title: A2 and D5 Fiber 2 DPA (58053)

description: A2 and D5 Fiber 2 DPA (58053)

value: Fiber 2 DPA

tag: soil type

value: Bessey Mix

tag: soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: date planted

tag: planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: average temperature (c)

value: 80 daytime - 70 nighttime

tag: day light regime

tag: light sources

tag: night duration

tag: age at harvest


title: ech4-ADK72

status: Public on Jul 25 2009

type: RNA

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

country: France

institute: INSERM U915

hyb_protocol: Each individual Cy3-labeled sample was mixed with an equal amount of Cy5-labeled reference sample (1 µg each), fragmented using the RNA Fragmentation Reagents (Ambion), vacuum dried and dissolved in 42 µL hybridization solution (5X Denhardt, 3.5X SSC, 0.3% SDS, 0.5 µg/µL Yeast tRNA (Life Technologies), 0.5 µg/µL polyA RNA (Sigma), 50% formamide, H2O). Denaturation was achieved by heating at 98°C for 2 min and was immediately followed by a preannealing step at 37°C for 30 min. Hereafter, 40 µL of each sample were pipetted onto the chips. Hybridization was performed at 42°C for 17 h using a Glass Array Hybridization Cassette (Telechem). At the end, the chips were washed in the following washing solutions (2X SSC, 0.1% SDS; 1X SSC; 0.2X SSC; 0.05X SSC) and dried by centrifugation (3 min, 1200 rpm).

scan_protocol: Hybridized arrays were scanned by fluorescence confocal microscopy (ScanArray Express, Perkin-Elmer). Fluorescence signal measurements were obtained separately for each fluorochrome at 10 µm/pixel resolution.

data_processing: Hybridization and background signals were measured using GenePix Pro 5.0 image analysis software (Axon Instruments). Technical biases were corrected by a Lowess normalization using a channel-by-channel procedure. For each microarray, Cy3 and Cy5 signal intensities were individually normalized to the median profile of all Cy3 or Cy5 signal intensities (values below background were filtered out).

molecule: total RNA

organism: Homo sapiens

source_name: adenocarcinoma cell line

label_protocol: Amino allyl RNA (aRNA) were generated using the Amino Allyl MessageAmp II aRNA AmplificationKit (Ambion) according to manufacturer's recommandations, and were subsequently labeled using Cy3 Post-labeling Reactive Dye Pack (Amersham).

growth_protocol: All cell lines were were maintained in complete medium composed of RPMI 1640 supplemented with 10% heat inactivated FCS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin and 2 mM L-glutamine and cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated and treated with DNAse I using the RNAse-Free DNAse Set and the RNeasy Mini Kit (Qiagen).

tag: cell type

value: cells isolated from pleural effusion

tag: tumor histology

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

tag: age

value: 60 years old

tag: gender

value: male

source_name: reference sample

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: ancestor versus CV101 biological replicate 2, sample A, hybridization 1

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

country: USA

institute: University of Montana

hyb_protocol: Hybridization was performed using protocols developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications: Slides were blocked (using 5X SSC, 0.1% SDS, 1% Roche Blocking Reagent) prior to hybridization as described (http://www.genomics.princeton.edu/dunham/MDhomemadeDNA.pdf) (Roche Applied Science, Mannheim, Germany).

scan_protocol: Hybridized arrays were scanned using an Axon 4000B scanner and software package GenePix  5.0 (Molecular Devices, Sunnyvale, CA).

data_processing: Total intensity normalized, background subtracted data obtained from log2 of processed experimental signal/processed reference signal. TIGR TM4 software suite was used.

organism: Escherichia coli K-12

source_name: evolved strain CV101, monoculture

label_protocol: Samples were labeled following the protocol developed at the J. Craig Venter Institute (http://pfgrc.tigr.org/protocols/protocols.shtml) with the following modifications:  20 μg of total RNA was reverse transcribed using 9 μg of random hexamer and 0.83 mM 1:1 aa-dUTP:dTTP labeling mixture.

extract_protocol: Total RNA was extracted using an SDS lysis/ hot phenol method developed by the Dunham lab http://www.genomics.princeton.edu/dunham/MDyeastRNA.htm. Briefly, frozen filters were mixed with 4 mL lysis solution (10 mM EDTA, 0.5% SDS, 10 mM Tris pH 7.4) and vortexed to remove cells. An equal volume of acid phenol (pH 4.5) was added and the mixture was incubated at 65°C for 1 hour with frequent mixing. The entire extraction was transferred to a phase-lock gel tube (5Prime Inc., Gaithersburg, MD) and centrifuged according to the manufacturer’s instructions. The aqueous layer was extracted twice more with chloroform:isoamyl alcohol (24:1) and precipitated with ethanol. Pellets were dried and dissolved in RNase free water, treated with 0.1U/µl RQ1 RNase-free DNase at 37°C for 1 hour (Promega, Madison WI), then further purified using the Qiagen RNeasy Mini kit. RNA quality was assessed on agarose denaturing gels as well as using a Bioanalyzer (Agilent Technologies) and quantified spectrophotometrically

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

source_name: ancestral strain JA122, monoculture

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: ancestor versus CV116 biological replicate 1, sample B, hybridization 1

source_name: evolved strain CV116, monoculture


title: A2 and D5 Fiber 2 DPA (58054)

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description: A2 and D5 Fiber 2 DPA (58054)

hyb_protocol: Hybridization by NimbleGen

scan_protocol: Scanning by NimbleGen

data_processing: The procedure for spot detection was performed by NimbleGen.  All values of the 42,429 genes with 7 redundant probes per gene were median polished with Tukey's biweight prior to performing a standard mixed linear model (LM) analysis of the data for expression differences between each fiber developmental stage within and between accessions of G. barbadense.

organism:
Gossypium arboreum
Gossypium raimondii

source_name: Fiber 2 DPA

label_protocol: Labelling by NimbleGen

extract_protocol: Hot-borate / Li precipitation method("Wilkins and Smart, 1996")

tag: genome

value: A-genome and D-genome physical mixture

tag: polyploid level:

tag: tissue & age

tag: soil type

tag: soil mix

value: ambient daylight

value: sun and 10 hour day sodium supplemental lighting

value: natural

value: 20 weeks

tag: developmental stage at harvest

value: Mature plant

tag: harvest time(hours after daybreak)

tag: harvested tissue type

value: Fiber

tag: number of plants harvested


title: ech1-Met5A

source_name: SV40 transformed mesothelial cells

tag: cell type

value: MeT-5A cell line (CRL-9444)


title: jfw Fiber 2 DPA (58052)

description: jfw Fiber 2 DPA (58052)

organism: Gossypium raimondii

value: D-genome

tag: polyploid level

value: Fiber 2 DPA

value: Bessey Mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: date planted

tag: planting location

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

tag: average temperature (c)

value: 80 daytime - 70 nighttime

tag: day light regime

tag: light sources

tag: night duration

tag: age at harvest


title: ech3-ADK60

value: cells isolated from pleural effusion

tag: tumor histology

value: pleural metastasis from adenocarcinoma of the lung (TITF-1 positive)

tag: age

value: 68-year old woman

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: jfw Fiber 2 DPA (58051)

description: jfw Fiber 2 DPA (58051)

tag: genome

tag: tissue & age

tag: soil type

tag: soil mix

value: ambient daylight


title: ech2-ADK3

value: pleural metastasis from adenocarcinoma probably from lung origin

value: 64 years old

tag: gender

value: male


title: ancestor versus CV115 biological replicate 1, sample B, hybridization 1

source_name: evolved strain CV115, monoculture

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: ancestor versus CV115 biological replicate 1, sample A, hybridization 2


title: jfw Fiber 2 DPA (58050)

description: jfw Fiber 2 DPA (58050)

value: D-genome

tag: polyploid level

tag: date planted

tag: planting location

tag: average temperature (c)

value: sun and 10 hour day sodium supplemental lighting

value: natural

value: 20 weeks

tag: developmental stage at harvest

value: Mature plant

tag: harvest time(hours after daybreak)

tag: harvested tissue type

value: Fiber

tag: number of plants harvested


title: ancestor versus CV103 biological replicate 1, sample B, hybridization 1

source_name: evolved strain CV103, monoculture


title: Fiber 2 DPA (58049)

description: Fiber 2 DPA (58049)

organism: Gossypium tomentosum

tag: genome

value: Fiber 2 DPA

value: Bessey Mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

value: 80 daytime - 70 nighttime

tag: day light regime

tag: light sources

tag: night duration

tag: age at harvest


title: ancestor versus CV103 biological replicate 1, sample A, hybridization 2

tag: parent strain


title: ancestor versus CV103 biological replicate 1, sample A, hybridization 1

tag: growth medium


title: ancestor versus CV101 biological replicate 1, sample A, hybridization 2

tag: culture condition


title: ancestor versus CV101 biological replicate 1, sample B, hybridization 1

tag: ancestral strain


title: ancestor versus CV101 biological replicate 1, sample A, hybridization 1


title: E. coli heat shock gene expression data using random priming method (replicate-2)

city: Beijing

first: liu

last: hanhua

address: 18 Life Science Parkway

country: China

institute: CBC

description: data of obtained images were extracted with LuxScan 3.0 Software (CapitalBio).

hyb_protocol: For hybridization, labeled control and experimental samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80μl hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). Microarrays were hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C and 0.2% SSC) for 5 min at room temperature.

scan_protocol: After hybridization, slides were scanned with a confocal scanner LuxScanTM 10KA (CapitalBio)

data_processing: The raw data were normalized using a space and intensity-dependant LOWESS program. Data from faint spots were removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array. For each experimental and control sample, amplification and hybridization were performed by a dye-swap strategy in two independent experiments. Differentially expressed genes were identified with at least 2 fold changes and q<0.001 criteria using SAM software .

label: Cy3, Cy5

organism: Escherichia coli

source_name: E.coli,43°C, 60min

label_protocol: Starting with 0.5 μg of total RNA, a T7 RNA promoter sequence is attached to a random hexamer, which is used for reverse transcription of RNAs. RNase H removes RNA and leaves RNA oligomers as primers for a DNA polymerase to synthesize dsDNA. The dsDNA was puriﬁed and served as a template in subsequent IVT reaction for cRNA ampliﬁcation. 5μg of ampliﬁed cRNA was then transcribed into cDNA using reverse transcriptase.Prepared cDNA targets were puriﬁed using a PCR puriﬁcation kit (Qiagen, Valencia, CA, USA) and vacuum evaporated to 14 μl. Random nonamers (2μg) were added, heated to 95°C for 3 min and snap cooled on ice. The fluorescence labeling reactions contained 5×Klenow buffer, dNTP(120 mM dATP, 120 mM dGTP, 120 mM dTTP, 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and 5U Klenow enzyme (TaKaRa, Dalian, China). Reaction was carried out at 37°C for 90 min and stopped by addition of 25mM EDTA, 0.25% SDS. Labeled DNA targets were purified and quantified by UV spectrophotometry.

