title: cirrhosis, biological rep 33

description: Gene expression using RMA method


title: cirrhosis, biological rep 32

status: Public on Jan 08 2009

type: RNA

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

country: USA

institute: Ohio State University

description: Gene expression using RMA method

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.

data_processing: The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver tissue with cirrhosis

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: Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Liver tissue samples were collected in liquid nitrogen or RNA later solution (Ambion, Inc, Austin, TX), and stored at -80°C until use.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).

treatment_protocol: Five mm frozen section slides were made and stained with H&E for Pathologist evaluation to determine tumor content. After Pathologist evaluation, normal/necrotic tissue was macrodissected. Twenty 20 mm sections were performed in a 15 ml tube with 10 ml of Trizol.

tag: Tissue

value: cirrhosis


title: cirrhosisHCC, match HCC rep 42

description: Gene expression using RMA method

source_name: liver tissue with cirrhosisHCC

value: cirrhosisHCC


title: cirrhosis, biological rep 29

description: Gene expression using RMA method


title: cirrhosis, biological rep 23

description: Gene expression using RMA method


title: cirrhosis, biological rep 22

description: Gene expression using RMA method


title: cirrhosis, biological rep 20

description: Gene expression using RMA method


title: cirrhosis, biological rep 21

description: Gene expression using RMA method


title: cirrhosis, biological rep 19

description: Gene expression using RMA method


title: HCC, biological rep 37

description: Gene expression using RMA method

source_name: liver tissue with HCC

value: HCC


title: HCC, biological rep 39

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 40

description: Gene expression using RMA method


title: cirrhosis, biological rep 16

description: Gene expression using RMA method


title: HCC, biological rep 38

description: Gene expression using RMA method


title: cirrhosis, biological rep 17

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 38

description: Gene expression using RMA method


title: HCC, biological rep 36

description: Gene expression using RMA method


title: cirrhosis, biological rep 13

description: Gene expression using RMA method


title: HCC, biological rep 34

description: Gene expression using RMA method


title: cirrhosis, biological rep 14

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 3

description: Gene expression using RMA method


title: HCC, biological rep 33

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 37

description: Gene expression using RMA method


title: cirrhosis, biological rep 18

description: Gene expression using RMA method


title: cirrhosis, biological rep 15

description: Gene expression using RMA method


title: cirrhosis, biological rep 12

description: Gene expression using RMA method


title: HCC, biological rep 40

description: Gene expression using RMA method


title: cirrhosis, biological rep 11

description: Gene expression using RMA method


title: HCC, biological rep 35

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 36

description: Gene expression using RMA method


title: HCC, biological rep 32

description: Gene expression using RMA method


title: cirrhosis, biological rep 10

description: Gene expression using RMA method


title: cirrhosis, biological rep 9

description: Gene expression using RMA method


title: cirrhosisHCC, biological rep 1

description: Gene expression using RMA method


title: cirrhosis, biological rep 7

description: Gene expression using RMA method


title: HCC, biological rep 30

description: Gene expression using RMA method


title: HCC, biological rep 29

description: Gene expression using RMA method


title: cirrhosis, biological rep 6

description: Gene expression using RMA method


title: HCC, biological rep 27

description: Gene expression using RMA method


title: cirrhosis, biological rep 3

description: Gene expression using RMA method


title: HCC, biological rep 25

description: Gene expression using RMA method


title: cirrhosis, biological rep 5

description: Gene expression using RMA method


title: cirrhosis, biological rep 4

description: Gene expression using RMA method


title: cirrhosis, biological rep 8

description: Gene expression using RMA method


title: HCC, biological rep 21

description: Gene expression using RMA method


title: HCC, biological rep 26

description: Gene expression using RMA method


title: cirrhosis, biological rep 2

description: Gene expression using RMA method


title: HCC, biological rep 20

description: Gene expression using RMA method


title: HCC, biological rep 24

description: Gene expression using RMA method


title: HCC, biological rep 23

description: Gene expression using RMA method


title: HCC, biological rep 19

description: Gene expression using RMA method


title: HCC, biological rep 28

description: Gene expression using RMA method


title: HCC, biological rep 16

description: Gene expression using RMA method


title: cirrhosis, biological rep 1

description: Gene expression using RMA method


title: HCC, biological rep 17

description: Gene expression using RMA method


title: HCC, biological rep 15

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 16

description: Gene expression using RMA method


title: HCC, biological rep 22

description: Gene expression using RMA method


title: HCC, biological rep 18

description: Gene expression using RMA method


title: cirrhosis, biological rep 24

description: Gene expression using RMA method


title: HCC, biological rep 13

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 1

description: Gene expression using RMA method


title: cirrhosisHCC, match HCC rep 12

description: Gene expression using RMA method


title: cirrhosis, biological rep 41

description: Gene expression using RMA method


title: HCC, biological rep 2

description: Gene expression using RMA method


title: HCC, biological rep 3

description: Gene expression using RMA method


title: HCC, biological rep 4

description: Gene expression using RMA method


title: SARST-V6_Drinking Water_Joinville

type: genomic

city: paris

first: Jean Baptiste

last: Poitelon

address: 9 rue Schoelcher

country: France

institute: EaudeParis

description: Characterization of the Bacterial Diversity of Drinking Water From Three Parisian Treatment Plants Using Genomic Approaches

