title: total RNA dEgd2/dBtt3 (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88470.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.59; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.59; Performer: Marta,,Del Alamo

source_name: total rna dEgd2/dBtt1

value: :egd2 btt1


title: Sertoli cell cloned embryo, 2-cell stage, biological rep4

status: Public on Apr 05 2013

type: RNA

city: Tokyo

first: Feng

last: Cao

address: 1-1-1 Sakuraoka, Setagaya-ku

department: Bioscience

country: Japan

institute: Tokyo University of Agriculture

description: Time-lapse gene expression data of Sertoli cell cloned embryos throughout preimplantation stages.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000

data_processing: The data were analyzed by GeneSpring GX 12.0 with RMA summarization algorithm and baseline to the median of all samples.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse Sertoli cell cloned embryo, 2-cell stage

label_protocol: cRNA amplify and label using Two-cycle target synthesis kit provided by Affymetrix with some modification for single embryos analysis (refer to Plos One, Fukuda, Cao, et al., 2010)

growth_protocol: Embryos incubated in drops of KSOM medium at 37C, 5% CO2,5%O2 and 90%N2 until collect.

extract_protocol: Total RNA is extract by Rneasy Micro kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Embryos were washed 3 times by PBS, transfer into 50μl lysis buffer included 1% 2-mercaptoethanol and store at -80℃ until use.

tag: method

value: Sertoli cell nuclear transfer

tag: Stage

value: 2-cell stage

tag: strain

value: donor cell:B6CBF1, recipient oocyte:B6D2F1


title: fibroblast_patient_1_C

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

description: reference: Artuch, R. et al. Cerebellar ataxia with coenzyme Q10 deficiency: diagnosis and follow-up after coenzyme Q10 supplementation. J Neurol Sci 246, 153-8 (2006). PubMed ID: 16677673

hyb_protocol: Each cRNA probe was hybridized to independent GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). Hybridization was performed overnight in the GeneChip Hybridization Oven 640 at 45ºC with shaking at 60 rpm; washes and staining of the probe were performed in the GeneChip fluidics station using buffers and protocols provided by the manufacturer. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

scan_protocol: High-quality scan of the arrays was performed with the GeneChip Scanner 3000. The full system was controlled by the GeneChip Operating Software (GCOS), and both the equipment and the software were provided by Affymetrix.

data_processing: Data extraction, cell intensity calculation and computational analysis were performed using GCOS and Expression Console Release Software from Affymetrix. The signal value was obtained using MAS5 and RMA algorithms at linear scale.

organism: Homo sapiens

source_name: human fibroblast, Q10 deficient patient 1, rep. 3

label_protocol: A cRNA probe was synthesized and fragmented from each RNA sample using Affymetrix protocols and kits provided by Qiagen.

extract_protocol: Cells were homogenized in 1 ml of Tripure Isolation Reagent (Roche) and RNA was extracted with chloroform and precipitated with 2-propanol by centrifugation at 12000 g for 10 min at 4ºC. After washing with 75% EtOH, RNA was resuspended in DEPC-treated water and treated with deoxiribonuclease I (Sigma) for removal of possible DNA contamination. Afterwards, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen), its concentration and purity were checked spectrophotometrically and its quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.

tag: age

tag: gender

value: girl

tag: clinical phenotype

value: (1) ataxia and cerebellar atrophy, (2) decreased mitochondrial enzimatic activities in complex I+III and complex II+III, and (3) CoQ concentration in muscle was decreased.

tag: treatment

value: After 16 months of CoQ supplementation, the patient is now able to walk unaided and cerebellar signs have disappeared.


title: Sertoli cell cloned embryo, 1-cell stage, biological rep5

source_name: Mouse Sertoli cell cloned embryo, 1-cell stage

value: 1-cell stage


title: Sertoli cell cloned embryo, 2-cell stage, biological rep5


title: Sertoli cell cloned embryo, 2-cell stage, biological rep1


title: AC_T_rep1

city: Wageningen

first: Ruud

middle: A

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45C in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

organism: Solanum lycopersicum

source_name: tomato fruit_turning/breaker

label_protocol: RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands.  corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, total RNA (100 ng) was used for whole transcript cDNA synthesis using the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands), and subsequently labeled using the Affymetrix GeneChip WT Terminal Labeling Kit [catalog number 901524] (Affymetrix, Santa Clara, CA).

growth_protocol: Tomato plants were grown in a greenhouse on rockwool with liquied nutrient solution

extract_protocol: Total RNA was extracted using an InviTrap Spin Plant RNA mini kit (Stratec, Berlin)

treatment_protocol: Fruits kept at -80C untill further use, and ground in liquied nitrogen before RNA extraction

tag: variety

value: Ailsa Craig

tag: tissue

value: ripening tomato fruit

tag: ripening stage

value: turning/breaker (T)


title: Sertoli cell cloned embryo, 1-cell stage, biological rep4


title: Sertoli cell cloned embryo, 2-cell stage, biological rep3


title: Sertoli cell cloned embryo, 2-cell stage, biological rep2


title: control_fibroblast_C

source_name: human fibroblast, neonatal, rep. 3

tag: cell type

value: Human dermal fibroblast (primary culture of cells) obtained from healthy voluntiers.

value: neonatal


title: AC_T_rep3


title: AC_MG_rep3

source_name: tomato fruit_mature green

value: mature green (MG)


title: Glio6 at 0.3% O2 with serum, biological rep4

city: La tronche

first: didier

last: wion

address: fortuné ferrini

country: France

institute: INSERM

description: cell culture in hypoxic conditions

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression console Suite (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Glioblastoma primary culture (with serum) cultivated at 0.3% of oxygen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured either in the presence of serum or in serum-free medium at different concentration of O2 (20%, 3% or 0.3%) in an hypoxic workstation

extract_protocol: Total RNA were extracted from cells with the MirVana isolation kit.

value: brain

value: primary culture

tag: cell line

tag: oxygen level

tag: serum

value: yes


title: fibroblast_patient_1_A

source_name: human fibroblast, Q10 deficient patient 1, rep. 1


title: AC_MG_rep2


title: fibroblast_patient_1_B

source_name: human fibroblast, Q10 deficient patient 1, rep. 2


title: total RNA dEgd2/dBtt3 (2)

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88472.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.74; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.74; Performer: Marta,,Del Alamo