extract_protocol: Total RNA was isolated from E.coli cells using NucleoSpin® RNA II kit according to the manufacturers’ instructions (Macherey Nagel, Duren, Germany). RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray and RT-PCR verification.

tag: strain

label: Cy5, Cy3

source_name: E.coli,37°C, 60min


title: AKA 8401 Fiber 2 DPA (58046)

description: AKA 8401 Fiber 2 DPA (58046)

organism: Gossypium arboreum

value: A-genome

tag: polyploid level

tag: tissue & age

tag: soil type

tag: soil mix

tag: date planted

value: ambient daylight


title: Fiber 2 DPA (58048)

description: Fiber 2 DPA (58048)

tag: planting location

tag: average temperature (c)

tag: developmental stage at harvest

tag: harvest time(hours after daybreak)

tag: harvested tissue type


title: Fiber 2 DPA (58047)

description: Fiber 2 DPA (58047)

tag: genome

tag: day light regime

tag: light sources

tag: night duration

tag: number of plants harvested


title: ancestor versus CV115 biological replicate 1, sample A, hybridization 1

tag: parent strain

tag: growth medium

tag: culture condition

tag: ancestral strain


title: ech7-meso13

source_name: mesothelioma cell line

tag: cell type

value: cells isolated from pleural effusion

tag: tumor histology

value: epithelioid mesothelioma

tag: age

value: 81 years old

tag: gender

value: male

tag: rna pool

value: comprised of equal quantities of RNA from all samples


title: liver_female_Low feeding level_animal8

status: Public on Jul 24 2009

city: Madrid

first: Ana

middle: I

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

description: no additional information

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GCOS

data_processing: Bioconductor, GCRMA

label: biotin

organism: Sus scrofa

source_name: liver sample at 211 days, female, low

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, MIAME recommendations

growth_protocol: Pigs were fed twice daily with the same pelleted diet until restriction diet

extract_protocol: RiboPure RNA isolation kit

treatment_protocol: Liver samples were mantained at -80ºC

tag: breed

value: Iberian

tag: tissue

value: liver

value: female

tag: feeding protocol

value: low


title: liver_male_High feeding level_animal4

description: no additional information

source_name: liver sample at 211 days, male, high

value: high


title: E. coli heat shock gene expression data using direct labeling method (replicate-2)

label_protocol: Prepared cDNA targets were puriﬁed using a PCR puriﬁcation kit (Qiagen, Valencia, CA, USA) and vacuum evaporated to 14 μl. Random nonamers (2μg) were added, heated to 95°C for 3 min and snap cooled on ice. The fluorescence labeling reactions contained 5×Klenow buffer, dNTP(120 mM dATP, 120 mM dGTP, 120 mM dTTP, 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and 5U Klenow enzyme (TaKaRa, Dalian, China). Reaction was carried out at 37°C for 90 min and stopped by addition of 25mM EDTA, 0.25% SDS. Labeled DNA targets were purified and quantified by UV spectrophotometry.

tag: strain

extract_protocol: Total RNA was isolated from E.coli cells using NucleoSpin® RNA II kit according to the manufacturers’ instructions (Macherey Nagel, Duren, Germany). RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray and RT-PCR verification


title: AKA 8401 Fiber 2 DPA (58045)

description: AKA 8401 Fiber 2 DPA (58045)

tag: genome

tag: polyploid level

tag: tissue & age

value: Fiber 2 DPA

tag: soil type

tag: soil mix

tag: date planted

tag: planting location

tag: average temperature (c)

tag: day light regime

value: sun and 10 hour day sodium supplemental lighting

value: natural

tag: age at harvest

value: 20 weeks

tag: developmental stage at harvest

value: Mature plant

tag: harvest time(hours after daybreak)

tag: harvested tissue type

value: Fiber


title: E. coli heat shock gene expression data using random priming method (replicate-1)

source_name: E.coli, 37°C, 60min


title: ancestor versus CV116 biological replicate 1, sample A, hybridization 1

tag: parent strain

tag: growth medium

value: Davis minimal medium with 0.0125% glucose

tag: culture condition

value: chemostat, dilution rate=0.2/hr.

tag: ancestral strain

value: chemostat, dilution rate = 0.2/hr


title: liver_male_Low feeding level_animal2

description: no additional information

source_name: liver sample at 211 days, male, low

tag: breed

tag: tissue

tag: gender

tag: feeding protocol


title: Bcl-6 GFP positive repeat 1

city: Sydney

first: Di

last: Yu

address: 384 Victoria Street

department: Immunology and inflammation

country: Australia

institute: The Garvan Institute of Medical Research

description: Bcl-6, GFP positive repeat1

hyb_protocol: according to manufacturer protocol

scan_protocol: according to manufacturer protocol

label: according to manufacturer protocol

organism: Mus musculus

source_name: Bcl-6 GFP positive repeat 1

label_protocol: according to manufacturer protocol

extract_protocol: Total RNAs were isolated using mirVana miRNA Isolation Kit (Applied Biosystems).

tag: cell type

value: CD4+ T cells


title: Bcl-6 GFP positive repeat 2

description: Bcl-6, GFP positive repeat2

source_name: Bcl-6 GFP positive Repeat 2


title: AKA 8401 Fiber 2 DPA (58044)

description: AKA 8401 Fiber 2 DPA (58044)

tag: genome

value: A-genome

tag: polyploid level

tag: tissue & age

tag: soil type

value: Bessey Mix

tag: soil mix

value: "50% Canadian Spagum Peat :40% Coarse Perlite :10% Mineral Soil (""Iowa Dirt"")"

tag: date planted

value: "Pohl Conservatory, Bessey Hall, Ames, IA"

value: 80 daytime - 70 nighttime

value: ambient daylight

tag: light sources

tag: night duration

tag: number of plants harvested


title: liver_female_High feeding level_animal7

description: no additional information

source_name: liver sample at 211 days, female, high

value: Iberian

value: liver

value: female

value: high


title: liver_female_Low feeding level_animal5

description: no additional information

value: low


title: liver_male_Low feeding level_animal3

description: no additional information

value: male


title: E. coli heat shock gene expression data using PAOD method (replicate-1)

source_name: E.coli, 43°C, 60min

label_protocol: PAOD method: 0.5μg of total RNA was polyadenylated using polyA-polymerase, and products were transcribed to ssDNA with oligo-dT primers that contain an optimized T7 promoter. RNase H removes RNA and leaves RNA oligomers as primers for a DNA polymerase to synthesize dsDNA. The dsDNA was puriﬁed and served as a template in subsequent IVT reaction for cRNA ampliﬁcation. 5μg of ampliﬁed cRNA was then transcribed into cDNA using reverse transcriptase.Prepared cDNA targets were puriﬁed using a PCR puriﬁcation kit (Qiagen, Valencia, CA, USA) and vacuum evaporated to 14 μl. Random nonamers (2μg) were added, heated to 95°C for 3 min and snap cooled on ice. The fluorescence labeling reactions contained 5×Klenow buffer, dNTP(120 mM dATP, 120 mM dGTP, 120 mM dTTP, 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and 5U Klenow enzyme (TaKaRa, Dalian, China). Reaction was carried out at 37°C for 90 min and stopped by addition of 25mM EDTA, 0.25% SDS. Labeled DNA targets were purified and quantified by UV spectrophotometry.

tag: strain


title: pathogen isolates: Polymyxa betae - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
regina (germplasm name); po: 0009005 root, (Organism Part); PO:0007520 root development stages (Development Stage); sand (Growth Media).
Four day old barley cv. Regina roots inoculated were inoculated with a zoospore suspension of 1 x 10 6 spores mL-1 P. betae in buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen).  Sample prepared for roots collected from ten seedlings from each of the ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) were combined for each treatment to give a time course pool.  RNA was extracted from this time course pool and used for subsequent experiments.

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: root (pathogen isolates: Polymyxa betae)

label_protocol: Affy-Eukaryotic Target Preparation

extract_protocol: Trizol total RNA extraction, Qiagen RNeasy column purification

tag: cultivar

value: Regina

value: root


title: pathogen isolates: Polymyxa betae - rep1


title: Bcl-6 GFP negative repeat 2

description: Bcl-6, GFP negative repeat2

source_name: Bcl-6 GFP negative repeat 2


title: pathogen isolates: Polymyxa betae - rep3


title: E. coli heat shock gene expression data using PAOD method (replicate-2)


title: liver_male_High feeding level_animal1

description: no additional information


title: liver_female_High feeding level_animal6

description: no additional information


title: pathogen isolates: Mock inoculated control - rep3

description:
regina (germplasm name); po: 0009005 root, (Organism Part); PO:0007520 root development stages (Development Stage); sand (Growth Media).
Four day old barley cv. Regina roots inoculated with zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) as mock inoculation control.  Sample prepared for roots collected from ten seedlings from each of the ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) were combined for each treatment to give a time course pool.  RNA was extracted from this time course pool and used for subsequent experiments.

source_name: root (pathogen isolates: Mock inoculated control)


title: Vector GFP positive repeat 1

description: Vector, GFP positive repeat1

source_name: Vector GFP positive repeat 1


title: Vector GFP negative repeat 2

description: Vector, GFP negative repeat2

source_name: Vector GFP negative repeat 2


title: Vector GFP positve repeat 2

description: Vector, GFP positive repeat2

source_name: Vector GFP positve repeat 2


title: Bcl-6 GFP negative repeat 1

description: Bcl-6, GFP negative repeat1

source_name: Bcl-6 GFP negative repeat 1


title: E. coli heat shock gene expression data using direct labeling method (replicate-1)

source_name: e.coli , 43°C, 60min

source_name: e.coli , 37°C, 60min


title: Vector GFP negative repeat 1

description: Vector, GFP negative repeat1

source_name: Vector GFP negative repeat 1


title: pathogen isolates: Mock inoculated control - rep2


title: GPI immunized

city: Tsukuba

first: Isao

last: Matsumoto

department: Clinical Immunology

country: Japan

institute: University of Tsukuba

hyb_protocol: Samples were hybridized with GeneChip Mouse 430A2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing: Quantile normalized gene level expression values from GeneBASE

source_name: DBA/1 splenocytes

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: mouse splenocytes after control or GPI immunized DBA/1 mice on day 10

extract_protocol: Total RNA was extracted from the splenocytes using Isogen (Nippon gene)

treatment_protocol: not applicable

value: splenocyte


title: pathogen isolates: Polymyxa graminis - rep3

description:
regina (germplasm name); po: 0009005 root, (Organism Part); PO:0007520 root development stages (Development Stage); sand (Growth Media).
Four day old barley cv. Regina roots inoculated were inoculated with a zoospore suspension of 1 x 10 6 spores mL-1 P. graminis in buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen).  Sample prepared for roots collected from ten seedlings from each of the ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) were combined for each treatment to give a time course pool.  RNA was extracted from this time course pool and used for subsequent experiments.

