title: 2026001-048-Pancreas-Aneuploid

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA) for 40 hours in a rotating 65°C oven. All hybridizations were done with a pooled commercial 46,XX reference (Promega, Madison WI GSM540609).

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 10.7 using default settings.

data_processing:
The aCGH data was assessed with a series of QC metrics, dye  normalized and centralized, then analyzed using an aberration detection algorithm (ADM2) which is included in Agilent Genomic Workbench 6.7 software. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average )
Log2(Cy5/Cy3) values included in Series supplementary file normalized.txt

source_name: Fresh frozen tissue

label_protocol: Extracted fresh frozen sourced genomic DNA was amplified using the phi29 based Illustra GenomiPhi V2 Amplification kit from GE Healthcare Bio-sciences Corp (Piscataway,NJ) according to our published protocols18.  A 100 ng aliquot of pooled 46,XX DNA (Promega, Madison, WI) was amplified with the matching amplification protocol to generate a suitable reference for each aCGH experiment using amplified DNA template.  In all cases the quality of the amplification product was assessed by gel electrophoresis.    Fresh frozen phi29 amplified and FFPE non-amplified DNAs were treated with DNAse 1 prior to Klenow based labeling. High molecular weight phi29 templates were digested for 30 minutes while the smaller fragmented FFPE samples were digested for only 1 minute. In each case 1ul of 10x DNase 1 reaction buffer and 2ul of DNase 1 dilution buffer were added to 7ul of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1.  In contrast the amplified FFPE sourced DNAs do not require DNase 1 treatment prior to Klenow-based labeling. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols

extract_protocol: DNA from sorted nuclei was extracted using an amended protocol from QIAamp® DNA Micro Kit from Qiagen (Valencia, CA).  Briefly each sorted sample was resuspended in 180ul buffer ATL and 20ul proteinase K then incubated for 3 hours at 56°C for complete lysis.  Samples were bound and washed according to QIAamp® DNA Micro Kit instructions, eluted into 50ul of H20, then precipitated overnight with 5ul 3 M sodium acetate and 180 ul 100% EtOH.  Each sample was then centrifuged for 30 minutes at 20,000 x g, washed in 1 ml of 70% EtOH for 30 minutes at 20,000 x g. The samples were carefully decanted and the DNA pellet was dried by speed vacuum then resuspension in a small volume (e.g. 10-50ul) of H20 for final concentrations suitable for accurate quantification.

treatment_protocol: All patients had prior gemcitabine treatment.

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

tag: gender

value: Female

tag: age (years)

tag: study therapy

value: FOLFOX

tag: time from first diagnosis of pda (months)

tag: overall survival (months)

source_name: Reference pooled 46XX

value: female

tag: phenotype


title: 2026001-046-Pancreas-Aneuploid

status: Public on Dec 31 2014

type: genomic

country: USA

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

value: Male

tag: prior therapy

value: BMN-673, IROX

value: irinotecan/erlotinib

value: normal


title: Fertilized_Eggs_Female12_rep1

type: RNA

city: St. John's

first: Matthew

last: Rise

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air. For each array two labeled cDNAs were combined (one sample, one reference) and 2 μl of LNA blocker (Genisphere) and 40 μl of prewarmed 2x formamide-based hybridization buffer (Genisphere) was added. These samples were incubated at 80°C for 10 minutes and then kept at 42°C. Pre-warmed arrays were put in Corning hybridization chambers, LifterSlips were applied and the samples were loaded under the LifterSlips. Hybridizations were performed overnight for ~16 hours in a water bath at 42°C. After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

data_processing: Signal intensity data was extracted from tiff images using Imagene v7.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged, and logratios for the dye-swap arrays were multiplied by -1 to give all logratios the same orientation.

label: AlexaFluor 647

molecule: total RNA

organism: Gadus morhua

source_name: Fertilized egg_low quality female

label_protocol: 5 μg of DNAse-treated and column-purified total RNA was labeled using the SuperScript Direct cDNA Labeling kit (Invitrogen) according to the manufacturer's protocol. Each RNA was labeled in 4 labeling reactions: two with AlexaFluor 647 and two with AlexaFluor 555.

growth_protocol: Eggs and sperm were harvested by stripping and collected in plastic collection beakers. Eggs were transferred into 1.5 L graduated glass ‘fertilization’ beakers by gentle pouring and sperm was added using a plastic transfer pipette. The egg and sperm mixture was gently stirred using the pipette and 100 ml UV-treated, filtered seawater was added and again stirred with the pipette. The mixture was left to incubate for 1 minute after which 500 ml UV-treated, filtered seawater was added and left to incubate for 5 minutes. After this incubation, the fertilization beaker was filled to 1.4 L mark with UV-treated, filtered seawater, placed on the bench in the walk-in cold room (6°C) and left undisturbed until the embryos reached first cleavage (2-cell stage), approximately 7 hours post-fertilization (hpf). At first cleavage stage, 7hpf embryo samples were collected from the 'fertilization beaker'. A sterile transfer pipette was used to fill three 1.5 ml RNase-free tubes with 0.25 ml of floating eggs from the ‘fertilization beaker’. Seawater was removed by pipette, and samples were flash frozen in liquid nitrogen and stored at -80 °C until RNA extraction.

