title: OT-1 Lck-/- replicate #4

tag: fraction

value: Sub-polysomal

value: Polysomal


title: 1.95c5-PRRT-1.1

status: Public on Nov 30 2016

type: genomic

city: Torrejón de Ardoz

first: Carlos

last: Briones

state: Madrid

address: Ctra de Torrejón a Ajalvir, km 4

department: Department of Molecular Evolution

country: Spain

institute: Centro de Astrobiología (CAB, CSIC-INTA)

hyb_protocol: Before hybridization, printed microarrays were washed in 2× saline-sodium citrate (SSC) buffer and 0.1% N-lauryl sarcosine, for 2 min at room temperature, followed by 2 additional min in 2× SSC. This step allowed removing unbound DNA from the microarray surface and washing the excess of spotting solution. Printed oligonucleotides were denatured by baking the slides for 2 min in boiling milli-Q water and cooling for 10 sec at room temperature. The oligonucleotides were immediately fixed by plunging the slides into ice-cold 100% ethanol for 2 min, followed by centrifugation at 500×g for 1 min (using an Arrayit minicentrifuge). Microarrays were prehybridized with 20 ul of hybridization buffer (6× SSC, 0.5% SDS, 1% BSA) for 45 min at 42°C, under a 24  24 mm cover slip in a hybridization chamber (Genetix). Finally, the microarrays were washed with distilled water, and dried by centrifugation. Hybridization with the labeled target (50 ng, equivalent to 0.3 pmol Alexa Fluor 647) was carried out in hybridization buffer at 50oC for 3 h, using microarray hybridization chambers (Genetix).

scan_protocol: Hybridized microarrays were washed at 45ºC in 2x SSC and 0.1% N-lauryl sarcosine for 5 min, then in 2x SSC for 5 min, rinsed in 0.2x SSC for 10 sec, and finally in distilled water for 5 min. Slides were dried by centrifugation at 500×g for 1 min and immediately scanned at 635 nm using either GenePix 4000B (Molecular Devices) or G2565AA  (Agilent) high resolution microarray scanners. Hybridization images were processed using GenePix Pro 6.0.0.68 (Molecular Devices) software in GenePix Scanner, and ScanArray Express 2.0 (Perkin Elmer) in Agilent one. No automatic normalization of images was performed.

data_processing: The selected raw fluorescence value for each spot was the median foreground signal after subtracting its local background. Technical replicates for each target-probe hybridization (4 spots per experiment) were clustered together. Since two different classes of signals (positive or negative) are expected, they were clustered into two groups using the K-means algorithm. Then, after removing the outliers from the positive group by applying the Grubb’s test with a significance level of 0.05, the mean of the positive signals was obtained. Two regions (containing the PR and RT probes, respectively) were separately normalized in each microarray by means of their own mean positive  signal. These two values were used as the normalization factor for each probe by applying the function (formula.pdf). where ǁPSǁ is the normalized probe signal, NRP is the total number of replicas per hybridized probe (typically, 4), IRP is the signal intensity of a replica probe i, NPS is the total number of positive probe signals per array region (either PR or RT), and IPS is the intensity of a positive probe signal i within such a region.

label: Alexa Fluor 647

molecule: genomic DNA

organism: Simian-Human immunodeficiency virus

source_name: Training sample from plasmid 1.95c5

label_protocol: The phosphorylated strand of the HIV-1 DNA targets to be hybridized was specifically degraded using lambda exonuclease (New England Biolabs), and the resulting ssDNA was fluorescently labeled with Alexa Fluor 647, using the Ulysis Alexa Fluor 647 Nucleic Acid Labeling Kit (Life Technologies)

extract_protocol:
HIV-1 DNA target molecules corresponding to the training set were amplified from the cloned sequences using Expand High Fidelity DNA polymerase (EHF, Roche), as specified by the manufacturer. PCR amplification of the full PR-coding region was carried out using the forward primer 5’PROT2HindIII-P (5’-TCAGAGCAGACCAGAGCCAACAGCCCCACC-3’, corresponding to nucleotides [nts] 2138 to 2167 of HIV-1 CAM-1 strain, GenBank accession  number D10112) phosphorylated at its 5’-end, and the reverse primer 140RD (5’-CATTGTACTGATATCTAATCCCTGG-3’, complementary to positions 2969-2993). In turn, PCR amplifications of the queried codons of the RT-coding region involved the phosphorylated forward primers RT1-P (5’-CCAAAAGTTAAACAATGGCCATTG-3’, nts 2606-2629) or 55F-P (5’-CAAAAATTGGGCCTGAAAATCC-3’, nts 2694-2715), and the reverse primers 153RD (5’-TATTGCTGGTGATCCTTTCC-3’, nts 3009-3028), 13RD (5’-GTTCATAACCCATCCAAAGG-3’,nts 3232-3251) or 20RD (5’-ATTGACAGTCCAGCTGTCTTTTTCTGGC-3’, nts 3289-3316). Longer amplicons containing the PR-RT-coding regions were obtained by PCR amplification using as primers 5’PROT2HindIII-P and either 20RD or RT3333R (5’-CCACTAACTTCTGTATGTCATTG-3’, nts 3311-3333).
Viral RNA was extracted from plasma samples using the ‘HIV Sample Preparation Module’ of the ‘ViroSeq HIV-1 Genotyping System’ (Applied Biosystems), as specified by the manufacturer. The extracted RNA was retrotranscribed and PCR amplified by means of the ‘OneStep RT-PCR Kit’ (Qiagen), since this system showed higher sensitivity for samples with low viral load than other two-step protocols essayed (data not shown). Primers used were 5’PROT1 (5’-AGGCTAATTTTTTAGGGAAAATCTGGCCTTCC-3’, nts 2080-2111) and 153RD for the PR region, and RT-INI (5’-ACAGTATTAGTAGGACCTACACC-3’, nts 2474-2496) and RT3333R for the RT region. The RT-PCR amplification of a single amplicon containing the PR-RT-coding regions involved primers 5’PROT1 and RT3333R, though this approach showed less efficiency for samples with viral load lower than 104 copies/ml. Upon RT-PCR, nested PCR amplifications of the PR-coding region were performed with EHF, using the forward primer 5’PROT2HindIII-P and the reverse primer 140RD (positive amplification was successful in 53 out of the 57 samples), while those of the RT-coding region involved different combinations of the forward primers RT1-P or 55F-P, and the reverse primers 153RD, 13RD or 20RD (51 samples amplified).

tag: plasmid/patient id

tag: region

value: PRRT

tag: scanner

value: ScanArray

tag: sequence(s)


title: OT-1 Lck-/- replicate #2

type: RNA

city: Edinburgh

first: Thomas

last: Tan

address: Charlotte Auerbach Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: 300 ng Cy-3 labelled sample and 300 ng Cy-5 labelled sample were pooled and fragmented using fragmentation buffer from the Agilent Gene Expression Hybridisation Kit (Agilent) for 30 min at 60°C. Fragmented samples were mixed 1:1 with Hybridisation Buffer (v/v) and hybridised to a 60K high-density oligonucleotide microarray overnight. Microarrays were loaded as per the manufacturer’s instructions and hybridisation was performed at 65°C, in an Agilent Hybridisation Oven with rotation set to 10 RPM.

scan_protocol: Following hybridisation, the microarray slides were washed in Gene Expression wash buffers 1 and 2 (Agilent) and immediately scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies).

data_processing: GenePix Pro 6.0 was used to quantify fluorescence intensities for individual spots on the microarray. All statistical analysis was performed in the statistical environment R, version 2.6.1 and the Limma (Smyth and Speed, 2003), RankProd (Breitling et al., 2004) and Siggenes (Schwender H., 2012) packages. Briefly, raw intensities for both channels (Cy5 Polysomal RNA and Cy3 Subpolysomal RNA) were background corrected and normalised by scaling. Dye-swapped samples were averaged to correct for bias. Differentially expressed genes between WT and OFF samples were identified using RankProd test.

molecule: total RNA

organism: Mus musculus

source_name: Mouse T lymphocyte, OT-1het, Rag-/-, Lck-/-

label_protocol: 1.5 μl subs RNA was Cy-3 labelled and 1.5 μl polys RNA was Cy-5 labelled using Agilent Low Input Quick Amp 2-colour Labelling Kit (Agilent). The level of dye incorporation was measured using a Nanodrop ND1000 spectrophotometer (LabTech, Sussex, UK).

growth_protocol: Ex vivo cells were cultured in IMDM supplemented with 10% FCS, L-glutamine, 100U/ml penicillin, 100U/ml streptomycin and 50μM 2β-ME

extract_protocol: Cells were harvested and lysed in Gradient Buffer (300 mM NaCl, 15 mM MgCl2, 15 mM Tris/HCl pH 7.5, 2 mM DTT, 100 μg/mL cycloheximide) supplemented with 1% Triton X-100, 0.5 U/μl RNAse inhibitor (Promega), and a cocktail of protease inhibitors (Sigma). Postnuclear supernatants were loaded onto 10%-50% sucrose step gradients in Gradient Buffer and separated by centrifugation at 38,000 rpm for 2 hours at 4°C in a SW-40 rotor (Beckman Coulter). RNA content was read across the gradients through a live 254 nm UV spectrometer (Isco) and each sample was collected in ten fractions. Fraction 1-5 were pooled and define as the sub-polysomal fraction, while Fraction 6-10 were pooled and defined as the polysomal fraction. Total RNA was extracted from the pooled fractions using Trizol reagent (Thermo Fisher Scientific) and further purified with acid phenol-chloroform and ethanol precipitation.

treatment_protocol: Cells were stimulated with 100nM SIINFEKL peptide antigen for 24h. Cells were treated with 100 μg/ml cycloheximide for 10 minutes before harvest. Cell pellets were flash-frozen in dry ice on stored at -80°C until extraction.

tag: tissue

value: Lymph node

tag: genotype/variation

value: OT-1 Lck-/-


title: FAPs_Cntrl_AMO_PDGF_50_rep2

city: Palo Alto

middle: A

last: Rando

state: CA

address: 3801 Miranda Ave

department: Neurology and Neurological Sciences

country: USA

institute: Stanford University School of Medicine

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Control AMO and 50uM PDGF-AA.

hyb_protocol: Fragmented biotin-labeled single stranded DNA was hybridized to Affymetrix Mouse Gene 1.0 Array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymertix Expression Console software using Affymetrix default RMA analysis settings.