source_name: root (pathogen isolates: Polymyxa graminis)


title: pathogen isolates: Polymyxa graminis - rep2


title: control immunized


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, normal, 1nM, 24 hr

status: Public on Jul 23 2009

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Transfected siRNAs regulate numerous transcripts sharing limited complementarity to the RNA duplex. This unintended (“off-target”) silencing can hinder the use of RNAi to define gene function. Here we describe position-specific, sequence-independent chemical modifications that reduced silencing of partially-complementary transcripts by all siRNAs tested. Silencing of perfectly-matched targets was unaffected by these modifications. The chemical modification also reduced off-target phenotypes in growth inhibition studies. Key to the modification was 2’-O-methyl ribosyl substitution at position 2 in the guide strand, which reduced silencing of most off-target transcripts with complementarity to the seed region of the siRNA guide strand. The sharp position-dependence of 2’-O-methyl ribosyl modification contrasts with the broader position dependence of base pair substitutions within the seed region, suggesting a role for position 2 of the guide strand distinct from its effects on pairing to target transcripts.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: HeLa

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: cell line

value: HeLa

tag: conditions

value: HeLa, mock, 24hr

value: HeLa, MAPK14-193, normal, 1nM, 24 hr


title: HeLa, mock, 24hr vs. HeLa, MPHOSH1-202, normal, 1nM, 24 hr

value: HeLa, MPHOSH1-202, normal, 1nM, 24 hr


title: pathogen isolates: Mock - rep1

source_name: root (pathogen isolates: Mock)

tag: tissue


title: pathogen isolates: Polymyxa graminis - rep1


title: HeLa, mock, 24hr vs. HeLa, MPHOSH1-202, normal, 0.1nM, 24 hr

value: HeLa, MPHOSH1-202, normal, 0.1nM, 24 hr


title: pathogen isolates: Mock - rep2


title: HeLa, mock, 24hr vs. HeLa, MAPK14-193, normal, 0.1nM, 24 hr

value: HeLa, MAPK14-193, normal, 0.1nM, 24 hr


title: Ramos pRTS-CA-IKK2 F+

status: Public on Jul 22 2009

city: Ulm

first: Kay

last: Klapproth

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

hyb_protocol: Hybridization on a Hybridization Oven 640 (Affymetrix). Arrays were stained and washed in a FS 450 Fluidics station (Affymetrix)

scan_protocol: Imaging on an Affymetrix GeneChip (3000) scanner. Raw data were generated using the GCOS 1.4 software (Affymetrix). Probe level data were obtained using the Robust Multichip Average (RMA) normalization algorithm [Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185?193 (2003)]

data_processing:
Data pre-processed with RMA.
Data analysis was performed using the BRB-ARRAYTOOLS software package (available at http://linus.nci.nih.gov/BRB-ArrayTools.html)

label: Biotin

source_name: BL Ramos cell line

label_protocol: 2 µg of total RNA were labeled using the GeneChip® One-Cycle Target Labeling assay kit (Affymetrix), according to the manufacturer´s instructions

extract_protocol: extraction with RNeasy Mini Kit (QIAGEN) according to manufacturer´s instructions

treatment_protocol: Ramos cells were transfected in triplicates with pRTS-GFP or pRTS-CA-IKK2, selected with hygromycin and transgene expression was induced with doxycycline (0,5mg/ml) for 48hrs. RNA was isolated with RNeasy mini kit (Qiagen, Venlo, Netherlands)

tag: transfection

value: human Burkitt lymphoma

tag: dsmz no.

value: ACC 603

tag: origin

value: established from the ascitic fluid of a 3-year-old boy with American-type Burkitt lymphoma in 1972; cells were described to be EBV-negative but EBV infectible, to carry the (8;14) translocation and p53 mutations


title: Ramos pRTS-CA-IKK2 E+

tag: cell type


title: Ramos pRTS-GFP A+

value: pRTS-GFP


title: Ramos pRTS-GFP C+


title: pathogen isolates: Mock inoculated control - rep1


title: Ramos pRTS-CA-IKK2 H+


title: pathogen isolates: Mock - rep3


title: Gersh_HA279_diff

city: Seattle

first: Burak

last: Kutlu

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: Re-differentiated cells after expansion from islets with NIH protocol

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: re-differentiated cells, NIH protocol

label_protocol: Affymetrix

extract_protocol: Qiagen

value: re-differentiated cells after expansion from islets


title: Zoarces viviparus evaluation data

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

description: Full details can be found in Kristiansson et al 2009.

hyb_protocol: Chemical fragmentation of the cRNA was performed at 94°C for 35 min, using 40 mM Tris-acetat, 100 mM K-acetate and 30 mM Mg-acetat at a concentration of 1.6 µg cRNA/µl giving an average fragment length of 100 bp. Fragmented cRNA (6 µg/array) was dissolved in hybridization buffer (final concentration: 5X SSPE, 20% formamide, 0.5 m BSA/ml, 0.1X TE, 0.1 mg mouse CotI, 0.01% Tween 20). Samples were denatured at 95°C for 3 min and hybridized to the arrays at 45°C for 15 h. Arrays were washed using 6xSSPE at 25°C and 0.5xSSPE at 45°C. Fluorescent staining of the hybridized cRNA was performed by incubating the arrays with SAPE (streptavidin, R-phycoerythrin conjugate, Invitrogen, Carlsbad, USA) diluted in 6xSSPE (5 µg SAPE/ml). Signal amplification was performed using biotinylated α-streptavidin antibodies (Vector Laboratories, Burlingame, USA) followed by and additional incubation with SAPE, according to the Consecutive Signal Enhancement protocol.

scan_protocol: Signals were detected using the CCD-based camera located in the Geniom instrument and quantified using the Geniom Wizard.

data_processing: The microarray data was imported into the statistical language R 2.7.2 and analyzed with Bioconductor. After log2-transformation, differences in intensity between the eight sub-arrays were removed using median normalization implemented in the R-package LIMMA.

organism: Zoarces viviparus

source_name: mRNA pool from 31 Z. viviparus

label_protocol: Biotinylated cRNA was prepared using the Message Amp II-Biotin Enhanced single round Amplification kit (Ambion) starting with 1 µg of total RNA and performing the in vitro transcription for 14 h.

extract_protocol: Total RNA was isolated by homogenization of liver samples in TRIzol (Invitrogen, Carlsbad, USA)/chloroform followed by RNeasy mini kit (Qiagen, Chatsworth, USA) for DNAse treatment and cleaning. Equal amount of total RNA from each of the 31 fish samples was pooled and used for cDNA synthesis.

treatment_protocol: Wild fish were caught using fyke nets. The laboratory exposure was performed as follows. Fish of both sexes were separated into 7 different tanks (5 fish/tank) containing 35 litres of seawater. The tanks were aerated and held at 10°C during the 72 h of exposure. The fish lengths were in the range of 20.9 to 24.8 cm and all fish were sexually mature. On day one, the fish in the three first tanks were injected intraperitoneally (0.2 ml/fish) with 15 mg paraquat/kg body weight (dissolved in 0.15M KCl), 1 mg cadmium (CdCl2)/kg (dissolved in 0.15M KCl) or 7 mg β-naphthoflavone/kg (dissolved in peanut oil). Z. viviparus in the following four tanks were exposed on day one and 48 h later to ethinylestradiol (EE2) (50 µg/l seawater, dissolved in EtOH); progesterone (100 µg/l seawater, dissolved in EtOH); methyltestosterone (100 µg/l seawater, dissolved in EtOH) or copper (CuCl2) (10 ng/l seawater).

tag: Zoarces viviparus of both sexes were caught in April, June and November during the years 2005-2007 from five different locations on the Swedish west coast. In addition, fish from laboratory exposures (paraquat, cadmium, β-naphthoflavone, ethinylestradiol, progesterone, methyltestosterone and copper) was also included. The pool encompassed 18 wild and 13 lab exposed fish.


title: G3BP immunoprecipitation

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu, Oko

institute: Kochi University Medical School

description: Immunoprecipitated transcripts from S2-013 using either mouse anti-G3BP monoclonal antibody or control IgG.

hyb_protocol: Cy3- and Cy5-conjugated cDNA targets were then purified by QIAquick PCR purification columns, combined, vacuum-concentrated, and diluted to 55 µl with hybridization solution containing final concentrations of 50% formamide, 4.1x Denhardts, and 4.4x SSC.  To reduce nonspecific hybridization, the hybridization solution also contained final concentrations of 15 µg human Cot1 DNA (Invitrogen), 12µg poly-deoxyadenylate, and 5 µg of yeast tRNA (Sigma).  After clarification by centrifugation, the cDNA/hybridization solution was applied to DNA microarrays and incubated at 42ºC for 16-20 h.

scan_protocol: After hybridization, microarray slides were washed by immersion in 2X SSC, 0.1%SDS for 5 min at room temperature, 1X SSC, 0.01% SDS for 5 min at room temperature, and 0.2X SSC for 2 min at room temperature.  The microarrays were dried by centrifugation for 5 min at 1000 rpm and scanned immediately with a ScanArray 4000 confocal laser system (Perkin-Elmer).

data_processing:
Fluorescent intensities were background subtracted, and normalization and filtering of the data were performed using the QuantArray software package (Perkin-Elmer). Total background subtracted intensities for each channel were used for normalization. Differential expression was defined as those genes exhibiting a 2-fold up or down average ratio in signal intensity (after normalization).
Differentially expressed genes are listed in the 'GSE17056_higher_aG3BP.txt' file, which is linked to the Series GSE17056 record as a supplementary file. All of the differentially expressed genes had transcripts that were more highly immunoprecipitated with anti-G3BP than with control IgG.
Raw intensities prior to background subtraction were requested from the submitter, but they were not able to be provided.

