title: RPMI2650CR CDDP S2

status: Public on Jun 14 2012

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

institute: Tohoku University School of Medicine

description:
miRNA profiing
Nasal cancer cell line with CDDP treatment
Processed data file: 252182711223_S01_2_2_GeneView.txt
Raw file: US80703200_252182711223_S01_miRNA-v1_95_May07_2_2.txt

hyb_protocol: Cy3 labeled RNAs were hybridized for 20hr at 55oC Human miRNA Microarray, 8x15K

scan_protocol: Microarray slides were scanned with the Agilent G2565BA microarray scanner

data_processing: Intensity data from microarray images were extracted with Feature Extraction Software 9.5.1 (Agilent Technologies). The GeneView txt files were specific files of miRNA data, which appeared automatically using the extraction protocol( miRNA-v1_95_May07).

source_name: Nasal cancer cell line

label_protocol: Cy3 labeled RNAs were prepared according to the standard Agilent protocol from 100 nanog total RNA (miRNA Microarray System with miRNA Complete Labeling and Hyb Kit, ver.2.1, Agilent)

growth_protocol: Cultured in RPMI2650 (Sigma) supplemented with 10% FBS (Invitrogene)

extract_protocol: Total RNAs including microRNAs were extracted using miRVanaTM microRNA Isolation kit (Applied Biosystems , Foster City, CA) according to the manufactures’ instructions

treatment_protocol: Incubate with or without 10μg/ml CDDP for 1/4 doubling time

tag: cell line

value: CDDP-resistant nasal squamous cell carcinoma (nasal SCC) cell line RPMI2650CR

tag: agent

value: CDDP


title: Brain from TM1 Female rep 2

status: Public on Jun 15 2012

type: RNA

city: N. Dartmouth

first: Robert

last: Drew

state: MA

address: 285 Old Westport Road

department: Biology

country: USA

institute: University of Massachusetts Dartmouth

description: Gene expression data from brain of domesticated TM1 zebrafish strain

hyb_protocol: Affymetrix Zebrafish Genome Arrays (~14,900 transcripts) were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 rpm), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.  This was followed by another round of SAPE.   All microarray procedures were performed at the Genomics Core Facility of the Center for Reproductive Biology at Washington State University (Pullman, WA).

scan_protocol: All microarrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: CEL files containing raw data were then processed and analyzed using R software and Bioconductor packages. Microarray hybridization data were examined for physical anomalies on the chip by pseudochip and residual error visualizations. Quality assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport.  The arrays were then pre-processed using the Robust Multi-array Average (RMA) procedure using the affy package. Next, unexpressed and low variability genes were removed by unbiased filtering.  Affymetrix present-marginal-absent (PMA) calls were determined using a P-value cut off for absent of greater than 0.04 and present less than 0.04; marginal calls were treated as absent. Unexpressed genes were then defined as having a signal less than the expression value at which 99% of genes were called as absent across all samples.  A filter on interquartile range was also applied to remove genes with low variability.  Genes with an interquartile range of less than 0.5 across all chips in the experiment were excluded, reducing the dataset further to 7,958 genes.  Signal intensities were also examined at the probe level to identify single feature polymorphisms (SFPs), differences at the probe level due to genetic polymorphisms rather than expression differences, which may also impact computed expression values.  Briefly, in R using previously described methods, the RMA normalized expression estimate for each probe set was subtracted from background corrected and normalized expression levels at individual probes within the probe set.  Normalized residuals were analyzed using significance analysis of microarrays (SAM) within the siggenes package to detect features with a significant effect for strain (FDR adjusted  < 0.01). A total of 3,199 genes with significant SFPs were then removed from the analysis.

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: Brain from domesticated TM1 strain, Univ of Idaho

label_protocol: For each array, 10 ug of total RNA were converted to cDNA.  Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Prior to the experiment, all zebrafish were reared in a recirculating zebrafish facility at the University of Idaho, designed by Aquaneering Inc. (San Diego, CA).  Fish were feed twice daily with a combination of commercial flake food and Artemia nauplii.  Temperature of the facility was maintained at 28ºC with a constant 14 h light: 10 h dark cycle.  These rearing conditions were maintained during the behavior assays.

extract_protocol: Total RNA was then extracted using the TRIzol method following manufacturer’s protocol (Invitrogen).

treatment_protocol: Sixteen adult fish (4 to 6 months old) from each strain were randomly assigned to 1-L aquaria (22 cm long, 15 cm high, 5 cm wide), one fish per aquarium.  The aquaria were delimited into six 2-cm vertical zones using thin twine tied across the front of the entire row of aquaria.  Fish were then observed using a high-throughput behavioral assay to quantity fear-related behaviors.  Following behavioral observations, fish were removed from the individual tanks and temporily placed in one of sixteen 3-L group tanks.  On the sampling day, each fish was anesthetized in 170 mg L−1 tricaine methanesulfonate (MS222, Western Chemical Inc., Ferndale, WA), briefly blotted on a paper towel, and rapidly measured for standard length and body mass.  The brain was then quickly removed and homogenized in TRIzol (Invitrogen, Carlsbad, CA).  Brains from all individuals in a tank were homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).

tag: strain

tag: tissue

value: Brain

tag: rearing history

value: Domesticated

tag: age

value: Adult

tag: Sex

value: Female


title: M PER417-003, Untreated plants, biological rep1

city: Yokohama

first: Tetsuya

last: Sakurai

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: Gene expression data from untreated M PER417-003 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacture's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent microarray (GPL14139) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (50 percentile) was performed for each chip.

organism: Manihot esculenta subsp. peruviana

source_name: Untreated M PER417-003 plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacture's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: After cutting of shoots from the cassava plants, the shoots were grown in  a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark).

extract_protocol: The total RNA was extracted from the plants before or after drought treatment using RNeasy Plant Mini kit (QIAGEN) according to manufacture’s instruction.

treatment_protocol: The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for  1 hour under 40-80 μmol photons m-2 sec-1 at 30ºC in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization.

value: Stem and leaves

value: 30 day-old plantlets  after cutting

tag: treatment

value: untreated

tag: cultivar


title: M PER417-003, Untreated plants, biological rep3


title: RPMI2650CR S2

description:
miRNA profiing
Nasal cancer cell line
Processed data file: 252182711223_S01_2_1_GeneView.txt
Raw file: US80703200_252182711223_S01_miRNA-v1_95_May07_2_1.txt

organism: Homo sapiens

value: control


title: M PER417-003, Drought-treated plants, biological rep1

description: Gene expression data from drought-stress-treated M PER417-003 plants

source_name: Drought-treated M PER417-003 plants

value: drought


title: M ECU72, Drought-treated plants, biological rep2

description: Gene expression data from drought-stress-treated M ECU 72 plants

organism: Manihot esculenta

source_name: Drought-treated M ECU72 plants

value: M ECU72


title: RPMI2650 CDDP S2

description:
miRNA profiing
Nasal cancer cell line with CDDP treatment
Processed data file: 252182711223_S01_1_2_GeneView.txt
Raw file: US80703200_252182711223_S01_miRNA-v1_95_May07_1_2.txt

value: Parental nasal squamous cell carcinoma (nasal SCC) cell line RPMI2650


title: M TAI16, Drought-treated plants, biological rep3

description: Gene expression data from drought-stress-treated M TAI16 plants

source_name: Drought-treated M TAI16 plants

value: M TAI16


title: RPMI2650 S2

description:
miRNA profiing
Nasal cancer cell line
Processed data file: 252182711223_S01_1_1_GeneView.txt
Raw file: US80703200_252182711223_S01_miRNA-v1_95_May07_1_1.txt


title: M TAI16, Untreated plants, biological rep3

description: Gene expression data from untreated M TAI16 plants

source_name: Untreated M TAI16 plants


title: M PER417-003, Untreated plants, biological rep2


title: M ECU72, Untreated plants, biological rep2

description: Gene expression data from untreated M ECU 72 plants

source_name: Untreated M ECU72 plants


title: M PER417-003, Drought-treated plants, biological rep2


title: M ECU72, Drought-treated plants, biological rep3


title: Subject 3L

city: Menlo Park

first: Denise

last: Nishita

state: CA

address: 333 Ravenswood Ave.

department: Molecular Genetics

institute: SRI International

scan_protocol: As described by manufacturer's protocol written by Fluidigm respectively

data_processing: In order to generate calibration curves for each of the six chips, the triplicate Ct values, SD, and CV for each point on the standard curve were averaged. Two different types of differential gene expression analyses were performed – the comparative standard curve (CSC) or delta delta CT method, and the relative standard curve (RSC) method. In the former method, the target gene amount is a function (2 to the – power) of the difference in normalized target assay cycle threshold between the sample and a calibrator (a standard curve). In the latter method, the sample Ct values are transformed into nanogram (ng) amounts based upon the standard curve produced from the aggregation of data from across all six chips.  The normalized signal, NormNg, calculated for each sample, is the ratio of the transformed ng in the target gene to the geometric mean of the transformed ng amounts of the four reference genes. Two-sided t-tests, as well as upper and lower one-sided t-tests, were performed for all assays in both methods of analysis.  False discovery rates were calculated and post-hoc multiple regression tests incorporating covariates were performed.

label: EvaGreen

source_name: Low Salivary Stress

label_protocol: Fluidigm standard protocol

extract_protocol: Saliva biospecimens were collected using the Oragene•RNA for Expression Analysis Self-Collection Kits, RE-100 (DNA Genotek, Ontario, Canada) and the manufacturer’s protocol, described in the Supplemental File.

tag: sample id

tag: stress (0-low, 1-high)

tag: sex (0-male 1-female)

tag: smoking status (0-non smoker, 1-former smoker, 2-current smoker)

tag: rna integrity score

tag: rna yield (ug)


title: M ECU72, Untreated plants, biological rep3


title: RPMI2650CR CDDP S1

description:
miRNA profiing
Nasal cancer cell line with CDDP treatment
Processed data file: 252182711222_S01_2_2_GeneView.txt
Raw file: US80703200_252182711222_S01_miRNA-v1_95_May07_2_2.txt


title: M TAI16, Drought-treated plants, biological rep2


title: M ECU72, Drought-treated plants, biological rep1


title: M ECU72, Untreated plants, biological rep1

description: Gene expression data from untreated M ECU72 plants


title: BIR replicate 2

type: genomic

city: marseille

first: bertrand

last: llorente

address: 31 chemin josephh aiguier

country: France

institute: cnrs

hyb_protocol: Precipitated labeled DNA was resuspended in 5 microliters of water and 50 microliters of DIG Easy Hyb (Roche Applied Science), denatured for 2 minutes at 95 Celcius degrees, placed on the surface of the array below a coverslip and hybridized overnight at 24 Celcius degrees.  The slides were washed in 6X SSPE, 0.05% Triton X-100 for 5 min, and in successive baths of 2X SSPE, 0.05% Triton, 0.2X SSPE, 0.05% Triton and 0.2X SSPE, for 3 min each and dried by a short centrifuge spin. For details see Decourty et AL. PNAS 2008.