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: Saccharomyces cerevisiae

source_name: total rna WT

label_protocol: not provided

extract_protocol: not provided

tag: genotype

value: WT

value: :egd2 btt1


title: Glio6 at 0.3% O2 with serum, biological rep3

description: cell culture in hypoxic conditions


title: Egd2 -CHX (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-03/92365.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 970, 6760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.12; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.12; Performer: Marta,,Del Alamo

source_name: total rna

tag: reference

value: total rna

source_name: totalrna

tag: cyclohexamide treatment

value: wt

tag: tap-tag


title: total RNA dEgd2/dBtt3 (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88474.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.83; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.83; Performer: Marta,,Del Alamo


title: Glio6 at 0.3% O2 with serum, biological rep2

description: cell culture in hypoxic conditions


title: total RNA dEgd1/dEgd2 (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88466.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.25; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.25; Performer: Marta,,Del Alamo

source_name: total rna dEgd1/dEgd2

value: :egd1 egd2


title: total RNA dEgd1/dEgd2 (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88464.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.04; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 37.04; Performer: Marta,,Del Alamo


title: Sertoli cell cloned embryo, 1-cell stage, biological rep3

tag: method

value: Sertoli cell nuclear transfer

tag: Stage

value: donor cell:B6CBF1, recipient oocyte:B6D2F1


title: Sertoli cell cloned embryo, 1-cell stage, biological rep2

value: 1-cell stage

tag: strain


title: IVF embryo, Morula stage, biological rep3

source_name: Mouse in vitro fertilized embryo, Morula stage

value: In vitro fertilization

value: Morula stage


title: IVF embryo, Blastocyst stage, biological rep2

source_name: Mouse in vitro fertilized embryo, Blastocyst stage

value: Blastocyst stage


title: Sertoli cell cloned embryo, 1-cell stage, biological rep1


title: SRP54 dEgd2/Btt2 (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88455.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.55; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.55; Performer: Marta,,Del Alamo

source_name: SRP54 dEgd2/Btt1 IP

value: egd2 btt1


title: Glio6 serum-free at 0.3% O2, biological rep5

description: cell culture in hypoxic conditions

source_name: Glioblastoma primary serum-free culture cultivated at 0.3% of oxygen

value: no


title: SRP54 dEgd2/Btt3 (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88456.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.79; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.79; Performer: Marta,,Del Alamo


title: Glio6 serum-free at 0.3% O2, biological rep4

description: cell culture in hypoxic conditions


title: IVF embryo, Morula stage, biological rep2


title: Membrane bound vs Free/Soluble mRNAs (2) -- glass beads delta NAC

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79243.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5200; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 382; Parameter Laser on time = 38413; Parameter Laser Power = 3.55; Parameter Scan Time = 12:02:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.06; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 507; Parameter Scan Power = 100; Parameter Laser on time = 38416; Parameter Laser Power = 3.20; Parameter Scan Time = 12:02:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.06; Performer: Daniel,,Hogan

source_name: free RNA

tag: fraction

value: free RNA

value: dNAC

source_name: membrane bound RNA

extract_protocol: Del Alamo Subcellular Fractionation and RNA Isolation; Free cytosolic polysomes and membrane-bound polysomes were fractionated by sedimentation velocity exactly as described [34],[85] starting with 250 ml of exponential growth cultures (of WT or ??egd1/egd2) in YPD. Total RNA from free and membrane-associated polysomes was purified with RNeasy Mini Columns Kit (Qiagen).; Protocol Type = Biological Sample; Performer: Daniel,,Hogan

value: membrane bound RNA


title: Glio6 at 0.3% O2 with serum, biological rep1

description: cell culture in hypoxic conditions

value: brain

value: primary culture

value: yes


title: Glio6 serum-free at 0.3% O2, biological rep2

description: cell culture in hypoxic conditions


title: Glio6 at 3% O2 with serum, biological rep1

description: cell culture in normoxic conditions

source_name: Glioblastoma primary culture (with serum) cultivated at 3% of oxygen


title: Glio6 at 3% O2 with serum, biological rep3

description: cell culture in normoxic conditions


title: AC_MG_rep1

value: Ailsa Craig

value: ripening tomato fruit

value: mature green (MG)


title: Glio6 at 3% O2 with serum, biological rep2

description: cell culture in normoxic conditions


title: Membrane bound vs Free/Soluble mRNAs (1) -- glass beads delta NAC

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79241.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5200; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 405; Parameter Laser on time = 38396; Parameter Laser Power = 3.55; Parameter Scan Time = 11:45:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 496; Parameter Scan Power = 100; Parameter Laser on time = 38399; Parameter Laser Power = 3.17; Parameter Scan Time = 11:45:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Daniel,,Hogan


title: Glio6 serum-free at 0.3% O2, biological rep3

description: cell culture in hypoxic conditions


title: SRP54 dEgd2/Btt1 (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-06/88454.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 5760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.40; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 36.40; Performer: Marta,,Del Alamo

value: total rna


title: IVF embryo, Blastocyst stage, biological rep3


title: IVF embryo, Blastocyst stage, biological rep1


title: Membrane bound vs Free/Soluble mRNAs (3) -- glass beads delta NAC

description:
Simple annotation: Subcellular fractionation, Chaperone
Image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79245.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5200; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 413; Parameter Laser on time = 38434; Parameter Laser Power = 3.54; Parameter Scan Time = 12:24:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.24; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-04-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 494; Parameter Scan Power = 100; Parameter Laser on time = 38437; Parameter Laser Power = 3.19; Parameter Scan Time = 12:24:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.24; Performer: Daniel,,Hogan


title: Glio6 serum-free at 0.3% O2, biological rep1

description: cell culture in hypoxic conditions


title: EGD1/betaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80976.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 411; Parameter Laser on time = 52586; Parameter Laser Power = 3.55; Parameter Scan Time = 11:55:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.14; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 477; Parameter Scan Power = 100; Parameter Laser on time = 52589; Parameter Laser Power = 3.15; Parameter Scan Time = 11:55:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.14; Performer: Daniel,,Hogan

source_name: total rna extract

source_name: affinity purified RNA

value: wt


title: IVF embryo, 8-cell stage, biological rep3

source_name: Mouse in vitro fertilized embryo, 8-cell stage

value: 8-cell stage


title: Egd2 -CHX (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-03/92363.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 970, 6760; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Marta,,Del Alamo


title: IVF embryo, Morula stage, biological rep1

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000

value: In vitro fertilization


title: IVF embryo, 8-cell stage, biological rep2


title: IVF embryo, 8-cell stage, biological rep1


title: Glio6 serum-free at 3% O2, biological rep5

description: cell culture in normoxic conditions

source_name: Glioblastoma primary serum-free culture cultivated at 3% of oxygen


title: Glio6 serum-free at 3% O2, biological rep4

description: cell culture in normoxic conditions


title: IVF embryo, 4-cell stage, biological rep2

source_name: Mouse in vitro fertilized embryo, 4-cell stage

value: 4-cell stage


title: IVF embryo, 4-cell stage, biological rep3


title: RPL16A IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80735.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 447; Parameter Laser on time = 52084; Parameter Laser Power = 3.51; Parameter Scan Time = 12:37:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.23; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 471; Parameter Scan Power = 100; Parameter Laser on time = 52088; Parameter Laser Power = 3.14; Parameter Scan Time = 12:37:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.23; Performer: Daniel,,Hogan


title: human embyonic stem cells differentiated into pancreatic cells

city: New York

first: Haiqing

last: Hua

state: NY

address: 3960 Broadway

institute: Columbia University

description:
1 of 1 samples
Chip ID: 5975034030

hyb_protocol: Hybridization according to Illumina protocols on Illumina HumanRef-8 v3 Expression BeadChip (GPL6883). Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal using GenomeStudio V2009.1. Background was subtracted.