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: 95% similarity threshold

label: not applicable

molecule: genomic DNA

organism: Bacteria

source_name: Joinville-le-Pont Drinking Water Treatment Plant

label_protocol: not applicable

extract_protocol: SARST-V6 library construction: we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis.

tag: Drinking Water From Treatment Plant


title: HCC, biological rep 10

description: Gene expression using RMA method


title: SARST-V6_Drinking Water_Orly

source_name: Orly Drinking Water Treatment Plant


title: HCC, biological rep 9

description: Gene expression using RMA method


title: HCC, biological rep 5

description: Gene expression using RMA method


title: HCC, biological rep 6

description: Gene expression using RMA method


title: SARST-V6_Drinking Water_Ivry

source_name: Ivry-sur-Seine Drinking Water Treatment Plant


title: cirrhosisHCC, match HCC rep 13

description: Gene expression using RMA method


title: HCC, biological rep 14

description: Gene expression using RMA method


title: HCC, biological rep 1

description: Gene expression using RMA method


title: HCC, biological rep 8

description: Gene expression using RMA method


title: cirrhosisHCC, biological rep 3

description: Gene expression using RMA method


title: HCC, biological rep 11

description: Gene expression using RMA method


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs axenic amastigote_replicate 2

city: Quebec

first: Barbara

last: Papadopoulou

state: Quebec

address: 2705 boulevard Laurier

country: Canada

institute: Centre de Recherche du CHUL

description: Biological replicate 2 of 4.

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed . For hybridization, labelled cDNA probes were dried and resuspended in 2.5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA, and then mixed. Mixed probes were applied on the array under a lifterslip. Hybridization was performed for 16h.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features.

data_processing:
Raw data from GenePix were imported in R 2.2.1 for normalization, and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done by using the ‘quantiles of A’ method for each array (Yang, 2003).
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed.
Data table VALUE column represents normalized log2 (amastigote/promastigote) ratios.

organism: Leishmania infantum

label_protocol: 10 µg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (GEHealthcare) and the SuperScript III RNase H- Reverse Transcriptase (Invitrogen). Probes were thereafter coupled to the fluorescent dye Alexa Fluor555 or Alexa Fluor647 (Invitrogen) following manufacturer recommendations. Fluorescent probes were then purified with MinElute Spin Columns (QIAGEN) and quantified spectrophotometrically.

growth_protocol: Promastigote cells were grown in MAA20 medium supplemented with 20% heat-inactivated fetal bovine serum and 15 µg/ml hemin at 25°C. Amastigote cells were isolated from infected mice or were grown in MAA20 medium supplemented with 20% heat-inactivated fetal bovine serum and 15 µg/ml hemin at 37°C.

extract_protocol: Total RNA was isolated from 108 Leishmania cells during the mid-log phase using RNeasy Plus Mini Kit (QIAGEN) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion) to avoid any genomic contamination.

tag: promastigote stage, replicate 2

tag: axenic amastigote stage, replicate 2


title: HCC, biological rep 31

description: Gene expression using RMA method


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs axenic amastigote_replicate 1

description: Biological replicate 1 of 4.

tag: promastigote stage, replicate 1

tag: axenic amastigote stage, replicate 1


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs axenic amastigote_replicate 4

description: Biological replicate 4 of 4.

tag: promastigote stage, replicate 4

tag: axenic amastigote stage, replicate 4


title: L. infantum MOHM/MA/67/ITMAP-263 promastigote vs axenic amastigote_replicate 3

description: Biological replicate 3 of 4.

tag: promastigote stage, replicate 3

tag: axenic amastigote stage, replicate 3


title: Scramble SiRNA time 48 of 20% serum induction replicat 5

status: Public on Jan 07 2009

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

description: scramble SIRNA  time 48

scan_protocol: Scanned on ScanArray express II (Packard) and using genepix 4.0 software (Axon)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: XTC.UC1 cells

label_protocol: protocol available on http://cardioserve.nantes.inserm.fr/ptf-puce/IMG/pdf/Pr_ration_Cibles-P1.2_Ampli_Marq_Ambion.pdf

extract_protocol: Total RNA extracted using RNeasy columns following manufacturer's instructions