scan_protocol: Scans of the microarrays were done on a GenePix 4000B scanner using the GenePix Pro software.

data_processing: The raw results were normalized by the ‘‘loess’’ algorithm for each microarray hybridization using R and the BioConductor package. For each deleted ORF, the median of the values for the different spots corresponding to the corresponding UPTAG and DOWNTAG was calculated. Note that the raw data file contains data for the up- and down- tags of all the yeast ORFs, named -U and -D respectively.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae systematic deletion mutant library

label_protocol: Labeled oligonucleotides were used to PCR amplifiy the tags from the genomic DNA.  For details see Decourty et AL. PNAS 2008.

extract_protocol: DNA was extracted using standard yeast protocol involving mechanical lysis with glass beads and vortex in the presence of phenol chloroform isoamyl alcohol (24:24:1). For details see Decourty et AL. PNAS 2008.

tag: minichromosome

value: transformation with linear minichromosome

value: transformation with circular minichromosome


title: BIR replicate 1


title: RPMI2650 CDDP S1

description:
miRNA profiing
Nasal cancer cell line with CDDP treatment
Processed data file: 252182711222_S01_1_2_GeneView.txt
Raw file: US80703200_252182711222_S01_miRNA-v1_95_May07_1_2.txt


title: M TAI16, Drought-treated plants, biological rep1


title: M TAI16, Untreated plants, biological rep1


title: M TAI16, Untreated plants, biological rep2


title: RPMI2650 S1

description:
miRNA profiing
Nasal cancer cell line
Processed data file: 252182711222_S01_1_1_GeneView.txt
Raw file: US80703200_252182711222_S01_miRNA-v1_95_May07_1_1.txt


title: RPMI2650CR S1

description:
miRNA profiing
Nasal cancer cell line
Processed data file: 252182711222_S01_2_1_GeneView.txt
Raw file: US80703200_252182711222_S01_miRNA-v1_95_May07_2_1.txt


title: Terbufos 2

city: Chicago

first: xiao

last: zhang

address: 680 N. Lake Shore Drive

institute: Northwestern University

description: genomic DNA from K562 cells treated with terbufos

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Bioconductor lumi package, version  2.0

label: C-Bio and A-DNP

source_name: K562 cell line

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: Terbufos

tag: concentration


title: Parathion 2

description: genomic DNA from K562 cells treated with parathion

value: Parathion

tag: cell line


title: Phorate 1

description: genomic DNA from K562 cells treated with phorate

value: Phorate


title: Chlorpyrifos 2

description: genomic DNA from K562 cells treated with chlorpyrifos

value: Chlorpyrifos


title: Chlorpyrifos 1


title: Fonofos 0

description: genomic DNA from K562 cells treated with fonofos

value: Fonofos


title: Phorate 0


title: Fonofos 2


title: Dichlorvos 1

description: genomic DNA from K562 cells treated with dichlorvos

value: Dichlorvos


title: Chlorpyrifos 0


title: Control 3

description: genomic DNA from K562 cells treated with EtOH (Ctrl)

value: ETOH


title: Parathion 0


title: Fonofos 1


title: Diazinon 1

description: genomic DNA from K562 cells treated with diazinon

value: Diazinon


title: Terbufos 0


title: Diazinon 2


title: Control 1


title: Diazinon 0


title: Control 0


title: Control 5


title: Dichlorvos 2


title: Terbufos 1


title: Control 2


title: Phorate 2


title: Dichlorvos 0


title: Parathion 1


title: Control 4


title: human dark zone, biological replicate 2

city: Cambridge

first: Gabriel

middle: D

last: Victora

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133plus2 gene chips. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned on Affymetrix GeneChip Scanner 3000 7G using Command Console Software.

data_processing: The data were RMA-normalized using Gene Pattern Expression File Creator Software (v.7.0).

source_name: human tonsil dark zone cells

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3'IVT Express Kit.

growth_protocol: Germinal center cells were isolated from pediatric tonsil specimens

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

tag: tissue source

value: pediatric tonsil specimens

tag: cell type

value: Germinal center B cells (CD19+CD38+IgD-)

tag: cell subpopulation

value: dark zone (CXCR4lo/CD83hi)


title: human dark zone, biological replicate 1


title: Quadriceps_Pompe_7_52wks

city: Framingham

first: Adam

middle: T

last: Palermo

address: 49 New York Ave

department: Functional Genomics

institute: Genzyme

hyb_protocol: Following fragmentation, 2.2 ug of  labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm.  RMA was run separately for biceps and quadriceps.

source_name: Quadriceps muscle, Pompe patient, 52 weeks rhGAA treatment

label_protocol: Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

extract_protocol: Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions.  Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.

tag: tissue

value: Quadriceps muscle

tag: patient

tag: diagnosis

value: Pompe

value: rhGAA

tag: treatment time (rhgaa)

value: 52 Weeks

tag: gender

value: F

tag: age at baseline

tag: motor status (52 weeks treatment)

value: Walking

tag: change in glycogen content (52 weeks treatment)

value: Decreased

tag: response

value: Positive Clinical Outcome


title: human dark zone, biological replicate 4


title: human light zone, biological replicate 1

source_name: human tonsil light zone cells

value: light zone (CXCR4hi/CD83lo)


title: human light zone, biological replicate 3


title: Quadriceps_Pompe_9_52wks

tag: treatment


title: human light zone, biological replicate 4


title: Quadriceps_Pompe_9_00wks

source_name: Quadriceps muscle, Pompe patient, 0 weeks rhGAA treatment

value: 00 Weeks


title: Quadriceps_Pompe_10_00wks

value: M


title: Quadriceps_Pompe_8_12wks

source_name: Quadriceps muscle, Pompe patient, 12 weeks rhGAA treatment

value: 12 Weeks

value: Standing


title: Quadriceps_Pompe_6_52wks


title: human dark zone, biological replicate 3


title: Quadriceps_Pompe_11_12wks

value: No gains

value: Stable

value: Poor Clinical Outcome


title: Quadriceps_Pompe_11_00wks


title: Quadriceps_Pompe_10_52wks


title: human light zone, biological replicate 2

value: pediatric tonsil specimens

value: Germinal center B cells (CD19+CD38+IgD-)


title: Quadriceps_Pompe_6_00wks

value: Quadriceps muscle

value: Pompe


title: Quadriceps_Pompe_7_12wks

value: rhGAA


title: Quadriceps_Pompe_8_52wks

value: 52 Weeks


title: Quadriceps_Pompe_8_00wks


title: Quadriceps_Pompe_10_12wks

value: Walking


title: Quadriceps_Pompe_9_12wks

value: F

value: Decreased


title: Quadriceps_Pompe_5_00wks

value: Positive Clinical Outcome


title: Quadriceps_Pompe_3_52wks


title: Quadriceps_Pompe_4_52wks

value: Increased


title: Quadriceps_Pompe_4_00wks

value: 00 Weeks

value: M


title: Quadriceps_Pompe_4_12wks

value: 12 Weeks


title: Quadriceps_Pompe_6_12wks


title: Quadriceps_Pompe_5_12wks


title: Quadriceps_Pompe_3_00wks

value: No gains


title: Quadriceps_Pompe_5_52wks


title: Quadriceps_Pompe_2_00wks

value: Stable


title: Quadriceps_Pompe_1_12wks

value: Poor Clinical Outcome


title: Quadriceps_Control_6

source_name: Quadriceps muscle, Control patient

value: Control


title: Biceps_Pompe_8

source_name: Biceps muscle, Pompe patient

value: Biceps muscle

value: 1y 5m


title: Quadriceps_Control_2

value: Quadriceps muscle


title: Quadriceps_Control_4


title: Quadriceps_Pompe_2_12wks

value: Pompe

value: rhGAA


title: Quadriceps_Pompe_2_52wks

value: 52 Weeks

value: Walking


title: Quadriceps_Control_5

value: F


title: Quadriceps_Pompe_3_12wks

value: Decreased


title: Biceps_Pompe_9


title: Quadriceps_Control_3


title: Biceps_Pompe_4


title: Quadriceps_Pompe_1_52wks

value: Increased


title: Biceps_Pompe_7


title: Biceps_Pompe_6


title: Quadriceps_Pompe_7_00wks

value: 00 Weeks

value: Positive Clinical Outcome


title: Quadriceps_Control_7


title: Quadriceps_Pompe_1_00wks

value: M


title: Biceps_Pompe_5


title: Biceps_Pompe_3


title: Biceps_Control_9

source_name: Biceps muscle, Control patient


title: Biceps_Control_7

value: 2y 3m


title: Biceps_Control_10

value: 2y 9m


title: Biceps_Control_6


title: Biceps_Pompe_2


title: Biceps_Control_2


title: Biceps_Control_4


title: Biceps_Control_8

value: 1y 9m


title: Biceps_Control_5

value: Control


title: Biceps_Control_1

value: Biceps muscle

value: 1y 2m


title: Biceps_Pompe_1


title: Cancer Epithelia_Patient ID 620

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

institute: The Institute for Next Generation Healthcare

description: Gene expression data of LCM-derived cells from fresh frozen tissues of cancer epithelium

hyb_protocol: Chips were hybridized to platform GPL570 platform (Affymetrix Human Genome U133 Plus2.0 Array) using Affymetrix HWS KIT and FS450_0004 Protocol

scan_protocol: Scan on 7G Affimetrix GeneChip scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis.

source_name: LCM-derived cells from snap-frozen tissues of cancer epithelium

label_protocol: RNA was amplified with Ovation Pico WTA System (NuGen) and labeled  with Encor Biotin Module (NuGen)

extract_protocol: Cells were collected from frozen sections using LCM. RNA was isolated with PicoPure RNA isolation KIT (LifeTechnologies). Concentration and Quality of RNA was measured with RNA PicoChip on Bioanalyzer

value: LCM-derived

tag: patient id

value: Ovarian Cancer Epithelium

tag: Stage

value: III/IV

tag: grade

tag: age


title: Cancer Epithelia_Patient ID 542

value: IV


title: Cancer Epithelia_Patient ID 551

value: IIIc/IV


title: Cancer Epithelia_Patient ID 606

value: III a


title: Cancer Epithelia_Patient ID 413

value: III


title: Cancer Stroma_Patient ID 413

description: Gene expression data of LCM-derived cells from fresh frozen tissues of cancer stroma

source_name: LCM-derived cells from snap-frozen tissues of cancer stroma

value: Ovarian Cancer Stroma


title: Cancer Epithelia_Patient ID 489


title: Cancer Epithelia_Patient ID 528

value: III c


title: Biceps_Control_3

value: 2y 1m


title: Cancer Epithelia_Patient ID 317

value: I c


title: Cancer Epithelia_Patient ID 369


title: Cancer Epithelia_Patient ID 651

value: IIIb/c


title: Cancer Epithelia_Patient ID 336


title: Cancer Epithelia_Patient ID 5883

value: II c


title: Cancer Epithelia_Patient ID 242

value: II b


title: Cancer Stroma_Patient ID 229


title: Cancer Epithelia_Patient ID 367

value: II


title: Cancer Epithelia_Patient ID 537


title: Cancer Epithelia_Patient ID 183


title: (normal) Ovarian Surface Epithelia_Patient ID 567

description: Gene expression data of cell brushings from the Ovarian Surface Epithelium