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit

growth_protocol: fibroblast, DMEM with 10% FBS; human iPS and ES, human embryonic stem cells cultured in knockout serum containing medium

extract_protocol: Qiagen Rneasy Plus Mini kit

treatment_protocol: stem cells were differentiated into endoderm using Activin A, then differentiated foregut endoderm using FGF10, then differentiated into pancreatic cells using retinoic acid, FGF10 and cyclopamine


title: RPL17 IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80738.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 423; Parameter Laser on time = 52035; Parameter Laser Power = 3.50; Parameter Scan Time = 11:48:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 487; Parameter Scan Power = 100; Parameter Laser on time = 52038; Parameter Laser Power = 3.16; Parameter Scan Time = 11:48:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Daniel,,Hogan


title: Egd2 -CHX (2bis)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-03/92366.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 6280; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.45; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.45; Performer: Marta,,Del Alamo


title: DeltaNACSrpgenomic (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81833.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 520, 4280; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Marta,,Del Alamo

source_name: total rna purified

value: egd1 egd2


title: Glio6 serum-free at 3% O2, biological rep2

description: cell culture in normoxic conditions

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


title: EGD1/betaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80978.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 407; Parameter Laser on time = 52618; Parameter Laser Power = 3.52; Parameter Scan Time = 12:27:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.48; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 477; Parameter Scan Power = 100; Parameter Laser on time = 52621; Parameter Laser Power = 3.14; Parameter Scan Time = 12:27:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.48; Performer: Daniel,,Hogan


title: EGD2/alphaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80975.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 442; Parameter Laser on time = 52568; Parameter Laser Power = 3.55; Parameter Scan Time = 11:37:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.86; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 465; Parameter Scan Power = 100; Parameter Laser on time = 52571; Parameter Laser Power = 3.18; Parameter Scan Time = 11:37:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.86; Performer: Daniel,,Hogan


title: U87 at 0.3% O2, biological rep2

description: cell culture in hypoxic conditions

source_name: U87 (glioblastoma) cultivated at 0.3% of oxygen


title: Glio6 serum-free at 3% O2, biological rep1

description: cell culture in normoxic conditions


title: human embyonic stem cells

description:
1 of 1 samples
Chip ID: 5975034030

value: human embyonic stem cells (Noggle et al, Nature, 2011)


title: Induced pluripotent cells differentiated into pancreatic cells

description:
1 of 1 samples
Chip ID: 5975034030

source_name: GCK G299R/+

tag: genotype/variation

value: GCK G299R/+; mutation in the glucokinase gene


title: Induced pluripotent cells

description:
1 of 1 samples
Chip ID: 5975034030

value: Induced pluripotent cells


title: IVF embryo, 4-cell stage, biological rep1

description: Time-lapse gene expression data of Sertoli cell cloned embryos throughout preimplantation stages.


title: IVF embryo, 2-cell stage, biological rep2

source_name: Mouse in vitro fertilized embryo, 2-cell stage

value: 2-cell stage


title: U87 at 0.3% O2, biological rep1

description: cell culture in hypoxic conditions


title: U87 at 20% O2, biological rep3

description: cell culture in hyperoxic conditions

source_name: U87 (glioblastoma) cultivated at 20% of oxygen


title: U87 at 0.3% O2, biological rep3

description: cell culture in hypoxic conditions


title: IVF embryo, 2-cell stage, biological rep3


title: RPL16A IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80734.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 451; Parameter Laser on time = 52069; Parameter Laser Power = 3.50; Parameter Scan Time = 12:21:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.02; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 471; Parameter Scan Power = 100; Parameter Laser on time = 52072; Parameter Laser Power = 3.15; Parameter Scan Time = 12:21:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.02; Performer: Daniel,,Hogan


title: fibroblast cells

description:
1 of 1 samples
Chip ID: 5975034030

value: fibroblast cells


title: HUVEC_replicative senescent_rep3

city: KUALA LUMPUR

first: Pooi-Fong

last: Wong

address: Faculty of Medicine

department: Pharmacology

country: Malaysia

institute: University of malaya

description: miRNA expression of replicative senescent HUVEC

hyb_protocol: 18 µl nuclease free water was added to resuspend the dried Cy3-labelled RNAs. 4.5 µl of the 10x GE Blocking Agent and 22.5 µl of 2x Hi-RPM Hybridization Buffer were added to each sample and incubated 100°C for 5 minutes. 45 µl mixture was then hybridized to Agilent Human MicroRNAs Miroarrays (G4770C) for 20 hours at at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minutes with moderate stirring at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with moderate stirring at 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner C using one color scan setting for the 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and output is 20 bit TIFF).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using protocol: miRNA_105_Jan09 and Grid: 021827_D_20081121.

source_name: HUVEC_PD > 48_replicate3

label_protocol: Total RNAs (100ng) were labeled with Cyanine 3-pCp using miRNA Complete Labeling and Hyb Kit (Agilent Technologies Inc., USA) according to manufacturer’s protocol. After labeling, Cy3-labelled RNAs were dried completely using vacuum concentrator (Genevac, USA) at 45oC to 55oC for 2 to 3 hours.

growth_protocol: HUVECs were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA) and maintained in endothelial cell medium (ECM) supplemented with 5% FBS, 1% endothelial cell growth supplement and 1% of penicillin/streptomycin (ScienCell Research Laboratories), at 37oC in a humidified atmosphere of 95% air/5% CO2.  Young and senescent cells used in experiments are cells with PD < 10 and PD > 48 respectively.

extract_protocol: Total RNAs were isolated from cells using miRNeasy mini kit (Qiagen) according to manufacturer’s protocol. RNA was quantified using Nanophotometer (Implen GmbH, Germany). RNA integrity was accessed using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA).