tag: XTC.UC1 cells

value: Scramble SiRNA time 48 of serum induction

tag: total RNA from pooled XTC


title: Scramble SiRNA time 48 of 20% serum induction replicat 3

description: scramble SIRNA  time 48


title: Scramble SiRNA time 48 of 20% serum induction replicat 2

description: scramble SIRNA  time 48


title: Scramble SiRNA time 48 of 20% serum induction replicat 1

description: scramble SIRNA  time 48


title: PRC SiRNA time 48 of 20% serum induction replicat 2

description: PRC SIRNA  time 48

value: PRC SiRNA time 48 of serum induction


title: Scramble SiRNA time 48 of 20% serum induction replicat 4

description: scramble SIRNA  time 48


title: PRC SiRNA time 48 of 20% serum induction replicat 4

description: PRC SIRNA  time 48


title: Scramble SiRNA time 24 of 20% serum induction replicat 4

description: scramble SIRNA  time 24

value: Scramble SiRNA time 24 of serum induction


title: PRC SiRNA time 48 of 20% serum induction replicat 1

description: PRC SIRNA  time 48


title: PRC SiRNA time 48 of 20% serum induction replicat 3

description: PRC SIRNA  time 48


title: PRC SiRNA time 24 of 20% serum induction replicat 2

description: PRC SIRNA  time 24

value: PRC SiRNA time 24 of serum induction


title: Scramble SiRNA time 24 of 20% serum induction replicat 3

description: scramble SIRNA  time 24


title: Scramble SiRNA time 12 of 20% serum induction replicat 3

description: scramble SIRNA  time 12

value: Scramble SiRNA time 12 of serum induction


title: Scramble SiRNA time 24 of 20% serum induction replicat 2

description: scramble SIRNA  time 24


title: Scramble SiRNA time 12 of 20% serum induction replicat 1

description: scramble SIRNA  time 12


title: Scramble SiRNA time 12 of 20% serum induction replicat 4

description: scramble SIRNA  time 12


title: PRC SiRNA time 24 of 20% serum induction replicat 3

description: PRC SIRNA  time 24


title: Scramble SiRNA time 12 of 20% serum induction replicat 2

description: scramble SIRNA  time 12


title: PRC SiRNA time 12 of 20% serum induction replicat 4

description: PRC SIRNA  time 12

value: PRC SiRNA time 12 of serum induction


title: PRC SiRNA time 24 of 20% serum induction replicat 1

description: PRC SIRNA  time 24


title: PRC SiRNA time 24 of 20% serum induction replicat 4

description: PRC SIRNA  time 24


title: PRC SiRNA time 12 of 20% serum induction replicat 3

description: PRC SIRNA  time 12


title: PRC SiRNA time 12 of 20% serum induction replicat 6

description: PRC SIRNA  time 12


title: PRC SiRNA time 12 of 20% serum induction replicat 5

description: PRC SIRNA  time 12


title: HCC, biological rep 12

description: Gene expression using RMA method


title: PRC SiRNA time 12 of 20% serum induction replicat 1

description: PRC SIRNA  time 12


title: PRC SiRNA time 12 of 20% serum induction replicat 2

description: PRC SIRNA  time 12


title: Scramble SiRNA time 0 of 20% serum induction replicat 3

description: scramble SIRNA  time 0

value: Scramble SiRNA time 0 of serum induction


title: Scramble SiRNA time 0 of 20% serum induction replicat 2

description: scramble SIRNA  time 0


title: PRC SiRNA time 0 of 20% serum induction replicat 5

description: PRC SIRNA  time 0

value: PRC SiRNA time 0 of serum induction


title: PRC SiRNA time 0 of 20% serum induction replicat 6

description: PRC SIRNA  time 0


title: LNCaP_input_2

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

description: Chromatin structure was analyzed in MCF7 and LNCaP cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Nagy et al. 2003; Hogan et al. 2006)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Scanned at the Dana-Farber microarray core facility

data_processing: Model-based analysis of tiling array (MAT), chip.dfci.harvard.edu/~wli/MAT/

source_name: LNCaP

label_protocol: Standard Affymetrix protocol

growth_protocol: MCF7 cells were grown in DMEM and LNCaP cells in RPMI. Media were supplemented with 10% FBS.

extract_protocol: Cells were cross-linked with 1% formaldehyde and processed as in (Nagy et al. 2003; Hogan et al. 2006)

tag: LNCaP


title: LNCaP_FAIRE_1


title: LNCaP_FAIRE_3


title: LNCaP_input_3


title: LNCaP_input_1


title: Scramble SiRNA time 0 of 20% serum induction replicat 4

description: scramble SIRNA  time 0


title: MCF7_FAIRE_3


title: MCF7_FAIRE_2


title: MCF7_FAIRE_1


title: DLD1_FOXA1

description: Duplicates of FOXA1 and input DNA.

source_name: DLD1 colon cancer cells

growth_protocol: DLD1 cells were grown in RPMI supplemented with 10% FBS.