source_name: Cell brushings from the ovarian surface epithelium

value: Ovarian Surface Epithelium


title: Cancer Epithelia_Patient ID 229


title: Cancer Stroma_Patient ID 369


title: Cancer Stroma_Patient ID 242


title: Cancer Stroma_Patient ID 367


title: Cancer Epithelia_Patient ID 617


title: (normal) Ovarian Surface Epithelia_Patient ID 552


title: (normal) Ovarian Surface Epithelia_Patient ID 563


title: Cancer Stroma_Patient ID 336


title: Cancer Stroma_Patient ID 183


title: Quadriceps_Control_1

value: Quadriceps muscle

value: Control

value: M


title: (normal) Ovarian Surface Epithelia_Patient ID 440

value: LCM-derived


title: (normal) Ovarian Surface Epithelia_Patient ID 434


title: (normal) Ovarian Surface Epithelia_Patient ID 463


title: (normal) Ovarian Surface Epithelia_Patient ID 448


title: (normal) Ovarian Surface Epithelia_Patient ID 541


title: (normal) Ovarian Surface Epithelia_Patient ID 452


title: (normal) Ovarian Surface Epithelia_Patient ID 475


title: (normal) Ovarian Surface Epithelia_Patient ID 470


title: Normal Stroma_Patient ID 448

description: Gene expression data of LCM-derived cells from fresh frozen tissues of normal stroma

source_name: LCM-derived cells from snap-frozen tissues of normal stroma

value: Ovarian Normal Stroma


title: Normal Stroma_Patient ID 475


title: (normal) Ovarian Surface Epithelia_Patient ID 437


title: Normal Stroma_Patient ID 434


title: Normal Stroma_Patient ID 463


title: Normal Stroma_Patient ID 437


title: Normal Stroma_Patient ID 440


title: Gut_CON/Stigma_replicate 4

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

institute: Max Planck Institute for Chemical Ecology

description: Pooled from 5 animals.

hyb_protocol: 825 ng of each Cyanine 3- and Cyanine 5-labeled cRNA was used for each array. Hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer's instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturer's instructions, using an Agilent microarray scanner.

data_processing: Data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data for both dye channels from output files were analyzed using GeneSpring microarray analysis software. The Sample data table includes the ratios (test/reference) log base 2 transformed normalized to median data. Data was averaged for structural and spike-in controls occurring several times in the microarray.

organism: Helicoverpa zea

source_name: Gut, cholesterol diet (CON)

label_protocol: Agilent Technologies spike-in RNA was added to 500 ng of total RNA and labeled using a combination of the QuickAmp Labeling kit (Agilent Technologies) for two-color arrays following the manufacturer's instructions. Labeled amplified cRNA samples were purified using Qiagen RNeasy MinElute columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >825 ng and the specific activity >8.0 pmol Cy3 or Cy5 per ug cRNA.

growth_protocol: Helicoverpa zea eggs were acquired from Benzon Research, Inc. (Carlisle, PA), and the emerging hatchlings were used in the experiments. Insects were reared under laboratory conditions (26 °C, 55% RH, 16:8 hr = L:D) in College Station, Texas, USA on an artificial diet. The artificial diets used in the experiment is the diet described in Jing (2011), and is a hybrid of two diets: (1) the standard corn-soy-milk (CSM) diet used to rear many different caterpillar species (Cohen, 2004), and (2) a sterol-free diet developed by Ritter and Nes (Ritter and Nes, 1981a) for rearing H. zea. Some of the diet components in the CSM diet contain sterols, so these individual components were sterol-washed prior to use (Behmer and Grebenok, 1998). After the diets were mixed, they were suspended in a 1% agar mix (in a 1:6 dry to wet ratio) and presented to the developing caterpillars as food blocks.

extract_protocol: Gut tissue was snap-frozen in liquid nitrogen. The frozen tissue was transferred to a liquid nitrogen-cooled mortar and ground. The homogenate was covered with 1 ml Trizol reagent (Invitrogen Corporation, Carlsbad, CA). Further steps were performed according to the manufacturer's instructions, replacing chloroform with 1-bromo-3-chloro-propane. Isolated RNA was quantified with a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE), while RNA quality was checked on a 1% agarose gel. Turbo DNase (Ambion) treatment was included to eliminate contaminating genomic DNA. The total RNA was further purified by using the RNeasy MinElute Clean up Kit (Qiagen) following the manufacturer's protocol. RNA integrity and quantity were verified on an Agilent 2100 Bioanalyzer, using RNA Nano chips (Agilent Technologies).

treatment_protocol: For the microarray experiment, H. zea caterpillars were reared on the diets until they molted into the 3rd instar; shortly after molting, their midguts were removed and processed for RNA extraction. For midgut extraction, larvae were ice-cold anesthesized prior to dissection, which took place under phosphate-buffered saline.

tag: developmental stage

value: 3rd instar larvae

value: midgut

value: cholesterol diet

source_name: Gut, stigmasterol diet (Stigma)

value: stigmasterol diet


title: Normal Stroma_Patient ID 452

tag: cell type


title: Gut_CON/Ch3one_replicate 3

description: Pooled from 5 animals.

source_name: Gut, cholestan-3-one diet (Ch3one)

value: cholestan-3-one diet


title: Gut_CON/Ch3one_replicate 1

description: Pooled from 5 animals.


title: Normal Stroma_Patient ID 470


title: Gut_CON/Ch3one_replicate 4

description: Pooled from 5 animals.


title: Gut_CON/ChStanol_replicate 2

description: Pooled from 5 animals.

source_name: Gut, cholestanol diet (ChStanol)

value: cholestanol diet


title: Gut_CON/Stigma_replicate 1

description: Pooled from 5 animals.


title: Gut_CON/ChStanol_replicate 4

description: Pooled from 5 animals.


title: Gut_CON/ChStanol_replicate 3

description: Pooled from 5 animals.


title: Gut_CON/Stigma_replicate 3

description: Pooled from 5 animals.


title: Gut_CON/ChStanol_replicate 1

description: Pooled from 5 animals.


title: Gut_CON/Ch3one_replicate 2

description: Pooled from 5 animals.


title: Gut_CON/Stigma_replicate 2

description: Pooled from 5 animals.


title: Mouse dark zone, biological replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse MOE430.2 gene chips. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned on Affymetrix GeneChip Scanner 3000 7G using Command Console Software

organism: Mus musculus

source_name: Mouse lymph node dark zone cells

growth_protocol: Germinal center cells were isolated from immunized mouse lymph nodes.

treatment_protocol: Mice were immunized subcutaneously with NP-KLH in alum and lymph nodes were harvested 12 days after immunization.

tag: strain

value: lymph node

value: Germinal center B cells (B220+CD38-CD95+)

tag: cell subpopulation

value: dark zone (CXCR4lo/CD83hi)


title: LIF/PD rep2

city: los angeles

first: Qilong

last: Ying

address: 1425 san pablo st BCC509b

institute: USC

description: Mouse embryonic stem cell, B6

hyb_protocol: Performed by UCLA DNA Microarray core facility

data_processing: The data analysis was performed by using Microarray Я US program provided by USC Norris Medical Library

source_name: ESC treated LIF/PD for 1hr

growth_protocol: GMEM medium (Sigma) supplemented with 10% fetal bovine serum (FBS) (Hyclone), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma)

extract_protocol: Total RNA was extracted by using TRIzol (Invitrogen)

treatment_protocol: GCSF (homemade), LIF (homemade), PD0325901 (Stemgent 1 µM)

tag: cell line

value: ESCs stably stably expressing a chimeric receptor (GRgp-Y118F)

tag: agent

value: LIF/PD


title: Control rep1

description: Mouse embryonic stem cell, B6

scan_protocol: Performed by UCLA DNA Microarray core facility

source_name: ESC untreated control

value: control


title: LIF/PD rep1

description: Mouse embryonic stem cell, B6

label_protocol: Performed by UCLA DNA Microarray core facility


title: Mouse light zone, biological replicate 4

source_name: Mouse lymph node light zone cells

tag: tissue

value: light zone (CXCR4hi/CD83lo)


title: Mouse dark zone, biological replicate 3


title: Mouse dark zone, biological replicate 4


title: Control rep2

description: Mouse embryonic stem cell, B6


title: GCSF rep2

description: Mouse embryonic stem cell, B6

source_name: ESC treated GCSF for 1hr

value: GCSF


title: Mouse light zone, biological replicate 2


title: 334 JVW-MT2 AA100 18/8

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA as implemented in the Bioconductor package xps.

source_name: HTLV-1-transformed cell line MT-2, high-dose ascorbic acid

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: The HTLV-1-infected CD4+ T cell line MT-2 was cultured at 200.000 cells/ml in the absence or presence of ascorbic acid (10, 50 or 100 µg/ml) and IFN-a2A (1000 IU/ml) for 48 hours. IFN-a2A (3.000.000 IU/ml, a gift of Blausiegel Farmacêutica, São Paulo, Brazil) and ascorbic acid (Sigma-Aldrich, Belgium) stock solutions were prepared in normal saline and milli-Q water, respectively. Working solutions were prepared in RPMI 1640 medium, supplemented with 10% heat inactivated foetal calf serum, 20 µg/ml gentamicin and 75 mM NaHCO3 (GIBCO Invitrogen, Belgium). MT-2 cells were grown in RPMI 1640 medium, supplemented with 10% heat inactivated foetal calf serum, 20 µg/ml gentamicin and 75 mM NaHCO3.

extract_protocol: QIAgen RNeasy kit. Protocols were carried out according to the manufacturer's instructions.

treatment_protocol: Treated for 48 hours with high-dose ascorbic acid (100 µg/ml).

value: HTLV-1-infected CD4+ T cells

value: ascorbic acid for 48 hours

tag: treatment dosage

value: 100 µg/ml (high)


title: Mouse dark zone, biological replicate 1


title: Mouse light zone, biological replicate 3


title: 356 JVW-MT2 AA10 25/8 C

source_name: HTLV-1-transformed cell line MT-2, low-dose ascorbic acid

treatment_protocol: Treated for 48 hours with low-dose ascorbic acid (10 µg/ml).

value: 10 µg/ml low


title: 352 JVW-MT2 con 25/8 C

source_name: HTLV-1-transformed cell line MT-2, untreated

treatment_protocol: Untreated for 48 hours.

value: untreated for 48 hours


title: 354 JVW-MT2 AA100 25/8 C


title: GCSF rep1

description: Mouse embryonic stem cell, B6


title: Mouse light zone, biological replicate 1


title: 344 JVW-MT2 AA100 25/8 A


title: 346 JVW-MT2 AA10 25/8 A


title: 353 JVW-MT2 IFNalpha 25/8 C

source_name: HTLV-1-transformed cell line MT-2, interferon-alpha

treatment_protocol: Treated for 48 hours with IFN-a2A (1000 IU/ml).