treatment_protocol: Not applicable

value: Endothelial cell

value: Umbilical vein

value: HUVEC

value: replicative senescent


title: IVF embryo, 2-cell stage, biological rep1


title: HUVEC_replicative senescent_rep1

source_name: HUVEC_PD > 48_replicate1


title: EGD1/betaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80977.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 397; Parameter Laser on time = 52598; Parameter Laser Power = 3.51; Parameter Scan Time = 12:08:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.29; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 478; Parameter Scan Power = 100; Parameter Laser on time = 52601; Parameter Laser Power = 3.14; Parameter Scan Time = 12:08:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.29; Performer: Daniel,,Hogan


title: U87 at 20% O2, biological rep2

description: cell culture in hyperoxic conditions

value: brain


title: EGD2/alphaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80973.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 456; Parameter Laser on time = 52536; Parameter Laser Power = 3.56; Parameter Scan Time = 11:05:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 487; Parameter Scan Power = 100; Parameter Laser on time = 52540; Parameter Laser Power = 3.16; Parameter Scan Time = 11:05:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Daniel,,Hogan

value: v


title: HUVEC_young_rep2

description: miRNA expression of young HUVEC

source_name: HUVEC_PD <10_replicate 2

value: young


title: HUVEC_replicative senescent_rep2

source_name: HUVEC_PD > 48_replicate2


title: HUVEC_young_rep1

description: miRNA expression of young HUVEC

source_name: HUVEC_PD <10_replicate 1


title: Metaphase II oocyte, biological rep2

source_name: Mouse metaphase II oocyte

value: Metaphase II oocyte


title: RPL17 IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80739.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 454; Parameter Laser on time = 52053; Parameter Laser Power = 3.50; Parameter Scan Time = 12:05:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.77; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 473; Parameter Scan Power = 100; Parameter Laser on time = 52056; Parameter Laser Power = 3.18; Parameter Scan Time = 12:05:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.77; Performer: Daniel,,Hogan

value: total rna

value: wt


title: IVF embryo, 1-cell stage, biological rep2

source_name: Mouse in vitro fertilized embryo, 1-cell stage

value: In vitro fertilization

value: 1-cell stage


title: IVF embryo, 1-cell stage, biological rep3


title: sh control D vs. IB10 A

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).

growth_protocol: pLKO-puro constructs (sh Kdm5c #1-TRCN0000097857 and sh Kdm5c #2- TRCN0000097858) expressing shRNAs that target Kdm5c were obtained from Sigma-Aldrich. As a control for the knockdown experiments, a non-targeting shRNA with the following sequence 5-CCGGGCGAACAAGAAGAAGGACAAACTCGAGTTTGTCCTTCTTCTTGTTCGCTTTTT was used. Viral production was performed in Cos7 by transfection of 2 µg each of pRSV-rev, pMDLg/pRRE, pMD2.G, and pLKO-shRNA using Fugene 6 (Roche). Viral-containing medium was collected at 48 h after transfection. Polybrene (8 ug/ml final concentration) was used to enhance infection efficiency. Infection was repeated 1-2 times with 25 h intervals. Puromycin selection was started 24 h after the last infection. Polyclonal cell lines were created by pooling surviving colonies. IB10 (E14 ES) mouse embryonic stem cells were cultured on gelatin-coated dishes in high glucose (4.5 g/l) DMEM (Gibco) media supplemented with 15% Fetal bovine serum, 100 µg/ml Pen/Strep, 2 mM L-glutamine, 100 µM ?-mercaptoethanol, 1 mM natrium pyruvate, 100 µM non-essential amino acids and leukemia inhibitory factor (LIF).

extract_protocol: Trizol

value: E14 ES

tag: treatment

value: control-sh

value: untreated


title: shKdm5c#2 D vs. IB10 A


title: DeltaNACSrpgenomic (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81832.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 520, 4280; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Marta,,Del Alamo

source_name: total rna

value: egd1 egd2


title: U87 at 20% O2, biological rep1

description: cell culture in hyperoxic conditions


title: shKdm5c#1 D vs. IB10 A


title: shKdm5c#1 B vs. IB10 A


title: Metaphase II oocyte, biological rep1


title: IVF embryo, 1-cell stage, biological rep1


title: Metaphase II oocyte, biological rep3


title: sh control B vs. IB10 A


title: senescent cells, replicate 3

first: Amaia

last: Lujambio

address: 1275 York Avenue

department: CBG

institute: MSKCC

description: Gene expression data from senescent stellate cells, with p53 expression

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

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

data_processing: RMA

label: Biotin

source_name: Murine hepatic stellate cells

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: DMEM supplemented with 10% FBS, 1% glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin

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

value: isolated senescent murine hepatic stellate cells

value: control

tag: genetic background


title: shKdm5c#2 B vs. IB10 A


title: IB10 A vs. sh control C


title: IB10 A vs. sh control A


title: senescent cells, replicate 2


title: DeltaNACSrpgenomic (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/81834.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 520, 4280; Software: type: feature extraction; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Marta,,Del Alamo 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Marta,,Del Alamo


title: IB10 A vs. shKdm5c#2 C


title: senescent cells, replicate 1


title: proliferating cells, replicate 3

description: Gene expression data from proliferating stellate cells, with p53 knockdown

value: isolated proliferating murine hepatic stellate cells

value: Doxycycline (1ug/ml)


title: RPL17 IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80737.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 417; Parameter Laser on time = 52117; Parameter Laser Power = 3.51; Parameter Scan Time = 13:09:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.54; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 493; Parameter Scan Power = 100; Parameter Laser on time = 52120; Parameter Laser Power = 3.14; Parameter Scan Time = 13:09:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.54; Performer: Daniel,,Hogan

source_name: total rna extract

source_name: affinity purified RNA


title: Mycelium_CYA_8d

status: Public on Apr 04 2013

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

hyb_protocol: 1.65 µg labeled cRNA was fragmented at 60 deg C on a heating block and the cRNA was prepared for hybridization according to the QALI protocol. 100 µl sample was loaded on a 4x44 Agilent Gasket Slide situated in an Agilent Technologies hybridization chamber. The 4x44 array was placed on top of the Gasket Slide. The array was hybridized at 65 deg C for 17 hours in an Agilent Technologies Hybridization oven.

scan_protocol: The array was washed following the QALI protocol and scanned in a G2505C Agilent Technologies Micro Array Scanner according to the same protocol.

data_processing: The raw array signal was processed by first removing the background noise using the normexp method, and the signal between arrays was made comparable using the quantiles normalization method, as implemented in the Limma package (Smyth et al., 2005). Multiple probe signals per gene were summarized into gene-level expression indices using Tukey's median polish, as performed in the last step of the RMA processing method (Irizarry, 2003).

organism: Aspergillus nidulans

source_name: Fungal mycelium, grown on CYA medium, cultivated for 8 days

label_protocol: 150 ng in 1.5 µL total RNA was labeled according to the One-Color Labeling for Expression Analysis, Quick Amp Low Input (QALI) manual version 6.5 May 2010 from Agilent Technologies. Yield and specific activity were determined on a NanoDrop ND-1000 spectrophotometer and verified on a Qubit 2.0 fluorometer (Invitrogen).

growth_protocol: All strains were three-point inoculated on the media and incubated at 32 deg C in darkness for 4, 8 or 10 days.