label: biotin

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with control AMO and 50uM PDGF-AA

label_protocol: Biotinylated single stranded cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Cells were grown for 2.5 days in DMEM supplemented with 10% FBS prior to treatment.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit as per the manufacturer’s instructions (Qiagen).

treatment_protocol: The media was switched to Ham’s F10 supplemented with 10% horse serum and transfected with 10 µM AMO as indicated for 48 hours. The media was then replaced with Opti-Mem and cells re-transfected with 10 µM AMO with 50uM PDGF-AA or control. After 48 hours, total RNA was extracted.

tag: gender

value: male

value: skeletal muscle

tag: cell type

value: fibro/adipogenic progenitors

tag: age

value: 8-12 weeks

tag: strain

tag: treatment

value: Control AMO, 50uM PDGF-AA


title: P23_T2

city: Los Angeles

first: Kamilla

last: Mundbjerg

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC Keck School of Medicine

hyb_protocol: DNA was bisulfite converted, restored, amplified, fragmented, and hybridized to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

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

data_processing: Methylumi R package

label: Cy5 and Cy3

organism: Homo sapiens

source_name: tumor_prostate_FFPE_patient 23

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using Qiagen miRNeasy FFPE kit and Rneasy plus mini kit

tag: patient id

value: patient 23

tag: tissue type

value: Prostate

tag: disease state

value: Tumor

tag: sample info

value: Primary tumor focus 2 from patient 23

tag: sample type

value: FFPE


title: 1.95c4-PRRT-2.2

source_name: Training sample from plasmid 1.95c4


title: FAPs_Cntrl_AMO_PDGF_50_rep1


title: 1.95c4-PRRT-2.1


title: OT-1 WT replicate #4

source_name: Mouse T lymphocyte, OT-1het, Rag-/-

tag: fraction

value: OT-1 Wild Type


title: OT-1 WT naive replicate #2

description: Gene expression in naïve CD8 T cells

hyb_protocol: 600 ng Cy-3 labelled sample fragmented using fragmentation buffer from the Agilent Gene Expression Hybridisation Kit (Agilent) for 30 min at 60°C. Fragmented samples were mixed 1:1 with Hybridisation Buffer (v/v) and hybridised to a 60K high-density oligonucleotide microarray overnight. Microarrays were loaded as per the manufacturer’s instructions and hybridisation was performed at 65°C, in an Agilent Hybridisation Oven with rotation set to 10 RPM.

data_processing: GenePix Pro 6.0 was used to quantify fluorescence intensities for individual spots on the microarray. All statistical analysis was performed in the statistical environment R, version 3.2.2 and the Limma (Smyth and Speed, 2003) and RankProd (Breitling et al., 2004) packages.

source_name: Mouse CD8 T lymphocyte, OT-1het, Rag-/-

label_protocol: 50 ng RNA was Cy-3 labelled using Agilent Low Input Quick Amp 1-colour Labelling Kit (Agilent). The level of dye incorporation was measured using a Nanodrop ND1000 spectrophotometer (LabTech, Sussex, UK).

extract_protocol: Total RNA was exracted using RNeasy column (Qiagen). RNA was first checked for quality using a 2100 Bioanalyser (Agilent). RNA with a RIN score of > 8 was used for microarray analysis.

treatment_protocol: Freshly isolated ex vivo lymphocytes were sorted for CD8b+ and CD44low, cell pellets were snap-frozen on dry ice.

tag: activation


title: cDNA_Exp3_a9

city: Jena

first: Friedrich

last: Becker

state: Thuringia

address: Beutenberg Strasse 11

department: Stem cell aging

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

description: skeletal muscle from hindlimbs

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent).

source_name: Gene expression after Hoxa9 - eGFP overexpression

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Satellite cells derived from young adult (3-4 months) C57BL/6J mice were FACS sorted and cultured in growth medium over night. Cells were transduced with lentiviral particales to induce stable genomic intergration and overexpresson of eGFP (control) or Hoxa9-eGFP. For analysis eGFP positive cells were FACS sorted 5 days after transduction.

value: cultured satellite cells

tag: genotype

value: genomically integrated Hoxa9 cDNA - eGFP cDNA


title: cDNA_Exp4_a9

description: skeletal muscle from hindlimbs


title: P23_AN

source_name: norm_prostate_FFPE_patient 23

value: Normal

value: Adjacent normal prostate sample from patient 23


title: cDNA_Exp1_a9

description: skeletal muscle from hindlimbs


title: 1.95c4-PRRT-1.1

tag: plasmid/patient id

tag: region

value: PRRT

tag: scanner

value: ScanArray


title: 1.95c5-PRRT-2

tag: sequence(s)


title: FAPs_5'ss_AMO_PDGF_0_rep1

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with intronic PDGFRα 5' splice site AMO and 0uM PDGF-AA.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with 5'ss AMO and 0uM PDGF-AA

tag: gender

value: male

tag: tissue

value: 5' Splice Site AMO, 0uM PDGF-AA


title: 1.95c2-PRRT-2.2

source_name: Training sample from plasmid 1.95c2


title: FAPs_5'ss_AMO_PDGF_0_rep2

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Intronic PDGFRα 5' splice site AMO and 0uM PDGF-AA.

value: skeletal muscle

tag: cell type

value: fibro/adipogenic progenitors

tag: age


title: FAPs_pA_AMO_PDGF_0_rep1

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Intronic PDGFRα polyA site AMO and 0uM PDGF-AA.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with pA AMOs and 0uM PDGF-AA

value: 8-12 weeks

tag: strain

tag: treatment

value: Polyadenylation Site AMOs, 0uM PDGF-AA


title: cDNA_Exp2_a9

description: skeletal muscle from hindlimbs


title: OT-1 Lck-/- replicate #1

value: Lymph node

value: Sub-polysomal

tag: genotype/variation

value: OT-1 Lck-/-

value: Polysomal


title: FAPs_Cntrl_AMO_PDGF_0_rep2

description: Gene expression data from WT fibro/adipogenic progenitors isolated from a noninjured animal and treated in vitro with Control AMO and 0uM PDGF-AA.

source_name: Fibro/adipogenic progenitors isolated from hindlimb skeletal muscles, treated with control AMO and 0uM PDGF-AA

value: Control AMO, 0uM PDGF-AA


title: 1.95c2-PRRT-2.1


title: cDNA_Exp4_SFLV

description: skeletal muscle from hindlimbs

source_name: Gene expression after eGFP overexpression (control)

value: cultured satellite cells

value: genomically integrated eGFP cDNA


title: P17_T2

source_name: tumor_prostate_FFPE_patient 17

tag: patient id

value: patient 17

tag: tissue type

value: Prostate

tag: disease state

value: Tumor

value: Primary tumor focus 2 from patient 17

value: FFPE


title: FAPs_pA_AMO_PDGF_0_rep2

value: male


title: FAPs_Cntrl_AMO_PDGF_0_rep1

value: skeletal muscle


title: 1.95c4-PRRT-1.2

value: PRRT

value: ScanArray


title: cDNA_Exp3_SFLV

description: skeletal muscle from hindlimbs


title: P17_AN

source_name: norm_prostate_FFPE_patient 17

value: Normal

tag: sample info

value: Adjacent normal prostate sample from patient 17

tag: sample type


title: cDNA_Exp2_SFLV

description: skeletal muscle from hindlimbs

tag: genotype


title: P17_T3

value: Primary tumor focus 3 from patient 17


title: P17_PL

source_name: met_lymphnode_FFPE_patient 17

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 17


title: P15_T3

source_name: tumor_prostate_FFPE_patient 15

value: patient 15

value: Primary tumor focus 3 from patient 15


title: genome-reduced strain PS38_rep4

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

hyb_protocol: 200 ng of Cy3-labeled cDNA were hybridized to a tiled microarray (tiling step of 22 nucleotides) following Agilent’s hybridization, washing and scanning protocol (One-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Probe intensities were computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described before (Nicolas et al., 2009; PMID 19561016). An aggregated expression value was
computed for each annotated CDS and previously identified RNA feature (Nicolas et al., 2012; PMID 22383849) as the median log2 intensity of probes lying entirely within the corresponding region. To control for possible cross-hybridization
artefacts, probe sequences were BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above a 1.5 cut-off were discarded (Wei et al., 2008; PMID 18385155). Gene-level intensities were scaled based on
the intensity values of ten different in-vitro synthesized transcripts contained in the One Color RNA Spike-In kit.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis genome-reduced strain

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation
on ice. Then, first-strand Master Mix, Actinomycin D (final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After RNA hydrolysis,
cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye, GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III protocol. cDNA and Cy-dye concentrations
were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: Cultures of the reference strain Δ6 and the deletion strains PG10 and PS38 were grown under vigorous agitation at 37 °C in LB medium supplemented with 0.5 % glucose until OD at 600 nm of 0.5.

extract_protocol:
Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165), followed by a DNase I treatment in order to eliminate residual genomic DNA and column
purification using the RNA Clean-Up kit (Norgen Biotech Corp.). RNA quality was checked by means of an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: genome size

value: genome size of 2.681 Mb


title: 1.95c2-PRRT-1.2

tag: plasmid/patient id

tag: region


title: 5 ng of DNA from tumor biopsy from patient 4

city: Copenhagen

first: Olga

last: Østrup

address: Blegdamsvej 9

department: Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital (Rigshospitalet)

description: Hybridized to OncoScan

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing:
BioDiscovery software NEXUS 7.5
data represents the SNP data of cfDNA analysed by OncoScan and tumor DNA analysed by CytoScanHD

label: Biotin

source_name: patient sample

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure; specifically QIAsymphony Circulating DNA Kit and Rneasy MIniPrep. DNA quality and quantity was controled by BioAnalyzer and Nanodrop.