source_name: Immunoprecipitated transcripts using control mouse IgG

label_protocol: To generate fluorescently-labeled single-stranded cDNA target, immunoprecipitated RNA was incubated with 2µg of anchored oligodeoxythymidylate primer in a total volume of 30µl at 70ºC for 10 min and chilled on ice.  To each sample was added 10X first strand buffer (6µl), 0.1M DTT (6µl), 20X aminoallyl-dNTP mix (3µl; 10mM dATP, 10mM dCTP, 10mM dGTP, 6mM dTTP, and 4mM aminoallyl-dUTP), RNase inhibitor (0.5µl) (RNasin, Promega), and StrataScript reverse transcriptase (3µl; 50U/µl).  After incubation at 48ºC for 60 min, an additional 50 units (1µl) of StrataScript was added to the samples and incubated for an additional 60 min. The reaction was stopped by adding 12 µl of 0.5M EDTA (pH 8).  Residual RNA was hydrolyzed by adding 12 µl of 1M NaOH to the mixture followed by incubation at 65ºC for 15 min and cooled to room temperature.  The reaction was neutralized with 16.8µl of 1N HCl.  First-strand cDNA was purified from unicorporated amino allyl-dUTPs on QIAquick PCR purification columns (Qiagen) according to manufacuter’s protocols, except that QIAquick wash buffer was replaced with 5 mM potassium phosphate buffer (pH 8.5) containing 80% ethanol, and cDNA was eluted with 4 mM potassium phosphate buffer (pH 8.5) and vacuum-dried.  cDNA was resuspended in 10 µl 0.05 M Na2CO3 buffer (pH 9), mixed with either Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia), and incubated for 90 min in the dark at room temperature.

extract_protocol: Protein G Sepharose beads were incubated with 5 µg of control mouse IgG for 16 h at 4°C and then with S2-013 cell lysate. The IP products were treated with proteinase K, extracted with phenol-chloroform, and precipitated with ethanol. Purified RNAs were subsequently treated with DNase I (Promega) and extracted using the RNeasy kit (Qiagen).

value: pancreatic cancer

tag: antibody

value: IgG

source_name: Immunoprecipitated transcripts using mouse anti-G3BP monoclonal antibody

extract_protocol: Protein G Sepharose beads were incubated with 5 µg of anti-G3BP antibody for 16 h at 4°C and then with S2-013 cell lysate. The IP products were treated with proteinase K, extracted with phenol-chloroform, and precipitated with ethanol. Purified RNAs were subsequently treated with DNase I (Promega) and extracted using the RNeasy kit (Qiagen).


title: mutant MSCs from root

city: Los Angeles

first: Cun-Yu

last: Wang

state: CA

address: 10833 Le Conte

institute: UCLA

description: Gene expression data from mutant cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 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.

source_name: Human dental root from an OFCD patient

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: Cells were grown in a humidified 5% CO2 incubator in DMEM alpha modified Eagle's medium supplemented with 15% fetal bovine serum

extract_protocol: Rneasy Kit extraction of total RNA was performed according to the manufacturer's instructions

value: Root apical papilla


title: wild type MSCs from Root

description: Gene expression data from  wild type cells

source_name: Human dental root from normal subject


title: Gersh_HA279_p4

description: Expanded islet cells obtained with NIH protocol

source_name: expanded islet cells, NIH protocol

value: expanded islets


title: Gersh_HA290_p3


title: islets_9

description: Fresh pancreatic islets

source_name: islets

value: fresh islets


title: Gersh_HA293_p3

growth_protocol: 25 ng/ml HGF

treatment_protocol: 25 ng/ml HGF


title: Hayek_HA290_p3

description: Expanded islet cells obtained with Whittier protocol

source_name: expanded islet cells, Whittier protocol


title: Hayek_HA293_diff

description: Re-differentiated cells after expansion from islets with Whittier protocol

source_name: re-differentiated cells, Whittier protocol


title: islets_8

description: Fresh pancreatic islets


title: Gersh_HA290_diff


title: Hayek_HA290_diff


title: Hayek_H298_diff


title: islets_6

description: Fresh pancreatic islets


title: Gersh_G298_P4


title: Hayek_HA293_p3


title: islets_7

description: Fresh pancreatic islets


title: islets_4

description: Fresh pancreatic islets


title: islets_5

description: Fresh pancreatic islets


title: Gersh_HA293_diff


title: Gersh_G298_diff


title: Hayek_H298_P4


title: PPRF_MIPC_2

description: Expanded islet cells obtained with PPRF protocol

source_name: expanded islet cells, PPRF protocol


title: islets_3

description: Fresh pancreatic islets


title: islets_2

description: Fresh pancreatic islets


title: PPRF-ILC-day6_2

description: Re-differentiated cells after expansion from islets with PPRF protocol day 6

source_name: re-differentiated cells, PPRF protocol, day 6

growth_protocol: INGAP 1.0 ug/mL

treatment_protocol: INGAP 1.0 ug/mL


title: PPRF_MIPC


title: Hayek_HA280_p3


title: PPRF-ILC-day2

description: Re-differentiated cells after expansion from islets with PPRF protocol day 2

source_name: re-differentiated cells, PPRF protocol, day 2


title: PPRF-ILC-day6


title: PPRF-ILC-day8_2

description: Re-differentiated cells after expansion from islets with PPRF protocol day 8

source_name: re-differentiated cells, PPRF protocol, day 8


title: PPRF-ILC-day2_2


title: PPRF-ILC-day4_2

description: Re-differentiated cells after expansion from islets with PPRF protocol day 4

source_name: re-differentiated cells, PPRF protocol, day 4


title: PPRF-ILC-day8


title: AML without MLL - sample 113

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org]

source_name: Human white blood cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No growth procolos were used

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: Leukemia samples

tag: Bone Marrow


title: AML without MLL - sample 116


title: AML without MLL - sample 114


title: AML without MLL - sample 115


title: Knockdown of CD24

description: Expression profiling of CD24 knockdown cells vs. control cells.

data_processing:
Fluorescent intensities were background subtracted, and normalization and filtering of the data were performed using the QuantArray software package (Perkin-Elmer). Total background subtracted intensities for each channel were used for normalization. Differential expression was defined as those genes exhibiting a 2-fold up or down average ratio in signal intensity (after normalization).

Differentially expressed genes are listed in the 'GSE17055_higher_siCD24.txt' and 'GSE17055_higher_control.txt' files, which are linked to the Series GSE17055 record as supplementary files.

Raw intensities prior to background subtraction were requested from the submitter, but they were not able to be provided.

source_name: pancreatic cancer cell line (S2-013 CD24 RNAi)

label_protocol: To generate fluorescently-labeled single-stranded cDNA target, 40µg of total RNA was incubated with 2µg of anchored oligodeoxythymidylate primer in a total volume of 30µl at 70ºC for 10 min and chilled on ice.  To each sample was added 10X first strand buffer (6µl), 0.1M DTT (6µl), 20X aminoallyl-dNTP mix (3µl; 10mM dATP, 10mM dCTP, 10mM dGTP, 6mM dTTP, and 4mM aminoallyl-dUTP), RNase inhibitor (0.5µl) (RNasin, Promega), and StrataScript reverse transcriptase (3µl; 50U/µl).  After incubation at 48ºC for 60 min, an additional 50 units (1µl) of StrataScript was added to the samples and incubated for an additional 60 min. The reaction was stopped by adding 12 µl of 0.5M EDTA (pH 8).  Residual RNA was hydrolyzed by adding 12 µl of 1M NaOH to the mixture followed by incubation at 65ºC for 15 min and cooled to room temperature.  The reaction was neutralized with 16.8µl of 1N HCl.  First-strand cDNA was purified from unicorporated amino allyl-dUTPs on QIAquick PCR purification columns (Qiagen) according to manufacuter’s protocols, except that QIAquick wash buffer was replaced with 5 mM potassium phosphate buffer (pH 8.5) containing 80% ethanol, and cDNA was eluted with 4 mM potassium phosphate buffer (pH 8.5) and vacuum-dried.  cDNA was resuspended in 10 µl 0.05 M Na2CO3 buffer (pH 9), mixed with either Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia), and incubated for 90 min in the dark at room temperature.

extract_protocol: Total RNA was extracted from control and CD24 RNAi S2-013 cells using the RNeasy kit with DNase I treatment.

value: S2-013 CD24 RNAi

tag: sample

source_name: pancreatic cancer cell line (S2-013 control)

value: control (neo)


title: AML without MLL - sample 109


title: AML without MLL - sample 106


title: AML without MLL - sample 111


title: AML without MLL - sample 112


title: Ramos pRTS-GFP D+

source_name: BL Ramos cell line


title: AML without MLL - sample 96


title: AML without MLL - sample 101


title: AML without MLL - sample 98


title: AML without MLL - sample 103


title: AML without MLL - sample 102


title: AML without MLL - sample 99


title: AML without MLL - sample 97


title: AML without MLL - sample 95


title: AML without MLL - sample 104


title: PPRF-ILC-day4


title: AML without MLL - sample 100


title: AML without MLL - sample 108


title: AML without MLL - sample 110


title: ALL without MLL - sample 89


title: AML without MLL - sample 94


title: AML without MLL - sample 93


title: AML without MLL - sample 91


title: AML without MLL - sample 92


title: ALL without MLL - sample 88


title: ALL without MLL - sample 90


title: ALL without MLL - sample 85


title: separated animals PVN, technical replicate 3

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

institute: German Research Center for Environmental Health

hyb_protocol: The pooled samples were hybridized on five Max-Planck Institute 24 k mouse cDNA arrays (Max-Planck Institute of Psychiatry, Munich, Germany) for each dye coupling combination (ten arrays total).

scan_protocol: The arrays were scanned on a PerkinElmer Life Sciences (Rodgau-Jügesheim, Germany) ScanArray 4000 laser scanner.

data_processing: The microarray data analysis was accomplished by the fixed circle quantification method using QuantArray (PerkinElmer Life Sciences) and raw data was normalized using a nonlinear regression method (Yang et al., 2002).

source_name: separated animals, PVN

label_protocol: Total RNA of the punched tissue was isolated with the Trizol (Invitrogen GmbH, Karlsruhe, Germany) method following the manufacturers protocol. Isolated RNA was then amplified in one round using the Ambion Amino Allyl MessageAmp aRNA kit (Ambion, Huntingdon, UK). RNA samples were quantified by spectrophotometry and RNA integrity checked on 1% agarose gels using a deionized formamide-based loading buffer. Equal amounts of total aRNA were pooled to one non-separated and one separated sample containing 40 µg of aRNA each and dye coupled using indirect labeling. To exclude dye bias, one-half of each sample was coupled to cyanine 3 (Cy3) and the other one-half to cyanine 5 (Cy5).