value: IFN-a2A for 48 hours


title: KO.uncut.R2

city: London

first: Kristjan

middle: R.

last: Jessen

address: Gower Street

country: United Kingdom

institute: University College London

description: Gene expression data from uncut schwannoma cells from adult c-Jun KO mice.

hyb_protocol: Labelled cDNA Microarray hybridisations were performed on Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: PICR scanner 3000

data_processing: Data were processed using R/Bioconductor.  The RMA (Robust Multichip Average) expression measure was calculated for each probe set using the Affy package's “rma” function with default settings.

source_name: c-Jun KO mouse, Schwann cell, uncut

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

extract_protocol: Total RNA was extracted with the RiboPure™ Kit from Ambion according to the manufacturer's instructions

treatment_protocol: The sciatic nerve of adult mice was cut at the sciatic notch. 7 days after injury, the distal stump and contralateral control nerve were excised and processed as indicated in the extract protocol.

value: Adult schwann cell

value: uncut

tag: genotype

value: c-Jun KO


title: KO.cut.R2

description: Gene expression data from cut schwannoma cells from adult c-Jun KO mice, 7 days after nerve cutting.

source_name: c-Jun KO mouse, Schwann cell, cut

value: cut


title: 336 JVW-MT2 AA10 18/8


title: 355 JVW-MT2 AA50 25/8 C

source_name: HTLV-1-transformed cell line MT-2, intermediate-dose ascorbic acid

treatment_protocol: Treated for 48 hours with intermediate-dose ascorbic acid (50 µg/ml).

value: 50 µg/ml (intermediate)


title: KO.cut.R1


title: 342 JVW-MT2 con 25/8 A


title: 343 JVW-MT2 IFN alpha 25/8 A


title: 345 JVW-MT2 AA50 25/8 A


title: CTRL.uncut.R2

description: Gene expression data from uncut schwannoma cells from adult WT mice.

source_name: WT mouse, Schwann cell, uncut

value: WT


title: Lyl1 KO LMPPs1

city: Houston

first: Margaret

middle: A

last: Goodell

state: TX

address: One Baylor Plaza, N1030

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Gene Chip Scanner 3000

data_processing: Array Star RMA

source_name: Lyl1-null murine LMPPs

label_protocol: Ambion Message Amp kit to amplify and label mRNA

growth_protocol: No growth- purification of native LMPPs from bone marrow of mice

extract_protocol: LMPPs were extracted from bone marrow and purified using flow cytometry for KSL (lack of lineage marker expression (Lin-) and postive expression for c-Kit and Sca-1) and high expression of Flt3. The RNA was extracted using RNAaqueous from Ambion.

treatment_protocol: WT versus knock-out LMPPs purified from 6-8 week old mice; KO allele described in Pub Med ID:  21387538

value: Lymphoid Primed Multipotent Progenitors (LMPPs)


title: 332 JVW-MT2 con 18/8


title: 335 JVW-MT2 AA50 18/8


title: KO.uncut.R1


title: 333 JVW-MT2 IFNalpha 18/8


title: CTRL.uncut.R1


title: WT LMPPs1

source_name: wildtype murine LMPPs

value: wildtype


title: Lyl1 KO LMPPs2


title: WT LMPPs2


title: CTRL.cut.R1

description: Gene expression data from cut schwannoma cells from adult WT mice, 7 days after nerve cutting.

source_name: WT mouse, Schwann cell, cut


title: CTRL.cut.R2


title: CA3_wt_290B

status: Public on Jun 13 2012

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Publication: Long-term proteasome dysfunction in the mouse brain by expression of aberrant ubiquitin; Fischer et al, Neurobiology of Aging 2008

hyb_protocol: According to manufacturer's instructions

data_processing: RMA normalized data, log2 values are provided

source_name: wild type

label_protocol: 2-cycle protocol. 1st round: Ambion MessageAmp RNA Amplificatin kit (AM1751); 2nd round: Ambion MessageAmp Enhanced Amplification Kit (AM1791)

extract_protocol: Qiagen RNeasy Mini kit

treatment_protocol: frozen brain sections were stained with 1% cresyl violet acetate and the CA3 region was isolated using the Palm Laser Beam system

tag: male

tag: wildtype

tag: age 540 days

tag: Hippocampal CA3 region

tag: laser-microdissected


title: CA3_wt_289B

scan_protocol: According to manufacturer's instructions


title: CA3_wt_291A

description: Publication: long-term proteasome dysfunction in the mouse brain by expression of aberrant ubiquitin; Fischer et al, Neurobiology of Aging 2008

data_processing: RMA normalized data, linear values are provided


title: CA3_wt_321B


title: CA3_Ubb+1tg_271A

description: Publication: Long-term proteasome dysfunction in the mouse brain by expression of aberrant ubiquitin; Fischer et al. Neurobiology of Aging 2008

source_name: Ubb+1 transgenic

tag: transgenic for Ubb+1

tag: line 3413


title: CA3_Ubb+1tg_277B


title: CA3_wt_290A


title: CA3_wt_289A


title: CA3_wt_321A


title: CA3_Ubb+1tg_274A


title: CA3_Ubb+1tg_277A


title: CA3_wt_331B


title: CA3_Ubb+1tg_276A


title: CA3_wt_291B


title: CA3_wt_287B


title: CA3_Ubb+1tg_274B


title: CA3_Ubb+1tg_271B


title: CA3_Ubb+1tg_276B


title: CA3_Ubb+1tg_270A


title: CA3_Ubb+1tg_273B


title: CA3_Ubb+1tg_270B


title: CA3_Ubb+1tg_273A


title: CA3_wt_287A


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 4

city: Guadalajara

first: Mario

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65164.gif

hyb_protocol: not provided

scan_protocol: GenePix

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

organism: Mycobacterium tuberculosis

source_name: H37Rv dosR MRO KO

label_protocol: not provided

extract_protocol: TB-Synthesis and Labeling of cDNA SKlab 01; 1. Bring 0.5-5 ?g RNA (Typically 3 ?g) to 11 ?l and add 2 ?l (~2 mg/ml) random hexamers. 2. Heat 10 min at 65C (or 2 min at 98C), snap cool on ice. 10 rxns 20 rxns 3. Add 11?l 5.0 ?l 5X First-Strand buffer (51) (102) 2.5 ?l 100 mM DTT (25.5) (51) 2.0 ?l dNTP (5 mM A,G,C and 0.2 mM T) (20.5) (41) 1.5 ?l Cy3 or Cy5 (Typically use Cy5 for sample that should change) (15.3) (30.6) Then add 1.2-1.8 ?l Stratascript or 0.8-1.2 ?l Superscript II RTase. 4. Incubate 10m at 25C followed by 90m at 42C in PCR machine. Can freeze or leave at 4C o/n.; Protocol Type = Labeling; Performer: Mario Alberto,,Flores-Valdez

value: MRO dosR KO

source_name: H37Rv dosR MRO KO +  pMVdosR

label_protocol: Amount of extract labeled = 2-3 ug of total RNA

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter OD at Harvest = 0.2; Parameter Growth Temperature = 37oC; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC); Performer: Mario Alberto,,Flores-Valdez

extract_protocol: TB-RNA Isolation and Purification SKlab 01; 1. Centrifuge 20-30 ml of early- to mid-log culture (O.D. 0.1-0.2) 4 min at 3700 rpm, at RT-37C. Pipette off supernatant and immediately freeze on dry ice and store at ?80C. 2. Add 1 ml Trizol (Gibco-BRL) to each of 4-8 pellets, suspend first pellet by vortexing,while other pellets are still frozen. Add suspension to 0.4 ml glass beads in a 2 ml screw cap tube. 3. Shake 30s at maximum speed in bead beater. Suspend next pellet and add to glass beads. Apply next sample to bead beater. Repeat bead beating two more times with each sample.Continue to periodically invert samples for at least 5 min in Trizol. 4. Centrifuge samples 45s at max speed, remove Trizol solution to a 2 ml screw cap tube containing half of the Heavy Phase Lock Gel I, supplied by 5 Prime 3 Prime, Inc. in 1.5 ml tubes and transferred with sterile stick to 2 ml tubes, and 300 ?l Chloroform:isoamyl alcohol (24:1). Invert rapidly for 15s, and continue inverting periodically for 2 min.a 5. Centrifuge 5-10m, remove aqueous layer (540 ?l) and add to a 1.5 ml tube containing 270 ?l isopropanol then add 270 ?l high salt solution (0.8M Na Citrate, 1.2M NaCl). Invert several times and spray with Staphene and remove from the P3. Typically ppted at 4C O/N. 6. Centrifuge 10m at 4C and remove isopropanol. Add 1 ml 75% EtOHb, invert several times and centrifuge 5m. 7. Remove EtOH by aspiration. Then, dry under vacuum for 2 min [Do not over dry]. 8. Suspend RNA in 90 ml RNase free water (don?t suspend in DNaseI buffer), may need to heat 10m at 55-60C to dissolve RNA. (Optional: obtain RNA concentration) 9. Add 10 ?l 10X DNaseI buffer to RNA (use no more than 80 ?g RNA) and add 4 ?l DNaseI (Ambion). Incubate 30m at 37C. Qiagen RNeasy purification. 1. Add 350 ?l RLT buffer (add 10 ?l BME to 1 ml RLT before using) and vortex. Add 260 ?l 95% EtOH (or 250 ?l 100% EtOH) to each sample and vortex. 2. Add to RNeasy spin column, centrifuge 15s, transfer column to a new 2 ml collection tube. Add 500 ?l RPE, centrifuge 15s, discard flow-through, add 500 ?l additional RPE and centrifuge 2m. If column still wet on sides, remove wash solution from tube and spin 1m to dry. 3. Transfer to a 1.5 ml collection tube, elute with 40 ?l RNase free water, centrifuge 1m. 4. Determine RNA concentration with A260/A280 readings. Dilute 1 ?l in 199 ?l TE. [200(dilution factor)x 40 ?g/A260x A260 = ?g/ml]. 5. Run 1 ?l RNA on 2% Agarose TAE gel. Run gel 45m at 100 volts. aIf Phase Lock Gel is not used, decrease Chloroform:isoamyl alcohol to 200?l. The yield will be less. Be careful not to remove any of the interface layer. bUsing 100% EtOH should be avoided in all steps of preparation of RNA intended for array analysis. Instead use 95% EtOH in preparation of solutions. Benzene contamination may fluoresce. cInstead of using the RNeasy purification, the DNaseI can be inactivated at 65-70C for 15m and then EtOH precipitated. The RNeasy purification may not be necessary in all applications. We find the purification gives more consistent results and is less time consuming, compared to precipitation. In addition, other purifications can be used. Note: The RNeasy column will remove much of the small tRNA and degraded RNA.; Protocol Type = Extract preparation; Performer: Mario Alberto,,Flores-Valdez

tag: experiment

value: dosR MRO KO + pMVdosR


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 2

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65523.gif

source_name: H37Rv MRO dosR KO

source_name: H37Rv MRO dosR KO +  pMVdosR

value: MRO dosR KO + pMVdosR


title: H37Rv WT vs dosR KO rep 3

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65159.gif

source_name: H37Rv WT


title: H37Rv WT vs dosR KO rep 2

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65519.gif


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 5

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65168.gif


title: H37Rv WT vs dosR KO rep 1

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65518.gif


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 3

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64909.gif

source_name: H37Rv MRO (dosRKO) + pMVdosR

value: MRO (dosRKO) + pMVdosR


title: metastasis_LRP_83a

first: Jianrong

last: Li

state: IL

address: 909 S Wolcott Avenue

department: Medicine

institute: University of Illinois at Chicago

description:
Test
miRNA profiling

data_processing:
The normalization was performed according to the manufacturers instructions using the Applied Biosystems 7900HT Fast Real-Time PCR System software package: http://www.appliedbiosystems.com/absite/us/en/home/support/software/real-time-pcr/ab-7900ht.html
For the normalization we used the average of two standard microRNAs: RNU-44 and RNU-48
Target gene signals normalized to RNU-44 and RNU-48 microRNAs; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RNU-44&RNU-48)]
Non-normalized_data worksheet reports raw Ct values.  Non-normalized data linked as supplementary file on the Series record.
Fold Change worksheet reports test/control (i.e., HRP/LRP) ratios.  Fold Change data linked as supplementary file on the Series record.

