title: Huvec PDLs44 pool B

type: other

city: Rome

first: Massimo

last: Federici

address: Via Montpellier 1

country: Italy

institute: University of Tor Vergata

description: The acquired images were analyzed with GenePix Pro 5.0 (Axon Instruments).

hyb_protocol: miRNA from PDLs44 cells was fluorescently labeled and hybridized to the Bioarrays according to the manufacturer’s instructions (Ambion Inc).

scan_protocol: The slides were scanned on the GenePix 4000B Microarray Scanner at the optimal wavelength for the Alexa555 (F532) and Alexa647 (F635) using lasers.

data_processing: MicroRNA spots were automatically segmented, local backgrounds (B635 and B532) and total intensities (F635 and F532) were calculated for each spot. The spots were flagged when they exhibited poor hybridization signals, when they were saturated (F635 or F532 median = 65535) or when signal to background ratio was below two.

molecule: other

source_name: Huvec PDLs44 (pool B)

label_protocol: miRNA from PDLs44cells was fluorescently labeled and hybridized to the Bioarrays according to the manufacturer’s instructions (Ambion Inc).

extract_protocol: Enriched miRNA was isolated from HUVEC (PDLs 44) with the mirVana miRNA Isolation Kit (Ambion Inc), which allows isolation of both enriched miRNA and larger RNA species separately.

tag: cell type

value: HUVEC (normal human umbilical vein endothelial cells)

value: population doubling levels (PDL) 44


title: 3_Scrotum

status: Public on Sep 29 2009

type: genomic

city: Seattle

first: Barbara

middle: J.

last: Trask

state: WA

address: 1100 Fairview Avenue N., C3-168, P.O. Box 19024

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
LCM collected tumor from patient 3, scrotum metastasis
Alternate patient ID 02-065

hyb_protocol: Labeled test and reference samples were each mixed with 125 micrograms of Cot-1 DNA (Invitrogen) and 30 micrograms of yeast tRNA, concentrated, and hybridized to arrays under conditions described previously (L.W. Loo et al., Cancer Res., 2004).

scan_protocol: See L.W. Loo et al., Cancer Res., 2004.

data_processing: A custom R script was used to log2-transform raw intensity values, calculate the ratio of red to green fluorescence intensities, and apply a block-based loess normalization procedure based on intensity. The log2 ratios for the two spots for each remaining clone were averaged.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 1 microgram of amplified material was labelled with Cy5-dUTP (GE Healthcare) using the Bioprime Array CGH kit (Invitrogen). Labeled material was cleaned using the columns included with the labeling kit.

extract_protocol: LCM-collected samples were incubated overnight in proteinase K buffer (1% Tween 20, 1 mg/ml Proteinase K, and 1 x TE) and DNA was isolated using the Qiagen QIAamp DNA Micro Kit (Qiagen Inc, Valencia, CA). Genomic material was amplified  by ligation-mediated PCR (LMP).

tag: tissue

value: Scrotum Metastasis

source_name: Female peripheral blood

label_protocol: 1 microgram of amplified material was labelled with Cy3-dUTP (GE Healthcare) using the Bioprime Array CGH kit (Invitrogen). Labeled material was cleaned using the columns included with the labeling kit.

extract_protocol: Reference DNA was obtained from the peripheral blood of a single female individual, isolated using the QIAamp DNA Blood Mini Kit (Qiagen Inc, Valencia, CA), and quantified using the Quant-iT PicoGreen dsDNA Assay (Invitrogen, Carlsbad, CA). The amplification method (i.e., LMP or WGA) and the amount of input DNA for all reference samples matched the test sample.

value: Female peripheral blood


title: Huvec PDLs8 pool B

hyb_protocol: miRNA from PDLs8 cells was fluorescently labeled and hybridized to the Bioarrays according to the manufacturer’s instructions (Ambion Inc).

source_name: Huvec PDLs8 (pool B)

extract_protocol: Enriched miRNA was isolated from HUVEC (PDLs 8) with the mirVana miRNA Isolation Kit (Ambion Inc), which allows isolation of both enriched miRNA and larger RNA species separately.

tag: age

value: population doubling levels (PDL) 8


title: 3_Prostate

description:
LCM collected tumor from patient 3, prostate primary
Alternate patient ID 02-065

value: Prostate Primary


title: Huvec PDLs44 pool A

source_name: Huvec PDLs44 (pool A)

label_protocol: miRNA from PDLs44 cells was fluorescently labeled and hybridized to the Bioarrays according to the manufacturer’s instructions (Ambion Inc).


title: 3_Skin

description:
LCM collected tumor from patient 3, skin metastasis
Alternate patient ID 02-065

value: Skin Metastasis


title: 10_LN2

description:
LCM collected tumor from patient 10, retroperitoneal Lymph Node metastasis
Alternate patient ID 05-144

value: Retroperitoneal Lymph Node Metastasis


title: 3_LN

description:
LCM collected tumor from patient 3, retroperitoneal Lymph Node metastasis
Alternate patient ID 02-065


title: 2_LN

description:
LCM collected tumor from patient 2, pericaval Lymph Node metastasis
Alternate patient ID 00-140

extract_protocol: LCM-collected samples were incubated overnight in proteinase K buffer (1% Tween 20, 1 mg/ml Proteinase K, and 1 x TE) and DNA was isolated using the Qiagen QIAamp DNA Micro Kit (Qiagen Inc, Valencia, CA). Genomic material was amplified  using a whole genome amplification (WGA) kit, WGA2 (Sigma-Aldrich, St. Louis, MO).

value: Pericaval Lymph Node Metastasis


title: 2_Prostate

description:
LCM collected tumor from patient 2, prostate primary
Alternate patient ID 00-140


title: 430A plus GDNF sample 1

type: RNA

city: New YOrk

first: Benson

middle: Che-i

last: Lu

state: NY

department: Genetics and Development

institute: Columbia University Medical Center

description: No additional information

hyb_protocol: GeneChip® Hybridization Oven 640 according to Affymetrix protocol

scan_protocol: GeneChip® Scanner 3000

data_processing: Sample comparisons and statistical analysis were performed using dChip 1.3 (built April 2009), using the Comparison Analysis feature to identify genes differentially expressed between the two groups. The following filtering criteria were used: the lower limit for fold-change between the means of the +GDNF and -GDNF samples must exceed 1.2 with a 90% confidence limit, and the absolute difference between the two group means must exceed 100.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse isolated ureteric bud, with GDNF, 16 hours

label_protocol: IVT and labeling were performed with BioArray HighYield RNA Transcript Labeling Kit (Affymetrix, P/N 900182).

extract_protocol: Cultured ureteric buds were removed from the Matrigel with a Wiretrol and added directly to 800 µL of TRIzol reagent (Invitrogen, Cat # 15596-018) and homogenized with a 26 gauge needle prior to chloroform addition.  After homogenization and before addition of chloroform, samples were quick frozen and stored at -80C.  To increase RNA precipitation, 25 ng/µL of RNase-free glycogen was added as a carrier to the aqueous phase.  RNA was isolated from batches of 30-40 pooled UBs, and the RNA samples were quantified and checked for integrity using the Agilent 2100 Bioanalyzer. RNA from approximately 5-6 different batches of cultured UBs was then pooled to obtain sufficient RNA (>8 ug) to prepare the probe for hybridization a single chip.

treatment_protocol: Cultured uteric buds grown in matrigel were treated with 100ng/mL GDNF for 16 hrs prior to extraction.

tag: strain

value: Swiss Webster

tag: developmental stage

value: ureteric buds

tag: treatment group

value: plus GDNF


title: Huvec PDLs8 pool A

source_name: Huvec PDLs8 (pool A)

label_protocol: miRNA from PDLs8 cells was fluorescently labeled and hybridized to the Bioarrays according to the manufacturer’s instructions (Ambion Inc).


title: 2_Liver

description:
LCM collected tumor from patient 2, liver metastasis
Alternate patient ID 00-140

value: Liver Metastasis


title: 1_Prostate

description:
LCM collected tumor from patient 1, prostate primary
Alternate patient ID 00-010


title: SpnR6_pcsB_IU1533vsIU1979_BHI_rep4

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio~1.0). Images were analysed using GenePix Pro 5.0 software (molecular Devices)

data_processing: Data were normalized with BASE (Bioarray Software Environment) using the Lowess normalization method without background subtraction.

organism: Streptococcus pneumoniae

source_name: IU1533, S. pneumoniae bacterial strain R6ΔbgaA’::kan-tit2-Pc-pcsB+

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight. Overnight cultures which displayed no lysis were diluted to an OD620 of ~0.005 into BHI and grown at 37C and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520

tag: IU1533-- S. pneumoniae bacterial strain R6, partial sequence of bgaA is replaced with a kanamycin cassette, a constitutive promoter and pcsB gene sequence.