extract_protocol: Per female, 3 batches of 0.25 ml of eggs were homogenized in TRIzol (Invitrogen) Bio-Gen PRO200 tissue homogenizer (PRO Scientific Inc., Oxford, CT) equipped with a 5 mm x 150 mm generator tip, at speed setting 2-3 for 30 seconds or until no solids were visible. The homogenate samples were passed through QIAshredder columns (Qiagen) following the manufacturer’s instructions. Total RNA was extracted from the TRIzol homogenate according to the manufacturers’ instructions, and the triplicate extractions were pooled for each individual female. Total RNA was treated with DNAse I (Qiagen) to remove genomic DNA, and then purified using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturer’s instructions.

value: fertilized egg

tag: developmental stage

value: 7h post-fertilization (7 hpf, ~ 2-cell stage)

tag: egg harvested from

value: low quality female

source_name: Fertilized egg_high quality female

value: high quality female


title: sample292

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

label: biotin

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: long-lived individuals


title: Fertilized_Eggs_Female12_dyeswap_rep1

description:
dye-swap
female12_ds_1


title: Control dnFoxO 1

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

description: Whole transcript expression profiling

hyb_protocol: Fragmented biotinylated cDNA were further processed by GeneChip® Hybridization, Wash, and Stain Kit, then hybridized on mouse Affymetrix Gene 1.0 ST arrays (Santa Clara, CA, USA) to measure the expression of 28,132 well-annotated genes.

scan_protocol: A total of 16 array images were acquired by GeneChip Scanner 3000 7G and quality assessed by Affymetrix Expression Console (Santa Clara, CA).

data_processing:
Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and robust multi-array analysis algorithm (RMA) and quantile normalization was used for data preprocessing {Bolstad, 2003 #4365}.
Brainarray MoGene 1.0 ST custom CDF file v.16 was used for probe annotation {Dai M, 2005}.

label: Btiotin

organism: Mus musculus

source_name: tibialis anteior muscle

label_protocol: Whole-transcript expression profiling experiments were carried out by the Boston University Medical Center Microarray Core Facility.  The GeneChip Whole-Transcript Sense Target Labeling and Control Reagents Kit was used to synthesize and amplify cDNA for biotinylation labeling per manufacturer’s instructions .

growth_protocol: CDF1 mice (~20g) were used for all experiments. Food and water were provided ad libitum.

extract_protocol: Muscles were harvested from mice anesthetized under isofluorane and were snap-frozen in liquid nitrogen.  Muscles were minced and homogenized in TRIzol for RNA extraction.

treatment_protocol: The tibialis anterior muscles of mice were injected with either AAV9-EV or AAV9-d.n.FoxO, and then assigned to a control or C26 group. To induce cancer cachexia in the C26 group, 5x105 C26 cells were subcutaneously injected into each flank on the same day as AAV delivery. Control mice received a subcutaneous injection of 1xPBS into each flank.  Muscles from C26 mice(and control mice) were harvested when the largest tumor reached 1.5 cm in diameter (~26 days post-inoculation).

value: tibialis anteior muscle

tag: sample type

value: from healthy, non-tumor bearing mice with AAV9 dominant negative FoxO transfection

tag: disease state

value: from healthy, non-tumor bearing mice

tag: treatment


title: human CPE Braak-0 donor 2

city: Amsterdam

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Biological CPE replicate 2 of 7 of healthy human choroid plexus

hyb_protocol: Labeled human CPE RNA and labeled human common reference sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.

source_name: healthy human choroid plexus epithelium (Braak 0)

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

treatment_protocol: With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the choroid plexus (10um) mounted on PEN-membrane slides

value: choroid plexus epithelium

tag: cell sampling

value: laser dissection microscopy

value: healthy

source_name: Total RNA from pooled healthy human RPE/choroid cells

value: RPE/chodoid


title: Fertilized_Eggs_Female12_rep2


title: 2026001-042-Pancreas-Aneuploid

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

value: Female

value: FOLFOX/erlotinib

value: female


title: 2026001-045-Pancreas-Aneuploid

value: Male

value: temazolamide

value: normal


title: sample291


title: 2026001-049-Pancreas-Aneuploid

value: Gemcitabine/Cisplatin/Erlotinib, FOLFOX, FOLFIRINOX, GTX, Velcade/Doxorubicin

value: doxorubicin/bortezomib


title: Control EV 1

description: Whole transcript expression profiling

value: from healthy, non-tumor bearing mice with AAV9-ev transfection

value: AAV9-ev transfection


title: 2026001-041-Pancreas-Aneuploid

value: FOLFIRINOX


title: Control EV 3

description: Whole transcript expression profiling

value: tibialis anteior muscle

value: from healthy, non-tumor bearing mice


title: sample289

value: long-lived individuals


title: sample290


title: 2026001-040-Pancreas-Aneuploid


title: A10

city: Berlin

first: Mario

last: Lorenz

address: Hessische Strasse 3-4

institute: Charité-Universtitätsmedizin Berlin

description: Basal expression in non-treated HUVEC

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505B, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 9.1.3.1) was used to read out and process the microarray image files.

