

description: Gene expression from liver of obese subject without diabetes


title: Peripheral blood from patient L041_007

description: Hybridized to 250K_Nsp

source_name: patient L041_007


title: Liver_Obese_noDM_rep3


title: Liver_Obese_noDM_rep2


title: Liver_Obese_noDM_rep1


title: Liver_Lean_rep5

description: Gene expression from liver of lean subject


title: Liver_Lean_rep4


title: Liver_Lean_rep3


title: Liver_Lean_rep2


title: Liver_Lean_rep1


title: Liver_Obese_DM_well-controlled_rep1


title: Esophageal squamous cell carcinoma from patient E1782

description: Hybridized to 250K_Nsp

source_name: patient E1782


title: Esophageal squamous cell carcinoma from patient E1796

description: Hybridized to 250K_Nsp

source_name: patient E1796


title: Lenses_42days_DBLmice_replicate3

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

description: Whole lenses were removed from mice and stored in RNAlater RNA stabilizing reagent (Qiagen, Hilden, Germany). 4 to 8 individual lenses were pooled and homogenized.

hyb_protocol: Hybridization was carried out for 16 hr at 45 °C. Chips were then washed with 6x SSPE and stained with streptavidin-phycoerythrin according to Affymetrix’s guidelines

scan_protocol: Chips were scanned using a confocal microscope scanner with the 560-nm long-pass filter (HP GeneArray Scanner 3000) according to Affymetrix’s guidelines.