source_name: IU1979, S. pneumoniae bacterial strain R6 ΔpcsB::ermAM, ΔbgaA’::kan-tit2-Pc-pcsB+

tag: IU1979-- S. pneumoniae bacterial strain R6, partial sequence of bgaA is replaced with a kanamycin cassette, a constitutive promoter and pcsB gene sequence. In addition, pcsB sequence at the native locus is replaced with antibiotic marker ermAM sequence


title: 1_LN1

description:
LCM collected tumor from patient 1, retroperitoneal Lymph Node metastasis
Alternate patient ID 00-010


title: SpnR6_pcsB_IU1533vsIU1979_BHI_rep2


title: wild-type vs stp1 delete 3% oxygen biological replicate #2

city: Baltimore

first: Clara

last: Bien

state: MD

address: 725 N. Wolfe St Physiology rm #107

department: Cell Biology

institute: Johns Hopkins University

hyb_protocol: Processed at the Johns Hopkins SKCCC Microarray Core Facility (http://microarray.onc.jhmi.edu/).

data_processing: Features were examined and flagged using Agilent Feature Extraction software. Per spot, per chip Lowess normalizations were performed using Agilent Genespring GX 7.3 software. Statistically significant genes were identified by Significance Analysis of Microarrays (SAM) using a 90th percentile false discovery rate.

organism: Cryptococcus neoformans

source_name: wild-type H99 3% oxygen

growth_protocol: C. neoformans yeast cells were grown at the for 2 hours at 30 degrees celcius in YES medium (for recipe, see http://www-rcf.usc.edu/~forsburg/media.html#YES). Low oxygen experiments were performed in a Invivo2 400 workstation (Biotrace, Inc.)

extract_protocol:
Total RNA was extracted from yeast cells and treated with DNase I (Roche).
1.  Spin down 20 ODs (~4x108) of cells in a conical tube.  Wash cells with 20 ml of DEPC treated water.

2.  Aspirate off water, and either freeze in liquid nitrogen and store at -80C or start procedure.

3.  Lyophilize pellets overnight on dry ice

4.  Add glass beads to dry pellet and vortex ~2 min

5.  Add 1 ml of RNA STAT 60 (Tel-Test, inc.) and incubate at room temp for 5 min

6.  Transfer liquid to 1.5 ml microfuge tubes.

7.  Add 200 ul chloroform. Shake vigorously for 15 seconds and let stand at RT for 3 min.  Centrifuge homogenate for 15 min at 12,000g at 4°C.

8.  Transfer upper, clear aqueous phase to new tube and add 0.5ml of isopropanol per 1 ml of RNA STAT added to homogenate. Mix well.  Incubate at room temp for 5-10 min and then spin 10 min at 20,000g at 4°C.  White precipitate will be at bottom of tube.

9.  Remove sup and wash RNA pellet once with 75% EtOH (EtOH made with DEPC water). Centrifuge for 5 min at 10,000g at 4°C.  Wash with at least an equal volume of 75% EtOH as RNA STAT used for homogenization.

10.  Air-dry RNA pellet.  Resuspend in 50-100 ul of DEPC water.  This should give an approximate concentration of about 1-2ug/ul

11. Determine RNA concentration

tag: genotype

value: wild-type

tag: growth condition

value: 3% oxygen

source_name: stp1 delete 3% oxygen

value: stp1 mutant


title: wild-type vs sre1 delete 3% oxygen biological replicate #1

scan_protocol: Processed at the Johns Hopkins SKCCC Microarray Core Facility (http://microarray.onc.jhmi.edu/).

source_name: sre1 delete 3% oxygen

value: sre1 mutant


title: U74Av2 plus GDNF sample 2

description: No additional information


title: wild-type vs stp1 delete 3% oxygen biological replicate #1

label_protocol: Processed at the Johns Hopkins SKCCC Microarray Core Facility (http://microarray.onc.jhmi.edu/).


title: U74Av2 plus GDNF sample 3

description: No additional information


title: SpnR6_pcsB_IU1533vsIU1979_BHI_rep3


title: wild-type vs sre1 delete 3% oxygen biological replicate #2


title: 1_Liver

description:
LCM collected tumor from patient 1, liver metastasis
Alternate patient ID 00-010


title: U74Av2 minus GDNF sample 2

description: No additional information

source_name: mouse isolated ureteric bud, without GDNF, 16 hours

value: minus GDNF


title: SpnR6_pcsB_IU1533vsIU1979_BHI_rep1


title: U74Av2 minus GDNF sample 1

description: No additional information


title: wild-type 21% oxygen vs 3% oxygen biological replicate #1

source_name: wild-type H99 21% oxygen

value: 21% oxygen


title: mNSC control at polysomal rna level, biological rep4

status: Public on Sep 28 2009

city: Heidelberg

first: sachin

last: kumar

state: Baden-Württemberg

address: Molecular Neurobiology; German Cancer Research Center; INF 581;

country: Germany

institute: DKFZ

description: primary neurosphere cultures

hyb_protocol: Affymetrix standard protocol

scan_protocol: The expression profiling analysis for mouse NSC was carried out at DKFZ (Heidelberg, Germany). Hybridization and scanning of samples from mNSC were performed at the Microarray Facility of Medical Research Center (Mannheim, Germany).

data_processing: For the polysomal mRNA of mNSC 7 gene chip arrays, and for the total mRNA of mNSC 8 gene chip arrays were analyzed. Data mining was performed by using the ChipInspector analysis software (Genomatix, Munich, Germany) which identifies significant changes based on single probes. The corresponding transcripts were then assigned after a user-defined number of significant probes. For all analyses, a transcript coverage greater than three probes was chosen. After intensity normalisation of each array, significantly changed genes were determined by significance analysis of microarrays (SAM), (Tusher et al., 2001). ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided.

molecule: polyA RNA

source_name: primary mouse neural stem cells isolated from 6 week old female mice

label_protocol: Affymetrix standard protocol

extract_protocol: Polysomal RNA from mouse NSC was isolated by using the phenol-choloroform method. The quality of isolated RNA was controlled by the Lab-on-Chip-System Bioanalyser 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: gender

value: female

tag: treatment

value: control

tag: protocol

value: polysomal RNA


title: mNSC control at polysomal rna level, biological rep1

description: primary neurosphere cultures


title: wild-type 21% oxygen vs 3% oxygen biological replicate #2


title: mNSC Treated with CD95L-T4 at polysomal rna level, biological rep3

description: primary neurosphere cultures

value: mNSC


title: mNSC Treated with CD95L-T4 at polysomal rna level, biological rep2

description: primary neurosphere cultures


title: U74Av2 plus GDNF sample 1

description: No additional information


title: mNSC control at total rna level, biological rep4

description: primary neurosphere cultures

extract_protocol: Total RNA from mouse NSC was isolated by using the miRvana kit. The quality of isolated RNA was controlled by the Lab-on-Chip-System Bioanalyser 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA).

value: total RNA


title: mNSC control at total rna level, biological rep2

description: primary neurosphere cultures


title: mNSC control at total rna level, biological rep1

description: primary neurosphere cultures


title: mNSC Treated with CD95L-T4 at total rna level, biological rep3

description: primary neurosphere cultures


title: mNSC Treated with CD95L-T4 at total rna level, biological rep1

description: primary neurosphere cultures

extract_protocol: Total RNA from mouse NSC was isolated by using the mirVana miRNA Isolation Kit (Applied Biosystems Inc, USA). The quality of isolated RNA was controlled by the Lab-on-Chip-System Bioanalyser 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA).


title: 12 DO_Unpaired2

status: Public on Sep 27 2009

city: Philadelphia

first: Gordon

middle: A.

last: Barr

state: PA

address: 3615 Civic Center Blvd

department: Anesthesiology and Critical Care Medicine

institute: Children's Hospital of Philadelphia

description: 12 DO_Unpaired2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Preprocessing, background correction and normalization (RMA) were done by GCRMA (http://www.bioconductor.org) for paired and unpaired groups for each separate experimental condition. Differential expression between paired and unpaired groups for each of the three conditions (8 day old; 8 day old CORT treated; 12 day old) was determined on logged (base 2) data by Ranked Products. Correction for multiple testing was with False Detection Rate as described.