extract_protocol: For RNA purification, 40-50 mg of frozen mycelium was placed in a 2 ml microcentrifuge tube, and precooled in liquid nitrogen containing three steel balls (two balls with a diameter of 2 mm and one ball with a diameter of 5 mm). The tubes were then shaken in a Retsch Mixer Mill at 5 deg C for 10 min, until the mycelium was ground to a powder. Total RNA was isolated from the powder using the Qiagen RNeasy Mini Kit, according to the protocol for isolation of total RNA from plant and fungi, including the optional use of the QiaShredder column. Quality of the purified RNA was verified using a NanoDrop ND-1000 and an Agilent 2100 Bioanalyzer.

treatment_protocol: Whole colonies from three-stab agar plates were sampled for transcriptional analysis by scraping the mycelium off the agar with a scalpel and transferring directly into a 50 mL Falcon tube containing app. 15 mL of liquid nitrogen. Care was taken to transfer a minimum of agar to the Falcon tube. The liquid nitrogen was allowed to evaporate before capping the lid and re-cooling the tube in liquid nitrogen before storing the tube at -80 deg C until use for RNA purification.

tag: tissue

value: mycelium

tag: growth medium

value: CYA

tag: sampling time

value: 8 days


title: Mycelium_CYA_10d

source_name: Fungal mycelium, grown on CYA medium, cultivated for 10 days

value: 10 days


title: IB10 A vs. shKdm5c#1 A

tag: cell line

tag: cell type


title: EGD2/alphaNAC IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (2)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80974.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 434; Parameter Laser on time = 52552; Parameter Laser Power = 3.52; Parameter Scan Time = 11:21:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 474; Parameter Scan Power = 100; Parameter Laser on time = 52555; Parameter Laser Power = 3.16; Parameter Scan Time = 11:21:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Daniel,,Hogan


title: proliferating cells, replicate 1


title: IB10 A vs. shKdm5c#1 C


title: proliferating cells, replicate 2


title: Mycelium_CYAs_10d

source_name: Fungal mycelium, grown on CYAs medium, cultivated for 10 days

value: CYAs


title: Mycelium_CYA_4d

source_name: Fungal mycelium, grown on CYA medium, cultivated for 4 days

value: 4 days


title: Mycelium_YESs_10d

source_name: Fungal mycelium, grown on YES medium, cultivated for 10 days

value: YES


title: Mycelium_YESs_4d

source_name: Fungal mycelium, grown on YES medium, cultivated for 4 days


title: IB10 A vs. shKdm5c#2 A


title: RPL16A IP  YPAD/5mM MgCl2/cyclohexamide/150 mM KCl (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80736.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 200, 5920; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 52100; Parameter Laser Power = 3.51; Parameter Scan Time = 12:52:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.38; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 469; Parameter Scan Power = 100; Parameter Laser on time = 52103; Parameter Laser Power = 3.14; Parameter Scan Time = 12:52:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.38; Performer: Daniel,,Hogan

value: total rna

value: wt


title: Serum_control_pooled, rep1

city: Shanghai

first: Dongwei

last: Dai

address: 168 Changhai Road

country: China

institute: Changhai Hospital

description: Serum samples from 10 controls were pooled into a single control sample.

hyb_protocol: Agilent Human 8 x 60K miRNA Array was performed on the two pooled samples. Hybridization was carried out according to the instructions of the Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data were acquired using the Agilent G2565BA Microarray Scanner System and Agilent Feature Extraction Software (Scan resolution 5μm, PMT 100%). Probe intensities were normalized using GeneSpring 12.0 through percentile shift normalization. Differentially expressed miRNAs were identified through Fold Change filtering (Fold change >2).

source_name: Venous blood, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.

extract_protocol: Trizol Reagent (Invitrogen, Carlsbad, CA) was used for serum denaturizing and the Qiagen miRNeasy Mini kit (Qiagen, Valencia, CA) for RNA collection and purification according to the manufacturer's protocol.

treatment_protocol: The whole blood was separated into serum and cellular fractions by centrifugation at 4,000 rpm for 10 min, followed by 12000 rpm for 15 min to completely remove cell debris. To detect the generalizable signatures of serum miRNAs for MMD, we pooled serum samples from 10 patients and 10 controls.

value: blood serum

tag: disease status


title: Mycelium_CYAs_8d

source_name: Fungal mycelium, grown on CYAs medium, cultivated for 8 days


title: Mycelium_CYAs_4d

source_name: Fungal mycelium, grown on CYAs medium, cultivated for 4 days


title: Serum_MMD_pooled, rep1

description: Serum samples from 10 patients were pooled into a single MMD sample.

source_name: Venous blood, MMD

value: moyamoya disease (MMD)


title: HB_BDCA1_BC2

city: Dallas

first: Chun

middle: I

last: Yu

state: TX

address: 3434 Live Oak St

institute: Baylor Institute for Immunology Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol and scanned with Illumina iScan.

data_processing: The data were background subtracted and average normalized using Illumina Genome Studio.

source_name: BDCA1+ mDCs from Human blood

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre).

extract_protocol: Total RNA were extracted using the RNAqueous-Micro Kit (Life Technologies) according to the manufacturer's instructions.

value: Human blood

tag: cell population

value: BDCA1+ mDCs

tag: donor

value: BC2 (Human blood sample 2)


title: HB_BDCA3_BC2

source_name: BDCA3+ mDCs from Human blood

value: BDCA3+ mDCs


title: HL_BDCA3_HL157

source_name: BDCA3+ mDCs from Human lungs

value: Human lungs

value: HL157  (Human lungs sample 157)


title: HB_BDCA1_BC1

value: BC1 (Human blood sample 1)


title: HL_BDCA1_HL157

source_name: BDCA1+ mDCs from Human lungs


title: HL_BDCA3_HL158

value: HL158  (Human lungs sample 158)


title: HML_BDCA3_Flu123

source_name: BDCA3+ mDCs from Humouse lungs

value: Humouse lungs

value: Flu123 (Humouse lungs sample 123)


title: HL_BDCA1_HL158


title: HB_BDCA3_BC3

value: BC3 (Human blood sample 3)


title: HMS_BDCA3_Flu120

source_name: BDCA3+ mDCs from Humouse spleen

value: Humouse spleen

value: Flu120 (Humouse lungs sample 120)


title: HMS_BDCA1_Flu123

source_name: BDCA1+ mDCs from Humouse spleen


title: HB_BDCA1_BC3


title: HMS_BDCA3_Flu123


title: HMS_BDCA1_Flu120


title: HML_BDCA1_Flu123

source_name: BDCA1+ mDCs from Humouse lungs


title: HML_BDCA3_Flu120


title: AML Patient 14

city: Cambridge

first: Weng Khong

last: Lim

state: Cambridgeshire

address: Tennis Court Road

country: United Kingdom

institute: Cambridge Systems Biology Centre

hyb_protocol: The cRNA is hybridised to the Illumina beadchip following the Direct Hybridisation assay

scan_protocol: Illumina bead array scanner was used according to manufacturer's instructions

data_processing: Beadsummary data was loaded into the R environment and processed using the beadarray package. VSN normalisation was performed. Only probes common between HumanHT-12 V4.0 and HumanWG-6 v3.0 were retained and considered for further analysis.