label: FAM

source_name: metastatic tumor cell

label_protocol: Real-time qPCR of microRNAs was performed using human Taqman MicroRNA Array A Card v2.0 (Applied Biosystems, Allston, MA)

extract_protocol: Total RNA was extracted with RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems, Allston, MA, USA)

tag: metastatic progression phenotype

value: LRP

tag: oligo- vs. poly-metastasis

value: OM

tag: gender

value: M

tag: primary histology

value: Soft tissue sarcoma


title: H37Rv WT + pMVdosR vs dosR KO rep 7

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64956.gif

tag: strain

source_name: H37Rv WT + pMVdosR

value: WT + pMVdosR


title: H37Rv WT + pMVdosR vs dosR KO rep 3

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64903.gif


title: metastasis_HRP_90a

description:
Test
miRNA profiling

value: HRP

value: PM

value: Adenosquamous


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 8

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64958.gif


title: H37Rv WT + pMVdosR vs dosR KO rep 4

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64906.gif


title: H37Rv WT vs dosR KO rep 5

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64953.gif

growth_protocol: Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter OD at Harvest = 0.2; Parameter Growth Temperature = 37oC; Parameter Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.05% Tween 80; Performer: Mario Alberto,,Flores-Valdez


title: H37Rv WT + pMVdosR vs dosR KO rep 2

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65521.gif


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 6

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64912.gif


title: metastasis_IRP_81c

description:
Test
miRNA profiling

value: IRP


title: metastasis_IRP_88c

description:
Test
miRNA profiling

value: Renal cell carcinoma


title: metastasis_LRP_87a

description:
Test
miRNA profiling

value: Adenocarcinoma


title: H37Rv WT vs dosR KO rep 4

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65161.gif

value: WT


title: metastasis_HRP_78b

description:
Test
miRNA profiling

value: Cholangiocarcinoma


title: H37Rv WT + pMVdosR vs dosR KO rep 1

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65520.gif

value: MRO dosR KO


title: metastasis_LRP_77a

description:
Test
miRNA profiling


title: metastasis_HRP_82b

description:
Test
miRNA profiling

value: Angiosarcoma


title: metastasis_LRP_76a

description:
Test
miRNA profiling

value: F

value: Squamous cell carcinoma


title: H37Rv WT + pMVdosR vs dosR KO rep 5

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65162.gif

source_name: H37Rv WT pMVdosR

value: WT pMVdosR


title: H37Rv WT + pMVdosR vs dosR KO rep 6

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64954.gif


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 7

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64957.gif

value: MRO dosR KO + pMVdosR


title: metastasis_IRP_79b

description:
Test
miRNA profiling

value: M

value: Melanoma


title: metastasis_LRP_75b

description:
Test
miRNA profiling

value: LRP

value: OM

value: Soft tissue sarcoma


title: H37Rv dosR KO + pMVdosR vs dosR KO rep 1

description:
Simple annotation: Absolute transcript levels, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65522.gif


title: metastasis_LRP_71c

description:
Test
miRNA profiling


title: metastasis_HRP_73c

description:
Test
miRNA profiling

value: HRP

value: PM


title: metastasis_HRP_69a

description:
Test
miRNA profiling


title: metastasis_LRP_68b

description:
Test
miRNA profiling

value: Adenoid cystic carcinoma


title: metastasis_IRP_67b

description:
Test
miRNA profiling

value: IRP

value: Renal cell carcinoma


title: metastasis_IRP_63a

description:
Test
miRNA profiling


title: metastasis_LRP_64c

description:
Test
miRNA profiling

value: Adenocarcinoma


title: metastasis_LRP_62b

description:
Test
miRNA profiling


title: metastasis_LRP_61b

description:
Test
miRNA profiling


title: metastasis_HRP_60e

description:
Test
miRNA profiling


title: metastasis_IRP_58b

description:
Test
miRNA profiling


title: metastasis_LRP_59b

description:
Test
miRNA profiling


title: metastasis_LRP_57b

description:
Test
miRNA profiling


title: Middle_age_18

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: healthy sample

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
The intensities of the images are extracted using Genome Studio V2011.2.  Methylation score of each CpG is represented as AVG_beta value.
Raw data file linked to Series record: Unmethylated (Signal_A) and methylated (Signal_B) signal intensities.

label: Cy3 and Cy5

source_name: Whole blood

label_protocol: Illumina Infinium Assay

extract_protocol: Peripheral blood was obtained from female healthy donors from different ages. Peripheral blood mononuclear cells (PBMC) were extracted using a Ficoll gradient. To separate CD19 and CD4 positive cells CD19 MicroBeads and CD4+ T cell Isolation kit II (Miltenyi Biotec) was applied following the manufacturer’s instructions. DNA was Phenol:Chloroform:Isoamylalcohol (Sigma), respectively. CD19+ B-cells were immortalized by Epstein-Barr-Virus (EBV) applying previous published protocol (Miller, G. & Lipman, M. Release of infectious Epstein-Barr virus by transformed marmoset leukocytes. Proc. Natl. Acad. Sci. U.S.A 70, 190-194 (1973)). Bisulphite modification of genomic DNA was carried out with the EZ DNA Methylation Kit (Zymo) following the manufacturer's protocol.

value: Female

tag: age

value: Middle age

value: Whole blood

tag: cell type

tag: disease state

value: Healthy donor


title: metastasis_IRP_56a

description:
Test
miRNA profiling


title: Middle_age_19

description: healthy sample

tag: tissue

value: Peripheral blood mononuclear cells (PBMC)


title: Middle_age_17

description: healthy sample


title: metastasis_LRP_48a

description:
Test
miRNA profiling

value: F


title: metastasis_LRP_49b

description:
Test
miRNA profiling


title: metastasis_HRP_46a

description:
Test
miRNA profiling

value: M


title: Middle_age_13

description: healthy sample


title: Middle_age_10

description: healthy sample


title: Middle_age_15

description: healthy sample


title: Middle_age_14

description: healthy sample


title: metastasis_LRP_45b

description:
Test
miRNA profiling


title: metastasis_LRP_52b

description:
Test
miRNA profiling


title: Middle_age_16

description: healthy sample


title: Middle_age_6

description: healthy sample


title: A549, +TNFα, Claudin 1 siRNA, rep3

city: Toronto

first: Mingyao

last: Liu

state: Ontario

address: 101 College Street

department: Surgery

country: Canada

institute: University of Toronto

description:
CLD_TNF_3
HuGene1_072909H_ML20_CLD TNF 3.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix CEL files were imported into Partek software (Partek Inc., St. Louis, MO) using the default Partek parameters for RMA pre-processing of the probe-level data.

source_name: Human lung adenocarcinoma A549 cells treated with TNFα, in presence of Claudin 1 siRNA

label_protocol: Standard Affymetrix protocol

growth_protocol: Human lung adenocarcinoma A549 cells were grown in DMEM medium supplied with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1% glutamine. Cells were cultured in a standard humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen, Valencia, CA), and cDNA was synthesized with High-Capacity cDNA Reverse Transcription kits (Applied Biosystems, Foster City, CA) on a PTC-100 Programmable Thermal controller (MJ Research Inc., Watertown, MA).

treatment_protocol: Cells were transfected with 50 nM Claudin 1 siRNAs using the oligofectamine reagent (Invitrogen). The medium containing siRNA was replaced with a fresh medium with or without TNFa 24 h after transfection. The siSTABLE V2 non-targeting siRNA#1 from Dharmacon (Lafayette, CO) was used as a negative control.

tag: sirna

value: Claudin 1

tag: treated with tnfα

value: YES


title: Middle_age_8

description: healthy sample


title: metastasis_LRP_54b

description:
Test
miRNA profiling

value: LRP

value: OM


title: Middle_age_3

description: healthy sample


title: Middle_age_9

description: healthy sample


title: metastasis_LRP_39b

description:
Test
miRNA profiling


title: Middle_age_12

description: healthy sample


title: Middle_age_7

description: healthy sample


title: metastasis_LRP_43b

description:
Test
miRNA profiling

value: Hepatocellular carcinoma


title: CB37

data_processing: Genome Studio V2011.2, [(Unmethylated and methylated) signal_intensities.txt is provided as a Series supplementary file]

label: Cy3, Cy5

source_name: Newborns

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: Newborn

tag: disease status

value: healthy sample

value: Cord blood

value: PBMNC


title: Middle_age_5

description: healthy sample


title: Middle_age_2

description: healthy sample


title: A549, +TNFα, Claudin 1 siRNA, rep2

description:
CLD_TNF_2
HuGene1_072909H_ML19_CLD TNF 2.CEL


title: Middle_age_4

description: healthy sample


title: CB70


title: metastasis_LRP_40c

description:
Test
miRNA profiling

value: Adenocarcinoma


title: CB40


title: metastasis_HRP_34e

description:
Test
miRNA profiling

value: HRP

value: PM

value: Soft tissue sarcoma


title: A549, +TNFα, Claudin 1 siRNA, rep1

description:
CLD_TNF_1
HuGene1_072909H_ML18_CLD TNF 1.CEL


title: metastasis_IRP_37b

description:
Test
miRNA profiling

value: IRP


title: metastasis_IRP_33a

description:
Test
miRNA profiling

value: Renal cell carcinoma


title: metastasis_LRP_36c

description:
Test
miRNA profiling


title: CB18


title: Middle_age_11

description: healthy sample

value: Female

value: Middle age

value: Whole blood

value: Peripheral blood mononuclear cells (PBMC)