extract_protocol: Cells were cross-linked with 1% formaldehyde and processed as in (Carroll et al. 2005)

tag: DLD1 colon cancer cells


title: MCF7_input_3


title: MCF7_input_4


title: MCF7_input_1


title: MCF7_input_2


title: PRC SiRNA time 0 of 20% serum induction replicat 3

description: PRC SIRNA  time 0


title: PRC SiRNA time 0 of 20% serum induction replicat 4

description: PRC SIRNA  time 0


title: Scramble SiRNA time 0 of 20% serum induction replicat 1

description: scramble SIRNA  time 0


title: PRC SiRNA time 0 of 20% serum induction replicat 2

description: PRC SIRNA  time 0


title: HCC, biological rep 7

description: Gene expression using RMA method


title: XTC during serum starvation replicat 2

description: control serum starvation

tag: XTC.UC1 cells during serum starvation


title: XTC during serum starvation replicat 1

description: control serum starvation


title: lung_control_rep1

city: Turku

first: Anna

last: Koskinen

address: Kiinamllynkatu 10

department: University of Turku

country: Finland

institute: Research centre of Applied and Preventive Cardiovascular Medicine (CAPC)

description: Replicate 1 of 4.

hyb_protocol: 750 ng of cRNA was hybridized to the Illumina Sentrix RatRef-12 BeadChip microarray (Illumina Inc., San Diego, USA) representing ~22 000 genes, following a standard protocol of Illumina Whole Genome Gene Expression with IntelliHyb, revision A.

scan_protocol: Array was scanned with BeadArray Reader from Illumina. Expression values were generated with Bead Studio 2.3.1 software (Illumina).

data_processing: Microarray data analysis was performed using R statistical analysis software (http://www.project.org) and the related Bioconductor module (http://www.bioconductor.org). The data was preprocessed using the quantile normalization method and various measures were inspected during the quality control step. Correlation between the normalized expression values of biological replicates were >0.9897 for the control group and >0.983 for the study group. The statistical analysis was carried out using Limma package.

organism: Rattus norvegicus

source_name: lung tissue, control

label_protocol: Hybridization was detected by using 1µg/ml Cy3-Streptavidin (GE Healthcare, Little Chalfont, Buckinghamshire, UK).

extract_protocol: RNA was extracted from lung homogenate by using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) followed by purification using RNeasy mini kit and RNase-free DNase I (Qiagen, Hilden, Germany).

treatment_protocol: Diabetes was induced in female rat with intraperitoneal injection of streptozotocin (35mg/kg) before the onset of pregnancy.

tag: Sprague-Dawley rat

tag: Age


title: lung_control_rep2

description: Replicate 2 of 4.


title: XTC during serum starvation replicat 3

description: control serum starvation


title: LNCaP_FAIRE_2


title: lung_DM_rep4

description: Replicate 4 of 4.

source_name: lung tissue, exposed to maternal diabetes


title: Scramble SiRNA time 24 of 20% serum induction replicat 1

description: scramble SIRNA  time 24


title: Choroidplexuspapilloma_LMD_patient8

status: Public on Feb 01 2009

city: Münster

first: Martin

last: Hasselblatt

address: Domagkstraße 19

department: Institute of Neuropathology

country: Germany

institute: University Hospital Münster

description: Cryosections (10 µm) from tissue obtained at surgery were prepared on a cryostat and mounted on foil slides (P.A.L.M. Microlaser Technologies GmbH, Martinsried, Germany). Sections were cresyl violet stained and air-dried. Laser microdissection was performed using a Zeiss system equipped with an UVA-laser. A total of 10,000 cells were microdissected from each sample and collected in microcentrifuge tubes containing Buffer RLT (RNeasy Micro Kit; Qiagen, Hilden, Germany).

hyb_protocol: Following fragmentation, cRNA was hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: Fluorescence was scanned on a GeneChip Scanner 3000 (Affymetrix)

data_processing: Fluorescence gradient correction using Expressionist Pro Refiner followed by normalization using Expressionist Analyst (Stratagene; Arithmetic Mean; Target Value: Fixed Value; Reference Value: 1000). Only Affymetrix probe intensities with a 'P' call were considered (p-value < 0.04). Intensities with 'A' or 'M' calls were set to null.

label: biotin-labeling

source_name: Tumor cells lasermicrodissected from choroid plexus papilloma (Grade I WHO)

label_protocol: RNA was amplified using the GeneChip® Two-Cycle cDNA Synthesis Kit (Affymetrix, Wooburn Green, UK) and subsequently in vitro transcribed to complementary RNA using the GeneChip® IVT Labeling Kit (Affymetrix).

extract_protocol: Total RNA from the sample was extracted using the RNeasy Micro Kit (Qiagen).

tag: Patient identifyier

value: WT

tag: Sex

value: male

tag: Age of patient

value: 37 years


title: lung_DM_rep2

description: Replicate 2 of 4.