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

organism: Mus musculus

source_name: Lenses from 42 day old DBL transgenic mice

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

tag: strain

value: DBL transgenic


title: Esophageal squamous cell carcinoma from patient E2644

description: Hybridized to 250K_Nsp

source_name: patient E2644


title: Lenses_42days_DBLmice_replicate2


title: Esophageal squamous cell carcinoma from patient E1756

description: Hybridized to 250K_Nsp

source_name: patient E1756


title: Esophageal squamous cell carcinoma from patient E1709

description: Hybridized to 250K_Nsp

source_name: patient E1709


title: Lenses_42days_WTmice_replicate3

source_name: Lenses from 42 day old wild type mice

value: WT


title: Lenses_42days_WTmice_replicate2


title: Lenses_42days_WTmice_replicate1


title: Esophageal squamous cell carcinoma from patient E1629

description: Hybridized to 250K_Nsp

source_name: patient E1629


title: Lenses_14days_WTmice_replicate3

source_name: Lenses from 14 day old wild type mice


title: Esophageal squamous cell carcinoma from patient E1610

description: Hybridized to 250K_Nsp

source_name: patient E1610


title: Lenses_14days_WTmice_replicate2


title: Peripheral blood from patient L002_014

description: Hybridized to 250K_Nsp

source_name: patient L002_014


title: Esophageal squamous cell carcinoma from patient E1578

description: Hybridized to 250K_Nsp

source_name: patient E1578


title: Lenses_14days_WTmice_replicate1


title: Lenses_14days_DBLmice_replicate1

source_name: Lenses from 14 day old DBL transgenic mice


title: Lenses_14days_DBLmice_replicate2


title: Esophageal squamous cell carcinoma from patient E1566

description: Hybridized to 250K_Nsp

source_name: patient E1566


title: Esophageal squamous cell carcinoma from patient E1589

description: Hybridized to 250K_Nsp

source_name: patient E1589


title: Esophageal squamous cell carcinoma from patient E1572

description: Hybridized to 250K_Nsp

source_name: patient E1572


title: Esophageal squamous cell carcinoma from patient E1584

description: Hybridized to 250K_Nsp

source_name: patient E1584


title: Lenses_2days_DBLmice_replicate3

source_name: Lenses from 2 day old DBL transgenic mice


title: Lenses_2days_DBLmice_replicate1


title: Lenses_2days_DBLmice_replicate2


title: Esophageal squamous cell carcinoma from patient E1635

description: Hybridized to 250K_Nsp

source_name: patient E1635


title: Esophageal squamous cell carcinoma from patient E1573

description: Hybridized to 250K_Nsp

source_name: patient E1573


title: Esophageal squamous cell carcinoma from patient E1576

description: Hybridized to 250K_Nsp

source_name: patient E1576


title: Lenses_42days_DBLmice_replicate1

source_name: Lenses from 42 day old DBL transgenic mice


title: Lenses_14days_DBLmice_replicate3


title: Esophageal squamous cell carcinoma from patient E1556

description: Hybridized to 250K_Nsp

source_name: patient E1556


title: Esophageal squamous cell carcinoma from patient E1575

description: Hybridized to 250K_Nsp

source_name: patient E1575


title: Esophageal squamous cell carcinoma from patient E1546

description: Hybridized to 250K_Nsp

source_name: patient E1546


title: Brassica rapa replicate 2

status: Public on May 03 2009

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

hyb_protocol: A consistent amount of Cy3-labeled cRNA (1.6 micrograms) were hybridized to the microarray, for 17 hours, prior to washing and scanning.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted from scanned images using Agilent’s Feature Extraction Software (Agilent Technologies). Gene expression data was loaded into the Rosetta Resolver® Gene Expression Analysis System version 7.0.0.1.9 and biological replicates were combined using an error-weighted average.

organism: Brassica rapa

source_name: Brassica rapa first true leaf

label_protocol: 500 ng of total RNA from each sample was amplified and labeled with a fluorescent dye (Cy3) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer’s protocol. The amount and quality of the fluorescently labeled cRNA was assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

growth_protocol: The seeds were germinated and grown on in long day glass house conditions (16 hours photoperiod) at 15 degrees Celsius (400W HQI metal halide lamps). Plants were pricked out after 11 days into Plantpak P15 modules containing Scotts Levington M2 compost and arranged into a four block randomised design with three plants each of each of the four genotypes per block and randomised within each block.  Leaves were harvested 15 days after pricking out, 26 days after sowing.  Leaf harvest was carried out as close to the midpoint of the light period as possible.  The first true leaf of each plant was excised as close to the petiole as possible and the weight was recorded.  Three leaf samples for each genotype from each experimental block were pooled and frozen in liquid nitrogen, giving a final harvest of four pooled leaf samples per genotype.

extract_protocol: RNA was prepared by grinding tissue in liquid nitrogen and extracting using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s protocol.

value: first true leaf


title: Esophageal squamous cell carcinoma from patient E1551

description: Hybridized to 250K_Nsp

source_name: patient E1551


title: Esophageal squamous cell carcinoma from patient E1535

description: Hybridized to 250K_Nsp

source_name: patient E1535


title: Esophageal squamous cell carcinoma from patient E1558

description: Hybridized to 250K_Nsp

source_name: patient E1558


title: Brassica oleracea replicate 4

organism: Brassica oleracea

source_name: Brassica oleracea first true leaf


title: Brassica napus 4 replicate 2

organism: Brassica napus

source_name: Brassica napus first true leaf


title: Brassica rapa replicate 3


title: Brassica napus 4 replicate 4


title: Brassica napus 4 replicate 1


title: Lenses_2days_WTmice_replicate3

source_name: Lenses from 2 day old wild type mice


title: Lenses_2days_WTmice_replicate2


title: Brassica napus 2 replicate 3


title: Brassica rapa replicate 4


title: Esophageal squamous cell carcinoma from patient E1542

description: Hybridized to 250K_Nsp

source_name: patient E1542


title: Brassica oleracea replicate 3


title: Lenses_2days_WTmice_replicate1

hyb_protocol: Hybridization was carried out for 16 hr at 45oC. Chips were then washed with 6x SSPE and stained with streptavidin-phycoerythrin according to Affymetrix’s guidelines


title: Esophageal squamous cell carcinoma from patient E1517

description: Hybridized to 250K_Nsp

source_name: patient E1517


title: Brassica napus 2 replicate 2


title: Brassica oleracea replicate 2


title: Esophageal squamous cell carcinoma from patient E1521

description: Hybridized to 250K_Nsp

source_name: patient E1521


title: Brassica rapa replicate 1


title: Keratinocytes_Erk1andErk2siRNA-B_rep2

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

description: Primary human keratinocytes were grown in vitro and treated with either a scrambled control siRNA, a pair of siRNA oligomers against Erk1 and Erk2, or an independent pair of siRNA oligomers against Erk1 and Erk2.  RNA was harvested four days later.  Three biological replicates were performed for each of the three groups. See PA Dumesic et al. 2009 Journal of Cell Biology for experimental details.