molecule: polyA RNA

source_name: HUVEC RNA Pool M5

label_protocol: 1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: The cells were cultured in medium M199 (Gibco BRL) supplemented with 20 % FCS, 12 µg/ml ECGS (endothelial cell growth supplement, Promocell), 5 U/ml heparin, 2 mM L-glutamine, 5 µg/ml ascorbic acid, 5 µg/ml glutathione, 100 U/ml penicillin, and 100 µg/ml streptomycin. The medium was refreshed every 2–3 days. Cells were subcultured after treatment with 0.01% trypsin/EDTA. Cells were passaged twice and maintained throughout the culture period in the same medium.

extract_protocol: Cells were harvested and total RNA was extracted from confluent cells at passage 2. Cells were lysed in Trizol reagent, and DNase-digested RNA was purified using RNeasy columns (Invitrogen, Karlsruhe, Germany).

treatment_protocol: Non-treated cells at passage 2.

tag: cell type

value: HUVEC

tag: Sex


title: 2026001-039-Pancreas-Aneuploid

tag: gender


title: sample288

value: sarcoidosis


title: 2026001-038-Pancreas-Aneuploid

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

tag: age (years)


title: A9

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool M4


title: A8

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool M3


title: 2026001-036-Pancreas-Aneuploid

value: Female

value: FOLFIRINOX, Gemcitabine/Abraxane, Doxil

tag: study therapy

value: Doxorubicin


title: 2026001-035-Pancreas-Aneuploid

value: MKO-646, Capecitabine/Nab-paclitaxel

value: Nab-paclitaxel/capecitabine

tag: time from first diagnosis of pda (months)

value: female


title: 2026001-034-Pancreas-Aneuploid

value: Male

value: 5FU/XRT, Gemcitabine, Irinotecan

value: irinotecan

tag: overall survival (months)

value: normal


title: sample286


title: sample287


title: A6

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool M1


title: sample285


title: sample283


title: A7

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool M2


title: sample284


title: A5

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool F5


title: 2026001-033-Pancreas-Aneuploid

tag: phenotype


title: human CPE Braak-0 donor 1

description: Biological CPE replicate 1 of 7 of healthy human choroid plexus

tag: tissue

value: choroid plexus epithelium

value: laser dissection microscopy

value: healthy

value: RPE/chodoid


title: 2026001-032-Pancreas-Aneuploid

tag: prior therapy

value: Gemcitabine/Abraxane, FOLFOX/Erlotinib

value: FOLFOX/erlotinib


title: A4

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool F4

value: HUVEC


title: sample282

value: sarcoidosis


title: A3

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool F3

value: Female


title: MBC replicate 5

city: Seville

first: Alicia

last: Báez

address: Avenue Manuel Siurot

country: Spain

institute: IBIS

hyb_protocol: Labeled cRNA was mixed and hybridized against the oligonucleotide microarray slides Whole Human Genome Microarray Kit, 4x44K  (Agilent Technologies).

scan_protocol: The microarrays were scanned in a GenePix® reader, with data acquired at wavelengths of 635nm and 532nm for Cy3 and Cy5, respectively. Acquisition software GenePix® Pro v6.0 automatically adjusts the PMTs so that they produce roughly the same response in both channels.

data_processing: Acquired data (.gpr files) wer transformed to .mev files with the ExpressConverter v2.1 and then analyzed with the open-source Multi-Experiment Viewer, MeV v4.5, software. The expression data were normalized and filtered using the Multi-experiment Viewer 4.7.1 software. To do this, we use the normalization algorithm included in this software and we applied the percentage cutoff filter (percent=100.0) and the variance filter (mode=percent mode value=50).

source_name: CD27+ cells total RNA from a healthy donor

label_protocol: 200 ng of RNA from each sample were reverse-transcribed into cRNA and labeled with the Two-Color Microarray Low Input Quick Amp Labeling Kit (Agilent Technologies). 6 samples of NBCs were pooled, labeled with cyanine 3-CTP (Cy3), and used as reference samples. 6 samples of normal PCs, 6 samples of mPCs and 5 samples of MBCs were labeled with cyanine 5-CTP (Cy5) and used as test samples.

extract_protocol:
isolation protocol:  Peripheral blood mononuclear cells were isolated by density gradient centrifugation using Ficoll-Paque solution (Amersham Biosciences, Uppsala). The isolation of PCs, mPCs and MBCs was performed by immunomagnetic separation in an AutoMACS pro separator using the CD138 MACS microbead Human Kit (for PCs and mPCs), and the Memory B cell isolation kit human (for MBCs) (both of Miltenyi Biotec, Bergisch Gladbach, Germany)
Total RNA was extracted from all samples with TRIzol® reagent (Life Technologies), according to the manufacturer's directions for each type of sample.

value: Peripheral blood

source_name: CD27- cells total RNA from healthy donors


title: A2

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool F2


title: M3 24h

description: Expression HUVEC after shear stress

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.2.1.3) was used to read out and process the microarray image files.

source_name: HUVEC cell pool M3 shear stress 6 dyn/cm2 24h

label_protocol: 0.5 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: The cells were cultured in medium M199 (Gibco BRL) supplemented with 20 % FCS, 12 µg/ml ECGS (endothelial cell growth supplement, Promocell), 5 U/ml heparin, 2 mM L-glutamine, 5 µg/ml ascorbic acid, 5 µg/ml glutathione, 100 U/ml penicillin, and 100 µg/ml streptomycin. The medium was refreshed every 2–3 days. Cells were subcultured after treatment with 0.01% trypsin/EDTA. Cells were maintained throughout the culture period in the same medium.