source_name: AML patient blasts

label_protocol: RNA samples are amplified using the TotalPrep 96-RNA amplification kit from Ambion (Applied Biosystems). RNA is converted into cDNA, and amplified by In Vitro Transcription (IVT) to generate biotin-labelled cRNA.

extract_protocol: RNA extraction was performed using Trizol(r) according to manufacturer's instructions

tag: gender

value: Male

tag: age

tag: status(dd(dead)/al(alive))

value: DD

tag: overall survival (months)

tag: karyotype

value: monosomy 7

tag: wbc

tag: fab subtype

tag: npm1 mutation

value: no

tag: secondary?

value: NO


title: AML Patient 19

value: AL


title: AML Patient 7

value: Female

value: yes

value: ITD


title: AML Patient 13


title: AML Patient 9


title: AML Patient 22


title: AML Patient 21


title: HB_BDCA3_BC1

tag: tissue

value: Human blood

value: BDCA3+ mDCs


title: MHZ7-shoot-air

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

institute: IGDB

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Rice Genome Array in the Hybridization Oven 640. GeneChips were washed and stained in Fluidics Station 450.

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

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.

organism: Oryza sativa

source_name: shoots in air

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (IVT Labeling Kit, Affymetrix). ，

growth_protocol: The seeds were soaked in tap-water and germinated at 37°C in the dark for two days (change the water daily).

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

treatment_protocol: For ethylene treatment, we reduced the amount of water to 1.5-1.7cm below the seeds.Three-day old seedlings were treated with ethylene (10 ppm) for 8 hours at 28°C in the dark. Seedling grown in the air  was used as control. We isolated RNA from roots and shoots of wild-type and mutant.

value: shoot


title: HML_BDCA1_Flu120

value: Humouse lungs

value: BDCA1+ mDCs


title: MHZ7-root-ethylene

description: Gene expression data

source_name: roots with ethylene treatment

value: root


title: MHZ7-shoot-ethylene

description: Gene expression data

source_name: shoots with ethylene treatment


title: WT-root-ethylene

description: Gene expression data


title: WT-shoot-ethylene

description: Gene expression data


title: L3.6pl, #1, PD0325901

city: San Francisco

first: Stephan

middle: Christoph

last: Gysin

state: California

address: 1450 3rd Street

department: HDFCCC

institute: UCSF

description:
222 84B_L3.6pl+
gene expression data of orthotopic tumors grown in pancreas of nude mice

hyb_protocol: Fragmented amplified cDNA was hybridized to AffymetrixHG-U133A 2.0 gene chips according to manufacturer's protocols (Affymetrix).

scan_protocol: Scanning was performed according to Affymetrix protocols

data_processing: Raw hybridization data was preprocessed using Affymetrix Expression Console software (program-id = 1.3.0.187).

label_protocol: 2ug of total RNA was converted to cDNA, amplified, and biotinylated using the Message Amp II mRNA amplification kit from Ambion

growth_protocol: Human pancreatic cancerderived cell lines were mixed 1:1 with Matrigel and injected subcapsularly into the pancreas of 6-week-old  female nu/nu mice.

extract_protocol: Orthotopic tumors were excised from euthanized mice and then portions were either snap frozen in liquid nitrogen or fixed in formalin

treatment_protocol: Tumor-bearing mice were treated with 15 mg/kg PD0325901 in HPMT [0.5% hydroxypropylmethylcellulose, 0.2%(v/v) Tween-80] once daily by oral gavage. Before isolation of tumor-derived mRNA, mice were drug dosed twice at 24 and then 12 hours before euthanasia.

value: pancreas

value: human pancreatic cancer cells

tag: host strain

value: 6-wk-old  female nu/nu mouse

tag: treated with


title: WT-shoot-air

description: Gene expression data


title: L3.6pl, #2, PD0325901

description:
223 82B_L3.6pl+
gene expression data of orthotopic tumors grown in pancreas of nude mice

tag: cell line


title: L3.6pl, #3, vehicle

description:
224 87C_L3.6pl-
gene expression data of orthotopic tumors grown in pancreas of nude mice

tag: cell type

value: vehicle control


title: SU86.86, #4, PD0325901

description:
220 2406_SU86.86+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: SU86.86, #3, PD0325901

description:
219 2405_SU86.86+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: WT-root-air

description: Gene expression data

source_name: roots in air


title: SU86.86, #1, vehicle

description:
217 2409_SU86.86-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: AML Patient 23

value: DD

value: TKD


title: SU86.86, #2, vehicle

description:
218 2410_SU86.86-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Hs766T, #2, PD0325901

description:
216 2381_Hs766T+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Panc-2.12, #2, vehicle

description:
210 2403_2.13-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: MHZ7-root-air

description: Gene expression data


title: Panc-2.12, #6, PD0325901

description:
214 2401_2.13+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: L3.6pl, #4, vehicle

description:
225 83C_L3.6pl-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Panc-2.12, #1, vehicle

description:
209 2402_2.13-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Panc-2.12, #4, PD0325901

description:
212 2399_2.13+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: MIAPaCa-2 #4, PD0325901

description:
205 2591_MIA+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: MIAPaCa-2, #5, PD0325901

description:
206 2592_MIA+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Panc-2.12, #5, PD0325901

description:
213 2400_2.13+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Hs766T, #1, vehicle

description:
215 2386_Hs766T-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: Panc-2.12, #3, vehicle

description:
211 2404_2.13-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: normal human pancreatic cancer cells specimen 3, replica 1

growth_protocol: human pancreatic cancer cell lines were grown in culture in 3 replicas for vehicle control and 3 replicas for treatment

extract_protocol: Cells were collected and RNA was extracted using Rneasy from QIAGEN

treatment_protocol: Cells were treated either with vehicle or 2mM CI-1040 for 24 hours

value: normal human pancreatic ductal epithelial cells


title: MIAPaCa-2 #1, vehicle

description:
201 2563_MIA-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: PL45, #2, vehicle

description:
207 2600_PL45-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: PL45, #3, PD0325901

description:
208 2595_PL45+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: L3.6sl untreated, replica 3

source_name: L3.6sl untreated


title: MIAPaCa-2 #2, vehicle

description:
202 2593_MIA-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: normal human pancreatic cancer cells specimen 3, replica 2