title: 2007-06-27 383ko T4

status: Public on Jan 06 2009

city: Stanford

last: Brotcke

state: CA

department: Microbiology and Immunology

institute: Stanford University

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75977.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 14800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 11:32:59; Parameter PMT Volts = 610; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62624; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 11:32:59; Parameter PMT Volts = 740; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135757; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke

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

organism: Francisella tularensis

source_name: Ref

label_protocol: not provided

extract_protocol: not provided

tag: Ref

source_name: Timepoints

tag: Timepoints


title: lung_DM_rep1

description: Replicate 1 of 4.


title: lung_control_rep3

description: Replicate 3 of 4.


title: 2007-06-27 gb2 gro383 T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75969.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.65; Parameter Scan Time = 11:07:15; Parameter PMT Volts = 600; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62900; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.65; Parameter Scan Time = 11:07:15; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136033; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.30; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 gro383 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75968.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.59; Parameter Scan Time = 10:58:55; Parameter PMT Volts = 580; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62891; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.59; Parameter Scan Time = 10:58:55; Parameter PMT Volts = 650; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: lung_DM_rep3

description: Replicate 3 of 4.


title: 2007-06-27 gb2 T4

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75967.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 10:50:30; Parameter PMT Volts = 600; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 10:50:30; Parameter PMT Volts = 710; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136016; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: lung_control_rep4

description: Replicate 4 of 4.


title: 2007-06-27 383ko T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75974.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 15560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.23; Parameter Scan Time = 11:50:26; Parameter PMT Volts = 570; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62642; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.23; Parameter Scan Time = 11:50:26; Parameter PMT Volts = 620; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135775; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75964.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 15200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 10:24:53; Parameter PMT Volts = 610; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62859; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 10:24:53; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135992; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 T4

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75959.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.90; Parameter Scan Time = 09:37:22; Parameter PMT Volts = 680; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62812; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.90; Parameter Scan Time = 09:37:22; Parameter PMT Volts = 780; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 383ko T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75976.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 14800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.22; Parameter Scan Time = 11:41:32; Parameter PMT Volts = 600; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62633; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.22; Parameter Scan Time = 11:41:32; Parameter PMT Volts = 700; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135766; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75957.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.68; Parameter Scan Time = 09:19:53; Parameter PMT Volts = 620; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62794; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.07; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.68; Parameter Scan Time = 09:19:53; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135927; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.05; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75958.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.76; Parameter Scan Time = 09:28:07; Parameter PMT Volts = 680; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62802; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.76; Parameter Scan Time = 09:28:07; Parameter PMT Volts = 770; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.18; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: PRC SiRNA time 0 of 20% serum induction replicat 1

description: PRC SIRNA  time 0


title: 2007-06-27 383ko gro383 T4

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75980.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 14800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.13; Parameter Scan Time = 10:07:22; Parameter PMT Volts = 630; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62538; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.13; Parameter Scan Time = 10:07:22; Parameter PMT Volts = 740; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135671; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 gro383 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75970.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.71; Parameter Scan Time = 11:15:55; Parameter PMT Volts = 620; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62908; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.71; Parameter Scan Time = 11:15:55; Parameter PMT Volts = 700; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136041; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 gro383 T4

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75963.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.32; Parameter Scan Time = 10:14:45; Parameter PMT Volts = 660; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62849; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.32; Parameter Scan Time = 10:14:45; Parameter PMT Volts = 800; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135982; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75966.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 15520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.47; Parameter Scan Time = 10:42:14; Parameter PMT Volts = 600; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62875; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.47; Parameter Scan Time = 10:42:14; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136007; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.29; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 gro383 T4

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75971.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 15200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 11:24:27; Parameter PMT Volts = 650; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 11:24:27; Parameter PMT Volts = 780; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 136050; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75956.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 14960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.65; Parameter Scan Time = 09:11:34; Parameter PMT Volts = 630; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62785; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.65; Parameter Scan Time = 09:11:34; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135918; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 gb2 T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75965.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 15200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.41; Parameter Scan Time = 10:33:45; Parameter PMT Volts = 650; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62867; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.41; Parameter Scan Time = 10:33:45; Parameter PMT Volts = 720; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135999; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: XTC during serum starvation replicat 4

description: control serum starvation

scan_protocol: Scanned on ScanArray express II (Packard) and using genepix 4.0 software (Axon)


title: 2007-06-27 U112 gro383 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75962.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.23; Parameter Scan Time = 10:04:34; Parameter PMT Volts = 620; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.23; Parameter Scan Time = 10:04:34; Parameter PMT Volts = 700; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135972; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 383ko gro383 T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75979.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 14800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.21; Parameter Scan Time = 11:02:04; Parameter PMT Volts = 650; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62550; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.21; Parameter Scan Time = 11:02:04; Parameter PMT Volts = 790; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135682; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 U112 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72188.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.29; Parameter Scan Time = 08:01:27; Parameter PMT Volts = 590; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58738; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.08; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.29; Parameter Scan Time = 08:01:27; Parameter PMT Volts = 640; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131871; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 U112 T9