extract_protocol: After 24 hours, cells were harvested and RNA was extracted with Trizol followed by DNase digestion.

treatment_protocol: Laminar shear stress of 6 dyn/cm2 was applied for 24 hours to fully confluent cell monolayers (passage 3) using a cone-and-plate system. Cells cultured under static conditions served as controls.

value: shear stress 6 dyn/cm2 24h


title: MBC replicate 4


title: M5 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool M5 static 24h

value: non-treated


title: M5 24h

description: Expression HUVEC after shear stress

source_name: HUVEC cell pool M5 shear stress 6 dyn/cm2 24h


title: sample281

source_name: RNA from blood


title: MBC replicate 2


title: MBC replicate 3


title: 2026001-029-Pancreas-Aneuploid

source_name: Fresh frozen tissue

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

value: FOLFIRI

source_name: Reference pooled 46XX

value: female


title: sample280

value: long-lived individuals


title: 2026001-027-Pancreas-Aneuploid

value: Male

value: Gemcitabine/Abraxane, IROX

value: irinotecan/oxaliplatin

value: normal


title: sample279


title: MBC replicate 1


title: PC replicate 6

source_name: CD138+ cells total RNA from a healthy donor

value: Bone Marrow


title: M2 24h

description: Expression HUVEC after shear stress

source_name: HUVEC cell pool M2 shear stress 6 dyn/cm2 24h


title: M3 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool M3 static 24h


title: A1

description: Basal expression in non-treated HUVEC

source_name: HUVEC RNA Pool F1


title: M2 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool M2 static 24h


title: sample278


title: 2026001-031-Pancreas-Aneuploid

value: Gemcitabine, Gemcitabine/Abraxane, CapOx, FOLFIRI and then 5FU due to reaction


title: sample277


title: 2026001-022-Pancreas-Aneuploid 2

value: Gemcitabine/Abraxane, FOLFIRINOX, Capecitabine, Capecitabine/Abraxane, Gemcitabine

value: Nab-paclitaxel/capecitabine


title: PC replicate 5


title: PC replicate 4


title: sample276

value: sarcoidosis


title: 2026001-028-Pancreas-Aneuploid

value: Female

value: doxorubicn/capecitabine


title: 2026001-022-Pancreas-Aneuploid 1


title: sample274


title: 2026001-018-Pancreas-Aneuploid


title: PC replicate 1

value: Peripheral blood


title: sample273


title: F2 24h

description: Expression HUVEC after shear stress

source_name: HUVEC cell pool F2 shear stress 6 dyn/cm2 24h

value: HUVEC

value: shear stress 6 dyn/cm2 24h


title: PC replicate 3


title: 2026001-015-Pancreas-Aneuploid

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

value: Gemcitabine, FOLFIRI, IRiOX, Gemcitabine/Abraxane, DOXIL

value: Doxorubicin


title: PC replicate 2


title: 2026001-024-Pancreas-Aneuploid

value: Male

value: female


title: sample272

value: others


title: mPC replicate 6

source_name: CD138+ cells total RNA from a patient with MM


title: F3 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool F3 static 24h

value: non-treated


title: F1 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool F1 static 24h


title: 2026001-014-Pancreas-Aneuploid

value: FOLFIRI

value: normal


title: sample271


title: mPC replicate 4

value: Bone Marrow

source_name: CD27- cells total RNA from healthy donors


title: mPC replicate 5


title: 2026001-021-Pancreas-Aneuploid

value: CAPOX


title: sample270

value: ductal adenocarcinoma


title: F3 24h

description: Expression HUVEC after shear stress

source_name: HUVEC cell pool F3 shear stress 6 dyn/cm2 24h

value: Female


title: 2026001-011-Pancreas-Aneuploid


title: mPC replicate 3


title: 2026001-006-Pancreas-Aneuploid

value: Mitomycin/capecitabine


title: F2 Basal

description: Expression in non-treated HUVEC

source_name: HUVEC cell pool F2 static 24h


title: 2026001-005-Pancreas-Aneuploid

value: Folfiri+Avastin, Mitomycin C, Doxi


title: F1 24h

description: Expression HUVEC after shear stress

source_name: HUVEC cell pool F1 shear stress 6 dyn/cm2 24h

value: HUVEC


title: sample268


title: mPC replicate 2

value: Peripheral blood


title: sample269

value: pancreatitis


title: mPC replicate 1


title: sample267


title: sample266


title: 2026001-004-Pancreas-Aneuploid

value: Pancreatic Ductal Adenocarcinoma-Liver metastasis

value: Gemcitabine/Abraxane, Irinotecan

value: irinotecan


title: sample265


title: 2026001-002-Pancreas-Aneuploid

value: Male

value: XELOX, Gemcitabine/Abraxane, Doxil

value: Doxorubicin

value: female


title: CytD_exp|infected_90min_CytD|experiment_4|replicate_3

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: CytochalasinD experiment

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution, 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies)