hyb_protocol: Performed by Stanford PAN Facility

scan_protocol: Performed by Stanford PAN Facility

data_processing: RMA preprocessing normalization by GeneSpring 7.3.

source_name: Primary human keratinocytes treated with siRNA against Erk1 and Erk2 (oligo pair B)

label_protocol: Performed by Stanford PAN Facility

growth_protocol: Keratinocyte SFM

extract_protocol: QIAGEN RNeasy

value: Primary human foreskin keratinocytes


title: Esophageal squamous cell carcinoma from patient E1510

description: Hybridized to 250K_Nsp

source_name: patient E1510


title: Esophageal squamous cell carcinoma from patient E1520

description: Hybridized to 250K_Nsp

source_name: patient E1520


title: Keratinocytes_scrambledsiRNA_rep3

source_name: Primary human keratinocytes treated with scrambled control siRNA


title: Brassica napus 2 replicate 1


title: Keratinocytes_Erk1andErk2siRNA-A_rep3

source_name: Primary human keratinocytes treated with siRNA against Erk1 and Erk2 (oligo pair A)


title: Keratinocytes_Erk1andErk2siRNA-B_rep1


title: Keratinocytes_scrambledsiRNA_rep1

data_processing: RMA normalization by GeneSpring 7.3.

value: Primary human foreskin keratinocytes.


title: Keratinocytes_Erk1andErk2siRNA-A_rep1


title: mock, replicate

status: Public on May 01 2009

city: Osaka

first: Toshihiro

last: Kai

state: Osaka

address: 3-1-98 Kasugade-naka, Konohana-ku

department: Genomics Research

institute: Dainippon Sumitomo Pharma Co., Ltd.

description: mock

hyb_protocol: Standard Affymetrix procedures ( using Affymetrix GeneChip Hybridization Oven 640 and Affymetrix Fluidics Station 450)

scan_protocol: Standard Affymetrix procedures( using Hewlett-Packard GeneArray Scanner G2500A)

data_processing: Data processing was carried out by GCOS1.1. MAS5.0 algorithm was used to generate signals and detection calls. Global normalization was performed to make average intensity of all probe sets equal to 100.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa, mock, 9 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

extract_protocol: We added RNAprotect Bacteria Reagent (QIAGEN) to medium before extraction. Then, we extracted RNA with RNeasy Midi Kit (QIAGEN) according to the manufacturer's instructions. Finaly, we used RNase-Free DNase set (QIAGEN) to remove genomic DNA contamination.

treatment_protocol: P. aeruginosa was grown in 15ml LB medium at 37°C shaking without or with AZM (Pfizer Laboratories) (0.5, 2 ug/ml).

tag: Strain


title: Keratinocytes_Erk1andErk2siRNA-A_rep2


title: AZM 2 ug/ml, replicate

description: 2 ug/ml AZM is 1/64 MIC

source_name: P. aeruginosa, AZM 2 ug/ml, 9 hours


title: AZM 2 ug/ml

description: 2 ug/ml AZM is 1/64 MIC


title: Brassica oleracea replicate 1


title: Esophageal squamous cell carcinoma from patient E1507

description: Hybridized to 250K_Nsp

source_name: patient E1507


title: AZM 0.5 ug/ml

description: 0.5 ug/ml AZM is 1/256 MIC

source_name: P. aeruginosa, AZM 0.5 ug/ml, 9 hours


title: Brassica napus 4 replicate 3


title: mock

description: mock


title: Abf1-degron_Reb1_expression_B

first: Hiten

last: Madhani

department: Biochemistry and Biophysics

description: No further information

hyb_protocol: equal amounts of labeled cDNA were combined, heated at 100degs for 5 minutes, iced 5 minutes, then supplemented with 25X Fragmentation buffer (Agilent), 10X blocking agent (Agilent), and 2X GEx Hybridization Buffer HI-RPM (Agilent) prior to appliation to the microarray.  Hybridizations were carried out at 65 degrees for 18 hours.  Arrays were washed once with room-temperature Gene Expression Wash Buffer 1 and once with Gene Expression Wash Buffer 2 at 37 degrees.