value: tumor biopsy


title: 10 ng of DNA from tumor biopsy from patient 4

description: Hybridized to OncoScan


title: 1.95c2-PRRT-1.1

tag: scanner

tag: sequence(s)


title: genome-reduced strain PS38_rep3


title: 2.94c64-PR-6.2

source_name: Training sample from plasmid 2.94c64

value: PR

value: GenePix


title: Circulating cell-free DNA from patient 10

description: Hybridized to OncoScan

tag: tissue

value: circulating cell-free DNA


title: genome-reduced strain PS38_rep2


title: 2.94c64-PR-5.2


title: 2.94c64-PR-6.1


title: genome-reduced strain PS38_rep1


title: P15_T2

tag: gender

value: male

value: Prostate

value: Tumor

value: Primary tumor focus 2 from patient 15

value: FFPE


title: genome-reduced strain PG10_rep3

value: genome size of 2.702 Mb


title: 2.94c64-PR-5.1


title: 25 ng of DNA from tumor biopsy from patient 4

description: Hybridized to OncoScan


title: Circulating cell-free DNA from patient 9

description: Hybridized to OncoScan


title: genome-reduced strain PG10_rep4


title: cDNA_Exp1_SFLV

description: skeletal muscle from hindlimbs

value: skeletal muscle

tag: cell type

value: cultured satellite cells

value: genomically integrated eGFP cDNA


title: genome-reduced strain PG10_rep2


title: 2.94c64-PR-4.2


title: P15_AN

source_name: norm_prostate_FFPE_patient 15

value: Normal

value: Adjacent normal prostate sample from patient 15


title: P15_PL

source_name: met_lymphnode_FFPE_patient 15

value: patient 15

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 15


title: P17_T1

value: patient 17

value: Primary tumor focus 1 from patient 17


title: Circulating cell-free DNA from patient 6

description: Hybridized to OncoScan

value: circulating cell-free DNA


title: genome-reduced strain PG10_rep1


title: 2.94c64-PR-4.1

value: PR

value: GenePix


title: Circulating cell-free DNA from patient 5, between treatment 2 and 3

description: Hybridized to OncoScan


title: reference strain Δ6_rep4

source_name: Bacillus subtilis Δ6 (deletion of prophages)

value: genome size of 3.89 Mb


title: P14_T2

source_name: tumor_prostate_FFPE_patient 14

value: patient 14

value: male

value: Prostate

value: Tumor

value: Primary tumor focus 2 from patient 14

value: FFPE


title: Circulating cell-free DNA from patient 5, in treatment 2

description: Hybridized to OncoScan


title: Circulating cell-free DNA from patient 7

description: Hybridized to OncoScan


title: 2.94c64-PR-2.1


title: Donor 5 - OKT33

city: Brasilia

first: Isabel

middle: Garcia

last: Sousa

state: Distrito Federal

address: Campus Universitario Darcy Ribeiro

department: Cell Biology

country: Brazil

institute: Univerty of Brasilia

description: Treated with OKT3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the housekeeping miRNA: RNU48.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RNU48)] for each donor.
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., Untreated T cells/Treated T cells) ratios for each donor.

label: TaqMan® Assays

source_name: Test

label_protocol: qPCR assays were performed using the TaqMan® Human MicroRNA Arrays customized plates according to the manufacturer’s instructions (Applied Biosystems). Approximately 600 ng of total RNA extracted from T cells was utilized for cDNA synthesis, which was accomplished using a TaqMan® MicroRNA Reverse Transcription Kit (Applied Biosystems). The miRNAs were then evaluated via qPCR using TaqMan® Universal Master Mix II (Applied Biosystems) following the manufacturer’s instructions. RNU48 small non-coding RNA (snRNA) was used as an internal control for data normalization.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: T cell (CD3+)

tag: activation agent

value: monoclonal antibody OKT3

tag: time


title: 2.94c64-PR-3.1


title: reference strain Δ6_rep3


title: Donor 5 - OKT32

description: Treated with OKT3


title: reference strain Δ6_rep2


title: 2.94c64-PR-1.2


title: Circulating cell-free DNA from patient 5, in treatment 3

description: Hybridized to OncoScan


title: reference strain Δ6_rep1


title: 2.94c64-PR-3.2


title: 2.94c64-PR-2.2


title: P14_T1

value: Primary tumor focus 1 from patient 14


title: Circulating cell-free DNA from patient 5, in treatment 1

description: Hybridized to OncoScan


title: Circulating cell-free DNA from patient 4

description: Hybridized to OncoScan


title: P15_T1

value: patient 15

value: Primary tumor focus 1 from patient 15


title: P14_PL

source_name: met_lymphnode_FFPE_patient 14

value: Lymph node

value: Metastasis

value: Lymph node metastasis sample from patient 14


title: Donor 5 - FvFcR3

description: Treated with FvFcR

value: recombinant fragment of humanized anti-CD3 (FvFcR)


title: Donor 5 - OKT31

description: Treated with OKT3


title: Circulating cell-free DNA from patient 8

description: Hybridized to OncoScan

value: circulating cell-free DNA


title: Circulating cell-free DNA from patient 2

description: Hybridized to OncoScan


title: 2.94c63-PR-4.2

source_name: Training sample from plasmid 2.94c63

value: PR

value: GenePix


title: Circulating cell-free DNA from patient 1

description: Hybridized to OncoScan


title: P14_AN

source_name: norm_prostate_FFPE_patient 14

value: patient 14

value: male

value: Normal

value: Adjacent normal prostate sample from patient 14


title: 2.94c63-PR-4.1


title: 2.94c63-PR-3.2


title: Diagnostic tumor biopsy from patient 5

description: Hybridized to OncoScan

value: tumor biopsy


title: Donor 5 - FvFcR1

description: Treated with FvFcR

value: T cell (CD3+)


title: 2.94c63-PR-3.1


title: 2.94c63-PR-2.2


title: 1.95c9-PR-3.2

source_name: Training sample from plasmid 1.95c9


title: Donor 4 - OKT31

description: Treated with OKT3

value: monoclonal antibody OKT3


title: Donor 4 - OKT32

description: Treated with OKT3


title: 2.94c63-PR-2.1


title: Donor 5 - UT2

description: T cell  untreated

source_name: Control

value: Control - unstimulated


title: Donor 5 - UT1

description: T cell  untreated


title: Donor 4 - OKT33

description: Treated with OKT3


title: Donor 5 - UT3

description: T cell  untreated


title: 2.94c63-PR-1.1


title: 1.95c9-PR-3.1


title: Circulating cell-free DNA from patient 3

description: Hybridized to OncoScan


title: 1.95c9-PR-2.1


title: Donor 4 - FvFcR1

description: Treated with FvFcR


title: Donor 4 - FvFcR2

description: Treated with FvFcR


title: Donor 4 - UT3

description: T cell  untreated


title: 1.95c9-PR-2.2


title: 1.95c9-PR-1.2


title: Donor 5 - FvFcR2

description: Treated with FvFcR


title: 2.94c63-PR-1.2


title: Donor 4 - UT1

description: T cell  untreated


title: Donor 3 - OKT33

description: Treated with OKT3


title: 1.95c9-PR-1.1


title: Donor 4 - FvFcR3

description: Treated with FvFcR


title: 1.95c5-PR-3.2

source_name: Training sample from plasmid 1.95c5


title: 1.95c5-PR-4.2


title: 1.95c5-PR-4.1


title: Donor 3 - OKT31

description: Treated with OKT3


title: Donor 3 - FvFcR3

description: Treated with FvFcR


title: Donor 3 - OKT32

description: Treated with OKT3


title: Donor 4 - UT2

description: T cell  untreated


title: 1.95c5-PR-3.1


title: 1.95c5-PR-1.2


title: 1.95c5-PR-2.1


title: Donor 3 - FvFcR1

description: Treated with FvFcR


title: Donor 3 - FvFcR2

description: Treated with FvFcR


title: 1.95c5-PR-1.1


title: Donor 3 - UT2

description: T cell  untreated


title: 1.95c2-PR-5.4

source_name: Training sample from plasmid 1.95c2

value: ScanArray


title: Donor 3 - UT3

description: T cell  untreated


title: 1.95c5-PR-2.2


title: Donor 3 - UT1

description: T cell  untreated


title: Donor 2 - OKT33

description: Treated with OKT3


title: 1.95c2-PR-5.3


title: 1.95c2-PR-5.1


title: Stat5b-CA x Blnk+/- Leukemia #4

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

institute: University of Minnesota

description: CD19+ and/or B220+ lymph node tumor cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring GX11

source_name: Leukemic cells from Stat5b-CA  x  blnk+/- mouse #5331

label_protocol: cRNA was labeled with biotin-11-CTP (Perkin Elmer Life Sciences) and biotin-16-UTP (Roche), and cleaned up and fragmented.

growth_protocol: Mice were maintained according to IACUC protocols at the University of Minnesota.

extract_protocol: Total RNA was isolated with a Qiagen RNeasy kit.  cRNA probes were synthesized with Ambion's Message Amp II kit, biotinylated and hybridized to the Affymetrix Mouse 430 2.0 microarray chip.

treatment_protocol: Sorted preB cells (WT, Stat5, & xid) were isolated from bone marrow, negatively selected against dump antibodies with Miltenyi magnetic beads.  They were then stained with B220, CD19, CD43 and IgM antibodies, and sorted with a FacsAria for B220+ CD19+ CD43- IgM- cells.  Tumor lymph node cells were positively selected for with Miltenyi magnetic beads binding B220 and CD19.

tag: strain


title: Stat5b-CA x Blnk+/- Leukemia #3

source_name: Leukemic cells from Stat5b-CA  x  blnk+/- mouse #4878


title: Stat5b-CA x Blnk+/- Leukemia #2

source_name: Leukemic cells from Stat5b-CA  x  blnk+/- mouse #4024


title: Stat5b-CA x Blnk+/- Leukemia #1

source_name: Leukemic cells from Stat5b-CA  x  blnk+/- mouse #3961


title: Donor 2 - OKT32

description: Treated with OKT3


title: Stat5b-CA x Blnk+/- Leukemia #5

source_name: Leukemic cells from Stat5b-CA  x  blnk+/- mouse #6107


title: Donor 2 - OKT31

description: Treated with OKT3


title: 1.95c2-PR-4.3


title: Stat5b-CA x xid Leukemia #3

source_name: Leukemic cells from Stat5b-CA  x  xid mouse #1546


title: Stat5b-CA x xid Leukemia #4

source_name: Leukemic cells from Stat5b-CA  x  xid mouse #5793


title: Donor 2 - FvFcR3

description: Treated with FvFcR


title: 1.95c2-PR-5.2


title: SpiB-overexpressing A549 cells Replicate 1

city: Tianjin

first: Zhe

last: Liu

address: Heping District Qixiangtai Road No. 22

country: China

institute: Tianjin Medical University

description: Biological replicate 1 of 3. Gene expression changes in SpiB-overexpressing A549 cells versus control vector-expressing A549 cells

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Slides were scanned with an Agilent scanner Type C.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11).

source_name: control vector-expressing A549 cells

label_protocol: 100ng of total RNA was used to produce polyadenylated RNA with polyA polymerase (Ambion, Austin, TX, USA).The products were transcribed to single-stranded DNA with oligo-dT primers. RNA was selectively degraded by RNase H, leaving RNA oligomers as primers for a DNA polymerase to synthesize double-stranded DNA (dsDNA). The dsDNA was purified and served as a template to generate antisense cDNA by cRNA reverse transcription.The fluorescence labeling reactions contained 5× Klenow buffer, dNTP (120 mM dATP, 120 mM dGTP, 120 mM dTTP, and 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and Klenow enzyme (TaKaRa, Dalian, China). The reaction was carried out at 37°C for 90 min and stopped by addition of 25 mM EDTA and 0.25% sodium dodecyl sulfate (SDS).

growth_protocol: A549 cells were grown in RPMI1640 medium with 10% FBS, transfected with control vector or SpiB expression vector.