extract_protocol: The brains of 6 animals per group were used. Frozen brains were sectioned at -20ºC in a cryostat microtome at 100 µm in the coronal plane through the level of the hypothalamic PVN. The sections were mounted on superfrost slides and tissue micropunches were taken using a sample corer of 1 mm diameter (Fine Science Tools, Heidelberg, Germany). The PVNs of two animals from the same group were pooled into one sample, giving a total of three samples for each treatment. Punches were immediately transferred to frozen 1.5 ml plastic tubes and stored ad -80ºC until RNA isolation. The accuracy of the punch was controlled by cresyl violet counterstaining of the punched sections and confirming the punch location under a light microscope.

value: mouse brain, hypothalamus, PVN

source_name: non-separated animals, PVN


title: separated animals PVN, technical replicate 2


title: ALL without MLL - sample 86


title: separated animals PVN, technical replicate 4


title: AML without MLL - sample 107


title: ALL without MLL - sample 84


title: non-separated animals PVN, technical replicate 4


title: non-separated animals PVN, technical replicate 5


title: separated animals PVN, technical replicate 1


title: ALL without MLL - sample 83


title: separated animals PVN, technical replicate 5


title: ALL without MLL - sample 82


title: ALL without MLL - sample 79


title: ALL without MLL - sample 80


title: non-separated animals PVN, technical replicate 2


title: ALL without MLL - sample 78


title: ALL without MLL - sample 77


title: non-separated animals PVN, technical replicate 3


title: non-separated animals PVN, technical replicate 1


title: female breast cancer P678 XXX

first: Matteo

last: Fassan

state: PD

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

hyb_protocol: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates. The hybridized chips were washed and processed to detect biotin-containing transcripts by streptavidin-Alexa647 conjugate and scanned on an Axon 4000B microarray scanner (Axon Instruments, Sunnyvale, CA).

scan_protocol: The microarrays were processed by using a method of direct detection of biotin-containing transcripts by streptavidin-Alexa647 conjugate. Processed slides were then scanned by using the PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at power 80 and PMT 70 setting and a scan resolution of 10 nm. Microarray images were analyzed using GENEPIX PRO 6.0 (Axon Instruments).

data_processing: Average values of the replicate spots of each miRNA were background subtracted, normalized, and further analyzed. Normalization was performed using quantiles. miRNAs that are differentially expressed between breast cancer and gynecomastia were identified using a random-variance t-test. The random-variance t-test is an improvement over the standard separate t-test as it permits sharing information among genes about within-class variation without assuming that all genes have the same variance. Genes were considered statistically significant if their p value was less than 0.01. A stringent significance threshold was used to limit the number of false positive findings.

source_name: primary breast cancer

label_protocol: Five μg of total RNA from each sample were reverse-transcribed using biotin end-labeled random-octamer oligonucleotide primer.

extract_protocol: Four 15 μm sections were obtained from each case. Tissue sections were deparaffinized with xylene at 50°C for 3 minutes. Total RNA extraction was undertaken using the RecoverAll kit (Ambion Inc, Austin, Tex) according to manufacturer’s instructions.

value: primary breast cancer

tag: histology

value: ductal carcinoma

tag: sex

value: Female


title: female breast cancer P685 EEEE

description: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates.


title: female breast cancer P686 FFFF


title: female breast cancer P668 NNN


title: female breast cancer P688 LLLL


title: female breast cancer P670 PPP


title: female breast cancer P674 TTT


title: ALL without MLL - sample 76


title: AML without MLL - sample 105


title: female breast cancer P666 RRRR


title: ALL without MLL - sample 75


title: female breast cancer P662 HHH


title: female breast cancer P664 JJJ


title: gynecomastia P1390 41

source_name: gynecomastia

value: gynecomastia

value: Male


title: ALL without MLL - sample 81


title: gynecomastia P1389 40


title: gynecomastia P1388 37


title: ALL without MLL - sample 70


title: ALL without MLL - sample 87


title: ALL without MLL - sample 71


title: male breast cancer P1384 32


title: male breast cancer P1385 33


title: male breast cancer P1383 29


title: gynecomastia P1386 35


title: male breast cancer P1382 28


title: ALL without MLL - sample 68


title: ALL without MLL - sample 74


title: ALL without MLL - sample 72


title: gynecomastia P1387 36


title: male breast cancer P1381 25


title: ALL without MLL - sample 66


title: ALL without MLL - sample 67


title: male breast cancer P1380 23


title: ALL without MLL - sample 63


title: ALL without MLL - sample 61


title: ALL without MLL - sample 69


title: ALL without MLL - sample 64


title: ALL without MLL - sample 59


title: ALL without MLL - sample 65


title: ALL without MLL - sample 60


title: ALL without MLL - sample 57


title: ALL without MLL - sample 58


title: male breast cancer P1377 19


title: male breast cancer P1376 18


title: male breast cancer P1379 22


title: male breast cancer P1374 15


title: male breast cancer P1378 20


title: male breast cancer P1373 14


title: ALL without MLL - sample 56


title: male breast cancer P1375 17


title: male breast cancer P1372 13


title: ALL without MLL - sample 54


title: ALL without MLL - sample 52


title: male breast cancer P1370 10


title: ALL without MLL - sample 51


title: male breast cancer P1371 11


title: male breast cancer P1369 9


title: ALL without MLL - sample 53


title: ALL without MLL - sample 73


title: ALL without MLL - sample 55


title: male breast cancer P1368 8


title: ALL without MLL - sample 50


title: ALL without MLL - sample 47


title: ALL without MLL - sample 49


title: ALL without MLL - sample 48


title: ALL without MLL - sample 46


title: ALL without MLL - sample 44


title: male breast cancer P1367 7


title: ALL without MLL - sample 45


title: male breast cancer P1366 4


title: male breast cancer P1365 3


title: male breast cancer P1364 2


title: ALL without MLL - sample 43


title: Shoot- -Fe-P biological rep2

city: Hangzhou

first: Luqing

last: Zheng

address: 388 Yuhangtanghe Road

institute: Colledge of Life Sciences, Zhejiang University

description: Gene expression data from 11-d-old rice (Oryza sativa) seedlings under -Fe-P conditions

hyb_protocol: Microarray analysis was carried out using an Affymetrix technology platform and Affymetrix GeneChip rice genome array. Briefly, fragmented cRNA was mixed with spiked controls and applied to Affymetrix Test chips, and good quality samples were then used to hybridize with the rice GeneChip. The hybridization, probe array washing and staining, and washing procedures were executed as described in the Affymetrix protocols.

scan_protocol: Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (Leiden Genome Technology Center).

data_processing: Data analysis was carried out using Avadis 4.3 (Strand Genomics) and Partek Genomics suite software, version 6.3. Raw intensity data were initially normalized using the MAS5 algorithm, which allowed probe identifier present calls to be determined.

organism: Oryza sativa

source_name: Shoot segments derived from 11-d-old rice (Oryza sativa) seedlings under -Fe-P conditions

label_protocol: The One-Cycle Target Labeling and Control Reagent kit (Affymetrix 900493) and the protocols optimized by Affymetrix were used to prepare biotinylated complementaryRNA (cRNA; from 5 mg of total RNA) for microarray hybridization (n = 2 per group).

growth_protocol: Rice seeds were germinated in distilled water for 2 d. After germination, 25 seedlings were transferred to a plastic net floating on the Yoshida nutrient solution (Yoshida et al., 1976).

extract_protocol: Total RNA was extracted using RNAzol (Campro Scientific) and glass beads according to the manufacturer’s instructions.

treatment_protocol: For –Fe+P treatment, FeCl3 and citric acid were removed. For +Fe-P treatment, NaH2PO4 was removed. While for –Fe–P treatment, FeCl3, citric acid, and NaH2PO4 were removed.

value: Shoot


title: ALL without MLL - sample 42


title: male breast cancer P1363 1


title: Shoot- -Fe-P biological rep1

description: Gene expression data from 10-d-old rice (Oryza sativa) seedlings under -Fe-P conditions

source_name: Shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under -Fe-P conditions


title: ALL without MLL - sample 41


title: ALL without MLL - sample 39


title: ALL without MLL - sample 40


title: ALL without MLL - sample 38


title: Shoot- +Fe-P biological rep2

description: Gene expression data from 10-d-old rice (Oryza sativa) seedlings under +Fe-P conditions

source_name: Shoot segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe-P conditions


title: Shoot- +Fe-P biological rep1

source_name: Shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under +Fe-P conditions


title: ALL without MLL - sample 62


title: ALL without MLL - sample 36


title: Shoot- -Fe+P biological rep2

description: Gene expression data from 10-d-old rice (Oryza sativa) seedlings under -Fe+P conditions

source_name: Shoot segments derived from 11-d-old rice (Oryza sativa) seedlings under -Fe+P conditions


title: ALL without MLL - sample 32


title: Shoot- -Fe+P biological rep1

source_name: Shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under -Fe+P conditions


title: ALL without MLL - sample 35


title: ALL without MLL - sample 33


title: ALL without MLL - sample 34


title: Shoot- +Fe+P biological rep2

description: Gene expression data from 10-d-old rice (Oryza sativa) seedlings under +Fe+P conditions

source_name: Shoot segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe+P conditions


title: ALL without MLL - sample 30


title: Shoot- +Fe+P biological rep1

source_name: Shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under +Fe+P conditions


title: ALL without MLL - sample 31


title: Root- -Fe-P biological rep2

source_name: Root segments derived from 11-d-old rice (Oryza sativa) seedlings under -Fe-P conditions

value: Root


title: ALL without MLL - sample 27

source_name: Human white blood cells


title: ALL without MLL - sample 28


title: ALL without MLL - sample 29


title: ALL without MLL - sample 25


title: ALL without MLL - sample 26


title: Root- -Fe-P biological rep1

source_name: Root segments derived from 10-d-old rice (Oryza sativa) seedlings under -Fe-P conditions


title: ALL without MLL - sample 23


title: ALL without MLL - sample 21


title: Root- +Fe-P biological rep1

source_name: Root segments derived from 10-d-old rice (Oryza sativa) seedlings under +Fe-P conditions


title: ALL without MLL - sample 20


title: ALL without MLL - sample 22


title: Root- +Fe-P biological rep2

source_name: Root segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe-P conditions


title: ALL without MLL - sample 19


title: ALL without MLL - sample 17


title: Root- -Fe+P biological rep2

source_name: Root segments derived from 11-d-old rice (Oryza sativa) seedlings under -Fe+P conditions


title: ALL without MLL - sample 16


title: Root- -Fe+P biological rep1

source_name: Root segments derived from 10-d-old rice (Oryza sativa) seedlings under -Fe+P conditions


title: ALL without MLL - sample 18


title: ALL without MLL - sample 15


title: ALL without MLL - sample 14


title: ALL without MLL - sample 9


title: ALL without MLL - sample 11


title: Root- +Fe+P biological rep1

source_name: Root segments derived from 10-d-old rice (Oryza sativa) seedlings under +Fe+P conditions


title: ALL without MLL - sample 7


title: ALL without MLL - sample 37


title: ALL without MLL - sample 8


title: ALL without MLL - sample 6


title: ALL without MLL - sample 13


title: ALL without MLL - sample 4


title: ALL without MLL - sample 12


title: Mtb isolate 8 versus isolate 10 rep_2

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

country: Canada

institute: Research Institute of McGill University Health Centre

hyb_protocol: Microarray hybridization was carried out in GE Healthcare hybridization buffer in the presence of yeast tRNA (0.2µg ml-1) at 42°C for 16 hours.  Following hybridization, microarray slides were washed three times (15 mins/wash) with 0.5X SSC + 0.01% SDS, 0.06X SSC + 0.01% SDS and 0.06X SSC.