label: Biotin

organism: Rattus norvegicus

source_name: Brain: Amygdala

label_protocol:
Using Enzo RNA Transcript Labeling Kit (Enzo Cat No: 42655), ds-cDNA ,as a templet, was incubated with T7 RNA Polymerase and Biotin-labeled NTP at 37ûC for 5 hours to yield Biotin-labeled cRNA.
The Biotin-labeled cRNA was cleaned-up employing RNeasy Mini Kit (Qiagen Cat No: 74103) and after precipitation, wash, air-dry, finally redissolved in DEPC H2O. The quality of the cRNA was tested by 260/280 ratio of OD and Gel Analysis which should show the size distribution over all of the bands since the lengths of RNAs vary extremely.The quantity of the cRNA was measured by the OD reading at 260 nm.

extract_protocol:
Fifty to eighty milligram fresh frozon tissue from each sample was used in this experiment.
Total RNA was isolated using Trizol Reagent (Invitrogen, Cat. No: 15596), which contains phenol and guanidine isothiocyanate, to maintain the integrity of the RNA during sample homogenization. Addition of chloroform followed by centrifugation separated the solution into a RNA-containing aqueous phase and an organic phase. Total RNA was then recovered from the aqueous phase using isopropanol. The precipited RNA pellet, after washed with 75% Ethanol and Air-Dried, was redissolved in DEPC H2O. The quality of the RNA was tested by Gel Analysis and 260/280 ratio of OD (Optical Density) which should be between 1.6 and 1.8.The quantity of the RNA was measured by the OD reading at 260 nm (1 OD equals 40 _g / ml of RNA).

treatment_protocol:
Rat pups, 8 or 12 days old, were assigned to one of the two treatment groups, each lasting 45 min: 1) Paired odor-shock; 2) Unpaired odor-shock. Pups were trained in individual 600 ml plastic beakers and were adapted for 10 min to recover from experimental handling. During the 45 min conditioning session, pups received 11Ð30-sec presentations of a peppermint odor (CS) and a 1 sec 0.5 mA tail shock (US; Lafayette), with an intertrial interval of 4 min. Peppermint odor was delivered by a flow dilution olfactometer (2 L/min flow rate) at a concentration of 1:10 peppermint vapor. Paired odor-shock pups received 11 pairings of the 30 sec odor with shock overlapping during the last 1 sec of the odor presentation. Unpaired odor-shock pups received the shock 2 min after each odor presentation.
To verify learning during the training session, pup behavior was monitored for 20 sec before the odor and the first 20 sec during the odor presentation to construct an acquisition curve. Pups were also observed during the 1 sec shock. A behavioral rating scale was used that recorded the number of limbs moving (0= no movement of the extremities; 5= movement of all 5 extremities including the head), and specific behaviors (i.e. head up for response to odor, wall climbing and vocalization to shock).
Y-maze. The day following conditioning, pups were tested in a Y-maze. This test required pups to choose between two arms of a Plexiglas Y-maze (start box: 8.5 cm width, 10 cm length, 8 cm height; choice arms: 8.5 X 24 X 8 cm), one arm containing the 20 µl of the peppermint odor on a KimWipe placed at the end of the alley and the other containing the familiar odor of 20 ml of clean pine shavings placed at the end of the alley. Two doors separated the start box and the alleys. A pup was placed in the start box for 5 sec before the door to each alley was opened. Each pup was given 60 sec to choose an arm. A response was considered a choice when a pupÕs entire body was past the entrance to the arm.

value: Postnatal 12 days

tag: agent

tag: group

value: Unpaired


title: 12 DO_Unpaired1

description: 12 DO_Unpaired1


title: mNSC control at polysomal rna level, biological rep3

description: primary neurosphere cultures


title: 8 DO_CORT_Unpaired1

description: 8 DO_CORT_Unpaired1

value: Postnatal 8 days

value: Corticosterone


title: 12 DO_Paired1

description: 12 DO_Paired1

value: Paired


title: 8 DO_CORT_Unpaired3

description: 8 DO_CORT_Unpaired3


title: 8 DO_CORT_Paired1

description: 8 DO_CORT_Paired1


title: 12 DO_Unpaired4

description: 12 DO_Unpaired4


title: mNSC Treated with CD95L-T4 at total rna level, biological rep4

description: primary neurosphere cultures


title: 8 DO_CORT_Unpaired2

description: 8 DO_CORT_Unpaired2


title: 12 DO_Paired2

description: 12 DO_Paired2


title: mNSC Treated with CD95L-T4 at total rna level, biological rep2

description: primary neurosphere cultures


title: 8 DO_saline_Unpaired7

description: 8 DO_saline_Unpaired7

value: Saline


title: 8 DO_CORT_Paired2

description: 8 DO_CORT_Paired2


title: 8 DO_CORT_Paired3

description: 8 DO_CORT_Paired3


title: 8 DO_saline_Unpaired6

description: 8 DO_saline_Unpaired6


title: mNSC Treated with CD95L-T4 at polysomal rna level, biological rep1

description: primary neurosphere cultures


title: Akita 2

status: Public on Sep 30 2009

city: Vancouver

first: Bradley

middle: P

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

description: CNV Profile of Pedigree Akita 2

hyb_protocol: Hybridization was performed by NimbleGen using standard protocols

scan_protocol: Scanning was performed by NimbleGen using standard protocols

data_processing: Data processing was performed by NimbleGen using standard protocols

organism: Canis lupus familiaris

source_name: Pedigree Akita 2

label_protocol: Labeling was performed by NimbleGen using standard protocols

extract_protocol: DNA was extracted from Blood samples using standard molecular biology protocols

tag: pedigree

value: Akita 2

value: blood

tag: cell line

source_name: Pedigree Boxer Reference

value: Boxer


title: 12 DO_Unpaired3

description: 12 DO_Unpaired3


title: 12 DO_Paired4

description: 12 DO_Paired4


title: 8 DO_saline_Unpaired5

description: 8 DO_saline_Unpaired5


title: 8 DO_saline_Unpaired2

description: 8 DO_saline_Unpaired2


title: 8 DO_saline_Paired2

description: 8 DO_saline_Paired2


title: 8 DO_saline_Paired4

description: 8 DO_saline_Paired4


title: 8 DO_saline_Paired7

description: 8 DO_saline_Paired7


title: 8 DO_saline_Unpaired1

description: 8 DO_saline_Unpaired1


title: 12 DO_Paired3

description: 12 DO_Paired3


title: 8 DO_saline_Paired1

description: 8 DO_saline_Paired1


title: 8 DO_saline_Paired6

description: 8 DO_saline_Paired6


title: 8 DO_saline_Unpaired4

description: 8 DO_saline_Unpaired4


title: 8 DO_saline_Unpaired3

description: 8 DO_saline_Unpaired3


title: time2_d1807

status: Public on Sep 26 2009

city: Adelaide

first: Anna

last: Tsykin

state: SA

address: Frome Road

department: Hanson Institute

country: Australia

institute: SA Pathology

hyb_protocol: cDNA was labeled with Cy5 or Cy3 dyes using CyScribe post-labeling kit according to manufacturer's instructions.

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments).

data_processing: Image analysis and spot identification and intensity extraction was performed using the Spot software package (http://experimental.act.cmis.csiro.au/Spot/index.php, CSIRO, Australia). Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots.  Morphological opening background correction was applied to mean spot signal intensities.  Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA package of BioConductor).

source_name: WT 18h

label_protocol: CyScribe First-Strand cDNA Labeling Kit from Amersham Biosciences, currently GE Healthcare.

growth_protocol: The mouse CTL-EN T-cell line expressing wild-type beta-c or the beta-c Ser585Gly mutant were factor-deprived for 12h in RPMI containing 0.5% CS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were stimulated with 50 ng/mL human GM-CSF for 12 hours.

value: wild type

tag: time point

value: 18 hours

source_name: WT 0h

value: 0 hours


title: time2 + interaction2_d1809

source_name: S 18h

value: S mutation

source_name: S 0h


title: - time2 – interaction2_d1810


title: time1 + interaction1_d1805

source_name: S 12h

value: 12 hours


title: 8 DO_saline_Paired5

description: 8 DO_saline_Paired5


title: mutation + interaction2_d1811


title: - time1 – interaction1_d1806


title: - time1_d1804

source_name: WT 12h


title: - mutation – interaction2_d1812


title: - mutation – interaction1_d1802


title: - time2_d1808


title: time1_d1803


title: 1_LN2

description:
LCM collected tumor from patient 1, unspecified Lymph Node metastasis
Alternate patient ID 00-010

tag: tissue

value: Unspecified Lymph Node Metastasis

source_name: Female peripheral blood

value: Female peripheral blood


title: mutation + interaction1_d1801


title: mutation + interaction_o366


title: - mutation_d1800


title: time + interaction_o372


title: - mutation - interaction_o365


title: mutation_o368


title: - mutation_o367


title: time_o369


title: - time_o370


title: MIAPaCa2 cells expressing alpha2 cytoplasmic deletion and maintained on collagenI