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

tag: cell line

value: Human lung adenocarcinoma epithelial cells

source_name: SpiB-overexpressing A549 cells


title: Donor 2 - FvFcR2

description: Treated with FvFcR

source_name: Test


title: SpiB-overexpressing A549 cells Replicate 2

description: Biological replicate 2 of 3. Gene expression changes in SpiB-overexpressing A549 cells versus control vector-expressing A549 cells


title: Stat5b-CA x xid Leukemia #5

source_name: Leukemic cells from Stat5b-CA  x  xid mouse #1547


title: SpiB-overexpressing A549 cells Replicate 3

description: Biological replicate 3 of 3. Gene expression changes in SpiB-overexpressing A549 cells versus control vector-expressing A549 cells


title: 1.95c2-PR-4.2


title: Donor 2 - FvFcR1

description: Treated with FvFcR


title: 1.95c2-PR-4.1


title: Donor 2 - UT2

description: T cell  untreated


title: Donor 2 - UT3

description: T cell  untreated


title: Stat5b-CA x xid Leukemia #1

source_name: Leukemic cells from Stat5b-CA  x  xid mouse #5400


title: Stat5b-CA x Pkrcb-/- Leukemia #4

source_name: Leukemic cells from Stat5b-CA x PKC-b-/- mouse #5481


title: Donor 2 - UT1

description: T cell  untreated


title: 1.95c2-PR-3.3


title: 1.95c2-PR-3.1


title: 1.95c2-PR-3.2


title: Stat5b-CA x Pkrcb-/- Leukemia #2

source_name: Leukemic cells from Stat5b-CA x PKC-b-/- mouse #4668


title: Donor 1 - FvFcR3

description: Treated with FvFcR


title: Stat5b-CA x xid Leukemia #2

source_name: Leukemic cells from Stat5b-CA  x  xid mouse #1543


title: Donor 1 - FvFcR1

description: Treated with FvFcR


title: Donor 1 - FvFcR2

description: Treated with FvFcR


title: 1.95c2-PR-1.2


title: 1.95c2-PR-2


title: Stat5b-CA x Pkrcb-/- Leukemia #3

source_name: Leukemic cells from Stat5b-CA x PKC-b-/- mouse #4683


title: 1.95c2-PR-1.1

source_name: Training sample from plasmid 1.95c2


title: Donor 1 - UT3

description: T cell  untreated

source_name: Control


title: Stat5b-CA Spontaneous Leukemia #6

source_name: Leukemic cells from Stat5b-CA mouse #1277


title: Stat5b-CA x Pkrcb-/- Leukemia #1

source_name: Leukemic cells from Stat5b-CA x PKC-b-/- mouse #5484


title: Ethanol 3

status: Public on Nov 29 2016

city: Chicago

first: Subhash

middle: C

last: Pandey

state: IL

address: 1601 West Taylor Street

department: Psychiatry

institute: University of Illinois at Chicago & Jesse Brown VA Medical Center

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing:
Detected signals greater than background plus 3 times the standard deviation derived for the color channel; the mean and the co-variance (CV = stdev x100/replicate mean) of each probe having a detected signal calculated
The data are processed in a MS Excel spreadsheet using a program routine that performs raw signal background subtraction using a local regression method
Data normalized using a cyclic LOWESS method. Signal normalization done with Log2 values using the mean and the standard deviation for individual miRNA across all samples

organism: Rattus norvegicus

source_name: Amygdala, Acute Ethanol Treated

label_protocol: Single sample chips using Cy3

extract_protocol: Total RNA extracted from the amygdaloid tissues using QIAgen RNeasy Mini Kit

value: Amygdala


title: Control 3

source_name: Amygdala, Normal Saline Treated


title: Stat5b-CA Spontaneous Leukemia #5

source_name: Leukemic cells from Stat5b-CA mouse #6885


title: Ethanol 1


title: Stat5b-CA Spontaneous Leukemia #1

source_name: Leukemic cells from Stat5b-CA mouse #6878


title: 2.94c64-PR-1.1

source_name: Training sample from plasmid 2.94c64


title: Stat5b-CA Spontaneous Leukemia #2

source_name: Leukemic cells from Stat5b-CA mouse #5161


title: Donor 1 - UT1

description: T cell  untreated


title: Control 2


title: Stat5b-CA Spontaneous Leukemia #4

source_name: Leukemic cells from Stat5b-CA mouse #2805


title: Donor 1 - UT2

description: T cell  untreated


title: Xid preB #2

description: CD19+ B220+ dump- IgM- CD43- Bone marrow cells

source_name: Sorted preB cells from Xid mouse #7804


title: Control 1


title: Stat5b-CA Spontaneous Leukemia #3

source_name: Leukemic cells from Stat5b-CA mouse #6218


title: Xid preB #3

source_name: Sorted preB cells from Xid mouse #3719


title: Ethanol 2


title: Xid preB #1

source_name: Sorted preB cells from Xid mouse #3716


title: control cell biological_rep2

city: Beijing

first: gaijing

last: Han

address: 17 nanli Panjiayuan

department: State Key Laboratory of Molecular Oncology

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression date of control cell

hyb_protocol: 0.6  μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and   hybridized to Affymetrix Human Transcriptome Array (HTA2.0) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C   GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area   61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set   to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: control cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: These cells were cultured in complete RPMI 1640 medium supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 mg/ml) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Cell lines transfected with human STMN1, or empty vector pCMV6, were established by transfection of pCMV6 vector (Origene) containing the full-length STMN1 cDNA, or pCMV6 vector alone, respectively, into esophageal cancer cell lines KYSE 170, using Lipofectamine TM 2000 as per manufacturer’s instructions. The stable clones were selected with 200ug/ml G418.

value: KYSE 170

tag: transfection

value: pCMV6 vector alone


title: R3110823-05

city: Charleston

first: Marion

last: Neely

state: SC

address: 331 Ft. Johnson Rd

department: NCCOS

institute: National Ocean Services

hyb_protocol: A total of 1.65 mg of Cy3 labeled cRNA was hybridized to the microarray.   The One-Color Microarray-Based Gene Expression Analysis Protocol (Version 6.5, May 2010) was followed for both the labeling and the hybridization.  Hybridization was carried out at 65°C in an Agilent hybridization oven rotating at 10rpm for 17 hours.

scan_protocol: Slides were scanned with an Agilent G2505B scanner equipped with Agilent Scan Control software, using the Extended Dynamic Range Scan Mode, 5µM scan, XDR PMT Hi 100% Lo 10%.   Images were extracted using Agilent Feature Extraction version 10.7.3.1.

data_processing: Text (.txt) files obtained from Agilent Feature Extraction (FE) were imported into Agilent’s GeneSpring 11.5.1 software and processed as Agilent single color arrays.  Normalized signal values were generated after thresholding the raw signals to 1.0, summarization (summarization is performed by computing the geometric mean), and log transformation, followed by 75th percentile shift normalization.

organism: Tursiops truncatus

source_name: Skin

label_protocol: Total RNA (50ng) was amplified and Cy 3 labeled using Agilent’s Low Input Quick Amp Labeling Kit.  The Cy3 labeled cRNA was quantified using a Nanodrop ND-1000.

extract_protocol:
Samples were obtained by remote dart biopsy using the method of Hansen et al. (2004), employing a modified 0.22-caliber rifle affixed with a video camera to collect images of dorsal fins for individual identifications. The rifle fired a bolt which consisted of a thin-walled, hollow arrow shaft and a hollow cylindrical collecting head approximately 2.5 cm in length and 1.0 cm in diameter. Each sample was a cylindrical shaped core of skin and blubber, weighing approximately 0.5–1.0 g. The sampling location on the body of the dolphin varied to some degree between individuals, but all the samples were collected within an area that measured approximately 50 cm x 30cm centered below the dorsal fin above the lateral midline.  Prior to each use, the collecting head was scrubbed, soaked in a 10% bleach solution, then rinsed twice, first with distilled water and then with ethanol. Retrieval of the sample in the collecting head, affixed to a float, was carried out by reel. Once on deck, the sample was removed from the sampling tip with sterile forceps and scalpel, then transferred to a cryovial and snap frozen and stored in liquid nitrogen until transfer to the laboratory.  In the laboratory, samples were they were stored under chain of custody at -80°C until processing
Approximately 0.05-0.15 g of skin was dissected from frozen integument biopsies using a scalpel, on dry ice, just medial to a white line demarking the fibrous layer of the dermis and further cut into pieces ≤ 0.2 cm thick.  The dissected sample was transferred to 1.5ml of RNAlater Ice (Ambion) that was prechilled to -80°C and soaked for at least 16 hours to transition tissue from -80 °C to - 20°C prior to processing. The sample was then removed from the RNAlater ice and placed in a 2.0 ml microcentrifuge tube containing 1ml Qiazol (Qiagen) and a 5mm stainless steel bead, and homogenized 3x using a Qiagen Tissuelyser at 20 Hz for 3 min. The sample was cooled on ice for 30 sec between sets.   The homogenate was transferred to a new 2.0ml microcentrifuge tube and incubated on the benchtop at room temperature for 5 minutes before adding 200µl of chloroform.  The tube was shaken vigorously for 15 seconds then incubated on the benchtop at room temperature for 3 minutes.  After 15 min centrifugation at 12,000 x g 4°C, 500 µl of the upper aqueous phase was transferred to a new 1.5ml microcentrifuge tube containing 500 µl of 70% ethanol, mixed by pipetting, and then immediately transferred to a Qiagen RNeasy spin column.  The protocol for Purification of Total RNA using the RNeasy Lipid Tissue Mini Kit with on-column DNase digestion (Qiagen RNeasy Lipid Tissue Handbook 02/2009) was followed exactly from this point on with a 60µl final elution in RNase-free water.  The RNA quantity determined using a Nanodrop ND-1000 spectrophotometer and quality was assessed using an Agilent 2100 Bioanalyzer.   Only samples with an RNA integrity number (RIN) of > 7.0 were used in the study.