scan_protocol: Scanned on ScanArray Lite (Packard) Images were quantified using ScanArray Express software (Packard).

data_processing: Mean fluorescence values for each spot, minus the surrounding background were used in the analysis.  Spots flagged as misrepresentative or those with a negative value following background correction were subsequently excluded from further analysis.  The fluorescence intensity ratios (Cy3/Cy5 or Cy5/Cy3, representing test/reference) were calculated for each spot, log10 transformed and then normalized with respect to the mean value of all fluorescence ratios. A Z- score [Z = (log10 fluorescence ratio - mean)/standard deviation] was calculated for each spot.

organism: Mycobacterium tuberculosis

source_name: Mtb PDIM positive isolate 8

label_protocol: 4µg samples of RNA were used in the preparation of cDNA labeled with either Cy3 or Cy5-NHS esters (GE Healthcare) via the aminoallyl indirect labeling method (Yu et al., 2002) in the presence of RevertAid M-MuLV Reverse Transcriptase (Fermentas).  Labeled  cDNA was subsequently purified using the QIAquick PCR Purification Kit (Qiagen) and samples to be co-hybridized on the same array were mixed and concentrated to 6µl in a Savant SpeedVac Concentrator.

extract_protocol: Bacterial pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 40 seconds. Resulting cell lysates were added to chloroform, centrifuged and nucleic acids were then precipitated from the aqueous phase with isopropanol. RNA was washed in 75% ethanol, then DNAse treated. For further purification, the Qiagen RNeasy kit was used according to the manufacturer's instructions.

tag: properties

value: Laboratory isolate PDIM producer

value: Derived from H37Rv ATCC27294

source_name: Mtb PDIM negative isolate 10

value: Laboratory isolate PDIM deficient mutant


title: Mtb isolate 10 versus isolate 8 rep_2

source_name: Mtb PDIM positive isolate 10

tag: strain


title: ALL without MLL - sample 2


title: Root- +Fe+P biological rep2

source_name: Root segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe+P conditions


title: ALL without MLL - sample 5


title: Mtb isolate 10 versus isolate 8


title: ALL without MLL - sample 1


title: 3E5-6(13600439)

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: no additional information

hyb_protocol: 1. Mark the slide with a diamond pen to indicate the array position. 2. Place slide face down on a chamber filled with 3x SSC and rehydrate for 5-10 min. Immediatly dry the array on a 100C heat block for 2-3 sec. 3. Place slide in glass chamber and prehybridize arrays in 6x SSC, 0.5% SDS, 1%BSA at 42C water bath for at least 1h. 4. Wash with H20 and denaturate the slides for 2 min by placing the slide in boiling water. Dry the slide. 5. Prepare the probe for hybridisation as follows:  -Resuspend the probe in 25 ul hybridization buffer containing 50% dionized formamide, 6x SSC, 0.5% SDS and 5x Denhardt`s.  -Tab the bottom of the tube to dissolve the probe. Try to avoid generating bubbles.  -Denaturate probe at 95C for 2min. Allow the probe to cool down at RT. 6. Wait for the probe to cool down and pipet onto an inverted cover slip, with the spots facing the cover slip and allow the probe to smoothly spread allover the array. Avoid making bubbles but don`t worry too much about the very small ones. Lift the slide up, turn it into its normal position and transfer into hybridisation chamber. 7. Pipet 2 drops of 3xSSC into the special trays of the chamber to keep it humidified. Seal the hybridisation chamber and place it in a 42C water bath for 12-16h. 8. Prepare the following washing solutions:  I - 0.1xSSC, 0.1% SDS  II - 0.1xSSC Don`t use distilled or millipore water for washing buffers. Use just de-ionised. 9. Remove slides from the HybChfmber and submerge them in washing solution I until the cover slip falls off. It may be necessary to aggressivly shake the slide a few times to remove the cover slip. Be careful not to scratch the array. 10. Place the slides in slide rack and transfer in a glass chamber containing washing solution I. Wash for 10 min with continuous shaking. Transfer into fresh solution I and wash for another 5 min. Transfer into solution II and wash for 5 min. Wash in fresh solution II for another 5 min. All washes are carried out at RT. Do not wash  with water. 11. Spin to dry the arrays by either placing them in falcontubes or by spinning the slidee rack, if you have the appropriate centrifuge buckets. 12 Scan the arrays.

scan_protocol: The slide was scanned on the ScanArray Lite instrument (Perkin Elmer) at 10um resolution.

data_processing: Data was processed using TIGR Spotfinder 3.1.1 (Circle segmentation method, QC filter on, Bcg correction off). Then it was normalised with TIGR MIDAS v2.19 program (LocFit normalisation, SD regularisation)

organism: Drosophila melanogaster

source_name: reference, mixture of rnas from all stages

label_protocol: Labeling was perfomed using Invitrogen SuperScript Direct cDNA Labeling System protocol

extract_protocol:
For RNA extraction protocol from BGRC webcite was used:
1.  To 50 mg frozen flies (or frozen fly tissue) in a 1.5 ml microcentrifuge tube add 1 ml Trizol reagent and homogenize immediately with a disposable plastic pestle.
(Note: Work quickly.  RNA is protected from RNase in the frozen tissue and in the phenolic solution but is susceptible to degradation during the homogenization process)
2.  Incubate at room temperature for 5 minutes.
3.  Centrifuge at 12,000 rcf for 10 minutes at 4oC to pellet insoluble debris such as exoskeleton.
4.  Transfer the supernatant to a new microcentrifuge tube.  (Note:  Take great care not to take pellet or fat layer, which can lead to phenol contamination of the aqueous layer when the phenol becomes trapped in fat micelles.)
5.  Add 200 ul of Chloroform (no isoamyl alcohol) to each tube.
6.  Shake vigorously by hand (do not vortex which will lead to DNA Contamination).
7.  Incubate tubes at room temperature for 3 minutes.
8.  Centrifuge at 10,000 rcf for 15 minutes at 4oC.
9.  Transfer upper aqueous phase (~0.6 ml) to a fresh RNAse-free microcentrifuge tube.  (Note: Make sure to avoid RNase contamination from this point on.)
10.  Add 0.5 ml isopropanol
11.  Incubate at room temperature for 10 minutes.
12.  Centrifuge at 12,000 rcf for 10 minutes at 4oC.
13.  Remove the supernatant and wash the pellet with 1ml 75% ethanol.
14.  Centrifuge at 7,500 rcf for 5 minutes. at 4oC.
15.  Remove the supernatant.
16.  Centrifuge briefly and carefully remove the last of the supernatant with a micropipette.
17.  Air dry for 10 minutes.  (Note:  Do not dry under vacuum or heat.)
18.  Resuspend the pellet in 100 ul RNase-free water.
19.  Quantify a 1/100 dilution of the RNA on spectrophotometer.

tag: reference

value: mixture of rnas from all stages

tag: development stage

value: 0-1h embryos

value: 5-6h embryos

value: 11-12h embryos

value: 1st instar larvae

value: 2nd instar larvae

value: 3rd instar larvae

value: 0-1h prepupae

value: 13-14 h pupae

value: 3 days adult males

value: 3 days adult females


title: 3L3(13600440)

description: no additional information


title: ALL without MLL - sample 10


title: ALL without MLL - sample 3


title: Mtb isolate 8 versus isolate 10


title: Mtb isolate 9 versus isolate 8

source_name: Mtb PDIM positive isolate 9


title: 3males(13600063)

description: no additional information

source_name: males


title: Mtb isolate 20 versus isolate 3

type: genomic

molecule: genomic DNA

source_name: Mtb PDIM positive isolate 20

label_protocol: 2µg of purified genomic DNA was directly labeled with Cy3 or Cy5-dCTP (GE Healthcare) using DNA polymerase I Klenow fragment and a mixture of 6-mer and 9-mer random primers (New England Biolabs)  and 120 µM each dATP, dTTP, dGTP, with 60 µM dCTP and 60 µM of either Cy3 dCTP or Cy5 dCTP label

extract_protocol: Bacteria were harvested by centrifugation (10 min, 3,000 rpm) at room temperature, resuspended in SET solution (25% Sucrose, 50mM EDTA, 50 mM Tris pH=8) containing 4 mg/ml of lysozyme. Cell lysates were treated with RNase, Proteinase K and after phenol-chloroform extraction, DNA was precipitated with isopropanol.

source_name: Mtb PDIM negative isolate 3


title: 3E11-12(13599889)

description: no additional information


title: Mtb isolate 4 versus isolate 8

source_name: Mtb PDIM negative isolate 4


title: 3females(13600059)

description: no additional information

source_name: females


title: 3L1(13599883)

description: no additional information


title: miRNA expression in cytokine-stimulated airway smooth muscle cells, replicate 2.2

city: Reno

first: Cherie

middle: A

last: Singer

state: NV

address: 1664 N. Virginia St

department: Pharmacology MS318

institute: University of Nevada School of Medicine

description: primary cultured human airway myocytes were obtained from 2nd-4th generation mainstem bronchi of patients undergoing lung resection surgery at the university of manitoba as previously described (naureckas et, et al, am j respir crit care med 1999;160: 2062-2066). Alternatively, human bronchial smooth muscle cells were obtained from Lonza (Walkersville, MD).

hyb_protocol: Arrays were hybridized and washed according to the mirVana bioarrays protocols. Hybridized arrays were washed and incubated with AlexaFluor capture reagents from the NCode system to amplify signal intensity in these samples.

scan_protocol: Hybridized slides were scanned using a Perkin Elmer ScanArray 4000 Microarray Scanner at the Nevada Genomics Center. GenePix 4.1 software was used to quantify raw signal intensities.