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description:
Stable cell population derived from cell line originally obtained from ATCC, cultured under selection
Pancreatic ductal adenocarcinoma, human, grade 3
Gene expression data from MP2/alpha2dCYTO

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip U133_plus2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized with GCRMA algorithm, detection calls from MAS 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were passaged one-two times per week, maintained at subconfluence, and harvested at ~70% confluence

extract_protocol: Total RNA was harvested according to the manufacturer's instructions for the RNeasy kit (Qiagen)

treatment_protocol: Cells were maintained under drug-selection in standard tissue culture or on plates coated with either 25ug/ml collagenI or 10ug/ml tenascin FNIII, no other special treatment


title: Stimulation control

city: Cherry Hill,

first: Eytan

middle: R

last: Barnea

state: NJ

address: 1697 Lark Lane

institute: BioIncept LLC

description: Gene expression modulated by cell stimulation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human PBMC

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

growth_protocol: Blood was collected from a male volunteer and PBMC were separated using the Ficoll Hypaque method. Cells were cultured in media for 24 hours in four different groups in duplicate viz., Media alone, Media + 50 nM PIF, Media + 50nM PIF +CD3 (10µg/ml)+ CD28 (10µg/ml) and Media + CD3 (10µg/ml) +CD28 (10µg/ml).

extract_protocol: RNA was isolated using Rneasy kit from Qiagen following manufacturers protocol

treatment_protocol: Cells were washed with phosphate buffered saline (PBS), pelleted and lysed using RNAlater RNA Stabilization Reagent and shipped to Biocodon Sciences, Texas, USA for custom array services

value: Peripheral Blood Mononuclear Cell

value: diploid somatic cell

tag: age

value: 24 hours in culture


title: Effect of PIF on PBMC gene expression

description: Gene expression modulated by PIF following stimulation with CD3 and CD28


title: MIAPaCa2 cells expressing alpha2 and maintained on collagenI

description:
Stable cell population derived from cell line originally obtained from ATCC, cultured under selection
Pancreatic ductal adenocarcinoma, human, grade 3
Gene expression data from MP2/alpha2CI


title: MIAPaCa2 cells expressing alpha2 and maintained in standard culture

description:
Stable cell population derived from cell line originally obtained from ATCC, cultured under selection
Pancreatic ductal adenocarcinoma, human, grade 3
Gene expression data from MP2/alpha2TC


title: mNSC control at total rna level, biological rep3

description: primary neurosphere cultures

tag: strain

value: female

value: control

value: total RNA


title: MIAPaCa2 cells expressing alpha9alpha2 chimera and maintained on tenascin FNIII

description:
Stable cell population derived from cell line originally obtained from ATCC, cultured under selection
Pancreatic ductal adenocarcinoma, human, grade 3
Gene expression data from MP2/alpha9alpha2


title: human embryonic stem cell

city: Beijing

first: Yang

address: Xueyuan Road 38

country: China

institute: Peking University

description: H1 ES cell line from Thomson Lab

hyb_protocol: 1. Mix the following for each target, scaling up volumes for hybridization to multiple probe arrays. 2. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 3. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture. 4. Remove the buffer solution from the probe array cartridge and fill with appropriate volume (Table 2.2.2) of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 5. Place probe array into the Hybridization Oven, set to 45°C. Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 6. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Section 2, Chapter 3 to prepare reagents required immediately after completion of hybridization.

scan_protocol: The scanner is also controlled by Affymetrix® Microarray Suite or GCOS. The probe array is scanned after the wash protocols are complete. Make sure the laser is warmed up prior to scanning by turning it on at least 15 minutes before use if you are using the Agilent GeneArray® Scanner, or 10 minutes if you are using the Affymetrix® GeneChip® Scanner 3000. If probe array was stored at 4°C, warm to room temperature before scanning. Refer to the Microarray Suite or GCOS online help and the appropriate scanner user’s manual formore information on scanning.

data_processing: Arrays were scanned using an Affymetrix GCS3000 device and images were analyzed using the GCOS software. Then the signals were processed/normalized by dChip software (2006).

source_name: human blastocyst

label_protocol:
Transfer the needed amount of template cDNA to RNase-free microfuge tubes and add
the following reaction components in the order indicated in the table below. If more
than one IVT reaction is to be performed, a master mix can be prepared by multiplying
the reagent volumes by the number of reactions. Do not assemble the reaction on ice,
since spermidine in the 10X IVT Labeling Buffer can lead to precipitation of the
template cDNA.

extract_protocol: Total RNA was puriﬁed with an RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as per the manufacturer's instructions.

tag: cell type

value: human embryonic stem cell


title: Media Control

description: Gene expression in control untreated cells


title: 8 DO_saline_Paired3

description: 8 DO_saline_Paired3

value: Postnatal 8 days

value: Saline

value: Paired


title: PIF Control

description: Gene expression modulated by PIF


title: cerebralcortex_adult_5

status: Public on Sep 25 2009

type: SAGE

anchor: NlaIII

city: UPM Serdang

first: King

middle: Hwa

last: Ling

state: Selangor Darul Ehsan

address: Faculty of Medicine and Health Sciences

department: Department of Obstetrics and Gynaecology

country: Malaysia

institute: Universiti Putra Malaysia

description: Library was constructed by using original 3' long SAGE protocol according to Saha et al., 2002. Using the transcriptome to annotate the genome. Nature biotechnology, 20(5):508-512.

source_name: Right hemisphere of the cerebral cortex, Adult

extract_protocol: Total RNA was extracted by using RNeasy® Lipid Tissue Midi Kit (Qiagen) according to the manufacturer's protocol.

value: Female

value: 5-6 months

value: Right hemisphere of the cerebral cortex

tag: condition

value: Normal adult mouse


title: Anaerobic glucose limited chemostat with the rim101 delta mutant-1

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: For the culture of the IMK229 (rim101delta) mutant and its isogenic reference CENPK113-7D, the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (De Nicola et al., 2007). De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ, Walker GM, Pronk JT, Daran JM & Daran-Lapujade P (2007) Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 73: 7680-7692.

data_processing: GCOS CHP file targetted at 150.

organism: Saccharomyces cerevisiae

source_name: Chemostat culture

growth_protocol:
Anaerobic glucose-limited chemostat cultures were grown at a dilution rate of 0.10 h-1 on a synthetic medium supplemented with the anaerobic growth factors Tween-80 and ergosterol as described previously (Tai et al., 2005). Independent duplicate fermentations were run for the snf7Δ strain. In brief, 2-l Applikon fermenters with a working volume of 1 l were used at a temperature of 30oC and a stirrer speed of 800 rpm. Culture pH was kept at 5.0 by the automatic addition of 2 M KOH. Oxygen and carbon dioxide concentrations in the off-gas were measured with a NGA 2000 Rosemount gas analyser. Substrate and metabolite concentrations in culture supernatants and media were analysed by high performance liquid chromatography on an Aminex HPX-87H column (Biorad, Hercules, CA) with 5 mM H2SO4 as the mobile phase. Culture dry weights were determined via filtration (Postma et al., 1989).
Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM & Pronk JT (2005) Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437-447.
Postma E, Verduyn C, Scheffers WA & van Dijken JP (1989) Enzymic analysis of the crabtree effect in glucose-limited chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol 55: 468-477.

treatment_protocol: liquid N2 quenching

value: mata mal2-8c suc2 rim101::loxP-kanr-loxP


title: human gut mesentery derived mesenchymal cell

description: fibrobast-like, CD117 positive

source_name: gut mesentery


title: Anaerobic glucose limited chemostat with the snf7delta mutant-3

hyb_protocol: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004) Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.

data_processing: MAS 5.0 CHP file targetted at 150.

growth_protocol:
Anaerobic glucose-limited chemostat cultures were grown at a dilution rate of 0.10 h-1 on a synthetic medium supplemented with the anaerobic growth factors Tween-80 and ergosterol as described previously (Tai et al., 2005). Independent triplicate fermentations were run for the snf7Δ strain and the reference strain CEN.PK113-7D. In brief, 2-l Applikon fermenters with a working volume of 1 l were used at a temperature of 30oC and a stirrer speed of 800 rpm. Culture pH was kept at 5.0 by the automatic addition of 2 M KOH. Oxygen and carbon dioxide concentrations in the off-gas were measured with a NGA 2000 Rosemount gas analyser. Substrate and metabolite concentrations in culture supernatants and media were analysed by high performance liquid chromatography on an Aminex HPX-87H column (Biorad, Hercules, CA) with 5 mM H2SO4 as the mobile phase. Culture dry weights were determined via filtration (Postma et al., 1989).
Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM & Pronk JT (2005) Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437-447.
Postma E, Verduyn C, Scheffers WA & van Dijken JP (1989) Enzymic analysis of the crabtree effect in glucose-limited chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol 55: 468-477.