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: 1. Wash twice cryopreserved THP-1 cells* (one vial contains 5 x 10^6 cells) with complete medium - cRPMI (RPMI-1640 medium supplemented with 1% L-glutamine, 1% Hepes, 0.1% 2ME and fetal bovine serum to a final concentration of 10%). Use 50 ml Flacon tubes and 20 ml medium to wash, spin down for 5 min at 1500 rpm (400xg, Heraeus Megafuge), 4°C.    2. Seed cells in 6 well plates/ T75 flask and expand cell numbers by sub culturing in T75 flasks in 10 ml cRPMI and later in T150 flasks in 50 ml cRPMI.  Sub-cultures are established by centrifugation with subsequent re-suspension at 2-5 x 10^5 viable cells/ml, every 2-3 day. Cells reach density of 8 x 10^5 cells/ml within this period of time. For proper viability and fitness of the cells do not exceed before sub-culturing 1x10^6 cells/ml. Use T150 flasks and maximum volume of 80 ml cRPMI per flask to generate large cell numbers (eg 15 x T150 flasks to get 5 x 10^8 cells). Incubate cell cultures at 37°C and 5% CO2.  3. Differentiation to macrophages** is triggered by addition of PMA (50 ng/ml) and overnight incubation. This is followed by 2 washes (cRPMI)*** and addition of complete media over 48 h post differentiation. This protocol elicits a uniform population of resting macrophages prior infection experiments. For T150 flasks use 2x10^7 cells/20 ml cRPMI (30 flasks per time-point for MS platforms), for 6 well plate use 10^6 cells/well/3 ml cRPMI (triplicates per time-point).  Transfer differentiated THP-1 cells to the BSL3 lab.

extract_protocol: 1. Preparation of Mtb infected THP-1 macrophages for RNA extraction/isolation: At different time-points following infection wash once the macrophage monolayer with RT PBS (Invitrogen, # 20012-043). Add 1 ml cold 4M GITC solution (Invitrogen, # 15577-018) per well and gently scrape the cells. Collect solution in 1 ml screw cap. Centrifuge at 12,000 × g for 10 min. at 4°C. Add 3 Vol. Trizol LS (Invitrogen, # 10296-010) to supernatant and homogenize (eukaryotic fraction). Store homogenate of eukaryotic fraction at -80°C freezer until further processed. Resuspend pellet by pipetting up and down in residual GITC. Add 1 ml Trizol (Invitrogen, # 15596-018) containing 20 g/ml linear acrylamide to the pellet (prokaryotic fraction). Use pipette to homogenate in Trizol. Store homogenate of prokaryotic pellet at -80°C freezer until further processed.  2. Isolation of total eukaryotic host RNA: Note:  process only 1ml from total homogenate, store remaining volume at –80°C for future processing. Thaw Trizol homogenate of eukaryotic fraction and incubate for 5 min. at RT (15 to 30°C). Add 0.2 ml of chloroform per 0.75 ml of Trizol LS for phase separation. Shake tubes vigorously by hand for 15 sec. and incubate them at RT for 5 min. Centrifuge at 12,000 × g for 15 min.at 4°C. Transfer the colorless aqueous (upper) phase to a clean tube (typical volume will be ~500 µl, assure not to carry over anything from the white interphase or the red phenol phase)

treatment_protocol: Mtb infection stocks will be freshly prepared by cultivation of WSL* (working seed lot – 10^8 bacteria per vial, cryopreserved in 7H9+glycerol 50%) in 9 ml 7H9+ADC at 37°C under shaking with 90 rpm for 5 days. When bacterial growth is visible (day 5-7) inoculate 45 ml 7H9 with 5 ml bacterial suspension.      1. Grow infection stock in 7H9+ADC 0,05% Tween 80 for about 5 days to OD 0.3-0.6.    2. Spin down bacteria: 20 min at 4.000 rpm, 4°C  3. Wash once with equal amount of cold PBS and discard clumps by filtration using 40 μm pore size filters (BD).   4. Determine bacteria number: OD580 0.1 >>>> 5 x 10^7 bacteria/ml  5. Dilute PBS washed infection stock with cRPMI and infect cells – MOI 5 for up to day 3 and MOI 1 for longer time-points  6. Wash away non-internalized bacteria 4h after infection (use room temperature PBS 20 ml per flask, twice) and place cells back in cRPMI  7. For infection of macrophages in plates, change the culture media to media containing Mtb and spin down to obtain a uniform infectivity, 2 min, 700 rpm  8. For infection of macrophages in flasks, add 1ml of media containing Mtb to the 25 ml of cRPMI per flask

tag: cell line

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: Retina_myopia_rep2

city: Durham

first: Terri

last: Young

state: NC

address: LaSale St.

department: Ophthalmology

institute: Duke University

description:
miRNA expression after 10 days without FDM induction
MmiRNA-T-M-002

hyb_protocol: Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit for the hybridization protocol.  Ozone covers were used.

scan_protocol: Agilent B Scanner, Scan area (61 x 21.6mm), Scan resolution 5um, extended Dynamic range selected, Dye channel green, Green PMT XDR Hi 100%, XDR Lo 5%

data_processing: Feature Extraction version 11, protocol miRNA_1100_Jul11

source_name: retina, control, replicate2

label_protocol: Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit was used for the labeling protocol.