value: skin

tag: location

value: Chandeleur Sound

tag: collection date

value: August 23 2011

tag: season

value: Summer


title: control cell biological_rep1

description: Gene expression date of control cell


title: RTE1P exp.2

city: Sendai

first: yuriko

last: saiki

state: Miyagi

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

department: Molecular Pathology

country: Japan

institute: Tohoku University School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RTE1P paclitaxel resistant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp labeling kit one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Studio City, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: TE1 derived paclitaxel resistant line RTE1P

value: esophageal cancer cell line


title: R3111215-01

value: male

value: Mississippi Sound

value: December 15 2011

value: Winter


title: WT_MP_rep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression of WT mice after treatment with MP

hyb_protocol: For each sample, 3 ug of Cy3 labeled cDNA was hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: Nigrostriatal tissue isolated from brain of mice treated with MP, replicate 1

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was isolated from the nigrostriatal tissue of three independent triplicates using the TRIzol (Ambion, Life Technologies, Grand Island, NY) and RNeasy mini kit columns with in-column DNAse treatment (Qiagen, Valencia, CA).

treatment_protocol: Adult (8-10-week- old), pathogen-free male mice (C57BL6/J from Jackson Laboratories, Bar Harbor, Maine) were housed one to a cage for a week for acclimatization before experimental dosing. Mice that contained disrupted α-synuclein (α-synuclein knockout mice, stock number 003692) were treated similarly. Age-matched wild type C57BL6/J mice that contained α-synuclein served as the control animals for knockout experiments. The animals were housed under standard conditions of temperature and humidity with a 12 h light/dark cycle and fed a standard pellet diet and water ad libitum. Animals were treated with normal saline (control), paraquat (10mg/kg, ip) and Maneb (30mg/kg, ip) twice a week for 6 weeks.

value: Brain (nigrostriatal tissue)

tag: genotype

value: wild type

tag: age

value: adult


title: ASKO_MP_rep2

description: Gene expression of alpha-sinuclein KO mice after treatment with MP

source_name: Nigrostriatal tissue isolated from brain of alpha-sinuclein KO mice treated with MP, replicate 2

value: alpha-sinuclein KO


title: WT_rep3

description: Gene expression of WT mice

source_name: Nigrostriatal tissue isolated from brain of WT mice, replicate 3


title: R3111216-01

value: female

value: December 16 2011


title: TE1 exp.2

source_name: TE1 parental


title: WT_MP_rep2

source_name: Nigrostriatal tissue isolated from brain of mice treated with MP, replicate 2


title: R3120121-02

value: January 21 2012


title: stathmin overexpression cell biological_rep2

description: Gene expression date after stathmin overexpression

source_name: stathmin overexpression cell

value: KYSE 170

value: pCMV6 vector (Origene) containing the full-length STMN1 cDNA


title: R3110824-01

value: skin

value: Chandeleur Sound

value: August 24 2011


title: R3110823-02

value: August 23 2011

value: Summer


title: R2120125-04

value: male

value: January 25 2012


title: ASKO_MP_rep1

source_name: Nigrostriatal tissue isolated from brain of alpha-sinuclein KO mice treated with MP, replicate 1


title: WT_rep2

description: Gene expression of WT mice

source_name: Nigrostriatal tissue isolated from brain of WT mice, replicate 2


title: R3110828-03

value: Mississippi Sound

value: August 28 2011


title: WT_MP_rep3

source_name: Nigrostriatal tissue isolated from brain of mice treated with MP, replicate 3

value: Brain (nigrostriatal tissue)

value: wild type


title: R3110823-03


title: R3111209-01

value: December 09 2011

value: Winter


title: stathmin overexpression cell biological_rep1


title: RTE1P exp1

value: TE1 derived paclitaxel resistant line RTE1P

value: esophageal cancer cell line


title: ASKO_MP_rep3

source_name: Nigrostriatal tissue isolated from brain of alpha-sinuclein KO mice treated with MP, replicate 3

value: alpha-sinuclein KO

value: adult


title: WT_rep1

description: Gene expression of WT mice

source_name: Nigrostriatal tissue isolated from brain of WT mice, replicate 1


title: R3110820-03

value: skin

value: female

value: August 20 2011


title: R3120123-01

value: Chandeleur Sound

value: January 23 2012


title: TE1 exp.1


title: R2110828-01

value: male

value: Summer


title: 1.95c2-PR-4.4

source_name: Training sample from plasmid 1.95c2

tag: plasmid/patient id

value: PR

value: ScanArray


title: high-grade primary myxofibrosarcoma 867

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from primary high-grade myxofibrsarcoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human 133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: frozen human tumor: high-grade primary myxofibrosarcoma

label_protocol: cRNA was prepared using biotinylated UTP and CTP from 2ug total RNA prior to hybridization to HG U133A arrays (Affymetrix)

extract_protocol: Total RNA was isolated using the Rneasy Lipid Tissue Mini kit (QIAGEN) according to the manufacturer's instructions.