value: Healthy donor


title: metastasis_HRP_29c

description:
Test
miRNA profiling

value: F

value: Adenoid cystic carcinoma


title: metastasis_LRP_32a

description:
Test
miRNA profiling

value: LRP

value: OM


title: CB12

value: Newborn

value: healthy sample

value: Cord blood


title: metastasis_HRP_28c

description:
Test
miRNA profiling

value: HRP

value: M


title: metastasis_LRP_31b

description:
Test
miRNA profiling

value: Adenocarcinoma


title: metastasis_LRP_47b

description:
Test
miRNA profiling


title: metastasis_LRP_24a

description:
Test
miRNA profiling


title: metastasis_HRP_26a

description:
Test
miRNA profiling

value: PM

value: Transitional cell carcinoma


title: metastasis_HRP_25c

description:
Test
miRNA profiling

value: Renal cell carcinoma


title: A549, -TNFα, Claudin 1 siRNA, rep1

description:
CLD_cont_1
HuGene1_072909H_ML15_CLD cont 1.CEL

source_name: Human lung adenocarcinoma A549 cells treated without TNFα, in presence of Claudin 1 siRNA

value: Claudin 1

value: NO


title: A549, -TNFα, Claudin 1 siRNA, rep2

description:
CLD_cont_2
HuGene1_072909H_ML16_CLD cont 2.CEL


title: metastasis_LRP_21a

description:
Test
miRNA profiling

value: Uterine sarcoma


title: CB5

value: PBMNC


title: metastasis_LRP_23a

description:
Test
miRNA profiling

value: F


title: metastasis_LRP_20a

description:
Test
miRNA profiling


title: A549, -TNFα, Claudin 1 siRNA, rep3

description:
CLD_cont_3
HuGene1_072909H_ML17_CLD cont 3.CEL


title: CB7


title: A549, +TNFα, control siRNA, rep3

description:
U_TNF_3
HuGene1_072909H_ML14_U TNF 3.CEL

source_name: Human lung adenocarcinoma A549 cells treated with TNFα, in presence of control siRNA

value: control (siSTABLE V2 non-targeting siRNA#1)

value: YES


title: A549, +TNFα, control siRNA, rep2

description:
U_TNF_2
HuGene1_072909H_ML13_U TNF 2.CEL


title: CB36


title: metastasis_IRP_44b

description:
Test
miRNA profiling

value: IRP


title: A549, -TNFα, control siRNA, rep2

description:
U_cont_2
HuGene1_072909H_ML10_U cont 2.CEL

source_name: Human lung adenocarcinoma A549 cells treated without TNFα, in presence of control siRNA


title: metastasis_LRP_18a

description:
Test
miRNA profiling

value: LRP

value: OM


title: metastasis_LRP_14c

description:
Test
miRNA profiling

value: Soft tissue sarcoma


title: metastasis_IRP_17b

description:
Test
miRNA profiling


title: Middle_age_1

description: healthy sample

value: Female

value: Middle age

value: Whole blood

value: Peripheral blood mononuclear cells (PBMC)

value: Healthy donor


title: metastasis_IRP_13a

description:
Test
miRNA profiling


title: metastasis_IRP_09a

description:
Test
miRNA profiling

value: PM

value: M

value: Adenocarcinoma


title: metastasis_HRP_07b

description:
Test
miRNA profiling

value: HRP

value: Squamous cell carcinoma


title: metastasis_LRP_08b

description:
Test
miRNA profiling


title: A549, -TNFα, control siRNA, rep3

description:
U_cont_3
HuGene1_072909H_ML11_U cont 3.CEL

value: NO


title: metastasis_IRP_16a

description:
Test
miRNA profiling

value: Osteosarcoma


title: metastasis_LRP_06b

description:
Test
miRNA profiling

value: F


title: ASML_CD44 knock-down cells

city: Heidelberg

first: Sanyukta

last: Rana

address: Im Neuenheimerfeld 365

department: Tumor Cell Biology

institute: University Hostipal Heidelberg

description: Gene expression, ASML_CD44 knock down, base line

hyb_protocol: Standard  hybridization protocol at DKFZ core facility

scan_protocol: Agilent Technologies Scanner G2505C US22502683 were used to scan the arrays.

data_processing: The scanned microarray images were normalized and statistics were performed by using Chipster and Panther programs.

organism: Rattus norvegicus

source_name: ASML_CD44 knock-down cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit at DKFZ core facility.

growth_protocol: Cell lines either at base line or during the treatment with exosomes were mainted in RPMI 1640 medium supplemented with 10%FCS and 750 µg/ml of G418.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: pancreatic adenocarcinoma cell

tag: protocol

value: CD44 knock-down


title: A549, -TNFα, control siRNA, rep1

description:
U_cont_1
HuGene1_072909H_ML9_U cont 1.CEL

value: control (siSTABLE V2 non-targeting siRNA#1)


title: metastasis_HRP_02c

description:
Test
miRNA profiling


title: ASML wild type cells

description: Gene expression, ASML base line

source_name: ASML wild type cells

value: wildtype


title: metastasis_HRP_05b

description:
Test
miRNA profiling


title: CB8

value: Newborn

value: healthy sample

value: Cord blood

value: PBMNC


title: ASTspan8 exosomes

description: Gene expression, ASTspan 8 base line

source_name: ASTspan8 exosomes

value: exosomes derived from pancreatic adenocarcinoma cell

value: ASTspan 8 base line


title: CB9


title: CB17


title: CB82


title: metastasis_HRP_03a

description:
Test
miRNA profiling

value: PM


title: RF_ASTspan8 exosomes

description: Gene expression, ASTspan8 exosomes treated

source_name: RF_ASTspan8 exosomes

value: endothelial fibroblasts cell

value: ASTspan8 exosomes treated


title: CB35


title: metastasis_IRP_01a

description:
Test
miRNA profiling

value: IRP

value: M

value: Renal cell carcinoma


title: Control_144h_rep2

city: Ljubljana

first: Janez

last: Kosel

state: Slovenia

address: Jamnikarjeva 101

country: Slovenia

institute: Biotechnical faculty

description: Gene expression after 144 h in S. cerevisiae from control mono fermentation

hyb_protocol: 600 ng of Cy3-labeled and linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing Agilent 10x blocking agent, nuclease-free water and 25x fragmentation buffer. Immediately after the fragmentation reaction, 25 µl of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmented cRNA and the mixture was hybridized to Yeast (V2) Gene Expression Microarray (G4813A-016322; one glass slide formatted with eight high-definition 15K arrays) for 17 hours at 65°C in a rotating Agilent hybridization oven. After 17 hours of incubation, microarrays were washed with Agilent wash buffer 1 (Triton X-102 containing) and with wash buffer 2 (Triton X-102 containing, pre-warmed to 37°C) and dried with Agilent slide holder.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner G2565AA using one color scan settings and the fluorescence intensities were obtained with QuantArray v3.0 software (PerkinElmer-Cetus). The resulting 32-bit TIFF files were quantified with the same software.

data_processing: Pre-processing was performed using the Biometric Research Branch (BRB)-ArrayTools V4.2 software. Firstly erasing manually flagged bad spots and subtracting the local background and secondly averaging features that are spotted in replicate on the array. Single channel Log2 transformed data were normalization according to the user specified array groups. Data of 16 samples was divided into 4 groups according to the 4 time points of sampling (22h, 92h, 144h and 187h) in other words each group was composed of all microarray data that was obtained from RNA samples of one of the 4 time points of fermentation. For each array group, a median reference array was created based on all the arrays in this group, and each array was normalized against this median reference array. For further information regarding this type of normalization se BRB-ArrayTools User’s Manual Version  4.2 (Biometrics Research Branch, National Cancer Institute and BRB-ArrayTools Development Team, The EMMES Corporation).

source_name: S. cerevisiae-only fermentation, 144 h, replicate 2

label_protocol:
The mixture of 200 ng of total RNA and 2 µl of 1:5000 diluted Agilent One-Color RNA Spike-In solution was reverse transcribed to cDNA and subsequently Cy3-labeled cRNA was synthesized using the Agilent Quick Amp kit (p/n 5190-0442) according to the Agilent protocol “One-Color Microarray-Based Gene Expression Analysis” Version 6.5
URL: http://www.genome.duke.edu/cores/microarray/services/agilent-microarrays/documents/LIQA_G4140-90040_GeneExpression_One-color_v6.5.pdf
. Cy3-labeled cRNA was purified by repeated rinsing through RNeasy mini spin columns (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The initial contaminations were artificially made (106 cell/ml of S. cerevisiae (industrial strain Lalvin EC1118) and 106 cell/ml of D. bruxellensis (strain ZIM 701); inoculum was adjusted according to the cell count under the Bürker-Türk cell counting chamber) at the beginning of fermentations carried out in 500 ml membrane bioreactors, where strains D. bruxellensis and S. cerevisiae were separated from each other with a dialysis membrane during 8 days of fermentation period at 22oC. All fermentations were done in an artificial wine must.

extract_protocol:
30-40 ml of cell suspension was centrifugated at 6500 g in order to obtain around 100 µl of cell pellet per sample. One millilitre of Tri reagent (Molecular Research Center, Inc.) and 300 µl of acid-washed glass beads (425-600 μm) were added to the cell pellet and the contents was vortexed for 20 min. After homogenization we added additional 6 ml of Tri reagent to each sample. Chloroform extraction and RNA precipitation were performed according to the manufacturer’s instructions (
URL: http://tools.invitrogen.com/content/sfs/manuals/9738M_D.pdf
).

treatment_protocol: The control fermentations (mono fermentation of S. cerevisiae or D. bruxellensis) were inoculated only on one side of the membrane reactor and the other side remained sterile. For mixed fermentations we inoculated the spoilage yeast on one side and the alcohol fermenting yeast on the other side of the same reactor separated by a dialysis membrane.