scan_protocol: Scanned with a GenePix 4000B at 5 uM

data_processing: A loess curve was calculated for the 1:1 DCP spike-in probes, and another loess curve was calculated for the bona fide S. cerevisiae probes.  Features were normalized using a composite loess algorithm (Nucleic Acids Res. 30:e15)

label_protocol: Total RNA spiked with RNA from the Agilent Dual Color RNAi spike-in kit was reverse transcribed to cDNA with MMLV reverse transcriptase in a reaction that included dT oligos and aminoallyl-dUTP for dye coupling

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: Cells were collected by 1 minute spins at room temperature and flash frozen in liquid nitrogen.  Cell pellets were resuspended in TRIZOL and lysed by 2x2.5 minute bead-beatings.  Total RNA was recovered by two chloroform extractions and an isopropanol precipitation.

tag: pGAL1::UBR1, Reb1:dT7 inserted into PRM1

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


title: Abf1-degron_Reb1_expression_C

description: No further information


title: Esophageal squamous cell carcinoma from patient E1614

description: Hybridized to 250K_Nsp

source_name: patient E1614

tag: tissue


title: Brassica napus 2 replicate 4

tag: cell type


title: Abf1-degron_Reb1_expression_D

description: No further information


title: Keratinocytes_Erk1andErk2siRNA-B_rep3


title: Sth1-degron_expression_D

description: No further information

tag: pGAL1::UBR1, pMET3::UBI4::DHFRts::3xHA::STH1, Reb1:dT7 inserted into PRM1


title: Abf1-degron_Reb1_expression_A

description: No further information


title: Sth1-degron_expression_B

description: No further information


title: Sth1-degron_expression_A

description: No further information


title: Esophageal squamous cell carcinoma from patient E1603

description: Hybridized to 250K_Nsp

source_name: patient E1603


title: CKO Wild Type TP2

city: Baltimore

first: Thomas

middle: W

last: Kensler

address: 615 N Wolfe St SPH Rm E7541

institute: Johns Hopkins School of Medicine

description: genetic control wild-type mice treated with CDDO-Im gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: The .CEL files were background-corrected using the bg.adjust.gcrma function of gcrma v.2.12.1 , then base 2 logarithm-transformed.  The transformed data was quantile-normalized using the normalize.AffyBatch.quantiles function of affy v.1.8.1 as implemented in R v.2.7.0.

source_name: genetic control for CKO mice, Alb-Cre:Keap1(flox/+), liver tissue

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

extract_protocol: Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.

treatment_protocol: received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS  and sacrificed 6 h later

tag: genotype

value: genetic control for cko mice, alb-cre:Keap1(flox/+)

tag: gender

value: male

tag: age

value: 9 weeks

value: Liver


title: CKO Wild Type V3

description: Basal genetic control wild-type gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

treatment_protocol: received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS)  and sacrificed 6 h later


title: Sth1-degron_expression_C

description: No further information


title: CKO Wild Type V1

treatment_protocol: received vehicle only (10% DMSO, 10% Cremophor-EL, 80% PBS) and sacrificed 6 h later


title: CKO Wild Type V2


title: CKO Wild Type TP3

treatment_protocol: received 30 umol CDDO-Im/kg body weight by gavage in vehicle of 10% DMSO, 10% Cremophor-EL, 80% PBS and sacrificed 6 h later


title: CKO TP2

description: conditional Keap1 knockout mice treated with CDDO-Im gene expression

source_name: conditional Keap1 knockout (Albumin-Cre:Keap1(flox/-)) on C57Bl/6J background, liver tissue

value: conditional keap1 knockout


title: CKO V4

description: Basal conditional Keap1 knockout gene expression


title: CKO TP3


title: Esophageal squamous cell carcinoma from patient E1532

description: Hybridized to 250K_Nsp

source_name: patient E1532

value: esophageal squamous cell carcinoma tumor


title: ChIP-chip using BSG95

status: Public on May 14 2009

city: Newcastle upon Tyne

first: Stephan

last: Gruber

address: Framlignton Place

department: ICaMB

institute: Newcastle University

description: Smc ChIP-chip using tagged version

hyb_protocol: 6ug of IN and IP mixed and hybridized to Nimblegen array

scan_protocol: Genepix 4000B

data_processing: calculated ratio files using Nimblescan (no normalization)