value: mata mal2-8c suc2 snf7::loxP-kanr-loxP


title: cerebralcortex_adult_3

source_name: Left hemisphere of the cerebral cortex, Adult

value: Left hemisphere of the cerebral cortex


title: cerebralcortex_adult_6

value: 6 months


title: Anaerobic glucose limited chemostat with the snf7delta mutant-2

scan_protocol: For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004) Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.


title: Anaerobic glucose limited chemostat with the rim101 delta mutant-2

scan_protocol: For the culture of the IMK229 (rim101delta) mutant and its isogenic reference CENPK113-7D, the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (De Nicola et al., 2007). De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ, Walker GM, Pronk JT, Daran JM & Daran-Lapujade P (2007) Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 73: 7680-7692.


title: human gut mesentery derived msenchymal cell-iPS cell

description: Induced pluripotent stem cells from gut mesentery derived mesenchymal cells by ectopic expression Oct4,Sox2 and Nanog

source_name: human mesenchymal cells from gut mesentery


title: cerebralcortex_e17_1

description: Library was constructed by using I-SAGE(tm) Kit (Invitrogen) according to the manufacturer's protocol.

source_name: Cerebral cortex, E17.5

extract_protocol: Total RNA was extracted by using RNeasy® Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's protocol.

value: Unknown

value: E17.5 (embryonic day)

value: Cerebral cortex

value: Normal mouse embryo


title: cerebralcortex_P1_1

description: Library was constructed by using original 3' short SAGE protocol as reported in Gunnersen et al., 2002. Global analysis of gene expression patterns in developing mouse neocortex using serial analysis of gene expression. Molecular and cellular neurosciences, 19(4):560-573.

source_name: Cerebral cortex, P1.5

value: P1.5 (Postnatal day)

value: Normal P1.5 mouse


title: Anaerobic glucose limited chemostat with the snf7delta mutant-1

label_protocol:
For the culture of GG3201 (snf7delta) and its isogenic reference CEN.PK113-7D the rapid broth quenching in liquid nitrogen, RNA isolation and transcriptome analysis with Affymetrix microarrays were performed as described previously (Daran-Lapujade et al., 2004)
Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH & Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279: 9125-9138.


title: cerebralcortex_e17_2

value: E17.5 (Embryonic day)


title: mutation_d1799

value: S mutation

value: 0 hours

value: wild type


title: cerebralcortex_adult_2

description: Library was constructed by using I-SAGE(tm) Long Kit (Invitrogen) according to the manufacturer's protocol.

value: Male

value: 4 months


title: cerebralcortex_Adult_1

source_name: Left hemisphere of the cerebral cortex, adult

value: Normal adult mouse


title: cerebralcortex_e15_2

description: Library was constructed by using original 3' short SAGE protocol according to Velculescu et al., 1995. Serial analysis of gene expression. Science, 270(5235):484-487.

source_name: Caudal cerebral cortex, E15.5

value: E15.5 (embryonic day)

value: Caudal part of the cerebral cortex


title: - time - interaction_o373

value: 12 hours


title: cerebralcortex_adult_4

value: Female

value: 5 months

value: Left hemisphere of the cerebral cortex


title: Deadpan_DamID_2

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description:
LM-PCR amplified gDNA (DamID - see Choksi et al., 2006).
DamID experiment to map Deadpan binding in the genome.

hyb_protocol: Hybridisation performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Scanning performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan  ChIP-Chip data extraction.

organism: Drosophila melanogaster

source_name: DamID processed gDNA from UAS-Dam-Deadpan embryos

label_protocol: Labelling performed by Nimblegen (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Embryos developed at 25oC.

extract_protocol: gDNA was extracted from embryos using the Qiagen DNeasy kit, 2.5ug of gDNA was precipitated and then digested with DpnI O/N. DpnI-digested DNA was ligated to an adaptor and then digested with DpnII. DpnII-digested DNA was PCR amplified and purified using a Qiagen PCR purification kit. For more info on specifics of DamID, please see http://research.nki.nl/vansteensellab/damid.htm or Choksi et al., 2006.

treatment_protocol: gDNA was extracted from embryos, DpnI digested and amplified using LM-PCR.

value: UAS-Dam-Deadpan

value: whole embryo

tag: developmental stage

value: embryo stage 10-11

source_name: DamID processed gDNA from UAS-Dam embryos

value: UAS-Dam


title: Snail_DamID_2

description:
LM-PCR amplified gDNA (DamID - see Choksi et al., 2006).
DamID experiment to map Snail binding in the genome.

source_name: DamID processed gDNA from UAS-Dam-Snail embryos

value: UAS-Dam-Snail


title: cerebralcortex_e15_3

source_name: Cerebral cortex, E15.5

value: Unknown

value: Cerebral cortex

value: Normal mouse embryo


title: Snail_DamID_1


title: cerebralcortex_e15_1

source_name: Rostral cerebral cortex, E15.5

extract_protocol: Total RNA was extracted by using RNeasy® Lipid Tissue Mini Kit (QIAGEN) according to the manufacturer's protocol.

value: E15.5 (embryonic days)

value: Rostral part of the cerebral cortex


title: TM194

status: Public on Sep 24 2009

city: São Paulo

first: Renato

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

hyb_protocol: Pre-hybridization Protocol - Solution: 5xSSC; 0,2% SDS; 1% BSA; 5xDenhardt's / Temperature: 42C / Time: 6-24h Hybridization - Solution: 5 X SSC; 0,1% SDS; 2 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, deionized formamide 40% / Temperature:42oC / Time:20-24 H / Touch Down: 70, 55, 50, 42 Washing - Round 1 - Solution: SSC 2x / Temperature:42 / Time:10 min. / Washing Number: 1 Washing - Round 2 - Solution: SSC 0,1x; SDS 0,1% / Temperature:42 / Time:10 min. / Washing Number: 2 Washing - Round 3 - Solution: SSC 0,1x / Temperature:42 / Time:10 min. / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing:
Lowess normalization
Raw data files are available at http://www.lbhc.hcancer.org.br/arraydata/Sarcomas/samples/

label: Alexa 555

label_protocol: Linearly amplified RNA samples (T7-based protocol) derived from 102 tumor tissues, and a pool of RNAs obtained from 15 distinct human cell lines as reference, were used. cDNA was synthesized in the presence of aminoallyl-dUTP (Sigma-Aldrich) and labeled using Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen).

extract_protocol: Pico Pure RNA Isolation Kit

tag: MPNST

label: Alexa 647

source_name: Reference pool

extract_protocol: Trizol

tag: Pool of RNA from 15 distinct human cell lines


title: TM198 ref pool 15


title: TM200 ref pool 15


title: TM198


title: TM160


title: TM200


title: TM179


title: SS36

tag: Synovial sarcoma


title: SS183 ref pool 15


title: TM160 ref pool 15


title: SS36 ref pool 15


title: Pros_DamID_2

description:
LM-PCR amplified gDNA (DamID - see Choksi et al., 2006).
DamID experiment to map Prospero binding in the genome.

source_name: DamID processed gDNA from UAS-Dam-Pros embryos

tag: genotype

value: UAS-Dam-Prospero


title: SS199 ref pool 15


title: TM194 ref pool 15


title: TM179 ref pool 15


title: Deadpan_DamID_1


title: Asense_DamID_1

description:
LM-PCR amplified gDNA (DamID - see Choksi et al., 2006).
DamID experiment to map Asense binding in the genome.