value: Lalvin EC1118

tag: biomass

value: S. cerevisiae

tag: growth phase

value: late stationary growth phase

tag: sampling time


title: CB10


title: CB13


title: CB15


title: Control_22h_rep2

description: Gene expression after 22 h in S. cerevisiae from control mono fermentation

source_name: S. cerevisiae-only fermentation, 22 h, replicate 2

value: exponential growth phase


title: Control_187h_rep2

description: Gene expression after 187 h in S. cerevisiae from control mono fermentation

source_name: S. cerevisiae-only fermentation, 187 h, replicate 2

value: autolytic growth phase


title: Control_92h_rep2

description: Gene expression after 92 h in S. cerevisiae from control mono fermentation

source_name: S. cerevisiae-only fermentation, 92 h, replicate 2

value: early stationary growth phase


title: CB20

value: Newborn

value: healthy sample


title: Mixed_187h_rep2

description: Gene expression after 187 h in S. cerevisiae from mixed fermentation

source_name: Mixed fermentation, 187 h, replicate 2

value: Lalvin EC1118 and ZIM 701

value: S. cerevisiae from mixed fermentation


title: Mixed_144h_rep2

description: Gene expression after 144 h in S. cerevisiae from mixed fermentation

source_name: Mixed fermentation, 144 h, replicate 2


title: Mixed_22h_rep2

description: Gene expression after 22 h in S. cerevisiae from mixed fermentation

source_name: Mixed fermentation, 22 h, replicate 2


title: Control_187h_rep1

source_name: S. cerevisiae-only fermentation, 187 h, replicate 1


title: A38NEW

source_name: Nonagenarians

value: 90 years

value: Whole blood

value: PBMNC


title: Control_144h_rep1

source_name: S. cerevisiae-only fermentation, 144 h, replicate 1


title: RF

description: Gene expression, base line

source_name: Endothelial cell lines

value: endothelial fibroblasts cell

value: base line


title: ASTspan8 exosomes_replicate 1

description: Gene expression, ASTspan 8 base line_replicate 1

source_name: ASTspan8 exosomes_replicate 1

value: exosomes derived from pancreatic adenocarcinoma cell

value: ASTspan 8 base line


title: RF_AS exosomes

description: Gene expression, AS exosomes treated

source_name: RF_AS exosomes

value: AS exosomes treated


title: Endothelial cell lines_ASTspan8 exosomes_replicate 1

source_name: Endothelial cell lines_ASTspan 8 exosomes_replicate 1

value: endothelial cell

value: ASTspan8 exosomes treated


title: Endothelial cell lines_ASTspan8 exosomes

source_name: Endothelial cell lines_ASTspan 8 exosomes


title: Mixed_92h_rep2

description: Gene expression after 92 h in S. cerevisiae from mixed fermentation

source_name: Mixed fermentation, 92 h, replicate 2


title: CB76

source_name: Newborns

value: Cord blood


title: Control_92h_rep1

source_name: S. cerevisiae-only fermentation, 92 h, replicate 1

value: Lalvin EC1118

value: S. cerevisiae


title: Control_22h_rep1

source_name: S. cerevisiae-only fermentation, 22 h, replicate 1

value: exponential growth phase


title: A37NEW

value: healthy sample


title: Mixed_144h_rep1

source_name: Mixed fermentation, 144 h, replicate 1

value: Lalvin EC1118 and ZIM 701

value: late stationary growth phase


title: Mixed_187h_rep1

source_name: Mixed fermentation, 187 h, replicate 1

value: S. cerevisiae from mixed fermentation

value: autolytic growth phase


title: Mixed_92h_rep1

source_name: Mixed fermentation, 92 h, replicate 1

value: early stationary growth phase


title: Mixed_22h_rep1

source_name: Mixed fermentation, 22 h, replicate 1


title: C. sporogenes early stationary phase Cells 2

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

country: Italy

institute: Università Cattolica del Sacro Cuore

description: This is the second of three biological replicates of early stationary phase cells sample. These data are derived from the first technical replicate.

hyb_protocol: The fragmented Cy5-aRNA was then mixed with hybridization buffer (6X SSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionised formamide, 0.1 mg/mL sheared salmon sperm DNA and 0.04% SDS) and hybridized to the Combimatrix 12K Chip at 45 °C for 16 h.

scan_protocol: Scanning was performed by using a ScanArray 4000XL scanner (Perkin-Elmer, USA) following the standard operating protocol.

data_processing: Data pre-processing was performed using Combimatrix Blist software (v. 0.6.2.) and Quantile normalization was applied. Subtraction of estimated non-specific binding using the cross-species hybridization data was done.

label: Cy5 dye

organism: Clostridium sporogenes

source_name: Isolated Clostridium sporogenes UC9000

label_protocol: The obtained aRNA, quantified (20 μg per sample) and purified, was labelled with Cy-5 dye; Cy5-aRNA was subsequently purified and its concentration was determined using a spectrophotometer.

growth_protocol: Clostridium sporogenes UC9000, isolated from milk, was used for all the experiments. The strain was routinely cultured in Reinforced Clostridial Medium-Lactate  broth (Oxoid, UK) at 37°C in anaerobic bags equipped with Anaerocult A packs (Merck, Germany).

extract_protocol: RNA isolated from cells was obtained using Nucleospin® RNAII kit (Macherey Nagel, Germany) according to the manufacturer’s instructions. A FastPrep homogenizer (MP Biomedicals) was employed to extract RNA from spores.

treatment_protocol: After germination in RCM-lactate medium, samples for early stationary phase cells were collected after 35 hours for RNA isolation.

tag: developmental stage

value: early stationary phase cell at 35h

tag: time


title: C. sporogenes early stationary phase Cells 3

description: This is the third of three biological replicates of early stationary phase cells sample. These data are derived from the first technical replicate.


title: A36NEW

value: 89 years

value: Whole blood

value: PBMNC


title: C. sporogenes early stationary phase Cells 1

description: This is the first of three biological replicates of early stationary phase cells  sample. These data are derived from the first technical replicate.


title: Endothelial cell lines_AS exosomes

description: Gene expression, AS exosomes treated

source_name: Endothelial cell lines_AS exosomes

value: AS exosomes treated


title: A27NEW

source_name: Nonagenarians

value: 91 years


title: Endothelial cells, control

description: Gene expression, base line

value: endothelial cell

value: base line


title: A34NEW


title: A26NEW

value: 90 years


title: C. sporogenes mid-log vegetative Cells 1

description: This is the first of three biological replicates of mid-log vegetative cells sample. These data are derived from the first technical replicate.

treatment_protocol: After germination in RCM-lactate medium, samples for mid-log vegetative cells were collected after 28 hours for RNA isolation.

value: mid-log vegetative cell at 28h


title: A549, +TNFα, control siRNA, rep1

description:
U_TNF_1
HuGene1_072909H_ML12_U TNF 1.CEL

source_name: Human lung adenocarcinoma A549 cells treated with TNFα, in presence of control siRNA

value: control (siSTABLE V2 non-targeting siRNA#1)

value: YES


title: C. sporogenes mid-log vegetative Cells 3

description: This is the third of three biological replicates of mid-log vegetative cells sample. These data are derived from the first technical replicate.


title: C. sporogenes mid-log vegetative Cells 2

description: This is the second of three biological replicates of mid-log vegetative cells sample. These data are derived from the first technical replicate.


title: A35NEW

value: healthy sample


title: CB23

value: Newborn

value: Cord blood


title: C. sporogenes Germinating Spores 3

description: This is the third of three biological replicates of germinating spore sample at 3h. These data are derived from the first technical replicate.

treatment_protocol: Spore germination was performed at controlled 37°C temperature in anaerobiosis. The germination medium used was RCM broth-lactate (Oxoid, UK). The monitoring of the germinating progression was achieved at regular intervals (every 30 min for a total of 50 hours time interval) by optical density measurements of 10-fold-diluted samples at 600 nm and the germination time course was also followed using SEM-microanalysis technique. At 3 hours time interval, 1.5-ml samples was collected for RNA isolation; this was considered the optimal time set with the highest percentage of germinated spores (drop in OD value and loss of calcium in microanalysis).

value: germinating spore at 3h


title: C. sporogenes Germinating Spores 2

description: This is the second of three biological replicates of germinating spore sample at 3h. These data are derived from the first technical replicate.


title: MPAO1 untreated rep.2

city: Braunschweig

first: Piotr

last: Bielecki

address: Inhoffenstr 7

department: Cell Biology

institute: Helmholtz Centre for Infection Research

description: P. Aeruginosa gene expression from planctonic culture

hyb_protocol: Standard affymetrix

scan_protocol: Standard affymetrix

data_processing: R version 2.6.0, Bioconductor 2.1. The quality of all chips was assessed by fitting a linear model to the probe level data using the function “fitPLM” from the “affyPLM” package. Subsequently, the distribution (boxplots) of RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) was manually analysed.

organism: Pseudomonas aeruginosa

source_name: MPAO1 untreated

label_protocol: Biotin incorporation during amplification

growth_protocol: Pseudomonas aeruginosa strains MPAO1 was grown overnight in ABT minimal medium supplemented with 0.5% casamino acids and inoculated 1% (v/v) in 200 mL of the same media and incubated at 37°C with shaking (250 rpm). When the culture reached middle exponential phase at an optical density of 0.5 at 600 nm (OD600), it was split into halves. One half was treated with 125 μM of Protoanemonin and the second served as a control. Cultures were harvested for proteomic and transcriptomic analysis (RNAprotect reagent, Qiagen) at the late exponential/early stationary phase at OD600 = 2.0 as described below. The experiment was performed in triplicate.

extract_protocol: QIAGEN RNAmini, Ambion MessageAMP. The total RNA from triplicates of each condition (biological replicates) were pooled together. Replicates of the microarray represent the technical replicates.

treatment_protocol: Cultures of MPAO1 were collected on RNAprotect reagent, centrifuged and frozen until RNA extraction.

tag: isolate

value: labratory strain MPAO1

tag: compound


title: A33NEW


title: A31NEW

value: 92 years


title: A32NEW

value: 89 years


title: MPAO1 untreated rep.1


title: MPAO1 treated with Protoanemonin rep.2

description: P. Aeruginosa gene expression from planctonic culture treated with 125μM Protoanemonin

source_name: MPAO1 treated with Protoanemonin

value: Protoanemonin


title: MPAO1 treated with Protoanemonin rep.1


title: C. sporogenes Dormant Spore 2

treatment_protocol: Spore suspensions were obtained by adapting the biphasic culture from Cerf (1967) to Clostridium sporogenes UC9000 previuosly isolated from raw milk. The culture was maintained anaerobically at 37°C for at least 4 days and left 15 days at room temperature. After this, the spores were harvested, cleaned from cellular debris, centrifuged and washed. Mature spores obtained were purified through a continuous Percoll gradient followed by four washes and resuspensions in PBS before RNA extraction.

value: dormant spore

value: baseline


title: C. sporogenes Dormant Spore 3


title: C. sporogenes Germinating Spores 1

description: This is the first of three biological replicates of germinating spore samples at 3h. These data are derived from the first technical replicate.


title: C. sporogenes Dormant Spore 1


title: A30NEW

value: 91 years

value: Whole blood

value: PBMNC


title: A29NEW

value: 90 years


title: IEL3.1

status: Public on Jun 12 2012

city: Leiden

first: Frederike

last: Schmitz

address: Albinusdreef 2

department: Immunohematology and Blood Transfusion

country: Netherlands

institute: LUMC

hyb_protocol: Standard Illumina Hybridization protocoll was used

scan_protocol: Standard Illumina Scaning protocoll was used

data_processing: Gene expression values were log2 transformed and normalized using the quantile method across all samples in R

source_name: intestinal cells

label_protocol: Biotinylated cRNA were prepared using Ambion Illumina TotalPrep RNA Amplification kit (Illumina, Son, The Netherlands)

growth_protocol: For RCDII cell lines: Biopsy specimens from RCDII patients were treated with 1mM DTT (Fluka, Buchs, Switzerland) and 0.75 mM EDTA (Merck, Darmstadt, Germany). After this, the biopsy specimen were cultured in Iscove’s modified Dulbecco’s medium (IMDM, Lonza, Verviers, Belgium) supplemented with 10% normal human serum (NHS) and 10 ng/ml IL-15 (R&D systems Europe, Abingdon, UK). Released cells were propagated on IMDM containing 10% NHS and 10 ng/ml IL-15 and restimulated approximately every 4 to 5 weeks with 1 μg/ml phytohemagglutinin, 10 ng/ml IL-15  and 1 x 10^6/ml irradiated allogenous peripheral blood mononuclear cells as feeder cells.  For the T cell lines: Control cell lines for P1 were a CD4+ T cell line (P1-CD4) and a CD8+ T cell line (P1-CD8) isolated from the same biopsy as RCDII cell line P1. For P3 a CD4+ T cell clone (P3-CD4) and a CD8+ T cell line (P1-CD8) was isolated from the same biopsy as RCDII cell line P3. Isolated cells were restimulated every 2 weeks and maintained on 10% normal human serum (NHS) containing 10 ng/ml IL-15 and 20 Cetus units/ml IL-2 (Proleukin, Chiron corporation, Emeryville, CA). CD3+ IEL lines (IEL 1-5) were isolated from 4 celiac disease patients and one patient with Crohn’s disease as follows: IEL released directly after DTT and EDTA treatment were cultured in IMDM containing 10% NHS supplemented with 10 ng/ml IL-15 and 20 Cetus units/ml IL-2 (Proleukin, Chiron corporation, Emeryville, CA) and restimulated every 2 weeks. The T-IEL lines were a mixed population of CD4+ and CD8+ T cells (T-IEL).