organism: Bacillus subtilis

source_name: input DNA

label_protocol: 1ug amplified DNA labelled by random priming (Cy3 for IN, Cy5 for IP)

growth_protocol: LB, 37C, exponential growth

extract_protocol: sonication, ChIP (human IgG-Dynabeads), amplification using Sigma WGA2 kit

treatment_protocol: formaldehyde cross-linking, lysozyme treatment

tag: before IgG purification

source_name: ChIP DNA

tag: after IgG purification


title: CKO V3


title: CKO V5


title: As4.1 cells, interleukin treatment_1

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: Gene expression data from As4.1 cells.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

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

source_name: As4.1 cells, treated with interleukin

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

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

treatment_protocol: Interleukin treatment

tag: As4.1 cells are a renin-expressing cell line.


title: PPARα KO Wyeth+Heat Shock treated 22

city: Research Triangle Park

first: beena

last: vallanat

address: 109 Tw Alexanser Dr

institute: EPA

description: Studies utilized wild-type and PPARα-null male mice 9–12 weeks of age on a mixed SV129/C57BL/6 background. Control and treated mice were provided with NIH-07 rodent chow (Zeigler Brothers, Gardeners, PA) and deionized, filtered water ad libitum.  Lighting was on a 12-hr light/dark cycle.  Mice were sacrificed 4 hrs, 24 hrs and 3 days after the heat stress.

hyb_protocol: Following fragmentation, 10 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 Affymetrix Scanner 3000

data_processing: The data were analyzed with Rosetta Resolve 7.0  using Affymetrix default profile builder analysis settings.

source_name: PPARα KO Wyeth+Heat Shock treated 22

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

extract_protocol: Liver RNA was isolated using a modified guanidium isothiocyanate method (TRIzol®; Invitrogen) and was further purified using silica membrane spin columns (RNeasy®; Qiagen, Valencia, CA).  RNA integrity was assessed by the RNA 6000 LabChip® kit using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

treatment_protocol: Lighting was on a 12-hr light/dark cycle.  Mice (n = 5-6 per group) were fed a control diet or a diet containing the PPARα agonist WY-14,643 (ChemSyn Science, Lenexa, KS) (WY) in the diet (500 ppm) for 1 week followed by a 40-min heat stress at 42°C or held at room temperature in wire rack cages.  Mice were sacrificed 4 hrs, 24 hrs and 3 days after the heat stress.    Heat in the exposure chamber was generated by a combination of the building reheat system, an in-line air heater and two small surface heaters.  The in-line heater (Riley Equipment Company, Inc., Houston, TX) was set to approximately 300 °F.  The heated air traveled through a 2 foot by 2 inch inlet tube constructed on PVC, stainless steel and Teflon into the bottom of the H1000 inhalation chamber.  A small diverter was placed in the bottom of the H1000 inhalation chamber to prevent a chimney effect in the chamber and increasing the efficiency of the heat distribution.  The stainless steel animal cage unit was placed in the center of the H1000 inhalation chamber and a feces/urine catch pan was placed in the top-most position of the chamber.  A small (1500 watt) heater was placed on either side of the H1000 inhalation chamber approximately 4 inches from the surface.  These heaters heated the stainless steel sides and heated the surface enough to allow the internal temperature of the chamber to reach approximately 43°C.  The temperature was monitored in three locations of the H1000 inhalation chamber:  front door above the animal cage unit, back door below the animal cage unit and in the center approximately two inches using probes (Rotronic Hygrometer Series 1200, Rotronic Instrument Corp., Huntington, NY).

value: whole liver

value: PPARα-null

value: 9–12 weeks

tag: background

value: mixed SV129/C57BL/6 background


title: CKO TP4


title: As4.1 cells, Vehicle treatment_1

description: Gene expression data from As4.1 cells.

source_name: As4.1 cells, control

treatment_protocol: Vehicle treatment


title: As4.1 cells, hydrogen peroxide treatment_2

description: Gene expression data from As4.1 cells.

source_name: As4.1 cells, treated with hydrogen peroxide

treatment_protocol: Hydrogen peroxide treatment