value: Frozen tumor

tag: samplename

tag: celname

value: PD_pMFH867 _HG-U133A.mas5.CHP

tag: samplestage

value: Primary

value: High

value: Upper extremity

value: Upper arm

value: > 10 cm       primary tumor size category

value: Deep Depth

value: F

value: Alive

value: NED


title: BW120221-02

tag: tissue

value: skin

value: Barataria Bay

value: February 21 2012

value: Winter


title: R3110828-01

tag: gender

value: female

value: Mississippi Sound

value: August 28 2011

value: Summer


title: high-grade primary myxofibrosarcoma 876

value: Frozen tumor

value: Primary

value: Lower extremity

value: Knee

value: > 5, <= 10 cm primary tumor size category

value: Superficial Depth

value: M


title: R3111208-02

value: male

value: December 08 2011


title: high-grade primary myxofibrosarcoma 853

value: High

value: Thigh

value: > 10 cm       primary tumor size category

value: Deep Depth

value: F

value: Alive

value: NED


title: R3110817-05

value: skin

value: female

value: Mississippi Sound

value: August 17 2011

value: Summer


title: high-grade primary myxofibrosarcoma 854

value: Frozen tumor

value: Primary

value: Lower extremity

value: > 5, <= 10 cm primary tumor size category

value: Dead

value: DOO


title: R3120121-05

value: male

value: Chandeleur Sound

value: January 21 2012

value: Winter


title: R2120123-02

value: January 23 2012


title: high-grade primary myxofibrosarcoma 916

value: High

value: Thigh

value: > 10 cm       primary tumor size category

value: Deep Depth

value: F

value: DOD


title: high-grade primary myxofibrosarcoma 819

value: Frozen tumor

value: Upper extremity

value: Shoulder


title: high-grade primary myxofibrosarcoma 9679

value: Primary

value: Lower extremity

value: > 5, <= 10 cm primary tumor size category


title: high-grade primary myxofibrosarcoma 1042

value: M

value: Alive

value: NED


title: high-grade primary myxofibrosarcoma 850

value: Dead


title: high-grade primary myxofibrosarcoma 35


title: high-grade primary myxofibrosarcoma 818

value: DUK


title: high-grade primary myxofibrosarcoma 909

value: PD_MXF909 _HG-U133A.mas5.CHP

value: High


title: high-grade primary myxofibrosarcoma 862

value: Thigh

value: Superficial Depth


title: high-grade primary myxofibrosarcoma 864

value: > 10 cm       primary tumor size category

value: Deep Depth

value: F


title: R2110816-05

value: skin

value: male

value: Mississippi Sound

value: August 16 2011

value: Summer


title: high-grade primary myxofibrosarcoma 908

value: Frozen tumor

value: Primary

value: Lower extremity

value: Calf

value: > 5, <= 10 cm primary tumor size category


title: high-grade primary myxofibrosarcoma 912

value: <= 5 cm       primary tumor size category

value: Alive

value: NED


title: BW120223-02

value: Barataria Bay

value: February 23 2012

value: Winter


title: high-grade primary myxofibrosarcoma 911

value: High

value: Thigh

value: > 10 cm       primary tumor size category

value: Deep Depth

value: F


title: BW120223-01

value: skin

value: male


title: high-grade primary myxofibrosarcoma 906

value: Frozen tumor

value: Primary

value: Upper extremity

value: Axilla


title: R3110829-01

value: Mississippi Sound

value: August 29 2011

value: Summer


title: R3110817-01

value: August 17 2011


title: high-grade primary myxofibrosarcoma 874

value: Lower extremity

value: > 5, <= 10 cm primary tumor size category

value: M

value: Alive

value: NED


title: R2110829-02

value: female


title: high-grade primary myxofibrosarcoma 871

value: High

value: Thigh

value: Deep Depth

value: AWD


title: high-grade primary myxofibrosarcoma 851

value: Frozen tumor

value: Primary

value: <= 5 cm       primary tumor size category

value: Dead

value: DOD


title: R3120121-03

value: skin

value: male

value: Chandeleur Sound

value: January 21 2012

value: Winter


title: high-grade primary myxofibrosarcoma 852

value: Lower extremity

value: Lower leg

value: Superficial Depth

value: M

value: Alive


title: TE120220-03

value: female

value: Barataria Bay

value: February 20 2012


title: high-grade primary myxofibrosarcoma 848

value: Frozen tumor

value: Primary

value: High

value: Upper extremity

value: Axilla

value: Deep Depth

value: NED


title: high-grade primary myxofibrosarcoma 879

value: Thigh

value: > 10 cm       primary tumor size category


title: high-grade primary myxofibrosarcoma 861

value: Lower extremity

value: <= 5 cm       primary tumor size category

value: F


title: high-grade primary myxofibrosarcoma 847

value: M

value: AWD


title: high-grade primary myxofibrosarcoma 856

value: > 5, <= 10 cm primary tumor size category

value: Superficial Depth

value: Alive


title: R3111219-02

value: skin

value: male

value: Mississippi Sound

value: December 19 2011

value: Winter


title: high-grade primary myxofibrosarcoma 875

value: Frozen tumor

value: Primary

value: High

value: Deep Depth


title: high-grade primary myxofibrosarcoma 866

value: Lower extremity

value: Thigh

value: NED


title: high-grade primary myxofibrosarcoma 832

value: Lower leg

value: M

value: Dead

value: DOD


title: R2120120-02

value: Chandeleur Sound

value: January 20 2012


title: high-grade primary myxofibrosarcoma 815

value: > 5, <= 10 cm primary tumor size category

value: Superficial Depth

value: F

value: Alive

value: AWD


title: high-grade primary myxofibrosarcoma 836

value: Frozen tumor

value: Primary

value: Upper extremity

value: Upper arm

value: <= 5 cm       primary tumor size category


title: high-grade primary myxofibrosarcoma 863

value: High

value: Lower extremity

value: Calf

value: > 10 cm       primary tumor size category

value: NED


title: BW120225-03

value: skin

value: female

value: Barataria Bay

value: February 25 2012

value: Winter


title: R3111209-04

value: male

value: Mississippi Sound

value: December 09 2011


title: high-grade primary myxofibrosarcoma 776

value: Frozen tumor

value: Primary

value: Thigh

value: Deep Depth

value: F

value: Alive

value: AWD


title: BW120221-05

value: February 21 2012


title: R3111216-02

value: December 16 2011


title: high-grade primary myxofibrosarcoma 855

value: High

value: Lower extremity

value: > 10 cm       primary tumor size category

value: M


title: high-grade primary myxofibrosarcoma 772

value: Upper extremity

value: Upper arm

value: Dead

value: DOD


title: high-grade primary myxofibrosarcoma 7671

value: Frozen tumor

value: > 5, <= 10 cm primary tumor size category

value: NED


title: R3110816-03

value: skin

value: female

value: Mississippi Sound

value: August 16 2011

value: Summer


title: high-grade primary myxofibrosarcoma 771

value: Primary

value: Thigh

value: Superficial Depth

value: Alive


title: R3111201-01

value: male

value: December 01 2011

value: Winter


title: high-grade primary myxofibrosarcoma 742

value: High

value: Lower extremity

value: Deep Depth

value: F


title: high-grade primary myxofibrosarcoma 683

value: Frozen tumor

value: Trunk

value: Buttock

value: > 5, <= 10 cm primary tumor size category

value: M

value: Dead

value: DOD


title: high-grade primary myxofibrosarcoma 6838

value: Primary

value: Thigh


title: high-grade primary myxofibrosarcoma 674

value: Thoracic

value: Chest Wall

value: Alive

value: NED


title: high-grade primary myxofibrosarcoma 679

value: High

value: > 10 cm       primary tumor size category

value: AWD


title: R3111208-01

value: skin

value: male

value: Mississippi Sound

value: December 08 2011

value: Winter


title: high-grade primary myxofibrosarcoma 730

value: Frozen tumor

value: Lower extremity

value: Knee

value: Superficial Depth

value: F


title: R3111220-01

value: female

value: December 20 2011


title: R2120127-01

value: Chandeleur Sound

value: January 27 2012


title: WT/NT_4

city: TSUKUBA CITY

first: Keiichi

last: Minami

state: IBARAKI

address: 17-2 WADAI

department: Tsukuba Research Institute

institute: Ono pharmaceutical

description: Gene expression after cells were cultured in 1% FBS containing media for 24hr

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray 8x60K (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 1 minute at room temperature with acetonitrile then dried immediately by nitrogen blower.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Wild-type MEF, Non-target shRNA, 1%FBS 24hr, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low-Imput QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MEFs were infected with lentiviruses expressing Non-target shRNA or Rb shRNA and selected.

extract_protocol: RNA was prepared using theRNeasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were cultured in the medium containing 1% FBS for 24 hours.

tag: cell type

value: MEF

value: Wild-type

tag: shRNA

value: Non-target shRNA


title: high-grade primary myxofibrosarcoma 663

value: Primary

value: High

value: Thigh

value: <= 5 cm       primary tumor size category

value: Deep Depth

value: M

value: Alive

value: NED


title: high-grade primary myxofibrosarcoma 660

value: Frozen tumor

value: Lower extremity

value: > 5, <= 10 cm primary tumor size category


title: high-grade primary myxofibrosarcoma 664

value: F

value: Dead

value: DOD


title: high-grade primary myxofibrosarcoma 662


title: SREBP1_KO/Rb_KD_4

source_name: SREBP1 KO MEF, Rb shRNA, 1%FBS 24hr, replicate 4

value: MEF

value: SREBP1 KO

value: Rb shRNA


title: high-grade primary myxofibrosarcoma 675

value: Primary

value: Thoracic

value: Chest Wall

value: > 10 cm       primary tumor size category


title: SREBP1_KO/NT_4

source_name: SREBP1 KO MEF, Non-target shRNA, 1%FBS 24hr, replicate 4

value: Non-target shRNA


title: high-grade primary myxofibrosarcoma 682

value: High

value: Trunk

value: Abdominal Wall

value: <= 5 cm       primary tumor size category

value: Deep Depth

value: AUK


title: R3110821-02

source_name: Skin

value: skin

value: male

value: Chandeleur Sound

value: August 21 2011

value: Summer


title: high-grade primary myxofibrosarcoma 666

value: Frozen tumor

value: Retro-intrabdominal

value: Retroperitoneum

value: > 5, <= 10 cm primary tumor size category

value: F

value: Alive

value: NED


title: R3110820-02

value: female

value: August 20 2011


title: high-grade primary myxofibrosarcoma 659

value: Primary

value: High

value: Lower extremity

value: Lower leg

value: > 10 cm       primary tumor size category

value: M


title: R3111214-01

value: skin

value: male

value: Mississippi Sound

value: December 14 2011

value: Winter


title: high-grade primary myxofibrosarcoma 628

value: Frozen tumor

value: Thigh

value: > 5, <= 10 cm primary tumor size category

value: Deep Depth

value: Dead

value: DUK


title: high-grade primary myxofibrosarcoma 632

value: Primary

value: Upper extremity

value: Upper arm

value: F

value: DOD


title: high-grade primary myxofibrosarcoma 633

value: High

value: Lower extremity

value: > 10 cm       primary tumor size category

value: Alive

value: NED


title: R3111202-01

value: skin

value: female

value: Mississippi Sound

value: December 02 2011

value: Winter


title: high-grade primary myxofibrosarcoma 658

value: Frozen tumor

value: Trunk

value: Paraspinal

value: > 5, <= 10 cm primary tumor size category

value: Superficial Depth

value: M


title: high-grade primary myxofibrosarcoma 6221

value: Primary

value: Thigh

value: F

value: Dead

value: DOD


title: high-grade primary myxofibrosarcoma 623

value: High

value: Upper extremity

value: Forearm

value: Deep Depth

value: Alive

value: NED


title: BW120220-01

value: skin

value: female

value: Barataria Bay

value: February 20 2012

value: Winter


title: high-grade primary myxofibrosarcoma 3132

value: Frozen tumor

value: Trunk

value: Abdominal Wall

value: > 5, <= 10 cm primary tumor size category


title: WT/NT_3

source_name: Wild-type MEF, Non-target shRNA, 1%FBS 24hr, replicate 3

value: MEF

value: Wild-type

value: Non-target shRNA


title: high-grade primary myxofibrosarcoma 2516

value: Primary

value: High

value: Lower extremity

value: Thigh

value: M


title: high-grade primary myxofibrosarcoma 2553

value: Upper extremity

value: Upper arm

value: Deep Depth

value: Dead

value: DOD


title: high-grade primary myxofibrosarcoma 905

value: Frozen tumor

value: Foot

value: Alive

value: NED


title: L428, cd3-macs depl after coculture with %, no dexamethasone [H_BR31]

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: L428, cd3-macs depl after monoculture no dexamethasone

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: 7 day-old co-cultures of L428 cells and primary T cells were MACS-depleted of T cells.

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

treatment_protocol: Conventional culture conditions. When indicated addition of 0.75µM dexamethasone.


title: R2120127-02

value: skin

value: female

value: Chandeleur Sound

value: January 27 2012

value: Winter


title: L428, cd3-macs depl after coculture with %, + dexamethasone [H_D_BR32]

source_name: L428, cd3-macs depl after monoculture + dexamethasone


title: R3110829-02

value: male

value: Mississippi Sound

value: August 29 2011

value: Summer


title: high-grade primary myxofibrosarcoma 0224

value: Primary

value: High

value: Trunk

value: Buttock

value: > 10 cm       primary tumor size category

value: F


title: R2110824-01

value: August 24 2011


title: WT/Rb_KD_4

source_name: Wild-type MEF, Rb shRNA, 1%FBS 24hr, replicate 4

value: MEF

value: Wild-type

value: Rb shRNA


title: high-grade primary myxofibrosarcoma 1041

value: Frozen tumor

value: Deep Depth

value: Dead

value: DOO


title: SREBP1_KO/Rb_KD_3

source_name: SREBP1 KO MEF, Rb shRNA, 1%FBS 24hr, replicate 3

value: SREBP1 KO


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR27]


title: WT/Rb_KD_2

source_name: Wild-type MEF, Rb shRNA, 1%FBS 24hr, replicate 2


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR25]


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR29]


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR28]


title: SREBP1_KO/NT_3

source_name: SREBP1 KO MEF, Non-target shRNA, 1%FBS 24hr, replicate 3

value: Non-target shRNA


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR17]


title: R3120127-07

value: skin

value: female

value: Chandeleur Sound

value: January 27 2012

value: Winter


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR18]


title: WT/NT_2

source_name: Wild-type MEF, Non-target shRNA, 1%FBS 24hr, replicate 2


title: SREBP1_KO/Rb_KD_1

source_name: SREBP1 KO MEF, Rb shRNA, 1%FBS 24hr, replicate 1


title: SREBP1_KO/NT_2

source_name: SREBP1 KO MEF, Non-target shRNA, 1%FBS 24hr, replicate 2


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR30]


title: R2120120-03

value: male

value: January 20 2012


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR21]


title: SREBP1_KO/Rb_KD_2

source_name: SREBP1 KO MEF, Rb shRNA, 1%FBS 24hr, replicate 2


title: WT/Rb_KD_1

source_name: Wild-type MEF, Rb shRNA, 1%FBS 24hr, replicate 1


title: WT/NT_1

source_name: Wild-type MEF, Non-target shRNA, 1%FBS 24hr, replicate 1


title: R3110813-02

value: Mississippi Sound

value: August 13 2011

value: Summer


title: R3120125-01

value: January 25 2012


title: R3111219-03

value: December 19 2011


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR14]


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR22]


title: SREBP1_KO/NT_1

source_name: SREBP1 KO MEF, Non-target shRNA, 1%FBS 24hr, replicate 1

value: MEF


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR15]


title: R3111205-01

value: December 05 2011


title: 231T-3 [gene-level]

first: Tieju

state: Tianjin

address: Qixiangtai Road No.22, Heping District

department: Pathology

description: Gene expression data from MDA-MB-231 cells with TRA2A overexpression

hyb_protocol: Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the Affymetrix GeneChip® Human Transcriptome Array 2.0.