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72197.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.73; Parameter Scan Time = 09:12:51; Parameter PMT Volts = 690; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58810; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.73; Parameter Scan Time = 09:12:51; Parameter PMT Volts = 800; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131943; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 gb2 T7

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72195.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.70; Parameter Scan Time = 08:57:50; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58795; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.70; Parameter Scan Time = 08:57:50; Parameter PMT Volts = 770; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131928; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 383ko gro383 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75978.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 14800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.10; Parameter Scan Time = 11:23:53; Parameter PMT Volts = 660; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 62615; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.10; Parameter Scan Time = 11:23:53; Parameter PMT Volts = 750; Parameter Scan Date = 2007-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 135748; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 383ko gro383 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76011.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 15040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.00; Parameter Scan Time = 09:43:09; Parameter PMT Volts = 640; Parameter Scan Date = 2007-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 63050; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.00; Parameter Scan Time = 09:43:09; Parameter PMT Volts = 720; Parameter Scan Date = 2007-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 136183; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 gb2 T5

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72192.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.55; Parameter Scan Time = 08:33:15; Parameter PMT Volts = 640; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58771; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.55; Parameter Scan Time = 08:33:15; Parameter PMT Volts = 670; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131904; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 U112 gro383 T2

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75961.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 15080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.13; Parameter Scan Time = 09:55:25; Parameter PMT Volts = 620; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 62830; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.13; Parameter Scan Time = 09:55:25; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-12; Parameter Pixel Size = 10; Parameter Laser on time = 135963; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-06-27 383ko T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76010.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 15160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.06; Parameter Scan Time = 09:34:47; Parameter PMT Volts = 620; Parameter Scan Date = 2007-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 63042; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.08; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.06; Parameter Scan Time = 09:34:47; Parameter PMT Volts = 670; Parameter Scan Date = 2007-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 136175; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 U112 T7

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72194.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.68; Parameter Scan Time = 08:50:26; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58788; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.68; Parameter Scan Time = 08:50:26; Parameter PMT Volts = 730; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131920; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 383 T5

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72193.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.59; Parameter Scan Time = 08:42:54; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58780; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.59; Parameter Scan Time = 08:42:54; Parameter PMT Volts = 720; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131912; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 gb2 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72189.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.37; Parameter Scan Time = 08:09:31; Parameter PMT Volts = 590; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58747; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.37; Parameter Scan Time = 08:09:31; Parameter PMT Volts = 640; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131880; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.08; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 383 T7

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72196.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.78; Parameter Scan Time = 09:05:30; Parameter PMT Volts = 690; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58803; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.78; Parameter Scan Time = 09:05:30; Parameter PMT Volts = 790; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131936; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 gb2 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72186.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.21; Parameter Scan Time = 07:44:51; Parameter PMT Volts = 620; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58722; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.06; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.21; Parameter Scan Time = 07:44:51; Parameter PMT Volts = 670; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131854; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 383 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72187.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.26; Parameter Scan Time = 07:53:20; Parameter PMT Volts = 620; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58731; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.26; Parameter Scan Time = 07:53:20; Parameter PMT Volts = 670; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: Ras85D(V12) embryos, 7-8 hours AEL, rep. 1

city: Boston

first: Gregory

middle: D.

last: Hurlbut

state: MA

address: 240 Longwood Ave,LHRRB-410A

department: Cell Biology

institute: Harvard Medical School

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Ras85D (Ras1V12), 7-8 hours after egg lay (AEL) (stage 11 mid-12 of embryonic development)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array 1. 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 by GC-RMA as part of the LIMMA package in the R programming language environment

organism: Drosophila melanogaster

source_name: Drosophila embryos, Ras85D(V12), 7-8 hours after egg lay (AEL)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Embryos of each type were collected on apple juice plates for one hour, incubated at 25°C for 5 hours and 30 minutes for the first time point and 6 hours and 45 minutes for the second time point; dechorionated by treatment with 50% Clorox bleach in dH2O at room temperature for 1 minute with agitation, washed with 0.5X PBS, 1% Tween, rinsed with ddH2O.  Embryos were then shock frozen and stored in liquid Nitrogen within 15 minutes. All collections were performed in parallel sets, which were slightly staggered to equalize the length of embryo submersion in liquid. Each collection contained approximately 500 embryos per 1.5 ml microcentrifuge tube.

extract_protocol: Frozen embryos were ground by pestle in the Trizol reagent (Invitrogen). RNA was extracted according to the manufacturer's instructions, with the inclusion of an additional Trizol extraction prior to RNA precipitation to increase RNA purity.