title: L3.6sl treated, replica 3

source_name: L3.6sl treated

value: 2mM CI-1040 for 24 hours


title: L3.6sl treated, replica 2


title: normal human pancreatic cancer cells specimen 3, replica 3


title: L3.6sl untreated, replica 2


title: MIAPaCa-2 #3, vehicle

description:
203 2594_MIA-
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: L3.6sl untreated, replica 1


title: L3.6sl treated, replica 1


title: L3.3 untreated, replica 1

source_name: L3.3 untreated


title: PL45 #1, PD0325901

description:
204 2564_PL45+
gene expression data of orthotopic tumors grown in pancreas of nude mice


title: L3.3 untreated, replica 3


title: L3.3 treated, replica 1

source_name: L3.3 treated


title: COLO357 treated, replica 3

source_name: COLO357 treated


title: L3.3 untreated, replica 2


title: COLO357 untreated, replica 3

source_name: COLO357 untreated


title: L3.6pl treated, replica 2

source_name: L3.6pl treated


title: COLO357 treated, replica 2


title: L3.3 treated, replica 2


title: COLO357 untreated, replica 2


title: L3.6pl treated, replica 3


title: COLO357 treated, replica 1


title: L3.6pl untreated, replica 3

source_name: L3.6pl untreated


title: L3.6pl treated, replica 1


title: L3.6pl untreated, replica 2


title: Panc-2.03 untreated, replica 3

source_name: Panc-2.03 untreated


title: L3.6pl untreated, replica 1


title: Panc-2.03 treated, replica 2

source_name: Panc-2.03 treated


title: Panc-2.03 treated, replica 3


title: PL45 treated, replica 3

source_name: PL45 treated


title: Panc-2.03 untreated, replica 2


title: Panc-2.03 treated, replica 1


title: Panc-2.03 untreated, replica 1


title: PL45 untreated, replica 3

source_name: PL45 untreated


title: PL45 treated, replica 1


title: PL45 untreated, replica 1


title: L3.3 treated, replica 3


title: MPanc-96 treated, replica 3

source_name: MPanc-96 treated


title: PL45 untreated, replica 2


title: PL45 treated, replica 2


title: Mpanc-96 untreated, replica 2

source_name: Mpanc-96 untreated


title: MPanc-96 treated, replica 2


title: MPanc-96 treated, replica 1


title: Mpanc-96 untreated, replica 1


title: Mpanc-96 untreated, replica 3


title: Capan-2 treated, replica 3

source_name: Capan-2 treated


title: Capan-2 treated, replica 1


title: Capan-2 treated, replica 2


title: Capan-2 untreated, replica 3

source_name: Capan-2 untreated


title: COLO357 untreated, replica 1


title: genomic DNA extracted from TS603 maintained in 5198 for 20 passages Biological replicated 1

type: genomic

first: Daniel

last: Rohle

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: methylation data in cell lines

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 was used to export data to Partek Genomics Suite Format

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Oligodendroglioma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: mutation

value: Oligodendroglioma

tag: treatment


title: genomic DNA extracted from TS603 maintained in DMSO for 20 passages Biological replicated 2

description: methylation data in cell lines

value: DMSO


title: genomic DNA extracted from TS603 maintained in DMSO for 20 passages Biological replicated 1

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in 5198 for 15 passages Biological replicated 1

description: methylation data in cell lines


title: Capan-2 untreated, replica 2


title: Panc-5.04 treated, replica 3

source_name: Panc-5.04 treated


title: genomic DNA extracted from TS603 maintained in DMSO for 15 passages Biological replicated 1

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in 5198 for 4 passages Biological replicated 2

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in 5198 for 20 passages Biological replicated 2

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in DMSO for 15 passages Biological replicated 2

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in DMSO for 4 passages Biological replicated 1

description: methylation data in cell lines


title: Panc-5.04 untreated, replica 3

source_name: Panc-5.04 untreated


title: Panc-5.04 treated, replica 2


title: Panc-5.04 treated, replica 1


title: genomic DNA extracted from TS603 maintained in DMSO for 2 passages Biological replicated 2

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in DMSO for 4 passages Biological replicated 2

description: methylation data in cell lines


title: SW1990 treated, replica 3

source_name: SW1990 treated


title: vehicle m10

description:
genomic DNA from TS603 treated xenografts
methylation data in xenografts

value: vehicle


title: 150mg/kg AGI-5198 m20


title: Panc-5.04 untreated, replica 2


title: genomic DNA extracted from TS603 maintained in 5198 for 4 passages Biological replicated 1

description: methylation data in cell lines


title: SW1990 treated, replica 2


title: genomic DNA extracted from TS603 maintained in 5198 for 2 passages Biological replicated 1

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in 5198 for 2 passages Biological replicated 2

description: methylation data in cell lines


title: genomic DNA extracted from TS603 maintained in 5198 for 15 passages Biological replicated 2

description: methylation data in cell lines


title: SW1990 untreated, replica 3

source_name: SW1990 untreated


title: genomic DNA extracted from TS603 maintained in DMSO for 2 passages Biological replicated 1

description: methylation data in cell lines


title: 450mg/kg AGI-5198 m39


title: 150mg/kg AGI-5198 m18


title: 450mg/kg AGI-5198 m40


title: vehicle m9


title: Capan-2 untreated, replica 1


title: vehicle m8


title: SW1990 treated, replica 1


title: Panc-5.04 untreated, replica 1


title: SW1990 untreated, replica 2


title: 150mg/kg AGI-5198 m19


title: SU86.86 treated, replica 3

source_name: SU86.86 treated


title: 150mg/kg AGI-5198 m17


title: vehicle m7


title: SW1990 untreated, replica 1


title: SU86.86 untreated, replica 3

source_name: SU86.86 untreated


title: vehicle m6


title: SU86.86 treated, replica 2


title: 150mg/kg AGI-5198 m16


title: SU86.86 untreated, replica 2


title: SU86.86 untreated, replica 1


title: 450mg/kg AGI-5198 m38


title: lung tumor - transgenic - 1

city: Hanover

first: Sarah

last: Freemantle

state: NH

department: Pharmacology and Toxicology

institute: Geisel School of Medicine at Dartmouth

description: Gene expression data from lung adenocarcinoma of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TG+5

hyb_protocol: Hybridizations were performed according to Affymetrix guidelines at the Dartmouth College Microarray Shared Resource using an Affymetrix GeneChip Workstation.