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing:
Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis.
Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label_protocol: The Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671 or equivalent) is used for the fragmentation and labeling of the cDNA.

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum.

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

treatment_protocol: MDA-MB-231 cells were treated with 10 nM paclitaxel-containing media or with TRA2A vector.

value: MDA-MB-231 cells


title: L428, cd3-macs depl after coculture with %, no dexamethasone [H_BR12]


title: R2110815-01

value: August 15 2011


title: R2110823-03

value: August 23 2011


title: L428, cd3-macs depl after coculture with Tcells, + dexamethasone [H_T_D_BR8]


title: R3110824-05

value: skin

value: August 24 2011


title: 231T-2 [gene-level]

source_name: MDA-MB-231 cells with TRA2A overexpression


title: L428, cd3-macs depl after coculture with %, + dexamethasone [H_D_BR20]


title: L428, cd3-macs depl after coculture with %, no dexamethasone [H_BR19]


title: R2110823-01

value: female

value: Chandeleur Sound


title: PTX-3 [gene-level]

description: Gene expression data from MDA-MB-231 cells with paclitaxel treatment


title: L428, cd3-macs depl after coculture with %, + dexamethasone [H_D_BR7]


title: BW120223-05

value: Barataria Bay

value: February 23 2012

value: Winter


title: L428, cd3-macs depl after coculture with Tcells, no dexamethasone [H_T_BR6]


title: 231T-1 [gene-level]


title: PTX-1 [gene-level]

source_name: MDA-MB-231 cells with paclitaxel treatment


title: PTX-2 [gene-level]


title: R3111209-03

source_name: Skin

value: male

value: Mississippi Sound

value: December 09 2011


title: R3111212-02

value: December 12 2011


title: control-3 [gene-level]

description: Gene expression data from Control MDA-MB-233 cells

source_name: Control MDA-MB-231 cells


title: control-2 [gene-level]

description: Gene expression data from Control MDA-MB-232 cells


title: R3110828-02

value: August 28 2011

value: Summer


title: TYP110111-02

value: January 11 2011


title: reference male mouse1/ 0GyK7

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

source_name: reference male mouse1

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: status

value: reference

value: tail

tag: generation

value: progeny


title: TYP20110111-01

value: skin


title: TYP20110110-03

value: January 10 2011


title: reference male mouse1/ 0GyK6

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

tag: strain


title: TYP100918-01

value: September 18 2010


title: control-1 [gene-level]

description: Gene expression data from Control MDA-MB-231 cells

tag: cell line

value: MDA-MB-231 cells


title: TYP100917-04

tag: location

value: Chandeleur Sound

value: September 17 2010


title: 0GyK7/ reference male mouse1


title: TYP100917-02

tag: collection date


title: 0GyK6/ reference male mouse1


title: TYP100916-02

value: September 16 2010

tag: season


title: TYP100915-03

value: male

value: September 15 2010


title: neuroblastoma, C2-ceramide and PJ34, 6h, biological rep3

city: Warsaw

first: Krzysztof

last: Gogolewski

address: Banacha 2a

department: Intitute of Informatics

country: Poland

institute: University of Warsaw

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide and PJ34 treated, 6h

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in GeneChip Expression Analysis Technical Manual (Affymetrix, Thermo Fisher Scientific).

data_processing: R/Bioconductor, oligo package

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0) and PARP-1 inhibitor 20µM PJ-34; after 6 hours

label_protocol: Biotinylated cRNA were prepared according to manufacturer instructions (Affymetrix, Thermo Fisher Scientific).

growth_protocol: The SH-SY5Y cells were cultured in MEM/F-12 Ham Nutrient Mixtures (1:1) supplemented with 15% heat-inactivated fetal bovine serum (FBS), 1% penicillin/streptomycin and 2mM glutamine. Cells were maintained at 37◦C in a humidiﬁed incubator containing 5% CO2.

extract_protocol: Total RNA was isolated and purified using the  Aﬀymetrics PrepEasy RNA spin KIT (Affymetrix, Thermo Fisher Scientific) following manufacturer´s instructions.

treatment_protocol: Prior to treatment, the cells were cultivated in low serum (2% FBS) medium and then were treated with: (i) 25µM C2–ceramide (d18:1/2:0); (ii) C2-eramide d18:1/2:0 (25µM) and PARP-1 inhibitor PJ-34 (20µM); (iii) pure medium for control samples.

value: bone marrow

tag: morphology

value: neuroblast


title: reference male mouse1/ 0GyK5


title: neuroblastoma, C2-ceramide and PJ34, 6h, biological rep2

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in GeneChip Expression Analysis Technical Manual (Affymetrix, Thermo Fisher Scientific).


title: reference male mouse1/ 0GyK4


title: 0GyK4/ reference male mouse1


title: TYP100915-02


title: 0GyK5/ reference male mouse1


title: 0GyK3/ reference male mouse1


title: neuroblastoma, C2-ceramide and PJ34, 6h, biological rep1


title: TYP100831-01

value: Mississippi Sound

value: August 31 2010


title: WT/Rb_KD_3

source_name: Wild-type MEF, Rb shRNA, 1%FBS 24hr, replicate 3

value: MEF

tag: genotype

value: Wild-type

value: Rb shRNA


title: neuroblastoma, biological control, untreated, 6h, biological rep2

description: Gene expression data from neuroblastoma (SH-SY5Y) control sample, 6h

source_name: neuroblastoma SH-SY5Y; control sample, untreated; after 6 hours


title: TYP100828-01

value: female

value: August 28 2010

value: Summer


title: reference male mouse1/ 0GyK1

value: reference

value: tail

value: progeny


title: 0GyK2/ reference male mouse1


title: neuroblastoma, biological control, untreated, 6h, biological rep1


title: TYP100818-01

value: skin

value: Barataria Bay

value: August 18 2010


title: neuroblastoma, biological control, untreated, 6h, biological rep3


title: 0GyK1/ reference male mouse1

value: male


title: reference male mouse1/ 0GyKF

value: parent


title: TYP100817-02

value: August 17 2010


title: TYP100915-01

value: Mississippi Sound

value: September 15 2010


title: neuroblastoma, C2-ceramide, 6h, biological rep2

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide treated, 6h

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0); after 6 hours

value: bone marrow

value: neuroblast


title: neuroblastoma, C2-ceramide, 6h, biological rep3


title: 0GyKM/ reference male mouse1


title: 231T-3 [exon-level]

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis.


title: neuroblastoma, C2-ceramide, 6h, biological rep1


title: 231T-1 [exon-level]


title: reference male mouse1/ 0GyK3


title: reference male mouse1/ 0GyJ5


title: 0GyKF/ reference male mouse1


title: control-2 [exon-level]


title: 0GyJ5/ reference male mouse1


title: PTX-1 [exon-level]


title: TYP100814-06

value: August 14 2010


title: reference male mouse1/ 0GyKM


title: neuroblastoma, C2-ceramide and PJ34, 3h, biological rep3

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide and PJ34 treated, 3h

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0) and PARP-1 inhibitor 20µM PJ-34; after 3 hours


title: TYP052810-02

value: female

value: Chandeleur Sound

value: Spring


title: control-3 [exon-level]


title: PTX-3 [exon-level]


title: 0GyJ4/ reference male mouse1

value: reference


title: PTX-2 [exon-level]


title: control-1 [exon-level]


title: TYP100816-01

value: August 16 2010

value: Summer


title: reference male mouse1/ 0GyK2

value: tail

value: progeny


title: R3110208-02

value: skin

value: February 08 2011

value: Winter


title: TE100909-03

value: male

value: September 09 2010


title: TYP052710-01


title: neuroblastoma, biological control, untreated, 3h, biological rep1

description: Gene expression data from neuroblastoma (SH-SY5Y) control sample, 3h

source_name: neuroblastoma SH-SY5Y; control sample, untreated; after 3 hours


title: R3110208-01

value: Mississippi Sound


title: neuroblastoma, C2-ceramide and PJ34, 3h, biological rep1

value: bone marrow


title: reference male mouse1/ 0GyJ3


title: R3100517-03


title: R3100515-01


title: neuroblastoma, C2-ceramide, 3h, biological rep3

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide treated, 3h

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0); after 3 hours

value: neuroblast


title: neuroblastoma, C2-ceramide, 3h, biological rep2


title: neuroblastoma, biological control, untreated, 3h, biological rep2


title: neuroblastoma, C2-ceramide and PJ34, 3h, biological rep2


title: R3100513-02

value: Barataria Bay


title: R3100512-03

value: female


title: R3100512-04


title: neuroblastoma, C2-ceramide and PJ34, 24h, biological rep2

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide and PJ34 treated, 24h

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0) and PARP-1 inhibitor 20µM PJ-34; after 24 hours


title: reference male mouse1/ 0GyJ4


title: neuroblastoma, C2-ceramide and PJ34, 24h, biological rep3


title: R3100512-02


title: neuroblastoma, C2-ceramide and PJ34, 24h, biological rep1


title: 0GyJ3/ reference male mouse1


title: R3100511-04


title: reference male mouse1/ 0GyJ2


title: neuroblastoma, biological control, untreated, 24h, biological rep3

description: Gene expression data from neuroblastoma (SH-SY5Y) control sample, 24h

source_name: neuroblastoma SH-SY5Y; control sample, untreated; after 24 hours


title: R3100511-01


title: 0GyJ1/ reference male mouse1


title: neuroblastoma, biological control, untreated, 24h, biological rep2


title: 231T-2 [exon-level]


title: neuroblastoma, biological control, untreated, 24h, biological rep1


title: R3100510-04


title: R3100510-03


title: neuroblastoma, C2-ceramide, 24h, biological rep3

description: Gene expression data from neuroblastoma (SH-SY5Y) C2-ceramide treated, 24h

source_name: neuroblastoma SH-SY5Y treated with  25µM C2–ceramide (d18:1/2:0); after 24 hours


title: neuroblastoma, C2-ceramide, 24h, biological rep2


title: R3100510-02


title: reference male mouse1/ 0GyJ1


title: neuroblastoma, biological control, untreated, 3h, biological rep3


title: R3100508-02


title: neuroblastoma, C2-ceramide, 24h, biological rep1


title: 0GyJF/ reference male mouse1

value: parent


title: reference male mouse1/ 0GyJF


title: GQ00212

city: Los Banos

last: Sreenivasulu

address: Metro Manila

country: Philippines

institute: IRRI

description: Gene expression of developing seed at 16 dpa (days post-anthesis)

hyb_protocol: Microarray hybridization was conducted in a SureHyb chamber assembly using the large-volume Hi-RPM Gene Expression Hybridization Kit. Hybridization was done in a hybridization oven set at 60°C rotating at 10 rpm for exactly 17 hours.