data_processing: The noise threshold was computed independently as the sum of the mean and ½ the standard deviation of the background-corrected positive signal levels of the 194 empty wells. Remaining spot replicates were averaged after exclusion of those replicates that caused abnormally large coefficients of variations. Twenty-two signal intensities were excluded in sets of replicates with coefficients of variation greater than 0.8. Of all 2504 sets of detectable replicates, 1% was associated with coefficients of variation greater than this chosen threshold of 0.8. This yielded 642 remaining features to be considered for further analysis, including controls. The ratios of cytokine-stimulated to non-treated, control miRNA expression were computed for each arrays, and then normalized per array via a simple division by the median ratio of each array. Normalized ratios were then averaged for each of the two different cultures assayed and log2-transformed. Empty values indicate that no signal was detected.

source_name: Human airway smooth muscle cells, cultured

label_protocol: The NCode miRNA labeling system (Invitrogen, Carlsbad, CA) was used for labeling and polyadenylation of miRNA followed by ligation of a capture sequence prior to hybridization overnight.

growth_protocol: Cells from passages four through seven were used in these experiments and grown in a humidified 5% CO2 atmosphere at 37°C in M199 supplemented with 10% new born calf serum (Invitrogen, Carlsbad, CA), 0.5 μg/L epidermal growth factor and 2 μg/L fibroblast growth factor. , MO). IFNγ was purchased from R&D Systems, Inc. (Minneapolis, MN).

extract_protocol: Total RNA was extracted using TRIzol reagent and purified using the PureLink miRNA isolation kit (Invitrogen, Carlsbad, CA). An aliquot of 2 μg miRNA was lyophilized and resuspended in 15.5 μL of RNAse free water for labeling.

treatment_protocol: Cultures were grown to confluence and growth-arrested for 48 hours in serum free media consisting of a 50:50 mix of F12/DMEM supplemented with 10 ml/liter ITS+Premix containing 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium (BD Bioscience, Bedford, MA). Cells were then treated with 10 ng/ml IL-1β, TNFα, and IFNγ for 24 hours or left untreated.

source_name: Human airway smooth muscle cells, non-cultured

value: non-treated airway smooth muscle cells


title: Mtb isolate 8 versus isolate 4


title: 2males(13582065)

description: no additional information


title: 3P14(13599882)

description: no additional information


title: DNA biological replicate 1, technical replicate 2

city: Berkeley

first: Russell

last: Vance

address: 415 Life Science Addition

institute: UC Berkeley

hyb_protocol: Labeled aRNA probe was hybridized in 3X SSC, 25mM HEPES pH 7, 0.25%SDS for 36h at 63°C.  Slides were washed and dried before scanning.

scan_protocol: Scanned on a GenePix 2000 Scanner.

data_processing: Log2 of Cy3/Cy5 representing log2(test/reference).  These values were generated and normalized in GenePix Pro.  Ratio-based normalization was performed by analyzing "good" features and setting the average ratio of medians (Cy5/Cy3) equal to 1. Good features were defined as unsaturated features with a foreground-minus-background value of at least 350, in either channel. Features that were present in at least 1 microarray were selected using Acuity software and were included in the data table.

source_name: B6 bone marrow derived macrophages

label_protocol: RNA was amplified using the Ambion Amino Allyl MessageAmp Kit to incorporate amino-allyl-UTP.  aRNA was labeled with Cy3 or Cy5 for 1h.

growth_protocol: B6 bone marrow derived macrophages were grown in RPMI + 10%FBS, 10%M-CSF, glutamine, and antibiotic.

extract_protocol: Ambion RNaqueous Kit was used to extract total RNA.

treatment_protocol: Macrophages were transfected with the compounds indicated above using Lipofectamine 2000.  RNA was harvested 6h post transfection.

tag: treatment

value: transfected with double-stranded poly dA::dT DNA

source_name: total RNA pooled from each experimental sample of B6 mouse macrophages


title: cyclic-di-GMP biological replicate 1

description: cyclic-di-GMP biological replicate 1

value: transfected with cyclic-di-GMP

value: total RNA pooled from each experimental sample of B6 mouse macrophages


title: 3PP0-1(13599890)

description: no additional information


title: DNA biological replicate 2

description: DNA biological replicate 2


title: cyclic-di-GMP biological replicate 2

description: cyclic-di-GMP biological replicate 2


title: Mtb isolate 3 versus isolate 20

value: Derived from H37Rv ATCC27294

value: Laboratory isolate PDIM producer


title: miRNA expression in cytokine-stimulated airway smooth muscle cells, replicate 2.1


title: Mtb isolate 8 versus isolate 9

source_name: Mtb PDIM negative isolate 9

value: Laboratory isolate PDIM deficient mutant


title: 3E0-1(13599887)

description: no additional information

value: mixture of rnas from all stages

value: 0-1h embryos


title: miRNA expression in cytokine-stimulated airway smooth muscle cells, replicate 1.2


title: 2PP01(13581599)

description: no additional information

value: 5-6h embryos

value: 11-12h embryos


title: DNA biological replicate 1, technical replicate 1

description: DNA biological replicate 1, technical replicate1


title: 3L2(13600058)

description: no additional information

value: 1st instar larvae

value: 2nd instar larvae


title: 2females(13581601)

description: no additional information

value: 3rd instar larvae

value: 0-1h prepupae


title: ALL without MLL - sample 24

source_name: Human white blood cells


title: 2L1(13587939)

description: no additional information

value: 13-14 h pupae

value: 3 days adult males


title: miRNA expression in human tracheal smooth muscle, 68 yo, replicate 1

description: None.

hyb_protocol: Arrays were hybridized and washed as directed according to the mirVana protocols

scan_protocol: Hybridized slides were scanned using a Perkin Elmer ScanArray 4000 Microarray Scanner.  GenePix 4.1 software was used to quantify raw signal intensities.

data_processing: Local background as computed by GenePix was subtracted from each signal value.   A noise threshold was computed using the empty wells and a noise threshold for each array was computed independently as the sum of the mean and ½ the standard deviation of the background-corrected positive signal levels of the 194 empty wells on each array. All spots with expression greater than this threshold were retained, and the remaining set of per-array replicates of each miRNA was examined for outliers based on the coefficient of variation.  Replicated spots were then averaged, and averaged spot intensities were normalized per array by division of the median array signal.

source_name: human tracheal smooth muscle

label_protocol: miRNA was then polyadenylated and labeled with Cy5 using the mirVana miRNA labeling kit

extract_protocol: miRNA was purified from 20 μg of total RNA fractionated using the flashPAGE system as directed by the manufacturer (Ambion, Austin, TX).  The filter-based flashPAGE clean-up kit was used to concentrate the purified miRNA.

tag: gender

value: male

tag: age

value: 68 years old

tag: race

value: unknown

tag: cause of death

value: lung cancer


title: miRNA expression in cytokine-stimulated airway smooth muscle cells, replicate 1.1

description: primary cultured human airway myocytes were obtained from 2nd-4th generation mainstem bronchi of patients undergoing lung resection surgery at the university of manitoba as previously described (naureckas et, et al,  am j respir crit care med 1999;160: 2062-2066).  Alternatively, human bronchial smooth muscle cells were obtained from Lonza (Walkersville, MD).

hyb_protocol: Arrays were hybridized and washed according to the mirVana bioarrays protocols.  Hybridized arrays were washed and incubated with AlexaFluor capture reagents from the NCode system to amplify signal intensity in these samples.

scan_protocol: Hybridized slides were scanned using a Perkin Elmer ScanArray 4000 Microarray Scanner at the Nevada Genomics Center.  GenePix 4.1 software was used to quantify raw signal intensities.

data_processing: The noise threshold was computed independently as the sum of the mean and ½ the standard deviation of the background-corrected positive signal levels of the 194 empty wells. Remaining spot replicates were averaged after exclusion of those replicates that caused abnormally large coefficients of variations. Twenty-two signal intensities were excluded in sets of replicates with coefficients of variation greater than 0.8. Of all 2504 sets of detectable replicates, 1% was associated with coefficients of variation greater than this chosen threshold of 0.8.  This yielded 642 remaining features to be considered for further analysis, including controls.  The ratios of cytokine-stimulated to non-treated, control miRNA expression were computed for each arrays, and then normalized per array via a simple division by the median ratio of each array. Normalized ratios were then averaged for each of the two different cultures assayed and log2-transformed.  Empty values indicate that no signal was detected.

growth_protocol: Cells from passages four through seven were used in these experiments and grown in a humidified 5% CO2 atmosphere at 37°C in M199 supplemented with 10% new born calf serum (Invitrogen, Carlsbad, CA), 0.5 μg/L epidermal growth factor and 2 μg/L fibroblast growth factor.   , MO). IFNγ was purchased from R&D Systems, Inc. (Minneapolis, MN).

treatment_protocol: Cultures were grown to confluence and growth-arrested for 48 hours in serum free media consisting of a 50:50 mix of F12/DMEM supplemented with 10 ml/liter ITS+Premix containing 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium (BD Bioscience, Bedford, MA).  Cells were then treated with 10 ng/ml IL-1β, TNFα, and IFNγ for 24 hours or left untreated.

tag: cell type

value: non-treated airway smooth muscle cells


title: miRNA expression in human tracheal smooth muscle, 87 yo, replicate 1

description: None.

value: female

value: 87 years old

value: myocardial infarction


title: WT whole embryo

type: other

city: bukyo-ku

first: kaoru

last: yamagata

state: Tokyo

address: yayoi 1-1-1

institute: university of tokyo

description: whole embryo of wild type mice at E18.5

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min.  Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried prior to a high-resolution scan.

scan_protocol: Scan on a GenePix 4000B (Axon Instruments, CA, USA).  Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.  We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.

molecule: other

source_name: WT whole embryo

label_protocol: mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer.

extract_protocol: To isolate miRNA fractions from total RNA, 100μｇ total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per the manufacturer’s recommendation.

tag: Strain

tag: Tissue

value: whole embryo


title: miRNA expression in human tracheal smooth muscle, 59 yo, replicate 2

description: None.

value: 59 years old

value: Caucasian


title: miRNA expression in human tracheal smooth muscle, 59 yo, replicate 1

description: None.


title: miRNA expression in human tracheal smooth muscle, 68 yo, replicate 2

description: None.


title: ER alpha KO

description: whole embryo of Estrogen receptor (ER) alpha knockout mice at E18.5

source_name: whole embryo of ER alpha KO


title: WT-OVX-3

description: Vehicle control of ovariectomized wild type mouse

source_name: uterus from ovariectomized wild type mouse

treatment_protocol: At 15 week old, female mice were ovariectomized, and after one week uteruses were dissected from mice.