scan_protocol: GeneChips were scanned at the Dartmouth College Microarray Shared Resource using an Affymetrix GeneChip Workstation

data_processing: Raw data was converted to GC-RMA in the GeneSifter Analysis Edition (Geospiza Inc.) for subsequent analysis

source_name: Murine cyclin E transgenic lung tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: FVB nontransgenic and human surfactant protein C promoter-driven human cyclin E expressing transgenes were allowed to age to 7-11 months

extract_protocol: Total RNA was extracted with Trizol as per the manufacturer's instructions

treatment_protocol: Normal lung tissue and adenocarcinomas were identified by gross pathology and isolated and stored in RNAlater (Qiagen)

tag: strain

value: FVB transgene human surfactant protein C promoter-driven wild-type human Cyclin E

value: m

value: lung adenocarcinoma


title: 150mg/kg AGI-5198 m15


title: lung tumor - transgenic - 2

description: Gene expression data from lung adenocarcinoma of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TG+12

tag: gender


title: SU86.86 treated, replica 1


title: MIAPaCa-2 treated, replica 3

source_name: MIAPaCa-2 treated


title: lung tumor - transgenic - 3

description: Gene expression data from lung adenocarcinoma of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TG+14


title: lung tumor - transgenic - 4

description: Gene expression data from lung adenocarcinoma of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TG+16


title: 450mg/kg AGI-5198 m36


title: normal lung - transgenic- 4

description: Gene expression data from normal lung of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TGT17

source_name: Murine cyclin E transgenic normal lung

value: lung


title: normal lung - transgenic- 2

description: Gene expression data from normal lung of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TGT13


title: normal lung - transgenic- 3

description: Gene expression data from normal lung of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TGT15


title: MIAPaCa-2 treated, replica 2


title: 450mg/kg AGI-5198 m33


title: vehicle m5


title: 450mg/kg AGI-5198 m34


title: 150mg/kg AGI-5198 m14


title: normal lung - transgenic- 1

description: Gene expression data from normal lung of lung-specific Cyclin E overexpressing mice, tissue adjacent to sample TGT6


title: MIAPaCa-2 untreated, replica 1

source_name: MIAPaCa-2 untreated


title: normal lung - nontransgenic - 3

description: Gene expression data from normal FVB murine lung tissue

source_name: Murine nontransgenic normal lung

value: FVB


title: vehicle m4


title: Panc-10.05 treated, replica 3

source_name: Panc-10.05 treated


title: MIAPaCa-2 treated, replica 1


title: normal lung - nontransgenic - 1


title: N-Ras KO

first: stephen

last: Lynch

address: 550 First Ave

institute: NYU Langone School of Medicine

description: N KO

hyb_protocol: labeled and fragmented cRNA hybridized to MG-430 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent Genespring GX11 program. No further adjustments were made to the data in the table.

source_name: thymocytes

label_protocol: Labeled target cRNA population was generated using the Double-Stranded cDNA Synthesis kit (Life Technologies) and the Bioarray HighYield RNA Transcript Labeling Kit (T7) (Enzo Life Sciences) according to the manufacturer's instructions.

growth_protocol: The generation of the N-Ras KO and H-Ras KO lines on the 129/SJ background was described elsewhere (Umanoff, et al., 1995; Esteban LM, et al, 2001). N-Ras  and H-Ras heterozygous mice were bred to produce homozygous KO mice and WT mice.  Mice were given ad libitum access to food and water. 12h/12h light/dark cycles.

extract_protocol: Total RNA was isolated from thymocytes using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Thymocytes were isolated from 6-20 week old N-ras KO mice, H-Ras KO mice and their WT littermates.

tag: genotype/variation

value: N-Ras KO

value: thymocytes

value: no treatment


title: MIAPaCa-2 untreated, replica 3

value: human pancreatic cancer cells


title: MIAPaCa-2 untreated, replica 2

value: vehicle control


title: WT stimulated 2

source_name: CD4+ T cell splenocytes

growth_protocol: The generation of the N-Ras KO line on the 129/SJ background was described elsewhere (Umanoff, et al., 1995). N-Ras heterozygous mice were bred to produce N-Ras homozygous KO mice and WT mice.  Mice were given ad libitum access to food and water. 12h/12h light/dark cycles.

extract_protocol: Total RNA was isolated from stimulated and unstimulated CD4+ T cells using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: CD4+ T cell splenocytes were isolated from 6-20 week old N-ras KO mice and their WT littermates.  CD4+T cells were then grown overnight in T cell growth media either with or without 1 microgram/mililiterl anti-CD3 and anti-CD28 antibodies.

value: WT

value: CD4+ T cell splenocytes

value: low level TCR stimulus


title: normal lung - nontransgenic - 2


title: 150mg/kg AGI-5198 m13


title: N-Ras KO stimulated 3


title: WT stimulated 1


title: N-Ras KO stimulated 1


title: vehicle m2


title: wildtype

description: WT

value: wildtype


title: vehicle m3

value: Oligodendroglioma


title: N-Ras KO stimulated 2


title: WT stimulated 3


title: 450mg/kg AGI-5198 m32


title: H-Ras KO

description: H KO

value: H-Ras KO


title: normal lung - nontransgenic - 4


title: 150mg/kg AGI-5198 m12


title: Panc-10.05 treated, replica 2

value: 2mM CI-1040 for 24 hours


title: WT control 3

value: control


title: mRNA expression in fertilized embryonic stem cells, rep 2

city: Cheongju

first: Nam-Hyung

last: Kim

state: Chungbuk

address: Gaeshin-dong

country: South Korea

institute: Chungbuk National University

description:
Sample 7
Fertilized embryonic stem cell (fESC, FE).

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8 Expression BeadChip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal values were transformed by logarithm and normalized by the quantile method.

source_name: Mouse fertilized embryonic stem cell (fESC)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: Total RNA extraction was performed with the mirVana extraction kit (Ambion).

value: female and male

value: fertilized embryonic stem cells

tag: chromosomes contained

value: both X and Y

tag: passage


title: mRNA expression in fertilized embryonic stem cells, rep 1

description:
Sample 6
Fertilized embryonic stem cell (fESC, FE).


title: WT control 2


title: WT control 1


title: Panc-10.05 untreated, replica 3

source_name: Panc-10.05 untreated


title: Panc-10.05 treated, replica 1


title: mRNA expression in parthenogenetic embryonic stem cells, rep 1

description:
Sample 4
Parthenogenetic embryonic stem cell (pESC, PA).

source_name: Mouse parthenogenetic embryonic stem cell (pESC)

value: female

value: parthenogenetic embryonic stem cells


title: N-Ras KO control 3

value: N-Ras KO


title: N-Ras KO control 2


title: 150mg/kg AGI-5198 m11

source_name: Oligodendroglioma


title: N-Ras KO control 1


title: mRNA expression in androgenetic embryonic stem cells, rep 3

description:
Sample 3
Androgenetic embryonic stem cell: aESC (AN).

source_name: Mouse androgenetic embryonic stem cell (aESC)

value: androgenetic embryonic stem cells


title: 450mg/kg AGI-5198 m31


title: vehicle m1

value: vehicle


title: Panc-10.05 untreated, replica 1

value: human pancreatic cancer cells

value: vehicle control


title: Panc-3.27 treated, replica 3

source_name: Panc-3.27 treated