extract_protocol: Total RNA was extracted from the cells using RNeasy Mini Kit (Qiagen, Venlo, the Netherlands) followed by DNAse digestion using the RNase-free DNAse kit (Qiagen), following the corresponding protocol.

treatment_protocol: When cell growth stagnated, rested cells  (for T cells approximately 2 weeks, for aberrant cells approximately 4 weeks) were ficolled to remove dead cells and debris and checked by FACS analysis for surface marker expression of CD4, CD8 and CD3. Cells were washed with cold PBS and kept on ice until isolation of total RNA.

tag: disease status of patient

value: celiac disease

tag: surface marker expression

tag: overall phenotype

value: T cell

tag: patients

value: control line from celiac disease patient

tag: cell line/clone

value: line

value: duodenum

tag: gender

value: F


title: IEL5.1

value: crohn's disease

value: control line from crohns disease patient

tag: tissue

value: colon


title: OLD21

tag: age

value: 98 years

value: healthy sample

tag: cell type


title: OLD24

value: 100 years

tag: disease status


title: IEL1.2

description: replicate

value: M


title: OLD23

value: 96 years


title: IEL5.2

description: replicate


title: IEL2.2

description: replicate


title: P3.2

description: replicate

value: RCDII

value: aberrant cell

value: line RCDII patient 3


title: OLD17

value: 95 years

value: Whole blood

value: PBMNC


title: IEL2.1

value: celiac disease

value: T cell

value: control line from celiac disease patient

value: line


title: IEL3.2

description: replicate

value: duodenum

value: F


title: IEL4.1


title: P2.2

description: replicate

value: line RCDII patient 2


title: P3.1


title: IEL1.1


title: P2.1


title: P1-CD8.1

value: CD3+CD4- CD8+

value: control line from RCDII patient 1


title: OLD18

value: 97 years

value: healthy sample


title: P1.2

description: replicate

value: RCDII

value: line RCDII patient 1


title: P1-CD4.2

description: replicate

value: CD3+CD4+ CD8-


title: P1-CD8.2

description: replicate


title: P1-CD4.1


title: CDH+NewBorn

value: Newborn

value: Cord blood

value: CD4+ cells


title: Cid14_swi6D_1

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
Oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R. Contrasts were computed on the oligo level by subtracting respective columns of expression. Differential expression values for individual features in the file sPombegenomicelementsV02_ALL.txt were calculated by averaging enrichment values for all the oligos overlapping the individual features, considering only features covered by at least 50 oligos. This produces the DamID_results.txt file [contains all 8014 features for which DamID enrichment was calculated, with a separate column for each of the 4 contrasts].
Results files linked as supplementary files on Series record.

organism: Schizosaccharomyces pombe

label_protocol: The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.4

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)

treatment_protocol: Harvested cells were spheroplasted to remove cell wall

tag: strain

tag: expression

tag: genotype/variation

value: Dam only


title: Cid14_wt_2

value: wt


title: Cid14_wt_1


title: OLD16

value: Whole blood

value: PBMNC


title: CDH+103

value: 103 years


title: P3-CD4.2

description: replicate

value: T cell

value: control clone from RCDII patient 3

value: clone

value: duodenum

value: M


title: P1.1

value: aberrant cell

value: line

value: F


title: LNA-205_Sample_D

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale Tumori

description: miR-205 silenced (LNA-205)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log(2) transformed and normalized using the lumi package in R

source_name: RWPE-1 cells transfected with 100nM LNA-205

label_protocol: Biotinylated cRNA were prepared with Illumina RNA TotalPrep amplification kit (Ambion)

tag: cell line

value: prostate epithelial cells


title: LNA-205_Sample_F

description: miR-205 silenced (LNA-205)


title: Ewing sarcoma sample mRNA EW251

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

hyb_protocol: As according to the manufacturer's instructions

scan_protocol: GCOS 1.4

data_processing: Data were normalized and combined using R 2.13.0 environment. We used the combineAffyBatch function in the matchprobes library to merge data from HG-U133A and HG-U133Plus2 GeneChips and we applied RMA normalization to the merged dataset

source_name: Ewing sarcoma sample EW251

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2µg total RNA

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

treatment_protocol: FrozenTumor biopsy

value: Ewing tumor


title: LNA-SCR_Sample_B

description: experimental control (scrambeld oligomer : LNA-Scr)

source_name: RWPE-1 cells transfected with 100nM LNA-Scr


title: Ewing sarcoma sample mRNA EW236

source_name: Ewing sarcoma sample EW236


title: Ewing sarcoma sample mRNA EW212

source_name: Ewing sarcoma sample EW212


title: Ewing sarcoma sample mRNA EW208

source_name: Ewing sarcoma sample EW208


title: Ewing sarcoma sample mRNA EW250

source_name: Ewing sarcoma sample EW250


title: LNA-SCR_Sample_A


title: LNA-SCR_Sample_C


title: Ewing sarcoma sample mRNA EW206

source_name: Ewing sarcoma sample EW206


title: LNA-205_Sample_E

description: miR-205 silenced (LNA-205)


title: OLD19

value: 97 years

value: healthy sample


title: Ewing sarcoma sample mRNA EW249

source_name: Ewing sarcoma sample EW249


title: Ewing sarcoma sample mRNA EW252

source_name: Ewing sarcoma sample EW252


title: IEL4.2

description: replicate

value: celiac disease

value: control line from celiac disease patient


title: Ewing sarcoma sample mRNA EW248

source_name: Ewing sarcoma sample EW248


title: Ewing sarcoma sample mRNA EW247

source_name: Ewing sarcoma sample EW247


title: Ewing sarcoma sample mRNA EW204

source_name: Ewing sarcoma sample EW204


title: Heart from mdx mouse 4

city: Oxford

first: Thomas

middle: C

last: Roberts

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

description:
Heart_mdx_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

hyb_protocol: Total labeled RNA was hybridised to the Affymetrix GeneChip miRNA array 2.0 using the manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with the Affymetrix Expression Console package.

data_processing: The processing and data analyses were performed in Affymetrix miRNA QCTool, as well as in DNA-Chip Analyzer (dChip) and Excel. The analysis was done according to the following workflow; BC-CG background adjustment, Quantile normalisation and Median Polish summarisation. Since the miRNA 2.0 array covers 131 organisms, we sorted out Mus musculus transcripts only.

source_name: Heart from mdx mouse 4

label_protocol: 1 ug of total RNA was labeled using the FlashTag Biotin HSR kit (Genisphere).

extract_protocol: The heart, quadriceps femoris, and diaphragm were dissected and flash frozen in liquid nitrogen-cooled isopentane. Samples were homogenised using Precellys 24 (Bertin Technologies, France), and RNA was extracted using TRIzol reagent (Invitrogen) as according to the manufacturer’s instructions. Each RNA sample was analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to assess RNA quality.

tag: background strain

tag: genotype

value: mdx

value: male

value: 8 weeks

value: heart

tag: mouse identifier

value: mdx 4


title: Heart from mdx mouse 3

description:
Heart_mdx_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from mdx mouse 3

value: mdx 3


title: Ewing sarcoma sample mRNA EW135

source_name: Ewing sarcoma sample EW135


title: Ewing sarcoma sample mRNA EW124

source_name: Ewing sarcoma sample EW124


title: Ewing sarcoma sample mRNA EW83

source_name: Ewing sarcoma sample EW83


title: Ewing sarcoma sample mRNA EW66

source_name: Ewing sarcoma sample EW66


title: Heart from mdx mouse 1

description:
Heart_mdx_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from mdx mouse 1

value: mdx 1


title: Ewing sarcoma sample mRNA EW207

source_name: Ewing sarcoma sample EW207


title: P3-CD4.1

source_name: intestinal cells

tag: disease status of patient

value: RCDII

value: CD3+CD4+ CD8-

value: T cell

value: control clone from RCDII patient 3

value: clone

value: duodenum

value: M


title: Ewing sarcoma sample mRNA EW48

source_name: Ewing sarcoma sample EW48

value: Ewing tumor


title: Ewing sarcoma sample mRNA EW19

source_name: Ewing sarcoma sample EW19


title: Ewing sarcoma sample mRNA EW98

source_name: Ewing sarcoma sample EW98


title: Heart from mdx mouse 2

description:
Heart_mdx_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from mdx mouse 2

value: mdx 2


title: ALL patient 5

city: NY

first: Teena

last: Bhatla

address: 550 first avenue

institute: NYU medical center

hyb_protocol: Biotinylated cRNA (20ng) was fragmented,10 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 150.

source_name: ALL

label_protocol: Total RNA (50 ng) was used as template in a single-amplification protocol (RiboAmp OA, Mountain View, CA) according to manufacturer's instructions.

growth_protocol: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA) and quality was verified by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: Leukemic bone marrow samples were used for RNA extraction without further treatment.

tag: disease state

value: bone marrow


title: Quadriceps from mdx mouse 4

description:
Quad_mdx_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from mdx mouse 4

value: mdx

value: quadriceps


title: Heart from WT mouse 1

description:
Heart_C57_1
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from C57 mouse 1

value: wild-type

value: male

value: 8 weeks

value: WT 1


title: Heart from WT mouse 2

description:
Heart_C57_2
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from C57 mouse 2

value: heart

value: WT 2


title: ALL patient 6 1 uM vorinostat

value: B-precursor acute lymphoblastic leukemia

tag: treatment

value: 1 uM vorinostat


title: Cid14_swi6D_2

value: Dam only


title: ALL patient 4 1 uM vorinostat


title: ALL patient 2 1 uM vorinostat


title: Heart from WT mouse 3

description:
Heart_C57_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from C57 mouse 3

value: WT 3


title: Quadriceps from mdx mouse 3

description:
Quad_mdx_3
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Quadriceps from mdx mouse 3

value: mdx 3


title: Heart from WT mouse 4

description:
Heart_C57_4
miRNA expression data from diaphragm, heart and quadriceps of mdx and WT C57/B10 mice.

source_name: Heart from C57 mouse 4

value: WT 4