scan_protocol: Microarray slides with an ozone barrier slide cover were read by an Agilent SureScan microarray scanner controlled by Scan Control software using a scan resolution of 3 µm double pass. Raw data were generated from the TIFF file using Agilent Feature Extraction software. The quality of the data was judged per batch using the PDF QC report and as a group using QC Validation software.

data_processing:
The data were normalized using GeneSpring GX (Agilent, Santa Clara, CA) following the quantile normalization algorithm.
Differentially expressed genes (DEGs) between haplotype 8 (high amylose) and haplotype 4 (waxy) with the most contrasting samples were analyzed. The Limma R package is used following the empirical Bayes method.The p-values adjustment method used was either Bonferroni.The top-ranked genes were selected having an  p-value below 0.05 and fold change above ±1

organism: Oryza sativa Indica Group

source_name: Developing Seed,16dpa,haplotype4,waxy

label_protocol: Labelling was done using One-Color Microarray-Based Gene Expression Analysis protocol using a custom 8 x 60K microarray slide for rice (Agilent, Germany). cDNA synthesis and cRNA labelling were done using a single-color Low Input Quick Amp Labeling Kit following manufacturer's protocol.

growth_protocol: The rice accessions belonging to HRDA were grown  during the 2013 dry season at IRRI using a phytotron glasshouse maintained with ambient light, 29°C/21°C day/night temperature, and 75-85% relative humidity. Soil preparation, fertilizer regime, pesticide application, and glasshouse maintenance were as previously described (Jagadish et al., 2011).

extract_protocol: Total RNA was extracted in a 2.0-mL RNAse-free tube from 200 mg pulverized seeds using 750 uL RNA extraction buffer (100 mM Tris-HCl pH 8.0, 150 mM LiCl, 50 mM EDTA and 1.5% SDS plus 1.5% β-mercaptoehanol freshly added before use) and 500 uL phenol:chloroform:isoamyl (25:24:1). RNA was precipitated from the supernatant at -20°C overnight using 700 µL isopropanol and 400 µL 1.2 M NaCl in a fresh 2-mL microfuge tube. The RNA pellet was re-suspended in 450 µL RLT buffer (Qiagen) with 10% β-mercaptoethanol and further purified using Qiagen RNeasy Plant Mini Kit based on the manufacturer’s recommendation (Qiagen, Germany). Purified total RNA extract was treated with RNAse-free DNAse (Qiagen, Germany) to ensure that no residual genomic DNA were present in the sample

treatment_protocol: No treatment was done. All  rice lines were grown under optional conditions as described in growth protocol. This is to catch any inherent transcriptomic variation within each accession.

value: Developing Seed

tag: type


title: GQ00170


title: reference male mouse1/ 0GyI6

value: reference


title: GQ00205


title: 0GyJM/ reference male mouse1


title: A9 mutant nodules soybean 21 Days 2

status: Public on Nov 28 2016

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

description: nodules soybean 21 dpi infected by B. diazoefficiens nifA mutant strain A9

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA from culture-grown bacteria were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com). Normalized signal values from the arrays were then processed using Genespring GX 7.3 (Agilent Technologies,CA, USA). only those genes which are “present” (i.e., expressed, based on the detection P-value ≤ 0.06) in 80% of all replicates were further considered. Moreover, we excluded all genes in analyses with bacteroids for which the expression was not at least two times higher than in the control hybridizations with root material only. Thereby, we excluded those signals that might have originated from cross-hybridization with plant RNA. For these cross-hybridization control experiments, the amount of plant RNA was normalized to the signal of the Glycine max 18S rRNA. For experiments comparing different conditions amongst bacteroids, each chip was normalized to the median. Values below 0.01 were set to 0.01. For statistical comparisons, the student t-test with a P-value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2, when comparing different conditions amongst symbiotic bacteria.

organism: Bradyrhizobium diazoefficiens

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix).   The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: B. diazoefficiens-induced nodules from 5 soybean plants were collected for each GeneChip hybridization experiment. Nodules were harvested at 21 days post inoculation (dpi) and immediately frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 4-to–20% acrylamide gradient gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada).

tag: host plant

value: soybean

tag: infected with

value: B. diazoefficiens nifA mutant strain A9

value: soybean root nodules

tag: time point

value: 21 dpi


title: A9 mutant nodules soybean 21 Days 3

source_name: nodules soybean 21 dpi infected by B. diazoefficiens nifA mutant strain A9

tag: tissue


title: R3100517-02

value: skin

tag: gender

value: Spring


title: 0GyI5/ reference male mouse1

value: progeny

value: tail


title: 0GyI4/ reference male mouse1

value: male


title: 0GyI6/ reference male mouse1


title: A9 mutant nodules soybean 21 Days 1


title: H1 mutant nodules soybean 21 Days 3

description: nodules soybean 21 dpi infected by B. diazoefficiens nifH mutant strain H1

value: B. diazoefficiens nifH mutant strain H1


title: reference male mouse1/ 0GyI5


title: reference male mouse1/ 0GyJM


title: CRC Patient 256

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

hyb_protocol: Standard Affymetrix procedures

data_processing: RMA-sketch normalization on the core probeset using Affymetrix Power Tools (APT) followed by batch correction using the ComBat algorithm.

source_name: primary colon adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated proximal colon cancer specimens were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using the AllPrep DNA/RNA Micro Kit (Qiagen).

tag: patient id

tag: analysis batch

tag: other geo code

tag: age at diagnosis

tag: tumor stage

value: Tumor stage IV

tag: primary site

value: left

tag: microsatellite status

tag: braf v600e status

tag: kras codon 12, 13, 61 status


title: CRC Patient 257

value: Tumor stage III


title: H1 mutant nodules soybean 21 Days 1

source_name: nodules soybean 21 dpi infected by B. diazoefficiens nifH mutant strain H1


title: CRC Patient 255


title: neuroblastoma, C2-ceramide, 3h, biological rep1

value: bone marrow

tag: morphology

value: neuroblast


title: CRC Patient 254


title: CRC Patient 243

value: MSS

value: wt


title: CRC Patient 245

value: female

value: mut


title: 0GyI2/ reference male mouse1

tag: generation

tag: strain

tag: status

value: reference


title: H1 mutant nodules soybean 21 Days 2

tag: host plant

value: soybean

tag: infected with

value: soybean root nodules

tag: genotype

value: 21 dpi


title: CRC Patient 253

tag: gender


title: CRC Patient 246

tag: patient id


title: GQ00125

tag: tissue

value: Developing Seed

tag: type


title: reference male mouse1/ 0GyI4

value: tail

value: progeny


title: CRC Patient 244

tag: analysis batch

tag: other geo code

tag: age at diagnosis

value: right

value: MSI-H


title: GQ00086


title: CRC Patient 242

value: male

tag: tumor stage

tag: primary site

tag: microsatellite status


title: CRC Patient 239

value: Tumor stage III

value: left

tag: braf v600e status

tag: kras codon 12, 13, 61 status


title: reference male mouse1/ 0GyI3

tag: strain

tag: generation


title: CRC Patient 238


title: CRC Patient 241


title: reference male mouse1/ 0GyIF

tag: status

value: parent


title: CRC Patient 240

value: MSS


title: CRC Patient 236

value: wt


title: CRC Patient 234


title: CRC Patient 230


title: CRC Patient 233

value: female


title: CRC Patient 232


title: 0GyI1/ reference male mouse1


title: CRC Patient 228

value: mut


title: reference male mouse1/ 0GyI1

value: reference


title: reference male mouse1/ 0GyIM


title: CRC Patient 226


title: CRC Patient 227


title: CRC Patient 222


title: 0GyJ2/ reference male mouse1


title: CRC Patient 225


title: 0GyIM/ reference male mouse1


title: CRC Patient 229


title: 0GyIF/ reference male mouse1


title: CRC Patient 224


title: CRC Patient 217


title: reference male mouse1/ 0GyI2


title: 0GyI3/ reference male mouse1


title: CRC Patient 235


title: CRC Patient 218


title: CRC Patient 223

value: Tumor stage IV


title: CRC Patient 220


title: CRC Patient 221


title: CRC Patient 219


title: CRC Patient 216


title: CRC Patient 213


title: CRC Patient 214


title: CRC Patient 215


title: CRC Patient 211


title: CRC Patient 212


title: CRC Patient 210


title: CRC Patient 209


title: CRC Patient 208


title: CRC Patient 206


title: CRC Patient 205


title: CRC Patient 204


title: CRC Patient 203


title: CRC Patient 207


title: CRC Patient 195


title: CRC Patient 202


title: CRC Patient 200


title: CRC Patient 231


title: CRC Patient 201


title: CRC Patient 194


title: CRC Patient 198


title: CRC Patient 197


title: CRC Patient 199


title: CRC Patient 193


title: CRC Patient 189


title: CRC Patient 192


title: CRC Patient 183


title: CRC Patient 186


title: CRC Patient 184


title: CRC Patient 182


title: CRC Patient 191


title: CRC Patient 179


title: CRC Patient 180


title: CRC Patient 185


title: CRC Patient 196


title: CRC Patient 190


title: CRC Patient 171


title: CRC Patient 168


title: CRC Patient 172


title: CRC Patient 178


title: CRC Patient 169


title: CRC Patient 173


title: CRC Patient 170


title: CRC Patient 181


title: CRC Patient 165


title: CRC Patient 164


title: CRC Patient 167


title: CRC Patient 160


title: CRC Patient 161


title: CRC Patient 163


title: CRC Patient 162


title: CRC Patient 188


title: CRC Patient 159


title: CRC Patient 155


title: CRC Patient 158


title: CRC Patient 152


title: CRC Patient 156


title: CRC Patient 237


title: CRC Patient 151


title: CRC Patient 149


title: CRC Patient 143


title: CRC Patient 154


title: CRC Patient 148


title: CRC Patient 142


title: CRC Patient 150


title: CRC Patient 146


title: CRC Patient 138