source_name: DamID processed gDNA from UAS-Dam-Asense embryos

value: UAS-Dam-Asense


title: SS192 ref pool 15


title: Asense_DamID_2


title: MIAPaCa2 cells  maintained under drug selection

description:
Stable cell population derived from cell line originally obtained from ATCC, cultured under selection
Pancreatic ductal adenocarcinoma, human, grade 3
Gene expression data from MP2/mock


title: SS192


title: Pros_DamID_3


title: SS199


title: SS183


title: Pros_DamID_1


title: SS162


title: SS177


title: Pros_DamID_4


title: SS157


title: SS148


title: SS176


title: SS154 ref pool 15


title: SS154


title: SS176 ref pool 15


title: SS177 ref pool 15


title: SS148 ref pool 15


title: SS145 ref pool 15


title: SS147 ref pool 15


title: SS152 ref pool 15


title: SS153 ref pool 15


title: SS153


title: SS149 ref pool 15


title: SS149


title: SS147


title: SS144


title: SS145


title: SS144 ref pool 15


title: SS143 ref pool 15


title: SS157 ref pool 15


title: SS152


title: SS162 ref pool 15


title: SS140


title: SP186

tag: Pleomorphic sarcoma


title: SP191


title: SS143


title: SP186 ref pool 15


title: SS140 ref pool 15


title: SS142


title: SP188


title: SP191 ref pool 15


title: SP188 ref pool 15


title: SP174 ref pool 15


title: SP138


title: SP161


title: SP135 ref pool 15


title: SP190 ref pool 15


title: SP175 ref pool 15


title: SS142 ref pool 15


title: SP175


title: SP174


title: SP190


title: SP161 ref pool 15


title: SP135


title: SP138 ref pool 15


title: SP134 ref pool 15


title: SP132 ref pool 15


title: SP132


title: SP126


title: SP131 ref pool 15


title: SP127


title: SP124 ref pool 15


title: SP125


title: SP126 ref pool 15


title: SP124


title: SH158 ref pool 15

tag: Schwanoma


title: SP127 ref pool 15


title: SP122 ref pool 15


title: SH158


title: SH155


title: SP125 ref pool 15


title: SP131


title: SA178

tag: Alveolar soft part sarcoma


title: NF98 ref pool 15

tag: Neurofibroma


title: SP134


title: SA113 ref pool 15


title: SH155 ref pool 15


title: SP122


title: NF98


title: SA113


title: NF96


title: SA178 ref pool 15


title: NF96 ref pool 15


title: NF170 ref pool 15


title: LPS89 ref pool 15

tag: Liposarcoma


title: NF170


title: LPS81


title: LPS75 ref pool 15

tag: Leiomyosarcoma


title: LPS68 ref pool 15


title: LPS137


title: LM46

tag: Leiomyoma


title: LPS137 ref pool 15


title: LPS68


title: LM45 ref pool 15


title: LM45


title: LES65 ref pool 15


title: LPS75


title: LES64


title: LES65


title: LPS81 ref pool 15


title: LPS89


title: LES63 ref pool 15


title: LES64 ref pool 15


title: LM46 ref pool 15


title: LES62


title: LES63


title: LES61


title: LES58


title: LES60 ref pool 15


title: LES60


title: LES61 ref pool 15


title: LES62 ref pool 15


title: LES57


title: LES56


title: LES52 ref pool 15


title: LES53 ref pool 15


title: LES56 ref pool 15


title: LES59


title: LES59 ref pool 15


title: LES57 ref pool 15


title: LES52


title: LES53


title: LES51


title: LES58 ref pool 15


title: LES182


title: LES49


title: LES48


title: LES173


title: LES182 ref pool 15


title: LES48 ref pool 15


title: LES49 ref pool 15


title: LES172 ref pool 15


title: LES51 ref pool 15


title: LES136 ref pool 15


title: LES172


title: GI43 ref pool 15

tag: GIST


title: GI169 ref pool 15


title: GI43


title: GI159


title: LES173 ref pool 15


title: GI159 ref pool 15


title: FS40 ref pool 15

tag: Fibrosarcoma


title: FS37 ref pool 15


title: FS40


title: FS39 ref pool 15


title: GI169


title: FS35 ref pool 15


title: FS39


title: FS164 ref pool 15


title: T-ALL JAK1 WT 6

city: Brussels

first: Laurent

last: Knoops

address: Av Hippocrate, 74

country: Belgium

institute: de Duve Institute

description: Gene expression data from blasts of JAK1 Wild-Type T-ALL

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS300 scanner

data_processing: The data were analyzed with Genechip expression console using the MAS5.0 Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: T-ALL JAK1 WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Thawed or freshly isolated cells (>90% blasts) were homogenized, and total RNA was extracted either using the Trizol reagent (Life Technologies) and further purified with the SV total isolation system (Promega) or using the RNeasy mini kit (Qiagen) according to manufacturer's protocol. RNA quality was checked by agarose gel electrophoresis and spectrophotometry.

value: T-ALL cell

tag: mutation

value: JAK1 WT


title: T-ALL JAK1 WT 7

tag: cell type


title: T-ALL JAK1 WT 2


title: T-ALL JAK1 R724H 2

description: Gene expression data from blasts of JAK1 mutated T-ALL

source_name: T-ALL JAK1 mutated

value: JAK1 mutated


title: FS164


title: FM97

tag: Desmoid-type fibromatosis


title: T-ALL JAK1 WT 4


title: LES136


title: T-ALL JAK1 WT 5


title: T-ALL JAK1 WT 8


title: FS41


title: T-ALL JAK1 R724H 1


title: T-ALL JAK1 WT 3


title: FM33 ref pool 15


title: FS35


title: FS37


title: FM32 ref pool 15


title: Dosed with CDC8 tobacco product, biological rep2

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HGU133 2.0+ Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Dosed with CDC8 tobacco product

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: Primary human bronchial/tracheal epithelial (NHBE) cells were grown in tissue culture.

extract_protocol: Qiagen RNeasy used for total RNA extraction and was performed according to manufacture's instructions.

treatment_protocol: NHBE cells were treated for 18 hr with cigarette smoke condensates (CSCs) prepared from 5 commercial and 4 research cigarettes, at doses of ~ 4 μg/ml nicotine.

value: Primary human bronchial/tracheal epithelial cells


title: FM97 ref pool 15


title: T-ALL JAK1 S512L


title: Dosed with CDC10 tobacco product, biological rep2

source_name: Dosed with CDC10 tobacco product


title: Dosed with CDC9 tobacco product, biological rep1

source_name: Dosed with CDC9 tobacco product


title: Dosed with CDC7 tobacco product, biological rep1

source_name: Dosed with CDC7 tobacco product


title: Dosed with CDC9 tobacco product, biological rep2


title: Dosed with CDC10 tobacco product, biological rep1


title: FM38


title: FM31 ref pool 15


title: Dosed with CDC6 tobacco product, biological rep1

source_name: Dosed with CDC6 tobacco product


title: Dosed with CDC6 tobacco product, biological rep2


title: FM30 ref pool 15


title: FM29


title: FM33


title: FM28


title: FM32


title: Dosed with CDC4 tobacco product, biological rep1

source_name: Dosed with CDC4 tobacco product


title: Dosed with CDC5 tobacco product, biological rep2

source_name: Dosed with CDC5 tobacco product


title: FM31


title: FM27


title: Dosed with CDC5 tobacco product, biological rep1


title: FM27 ref pool 15


title: 061006_Undosed control, biological rep2

source_name: Undosed control


title: FM38 ref pool 15


title: Dosed with CDC1 tobacco product, biological rep1

source_name: Dosed with CDC1 tobacco product


title: T-ALL JAK1 WT 1


title: FM26 ref pool 15


title: FS41 ref pool 15


title: FM28 ref pool 15


title: Dosed with CDC8 tobacco product, biological rep1


title: Dosed with CDC4 tobacco product, biological rep2


title: FM34


title: Dosed with CDC1 tobacco product, biological rep2


title: FM25


title: FM29 ref pool 15


title: GSY10A

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48035.gif
Strain Name: GSY10A

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1400, 7760; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 145052; Parameter Laser Power = 1.39; Parameter Scan Time = 10:56:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.01; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 509955; Parameter Laser Power = 2.14; Parameter Scan Time = 10:56:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.01; Performer: Barbara,,Dunn

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: S288C sonicated genomic DNA 4ug

label_protocol: not provided

extract_protocol: not provided

tag: S288C sonicated genomic DNA 4ug

source_name: GSY10 sonicated DNA 4 ug

tag: GSY10 sonicated DNA 4 ug


title: FM26

tag: Pool of RNA from 15 distinct human cell lines


title: 061006_Undosed control, biological rep1


title: FM195 ref pool 15


title: FM193


title: FM196 ref pool 15


title: Dosed with CDC2 tobacco product, biological rep2

source_name: Dosed with CDC2 tobacco product


title: FM197 ref pool 15

source_name: Reference pool


title: FM168


title: Dosed with CDC3 tobacco product, biological rep2

source_name: Dosed with CDC3 tobacco product


title: FM197


title: FM196


title: FM25 ref pool 15


title: FM166 ref pool 15


title: GSY3A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48033.gif
Strain Name: GSY3A