extract_protocol: Total RNA was isolated from the whole eye, retina and sclera using mirVanaTM miRNA kit (Applied Biosystems, Austin, Texas) according to the manufacturer’s instructions. Total RNA concentration was measured using NanoDrop spectrophotometry. The quality of the total RNA was assessed using the Agilent RNA 600 Nano kit (Agilent Technologies, Santa Clara, CA) following the manufacturer’s instructions.

treatment_protocol: C57BL/6J mice were purchased from the Jackson Laboratory. Form-deprivation was induced in fifteen postnatal day 24 (P24) mice by applying a unilateral frosted hemispherical plastic diffuser over the right eyes for ten days. The contralateral untreated left eyes were used as control. At the end of form-deprivation induction (P34) both myopic and control eyes were isolated and retina and sclera were dissected out in RNAlatter.

tag: strain

value: retina

value: control

tag: age

value: 34 days


title: CytD_exp|infected_90min_CytD|experiment_6|replicate_3

description: CytochalasinD experiment


title: Retina_myopia_rep3

description:
miRNA expression after 10 days without FDM induction
MmiRNA-T-M-003

source_name: retina, control, replicate3


title: sample264

source_name: RNA from blood

tag: disease

value: melanoma


title: CytD_exp|infected_90min_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: Retina_myopia_rep1

description:
miRNA expression after 10 days without FDM induction
MmiRNA-T-M-001

source_name: retina, control, replicate1


title: CytD_exp|infected_90min_CytD|experiment_3|replicate_3

description: CytochalasinD experiment


title: CytD_exp|infected_90min_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: sample263


title: CytD_exp|infected_90min_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: Retina_control_rep3

description:
miRNA expression after 10 days of FDM induction
MmiRNA-T-C-003

source_name: retina, myopic, replicate3

value: myopic


title: sample260


title: sample261


title: Retina_control_rep2

description:
miRNA expression after 10 days of FDM induction
MmiRNA-T-C-002

source_name: retina, myopic, replicate2


title: Retina_control_rep1

description:
miRNA expression after 10 days of FDM induction
MmiRNA-T-C-001

source_name: retina, myopic, replicate1


title: sample259


title: 2026001-012-Pancreas-Aneuploid

source_name: Fresh frozen tissue

value: Gemcitabine, FOLFOX

value: FOLFOX

source_name: Reference pooled 46XX

value: normal


title: CytD_exp|infected_90min_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: Sclera_myopia_rep3

description:
miRNA expression after 10 days without FDM induction
MmiRNA-S-M-003

source_name: sclera, control, replicate3

value: sclera


title: CytD_exp|infected_90min_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_90min_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: sample258


title: Sclera_myopia_rep1

description:
miRNA expression after 10 days without FDM induction
MmiRNA-S-M-001

source_name: sclera, control, replicate1


title: CytD_exp|infected_90min_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: sample257


title: Sclera_myopia_rep2

description:
miRNA expression after 10 days without FDM induction
MmiRNA-S-M-002

source_name: sclera, control, replicate2


title: CytD_exp|infected_90min_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: sample262


title: Sclera_control_rep2

description:
miRNA expression after 10 days of FDM induction
MmiRNA-S-C-002

source_name: sclera, myopic, replicate2


title: CytD_exp|infected_90min_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: Sclera_control_rep3

description:
miRNA expression after 10 days of FDM induction
MmiRNA-S-C-003

source_name: sclera, myopic, replicate3


title: sample255

value: sarcoidosis


title: CytD_exp|infected_90min_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: Sclera_control_rep1

description:
miRNA expression after 10 days of FDM induction
MmiRNA-S-C-001

source_name: sclera, myopic, replicate1


title: sample256


title: CytD_exp|infected_90min_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: sample254


title: sample253


title: WholeEye_myopia_rep6

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-006

source_name: whole eye, myopic, replicate6

value: whole eye


title: sample252


title: CytD_exp|infected_90min_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: sample251


title: WholeEye_myopia_rep5

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-005

source_name: whole eye, myopic, replicate5


title: WholeEye_myopia_rep3

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-003

source_name: whole eye, myopic, replicate3


title: WholeEye_myopia_rep4

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-004

source_name: whole eye, myopic, replicate4


title: sample250

source_name: RNA from blood


title: sample249


title: CytD_exp|infected_90min_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_6|replicate_3

description: CytochalasinD experiment


title: sample248

value: ductal adenocarcinoma


title: sample247


title: CytD_exp|infected_90min_w/o_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: CytD_exp|infected_90min_CytD|experiment_1|replicate_1

description: CytochalasinD experiment


title: CytD_exp|infected_90min_CytD|experiment_2|replicate_1

description: CytochalasinD experiment


title: WholeEye_control_rep6

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-006

source_name: whole eye, control, replicate6


title: WholeEye_myopia_rep2

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-002

source_name: whole eye, myopic, replicate2


title: sample246

value: others


title: WholeEye_control_rep4

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-004

source_name: whole eye, control, replicate4


title: WholeEye_control_rep3

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-003

source_name: whole eye, control, replicate3


title: WholeEye_myopia_rep1

description:
miRNA expression after 10 days without FDM induction
MmiRNA-M-001

source_name: whole eye, myopic, replicate1


title: Biceps_Femoris_Growth_Restricted_Gestation_rep5

city: Denver

first: Laura

last: Brown

state: CO

address: Mail Stop C263 12348 East Montview Boulevard

department: Center for Women's Health Research

institute: University of Colorado Anschutz Medical Campus

description: Gene expression data from Biceps femoris muscle at 90% gestation under growth restricted conditions

hyb_protocol: 10ug of cRNA were hybridized on Affymetrix® GeneChip Bovine Genome Arrays with rotation at 60rpm for 16 hours at 45C.  Chips were washed and scanned in GeneChip Fludics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Microarray Suite 5.0 method (MAS5.0) in Affymetrix Expression Console version 1.1 using default settings.