tag: Gender

value: the uterus


title: monoGMP biological replicate 1

description: monoGMP biological replicate 1

value: transfected with monoGMP

value: total RNA pooled from each experimental sample of B6 mouse macrophages


title: 2L2(13587938)

description: no additional information

source_name: reference, mixture of rnas from all stages

value: mixture of rnas from all stages

value: 0-1h embryos

value: 5-6h embryos

value: 11-12h embryos

value: 1st instar larvae

value: 2nd instar larvae

value: 3rd instar larvae

value: 0-1h prepupae

value: 3 days adult females


title: miRNA expression in human tracheal smooth muscle, 20 yo, replicate 2

description: None.

value: male

value: 20 years old

value: African American

value: suicide


title: 2E11-12(13581603)

description: no additional information

value: 13-14 h pupae

value: 3 days adult males


title: 2P14(13587937)

description: no additional information


title: 2E5-6(13587744)

description: no additional information


title: 2E0-1(13581602)

description: no additional information


title: miRNA expression in human tracheal smooth muscle, 20 yo, replicate 1

description: None.

hyb_protocol: Arrays were hybridized and washed as directed according to the mirVana protocols.


title: WT-OVX-E2-2

description: E2 treatment of ovariectomized wild type mouse

source_name: uterus from ovariectomized and E2 treated wild type mouse

growth_protocol: 16 weeks old

treatment_protocol: At 15 week old, female mice were ovariectomized, and after one week, estradiol (E2) was delivered at a concentration of 0.050 mg/kg body weight/day. 24 hours after chemical treatment, uteruses were dissected.

value: female

value: the uterus


title: 1PP01(13587687)

description: no additional information

value: mixture of rnas from all stages


title: 1P14(13587688)

description: no additional information

value: 0-1h embryos


title: WT-OVX-E2-1


title: 1females(13587686)

description: no additional information

value: 5-6h embryos


title: WT-OVX-2

treatment_protocol: At 15 week old, female mice were ovariectomized, and after one week uteruses were dissected.


title: 1E5-6(13587936)

description: no additional information

value: 11-12h embryos


title: M/E-cells expression constitutively active Mef2c

city: Hamburg

first: Carol

last: Stocking

address: Martinistrasse 52

institute: Heinrich-Pette-Institut

description:
M/E-cells are rescued with an HDAC-binding mutant form of Mef2c (constitutively active).
murine bone marrow cells_immortalized by MLL/ENL-expression_6h,24h,48h pooled expansion medium

hyb_protocol: hybridization was done at the facilities of Miltenyi Biotec, Bergisch-Gladbach, Germany. In Brief, the hybridization procedure was performed according to the Agilent 60-mer oligo microarray  processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent  Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was  hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays  4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine  for 1 min at room temperature followed by a second wash with preheated  0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing  step was performed with acetonitrile for 30 sec.

scan_protocol: scanning was done at the facilities of Miltenyi Biotec, Bergisch-Gladbach, Germany. Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: data processing was done at the facilities of Miltenyi Biotec, Bergisch-Gladbach, Germany. The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files.

source_name: murine bone marrow cells, immortalized, 6h,24h,48h in expansion medium

label_protocol: labeling of T7-based amplificated cRNA was done at the facilities of Miltenyi Biotec, Bergisch-Gladbach, Germany. In Brief: RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer's protocol. Yield of cRNA and dye-incorporation was measured with ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: M/E-cells were grown in RPMI supplemented with 10% FCS, 1% Penicillin/Streptamycin, 1% Glutamine, 10 ng/ml recombinant murine IL6, GM-CSF, IL3 and 100 ng/ml murine recombinant SCF.

extract_protocol: extraction of total RNA was done at the facilities of Miltenyi Biotec, Bergisch-Gladbach, Germany. In Brief: Use of standard RNA extraction protocol (NucleoSpin® RNA II, Macherey-Nagel), the three samples of both M/E-celllines was pooled.

treatment_protocol: M/E-cells were harvested at three different time-points: 6h, 24h and 48h after seeding in fresh expansion-medium

value: bone marrow cells

tag: genotype

value: M/E-Mef2c del/-


title: 1E0-1

description: no additional information

value: 1st instar larvae

value: 2nd instar larvae

value: 3rd instar larvae


title: WT-OVX-1


title: MCF-7 Mock_5

description: Vehicle treatment for 24 hr of MCF-7 cells

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min. Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried prior to a high-resolution scan.

scan_protocol: Scan on a GenePix 4000B (Axon Instruments, CA, USA). Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays. We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.

source_name: MCF-7 cells

treatment_protocol: MCF-7 cells cultured in phenol red-free DMEM containing 10% charcoal-stripped FBS for 2 days and vehicle treatment for 24 hr.

tag: cell line

value: MCF-7 cells

tag: agent

value: vehicle treatment

tag: time point

value: 24 hr


title: MCF-7 E2 4h_2

description: E2 treatment for 4 hr of MCF-7 cells

treatment_protocol: MCF-7 cells cultured in phenol red-free DMEM containing 10% charcoal-stripped FBS for 2 days and E2 (100 nM) treatment for 4 hr.

value: E2 (100 nM) treatment

value: 4 hr


title: MCF-7 E2 4h_1

description: E2 treatment for 4 hr of MCF-7 cells


title: MCF-7 E2 24h_3

description: E2 treatment for 24 hr of MCF-7 cells

treatment_protocol: MCF-7 cells cultured in phenol red-free DMEM containing 10% charcoal-stripped FBS for 2 days and E2 (100 nM) treatment for 24 hr.


title: MCF-7 Mock_3


title: M/E-cells with Mys-iPAC control

description:
M/E-cells do not express a functional form of Mef2c
murine bone marrow cells_immortalized by MLL/ENL-expression_6h,24h,48h pooled expansion medium


title: MCF-7 Mock_4


title: MCF-7 Mock2

description: Vehicle treatment for 4 hr of MCF-7 cells

treatment_protocol: MCF-7 cells cultured in phenol red-free DMEM containing 10% charcoal-stripped FBS for 2 days and vehicle treatment for 4 hr.


title: 1males(13587692)

description: no additional information

value: 0-1h prepupae

value: 13-14 h pupae

value: 3 days adult males

value: 3 days adult females

source_name: Males


title: CKO3

city: New Haven

first: Rachel

last: Rutishauser

state: CT

address: 1 Gilbert St., TAC Building

department: Immunobiology

institute: Yale University

description: CKO replicate 3

hyb_protocol: Hybridizations of biotinylated cRNA to Illumina Sentrix MouseRef-8 BeadChip v1.0 Expression BeadChips (Illumina, San Diego, CA) were perfomed at the Genomic Resource Center at the Rockefeller University as per the manufacturer's protocol.

scan_protocol: BeadChips were scanned according to the Manufacturer's protocol.

data_processing: The data were normalized using quantile-quantile normalization algorithm implemented in Affy microarray analysis package for Bioconductor (Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England) 19, 185-193 (2003).)

source_name: day 8 LCMV tetramer+ CD8+ T cells; FACS sorted

label_protocol: 0.1 mg of total RNA was amplified and biotinylated cRNA was generated by using the IlluminaRNA Amplification Kit (Ambion, Austin, TX). RNA was analyzed for integrity with an Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Mice raised in specific-pathogen free conditions with and experiments were performed with approved Institutional Animal Care and Use Committee protocols.

extract_protocol: RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) followed by Rneasy mini elute Kit (Qiagen, Valencia, CA).

treatment_protocol: Mice were infected with 2x10^5 PFU LCMV-Armstrong. Splenocytes were harvested 8 days later, stained with an antibody to CD8 and Class I MHC tetramers (DbGP33-41 and DbNP396-404), and sorted by FACS.

value: spleen

value: Blimp-1flox/flox x GranzymeB-cre+

tag: replicate


title: MCF-7 Mock1


title: CKO4

description: CKO replicate 4


title: CKO1

description: CKO replicate 1


title: MCF-7 E2 24h_2

description: E2 treatment for 24 hr of MCF-7 cells


title: 1L3(13582027)

description: no additional information

value: mixture of rnas from all stages

value: 0-1h embryos

value: 5-6h embryos

value: 11-12h embryos


title: 1L1(13582025)

description: no additional information

value: 1st instar larvae

value: 2nd instar larvae


title: MCF-7 E2 24h_1

description: E2 treatment for 24 hr of MCF-7 cells

value: MCF-7 cells


title: CKO2

description: CKO replicate 2


title: WT4

description: WT replicate 4

value: wildtype


title: WT3

description: WT replicate 3


title: CpG ODN - 12 hr - repeat 2 - mAdbID:93892

status: Public on Jul 21 2009

city: Frederick

first: Debra

last: Tross

state: MD

institute: NCI

description: mAdb experiment ID: 93892

hyb_protocol: Hybridization Protocol Other: Hybridization was performed to 36K mouse 60 mer oligonucleotide array slides (NCI Mouse Array Set Mm MEEBO v1.3) at 42ƒÏC for 18 h in a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) followed by washing, centrifugation and air drying (Klaschik et al., 2007).

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49101;; 3.55541 Temperature: 27.1203

data_processing:
Data Processing Protocol
Calculation Method: An intensity filter of 120 minimum was used for both red and green channels. Lowess normalization was applied. Data missing from 50% of the arrays was filtered out. Ratios were log base 2 transformed.

source_name: Universal Mouse Reference RNA

label_protocol:
Cy3 Sample Labeling Protocol
Other: Synthesized cDNA samples were purified using a MinElute PCR Purification Kit (Qiagen Sciences, Valencia, CA) and labeled with Cy3 (universal reference cDNA) as described previously (Klaschik et al., 2007).

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: CpG ODN Treated - 12 hours

label_protocol:
Cy5 Sample Labeling Protocol
Other: Synthesized cDNA samples were purified using a MinElute PCR Purification Kit (Qiagen Sciences, Valencia, CA) and labeled with Cy5 (sample cDNA) as described previously (Klaschik et al., 2007).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted from resting and stimulated RAW 264.7 cells using TRIzol Reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: small molecule
Agent: CpG Oligonucleotide
Treatment dose: 3.2 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN for 12 hr.

value: Macrophages


title: 1L2(13582030)

description: no additional information

value: 3rd instar larvae


title: poly(I:C) - 12 hr - repeat 3 - mAdbID:93929

description: mAdb experiment ID: 93929

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48;; 3.57 Temperature: 28.25

source_name: poly(I:C) Treated - 12 hours

treatment_protocol:
Treatment type: small molecule
Agent: poly(I:C)
Treatment dose: 32 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 32 ug/ml poly(I:C) for 12 hr.


title: Untreated - 4 hr - repeat 3 - mAdbID:92653

description: mAdb experiment ID: 92653

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48979;; 3.52794 Temperature: 26.2047

source_name: Untreated - 4 hours