tag: Transgene

value: arm-GAL4, UAS-Ras85D(V12)

tag: Genotype

value: progeny of homozygous arm-GAL4 females crossed with homozygous UAS-Ras85D(V12) males

value: 7-8 hours after egg lay (developmental stage 11 mid-12)

tag: Reared at 25 degrees C


title: Ras85D(V12) embryos, 7-8 hours AEL, rep. 2


title: Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 2

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Ras85D (Ras1V12), 5:45-6:45 hours after egg lay (AEL) (stage 10-11 mid of embryonic development)

source_name: Drosophila embryos, Ras85D(V12), 5:45-6:45 hours after egg lay (AEL)

value: 5:45-6:45 hours after egg lay (developmental stage 10-11 mid)


title: 2007-02-02 U112 T5

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72191.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.49; Parameter Scan Time = 08:25:32; Parameter PMT Volts = 630; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58763; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.49; Parameter Scan Time = 08:25:32; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131896; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 3


title: DC_unstimulated_3

city: Firenze

first: Luca

last: Beltrame

address: Viale Pieraccini 6

department: Department of Pharmacology

country: Italy

institute: University of Firenze

description: Gene expression data from dendritic cells, unstimulated

hyb_protocol: Hybridization was performed according to the standard Affymetrix Protocols on HG-U133A 2.0 arrays

scan_protocol: Scanning was performed with a GeneChip Scanner 3000

data_processing: CEL files were processed using the Robust Multi-array (RMA) procedure (Irizarry et al.) using custom, re-annotated chip definition files (CDFs) as described by Dai et al. (2005)

source_name: Dendritic cells, unstimulated

growth_protocol: PBMC were isolated from buffy coats by density gradient centrifugation using Biocoll (BIOCHROM). CD14+ monocytes were isolated from PBMC by positive selection using MACS anti-CD14 microbeads and a Midi-MACS® magnetic cell sorting device (both from Miltenyi Biotec, Bergisch- Gladbach,Germany). Cells were cultured in RPMI 1640 medium (GIBCO BRL) supplemented with 2 mM L-glutamine (Sigma), 1% (vol/vol) non-essential amino acids (Gibco BRL), 100 mM sodium pyruvate (SIGMA), 50 U/ml of penicillin and 50 mg/ml of streptomycin (Gibco BRL) containing 10% (vol/vol) FCS (Hyclone). Differentiation of monocytes into dendritic cells was promote by addition of granulocyte-macrophage colony-stimulating factor (GM-CSF 1000U/ml) and recombinant IL-4 (1000U/ml, both from Gentaur) for 5 days.

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

tag: Type

value: monocyte-derived dendritic cells


title: Ras85D(V12) embryos, 7-8 hours AEL, rep. 3


title: 2007-02-02 383 T3

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72190.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.41; Parameter Scan Time = 08:17:33; Parameter PMT Volts = 570; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.41; Parameter Scan Time = 08:17:33; Parameter PMT Volts = 610; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 383 T9

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72199.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 560, 7040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.88; Parameter Scan Time = 09:27:33; Parameter PMT Volts = 700; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58824; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.88; Parameter Scan Time = 09:27:33; Parameter PMT Volts = 810; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131957; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: 2007-02-02 U112 T1

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72185.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.19; Parameter Scan Time = 07:35:52; Parameter PMT Volts = 580; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58714; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.03; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.19; Parameter Scan Time = 07:35:52; Parameter PMT Volts = 620; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131847; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: DC_unstimulated_2


title: 2007-02-02 gb2 T9

description:
Simple annotation: Transcription, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72198.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 600, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Anna,,Brotcke Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.82; Parameter Scan Time = 09:20:18; Parameter PMT Volts = 700; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 58818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.82; Parameter Scan Time = 09:20:18; Parameter PMT Volts = 810; Parameter Scan Date = 2007-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 131950; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Anna,,Brotcke


title: DC_unstimulated_1


title: DC_stimulated_yeast_exponential_phase_2

description: Gene expression data from dendritic cells, stimulated with yeast in exponential phase

source_name: Dendritic cells, stimulated with yeast in exponential phase

treatment_protocol: 3 * 10^6 DCs were stimulated with yeast (Saccaromyces cerevisiae strain SK1) grown in exponential phase (12 hours of growth). An equal number of cells was used as an untreated control. Treated and untreated cells were harvested after 4 hours.


title: NotchICD+Ras85D(V12) embryos, 7-8 hours AEL, rep. 1

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Notch (Notch intracellular domain) and activated Ras85D (Ras1V12), 7-8 hours after egg lay (AEL) (stage 11 mid-12 of embryonic development)

source_name: Drosophila embryos, NotchICD+Ras85D(V12), 7-8 hours after egg lay (AEL)

value: arm-GAL4, UAS-NotchICD, UAS-Ras85D(V12)

value: progeny of homozygous arm-GAL4 females crossed with homozygous UAS-NotchICD; UAS-Ras85D(V12) males


title: NotchICD embryos, 7-8 hours AEL, rep. 1

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Notch (Drosophila Notch intracellular domain), 7-8 hours after egg lay (AEL) (stage 11 mid-12 of embryonic development)