organism: Ovis aries

source_name: Ovine biceps femoris at 90% gestation in growth restricted conditions

label_protocol: 300ng of total RNA was primed with T7 oligo primer to synthesize the first strand cDNA.  The single-stranded cDNA was converted to double-stranded DNA template for transcription.  The cDNA was used directly in 3' IVT reaction to synthesize Biotin-Modified cRNA.

growth_protocol: A naturally occurring model of placental insufficiency was induced by housing pregnant ewes in an environmental chamber with elevated ambient temperatures of 40˚C and 35°C cycled every 12 hours with 40% humidity for 80 days (IUGR group).  Control ewes were housed in the same facilities at ambient temperature and pair fed to match heat chamber ewes.

extract_protocol: Total RNA was isolated from frozen biceps femoris muscle using Trizol LS (Invitrogen) and further purified using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. One animal was used per sample.

treatment_protocol: At 135 days gestation, pregnant ewes were anesthetized with ketamine and fetuses were delivered via maternal laparotomy and hysterotomy. The biceps femoris muscle in the fetal hindlimb was exposed and a biopsy of the mid-belly portion of the muscle was obtained. Muscle biopsies were flash frozen in liquid nitrogen.

value: Biceps femoris

tag: gestational age

value: 135 days gestation

tag: growth condition

value: intrauterine growth restriction


title: Biceps_Femoris_Growth_Restricted_Gestation_rep6


title: sample243

value: pancreatitis


title: WholeEye_control_rep2

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-002

source_name: whole eye, control, replicate2


title: WholeEye_control_rep5

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-005

source_name: whole eye, control, replicate5


title: CytD_exp|infected_90min_w/o_CytD|experiment_3|replicate_3

description: CytochalasinD experiment

value: Mycobacterium tuberculosis (Mtb)


title: WholeEye_control_rep1

description:
miRNA expression after 10 days of FDM induction
MmiRNA-C-001

source_name: whole eye, control, replicate1

value: control


title: sample275


title: CytD_exp|infected_90min_w/o_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: Biceps_Femoris_Growth_Restricted_Gestation_rep4


title: sample241


title: Biceps_Femoris_Growth_Restricted_Gestation_rep1


title: Biceps_Femoris_Growth_Restricted_Gestation_rep3


title: sample244


title: Biceps_Femoris_Growth_Restricted_Gestation_rep2


title: sample240


title: Biceps_Femoris_Normal_Gestation_rep5

description: Gene expression data from Biceps femoris muscle at 90% gestation under normal gestational growth conditions

source_name: Ovine biceps femoris at 90% gestation in control conditions

value: normal gestation


title: sample239


title: CD_colonbiopsy_rep2

city: Houston

first: Jeremy

middle: S

last: Schaefer

state: TX

address: 1941 East Rd

department: Diagnostic Sciences

institute: The University of Texas Health Science Center at Houston School of Dentistry

description: Biological replicate 2 of 2. CD colon biopsy.

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (version 5th Generation arrays, hsa, mmu and rno).   Analysis of the scanned slides showed that the labeling was successful as all capture probes for the control spike-in oligo nucleotides produced signals in the expected range.

scan_protocol: The quantified signals (background corrected) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm, which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. The positive effect of this normalization is illustrated in the MA-plots for each slide. An example is found in section 3 in this document (all MA plots are found in the folder named ‟Graphics‟).

source_name: Colon pinch biopsy

label_protocol: The samples were labeled using the miRCURY™ Hy3/Hy5 Power labeling kit. Individual samples were labeled with Hy3 (test) while the reference sample (containing equal amounts of RNA from all 5 samples) was labeled with Hy5.

extract_protocol: Total RNA extracted using miRNeasy kit following manufacturer's instructions

tag: disease state

value: Crohn's disease

value: Colon

source_name: Total RNA from pooled colon biopsies.

tag: sample type

value: Total RNA from pooled colon biopsies.


title: UC_colonbiopsy_rep2

description: Biological replicate 2 of 2. UC colon biopsy.

data_processing: The quantified signals (background corrected) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm, which we have found produces the best within-slide normalization to minimize the intensity-dependent differences between the dyes. The positive effect of this normalization is illustrated in the MA-plots for each slide. An example is found in section 3 in this document (all MA plots are found in the folder named ‟Graphics‟).

value: ulcerative colitis


title: UC_colonbiopsy_rep1

description: Biological replicate 1 of 2. UC colon biopsy.


title: sample242


title: sample238


title: sample237


title: Non-IBD_colonbiopsy_rep1

description: Biological replicate 1 of 1. Control non-IBD colon biopsy.