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1520, 8360; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 145041; Parameter Laser Power = 1.39; Parameter Scan Time = 10:45:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.94; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 509944; Parameter Laser Power = 2.15; Parameter Scan Time = 10:45:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.94; Performer: Barbara,,Dunn

source_name: GSY3 sonicated DNA 4 ug

tag: GSY3 sonicated DNA 4 ug


title: FM34 ref pool 15


title: FM166


title: Dosed with CDC7 tobacco product, biological rep2


title: Dosed with CDC3 tobacco product, biological rep1


title: FM195


title: FM30


title: FM165 ref pool 15


title: FM168 ref pool 15


title: Sc-ale vs. Sc DNA

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2340.gif
Strain Name: Sc-ale

scan_protocol: GenePix

source_name: DBY7286 genomic DNA

tag: DBY7286 genomic DNA

source_name: ale (S. cerevisiae) genomic DNA

tag: ale (S. cerevisiae) genomic DNA


title: Multiple Sclerosis 19

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: Hybridization for 16 hours at 42°C has been carried out overnight according to manufacturs instructions. Then, the biochip was washed automatically and a program for signal enhancement was processed with the Geniom Real Time Analyzer

scan_protocol: The resulting detection pictures were evaluated using the Geniom Wizard Software.

data_processing: For each array, the median signal intensity was extracted from the raw data file such that for each miRNA seven intensity values have been calculated corresponding to each replicate copy of miRBase on the array. Following background subtraction the seven replicate intensity values of each miRNA were summarized by their median value. To normalize the data across different arrays, quantile normalizatio  was applied.

source_name: blood of MS patient

label_protocol: Sample labeling with biotin has been carried out either by using the miRVANA™ miRNA Labeling Kit (Applied Biosystems Inc, Foster City, California USA) or by microfluidic-based enzymatic on-chip labeling of miRNAs (MPEA).

extract_protocol: It is a known fact that that gene expression in peripheral blood changes post-phlebotomically within a few minutes via transcript induction and degradation (Rainen, Oelmueller et al. 2002; Kruhoffer, Dyrskjot et al. 2007).  To counter this problem, the PAXgeneTM blood sample tubes have been developed. These tubes contain a solution that lyses blood cells and at the same time stabilizes the RNA. By that, the ex vivo changes of expression profiles are avoided. The RNA can be stabilized by PAXgene™ system can stabilize RNA for three days at 18-25°C, for five days at 2-8°C, and over a longer period (at least 6 months) at -20°C to -70°C. The PAXgene™ tubes contain 6,9 ml of RNA stabilizing solution and are suitable for the sampling of 2,5 ml blood per tube. Two tubes at 2,5 ml blood were sampled from each patient and healthy blood donor, which equals 5 ml per person. After 8-10fold reversal of the tubes, they were stored over night at 4°C. For a longer storage over several days tubes were frozen at -20°C. Before RNA isolation the blood was incubated for at least 2 hours at room temperature (RT).  2 Isolation of total RNA including miRNA    The contents of both blood sampling tubes of each patient and healthy donor was pooled and centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL  were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step  with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

tag: class label

value: MS


title: Multiple Sclerosis 20


title: FM193 ref pool 15


title: FM165


title: cv. Capelle Desprez 5 DAP  drought stressed seed Replicate 2

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

description: 5 DAP stressed and control seed

hyb_protocol: The hybridization and washing was performed as described in Agilent protocol.

scan_protocol: Scanned on Agilent scanner G2505B

data_processing: Image analysis and normalization was done by Agilent Feature Extraction 10.1 software using default GE2-v5_10_Apr08 protocol (Linear and Lowess)

organism: Triticum aestivum

source_name: Total RNA from cv. Capelle Desprez 5 DAP  drought stressed seed , labelled by Cy3

label_protocol: 1 µg total RNA was used to synthesize Cy3  labeled aRNA using AMBION (Austin, USA) Amino Allyl MessageAmpTM II aRNA Amplification Kit

extract_protocol: RNA extracted using RNAzol (SIGMA)

tag: genotype

value: cv. Capelle Desprez

tag: day after pollination

value: 5 DAP

tag: type of stress

value: drought

source_name: Total RNA from Total RNA from cv. Capelle Desprez 5 DAP  control seed  labelled by Cy5, labelled by Cy5

label_protocol: 1 µg total RNA was used to synthesize Cy5  labeled aRNA using AMBION (Austin, USA) Amino Allyl MessageAmpTM II aRNA Amplification Kit

value: control


title: Dosed with CDC2 tobacco product, biological rep1


title: Multiple Sclerosis 16


title: cv. Plainsman V 5 DAP  heat & drought stressed seed Replicate 1

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Plainsman V 5 DAP  heat&drought stressed seed , labelled by Cy5

value: cv. Plainsman V

value: heat&drought

source_name: Total RNA from Total RNA from cv. Plainsman V 5 DAP  control seed  labelled by Cy3, labelled by Cy3


title: Multiple Sclerosis 17


title: Multiple Sclerosis 14


title: Multiple Sclerosis 15


title: GSY2A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48031.gif
Strain Name: GSY2A

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1400, 7960; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 145030; Parameter Laser Power = 1.39; Parameter Scan Time = 10:34:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.89; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 509933; Parameter Laser Power = 2.16; Parameter Scan Time = 10:34:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.89; Performer: Barbara,,Dunn

source_name: GSY2 sonicated DNA 4 ug

tag: GSY2 sonicated DNA 4 ug


title: cv. Capelle Desprez 5 DAP  drought stressed seed Replicate 1

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Capelle Desprez 5 DAP  drought stressed seed , labelled by Cy5

source_name: Total RNA from Total RNA from cv. Capelle Desprez 5 DAP  control seed  labelled by Cy3, labelled by Cy3


title: cv. Capelle Desprez 5 DAP  heat & drought stressed seed Replicate 2

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Capelle Desprez 5 DAP  heat&drought stressed seed , labelled by Cy3


title: cv. Capelle Desprez 5 DAP  heat & drought stressed seed Replicate 1

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Capelle Desprez 5 DAP  heat&drought stressed seed , labelled by Cy5


title: cv. Plainsman V 5 DAP  drought stressed seed Replicate 1

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Plainsman V 5 DAP  drought stressed seed , labelled by Cy5


title: Multiple Sclerosis 11


title: S288cVsS288cGenomicDNA-a

description:
Simple annotation: control, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33093.gif
Strain Name: S288C

scan_protocol: Scanner Model: GenePix 4000A


title: Multiple Sclerosis 18


title: cv. Plainsman V 5 DAP  drought stressed seed Replicate 2

description: 5 DAP stressed and control seed

source_name: Total RNA from cv. Plainsman V 5 DAP  drought stressed seed , labelled by Cy3

source_name: Total RNA from Total RNA from cv. Plainsman V 5 DAP  control seed  labelled by Cy5, labelled by Cy5


title: Multiple Sclerosis 10


title: Multiple Sclerosis 4


title: Multiple Sclerosis 9


title: Multiple Sclerosis 13


title: Multiple Sclerosis 8


title: Multiple Sclerosis 2


title: Multiple Sclerosis 6


title: Multiple Sclerosis 5


title: Multiple Sclerosis 3


title: Multiple Sclerosis 12


title: Multiple Sclerosis 7


title: Control 18

source_name: blood of control


title: Control 21


title: Multiple Sclerosis 1


title: Control 20


title: Control 19


title: Control 16


title: Control 17


title: Control 13


title: Control 14


title: Control 15


title: Control 11


title: Control 8


title: Control 10


title: Control 6


title: Control 9


title: Control 5


title: Control 7


title: Control 12


title: Control 4


title: Control 2


title: Control 3


title: Control 1


title: Normal Control 19


title: Normal Control 13


title: Normal Control 16


title: Normal Control 15


title: Normal Control 17


title: Normal Control 18


title: Normal Control 9


title: Normal Control 11


title: Normal Control 7


title: Normal Control 5


title: Normal Control 10


title: Normal Control 12


title: Normal Control 2


title: Normal Control 3


title: Normal Control 8


title: Normal Control 4


title: Normal Control 6


title: Tumor Sample 17

source_name: blood of tumor patient

value: lung tumor


title: Normal Control 14


title: Normal Control 1


title: Tumor Sample 16


title: SA1-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69981.gif
Strain Name: SA1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1080, 5400; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 290389; Parameter Laser Power = 1.40; Parameter Scan Time = 15:28:54; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.84; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 730; Parameter Scan Power = 100; Parameter Laser on time = 655299; Parameter Laser Power = 2.06; Parameter Scan Time = 15:28:54; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.84; Performer: Boris,,Stambuk

source_name: S288c  1 ug genomic DNA sonicated

tag: S288c  1 ug genomic DNA sonicated

source_name: SA-1 1 ug genomic DNA HaeIII cut

tag: SA-1 1 ug genomic DNA HaeIII cut


title: GSY11B

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48038.gif
Strain Name: GSY11B