source_name: Drosophila embryos, NotchICD, 7-8 hours after egg lay (AEL)

value: arm-GAL4, UAS-NotchICD

value: progeny of homozygous arm-GAL4 females crossed with homozygous UAS-NotchICD males


title: NotchICD embryos, 7-8 hours AEL, rep. 3


title: DC_stimulated_yeast_exponential_phase_3


title: NotchICD+Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 1

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Notch (Notch intracellular domain) and activated Ras85D (Ras1V12), 5:45-6:45 hours after egg lay (AEL) (stage 10-11 mid of embryonic development)

source_name: Drosophila embryos, NotchICD+Ras85D(V12), 5:45-6:45 hours after egg lay (AEL)


title: NotchICD+Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 2


title: GAL4 control, 7-8 hours AEL, rep. 1

description: Transgenic Drosophila embryos expressing armadillo controlled GAL4, 7-8 hours after egg lay (AEL) (stage 11 mid-12 of embryonic development)

source_name: Drosophila embryos, arm-GAL4, 7-8 hours after egg lay (AEL)

value: progeny of homozygous arm-GAL4 females crossed with w1118 males


title: NotchICD+Ras85D(V12) embryos, 7-8 hours AEL, rep. 2


title: Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 1


title: NotchICD embryos, 5:45-6:45 hours AEL, rep. 3

description: Transgenic Drosophila embryos expressing armadillo-GAL4 controlled activated Notch (Drosophila Notch intracellular domain), 5:45-6:45 hours after egg lay (AEL) (stage 10-11 mid of embryonic development)

source_name: Drosophila embryos, NotchICD, 5:45-6:45 hours after egg lay (AEL)


title: NotchICD embryos, 5:45-6:45 hours AEL, rep. 2


title: GAL4 control, 5:45-6:45 hours AEL, rep. 3

description: Transgenic Drosophila embryos expressing armadillo controlled GAL4, 5:45-6:45 hours after egg lay (AEL) (stage 10-11 mid of embryonic development)

source_name: Drosophila embryos, arm-GAL4, 5:45-6:45 hours after egg lay (AEL)


title: NotchICD+Ras85D(V12) embryos, 7-8 hours AEL, rep. 3


title: GAL4 control, 5:45-6:45 hours AEL, rep. 2


title: NotchICD embryos, 5:45-6:45 hours AEL, rep. 1


title: NotchICD+Ras85D(V12) embryos, 5:45-6:45 hours AEL, rep. 3


title: GAL4 control, 7-8 hours AEL, rep. 2


title: GAL4 control, 7-8 hours AEL, rep. 3


title: DC_stimulated_yeast_exponential_phase_1


title: GAL4 control, 5:45-6:45 hours AEL, rep. 1


title: Biophenotypic leukemia patient #21

city: Memphis

first: Xueyuan

last: Cao

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St Jude Children's Research Hospital

description: Gene expression data for pediatric patient diagnostic sample.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed at 25°C with 6 X SSPE (0.9M NaCl, 60 mM NaH2PO4, 6 mM EDTA + 0.01% Tween 20) followed by a stringent wash at 50°C with 100 mM MES, 0.1M NaCl2, 0.01% Tween 20.

scan_protocol: Arrays were scanned using a laser confocal scanner (Agilent, Palo Alto, CA).

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: diagnostic BM aspirates or peripheral blood, patient #21

label_protocol: cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter coupled double stranded cDNA as template and the T7 RNA Transcript Labeling Kit (ENZO Diagnostics Inc., Farmingdale NY).

tag: Pediatric patient sample


title: Biophenotypic leukemia patient #33

source_name: diagnostic BM aspirates or peripheral blood, patient #33


title: Biophenotypic leukemia patient #18

source_name: diagnostic BM aspirates or peripheral blood, patient #18


title: Biophenotypic leukemia patient #31

source_name: diagnostic BM aspirates or peripheral blood, patient #31


title: Biophenotypic leukemia patient #28

source_name: diagnostic BM aspirates or peripheral blood, patient #28


title: Biophenotypic leukemia patient #4

source_name: diagnostic BM aspirates or peripheral blood, patient #4


title: Biophenotypic leukemia patient #20

source_name: diagnostic BM aspirates or peripheral blood, patient #20


title: Biophenotypic leukemia patient #6

source_name: diagnostic BM aspirates or peripheral blood, patient #6


title: Biophenotypic leukemia patient #16

source_name: diagnostic BM aspirates or peripheral blood, patient #16


title: Biophenotypic leukemia patient #11

source_name: diagnostic BM aspirates or peripheral blood, patient #11


title: Biophenotypic leukemia patient #25

source_name: diagnostic BM aspirates or peripheral blood, patient #25


title: Biophenotypic leukemia patient #15

source_name: diagnostic BM aspirates or peripheral blood, patient #15