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1480, 26660; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 145068; Parameter Laser Power = 1.39; Parameter Scan Time = 11:16:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.12; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 509971; Parameter Laser Power = 2.16; Parameter Scan Time = 11:16:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.12; Performer: Barbara,,Dunn

source_name: S288C sonicated genomic DNA 4ug

source_name: GSY11 sonicated DNA 4 ug

tag: GSY11 sonicated DNA 4 ug


title: PCF stationary 2

city: Seattle

first: Dhileep

last: Sivam

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

description: Procyclic form cells were grown in SDM-79 to a density of ~7.5 X107 cells/ml.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data pair file (.txt) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Trypanosoma brucei brucei TREU927

source_name: T. brucei strain TREU927/4 PCF stationary

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: In vivo cells were grown in irradiated Wistar rats.  In vitro cultured bloodform cells were grown in HMI-9 supplemented with 10% FCS. Procyclic cells were grown in SDM-79 with 15% FCS.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA).  RNA quality was determined by analysis with an Agilent 2100 bioanalyzer

tag: life cycle stage

value: stationary procyclic form cells


title: Tumor Sample 13


title: Tumor Sample 14


title: PCF stationary 3


title: Tumor Sample 15


title: PCF log 3

description: Procyclic form cells were grown in SDM-79 to ~5X106 cells/ml split 1:1 and grown an additional 24 hours before harvest at a density of 6-7x106 cells/ml

source_name: T. brucei strain TREU927/4 PCF log

value: log-phase procyclic form cells


title: Tumor Sample 11


title: Tumor Sample 12


title: PCF log 2


title: PCF stationary 1


title: Tumor Sample 10


title: SA1-2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70239.gif
Strain Name: SA1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1440, 6440; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 314311; Parameter Laser Power = 1.43; Parameter Scan Time = 14:35:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.58; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 679221; Parameter Laser Power = 2.14; Parameter Scan Time = 14:35:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.58; Performer: Boris,,Stambuk

source_name: SA-2 1 ug genomic DNA HaeIII cut

tag: SA-2 1 ug genomic DNA HaeIII cut


title: S288C self 2

description:
Simple annotation: control, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69659.gif
Strain Name: S288C

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 640, 4280; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 310524; Parameter Laser Power = 1.30; Parameter Scan Time = 14:54:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.75; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 675434; Parameter Laser Power = 2.09; Parameter Scan Time = 14:54:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.75; Performer: Barbara,,Dunn

source_name: S288C genomic DNA 1lg sonicated

tag: S288C genomic DNA 1lg sonicated


title: GSY155

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65000.gif
Strain Name: GSY155

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 6280; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 680; Parameter Laser on time = 243969; Parameter Laser Power = 1.42; Parameter Scan Time = 15:25:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.71; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 740; Parameter Scan Power = 100; Parameter Laser on time = 608929; Parameter Laser Power = 2.05; Parameter Scan Time = 15:25:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.71; Performer: Barbara,,Dunn

source_name: S288C genomic DNA 1 ug sonicated

tag: S288C genomic DNA 1 ug sonicated

source_name: GSY155 genomic DNA 1 ug HaeIII-cut

tag: GSY155 genomic DNA 1 ug HaeIII-cut


title: GSY154

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65003.gif
Strain Name: GSY154

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 6280; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 670; Parameter Laser on time = 244000; Parameter Laser Power = 1.42; Parameter Scan Time = 15:57:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.92; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 730; Parameter Scan Power = 100; Parameter Laser on time = 608960; Parameter Laser Power = 2.03; Parameter Scan Time = 15:57:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.92; Performer: Barbara,,Dunn

source_name: GSY154 genomic DNA 1 ug HaeIII-cut

tag: GSY154 genomic DNA 1 ug HaeIII-cut


title: GSY149

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64992.gif
Strain Name: GSY149

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 6040; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 690; Parameter Laser on time = 243959; Parameter Laser Power = 1.42; Parameter Scan Time = 15:15:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.70; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 243959; Parameter Laser Power = 1.42; Parameter Scan Time = 15:15:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.70; Performer: Barbara,,Dunn

source_name: GSY149 genomic DNA 1 ug HaeIII-cut

tag: GSY149 genomic DNA 1 ug HaeIII-cut


title: Tumor Sample 9


title: S288cVsS288cGenomicDNA-b

description:
Simple annotation: control, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33091.gif
Strain Name: S288C


title: CAT1_2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69974.gif
Strain Name: CAT1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1120, 6960; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 285165; Parameter Laser Power = 1.39; Parameter Scan Time = 17:52:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.42; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 650075; Parameter Laser Power = 2.20; Parameter Scan Time = 17:52:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.42; Performer: Boris,,Stambuk

source_name: CAT-2 1 ug genomic DNA HaeIII cut

tag: CAT-2 1 ug genomic DNA HaeIII cut


title: VR1-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69979.gif
Strain Name: VR1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 5800; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 290481; Parameter Laser Power = 1.39; Parameter Scan Time = 17:00:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.07; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 660; Parameter Scan Power = 100; Parameter Laser on time = 655391; Parameter Laser Power = 2.11; Parameter Scan Time = 17:00:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.07; Performer: Boris,,Stambuk

source_name: VR1-1 1 ug genomic DNA HaeIII cut

tag: VR1-1 1 ug genomic DNA HaeIII cut


title: Tumor Sample 7

tag: class label


title: Tumor Sample 8


title: BG1-2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69972.gif
Strain Name: BG1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1160, 6600; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 630; Parameter Laser on time = 285143; Parameter Laser Power = 1.39; Parameter Scan Time = 17:31:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.51; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 650052; Parameter Laser Power = 2.22; Parameter Scan Time = 17:31:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.51; Performer: Boris,,Stambuk

source_name: BG-2 1 ug genomic DNA HaeIII cut

tag: BG-2 1 ug genomic DNA HaeIII cut


title: Tumor Sample 6


title: PCF log 1


title: In vitro BF #2 7-30-08

description: Cells were grown to ~8X105 cells/ml in HMI-9 before harvest

source_name: T. brucei strain TREU927/4 cBF

value: In vitro cultured bloodform


title: In vitro BF #2 9-8-08


title: In vitro BF #3 2-28-08


title: Slender 301 G

description: Cells were isolated from irradiated Wistar rats.  Analysis of procyclin expression four hours after cells were induced to differentiate with 6 mM cis aconitate indicates that less than 1% of the cells were stumpy

source_name: T. brucei strain TREU927/4slender

value: In vivo slender form


title: Tumor Sample 5

source_name: blood of tumor patient


title: Tumor Sample 3


title: GSY150

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64995.gif
Strain Name: GSY150

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1120, 6320; Software: type: feature extraction; Performer: Barbara,,Dunn Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 243930; Parameter Laser Power = 1.42; Parameter Scan Time = 14:48:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.56; Performer: Barbara,,Dunn Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 608890; Parameter Laser Power = 2.01; Parameter Scan Time = 14:48:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 38.56; Performer: Barbara,,Dunn

source_name: GSY150 genomic DNA 1 ug HaeIII-cut

tag: GSY150 genomic DNA 1 ug HaeIII-cut


title: Slender 301 B

description: Cells were isolated from irradiated Wistar rats.  Analysis or procyclin expression four hours after cells were induced to differentiate with 6mM cis aconitate indicates that less than 1% of the cells were stumpy


title: Tumor Sample 4


title: CAT1_1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69973.gif
Strain Name: CAT1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1120, 7040; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 285175; Parameter Laser Power = 1.39; Parameter Scan Time = 18:02:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.41; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 650085; Parameter Laser Power = 2.19; Parameter Scan Time = 18:02:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 40.41; Performer: Boris,,Stambuk

source_name: S288c  1 ug genomic DNA sonicated

source_name: CAT-1 1 ug genomic DNA HaeIII cut

tag: CAT-1 1 ug genomic DNA HaeIII cut


title: PE2_2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69977.gif
Strain Name: PE2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.4; Parameter Image Origin = 1040, 5800; Software: type: feature extraction; Performer: Boris,,Stambuk Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 290491; Parameter Laser Power = 1.39; Parameter Scan Time = 17:09:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.08; Performer: Boris,,Stambuk Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.3; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 655401; Parameter Laser Power = 2.11; Parameter Scan Time = 17:09:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000A [47263]; Parameter Focus Position = 0; Parameter Scan Temperature = 39.08; Performer: Boris,,Stambuk

source_name: PE2-2 1 ug genomic DNA HaeIII cut

tag: PE2-2 1 ug genomic DNA HaeIII cut


title: Slender 301 P 1