value: normal


title: CD_colonbiopsy_rep1

description: Biological replicate 1 of 2. CD colon biopsy.


title: Biceps_Femoris_Normal_Gestation_rep4


title: sample235


title: sample234


title: sample233


title: Biceps_Femoris_Normal_Gestation_rep3


title: Biceps_Femoris_Normal_Gestation_rep1


title: Biceps_Femoris_Normal_Gestation_rep2


title: CytD_exp|infected_90min_w/o_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: sample232


title: sample236


title: Atino80-5_rep3

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

country: China

institute: Fudan University, School of life sciences

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4x44K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  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 (G2505B) using one color scan (Scan Area 71x21.6 mm, Scan resolution 5 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 021169_D_F_20090824) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Atino80-5 mutant_12-day-old seedling

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared and purified by RNAeasy Mini Kit (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown on MS medium at 22℃ under a light intensity of about 100 μEm-2s-1 in a 16 hrs-light/8 hrs-dark photoperiod.

extract_protocol: Total RNA was prepared using the TRIzol kit (Invitrogen).

tag: genotype/variation

value: Atino80-5 mutant

value: whole seedling


title: Atino80-5_rep1


title: sample231


title: CytD_exp|infected_90min_w/o_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: sample230


title: sample229


title: Atino80-5_rep2


title: CytD_exp|infected_90min_w/o_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: sample228


title: wild type_rep1

source_name: wild type_12-day-old seedling

value: wild type


title: sample227

value: ductal adenocarcinoma


title: CytD_exp|infected_90min_w/o_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: iPS_C9_7245_3

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] '7245', clone 3
single replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: ALS C9orf72 7245, iPSc clone 3

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: gender

value: female

tag: culture conditions

value: mTeSR-1 + matrigel


title: iPS_C9_T2_7

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] 'T2', clone 7
single replicate

source_name: ALS C9orf72 T2, iPSc clone 7

value: male


title: sample226

source_name: RNA from blood


title: CytD_exp|infected_90min_w/o_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: CytD_exp|infected_90min_w/o_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: iPS_C9_7245_1

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] '7245', clone 1
single replicate

source_name: ALS C9orf72 7245, iPSc clone 1


title: wild type_rep2


title: iPS C9_T2_6

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat] 'T2', clone 6
single replicate

source_name: ALS C9orf72 T2, iPSc clone 6


title: CytD_exp|infected_90min_w/o_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: sample225

value: others


title: sample224


title: sample222


title: sample220


title: sample221


title: sample219


title: sample223

value: pancreatitis


title: CytD_exp|infected_90min_w/o_CytD|experiment_2|replicate_1

description: CytochalasinD experiment

value: Mycobacterium tuberculosis (Mtb)


title: CytD_exp|infected_5min_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: CytD_exp|infected_5min_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: FAT.SA03806

city: San Antonio

first: Christopher

middle: P

last: Jenkinson

state: Texas

address: 7703 Floyd Curl Drive

department: Medicine

institute: University of Texas Health Sciences Center at San Antonio

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNAs were prepared with the Ambion MessageAmp kit for Illumina arrays

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

value: abdominal subcutaneous adipose tissue, fasted

tag: sample id

value: F

tag: bmi (kg/m2)

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: CytD_exp|infected_5min_CytD|experiment_6|replicate_3

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: FAT.SA03804

tag: tissue

value: M

tag: age


title: CytD_exp|infected_90min_w/o_CytD|experiment_1|replicate_1

description: CytochalasinD experiment


title: lung adenocarcinoma 8 rep2

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

hyb_protocol: Labeled RNA in 45 ul volume was hybdridized for 20 h at 45 ºC under rotation at 20 r.p.m. to Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarrays using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.

scan_protocol: Microarray slides were scanned on an Agilent® G2505C microarray scanner and data from images was extracted using Agilent® Feature Extraction software (version 9.5.3).

data_processing: AgiMicroRna Bioconductor package (version 2.10.1) was used in R 3.0.1. Data from all 16 microarrays was processed together. The RMA method was used for summarization. Background correction was not applied. Quantile method was used for inter-array normalization.

label: cyanine 3-cytidine bisphosphate (pCp)

source_name: resected cancer tissue with >70% tumor content

label_protocol: RNA (120 ng) was labeled with cyanine 3-cytidine bisphosphate (pCp) using reagents and methods provided with the Agilent® miRNA Complete Labeling and Hybridization Kit.

extract_protocol: The affinity spin column–based Roche® High Pure™ FFPE RNA kit was used to extract total RNA from eight resected stage I lung adenocarcinoma FFPE tumor specimens (~3 mm3) with >70% tumor content. RNA was quantified by RiboGreen fluorescence assay.

tag: tissue type

value: lung adenocarcinoma

tag: pathologic stage

value: I

tag: microarray experiment


title: sample218

tag: disease


title: FAT.SA03796

tag: sample id

tag: gender

tag: bmi (kg/m2)


title: CytD_exp|infected_5min_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: FAT.SA03795

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: FAT.SA03801

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: sample217


title: lung adenocarcinoma 7 rep2


title: sample216


title: FAT.SA03799

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: FAT.SA03789

tag: tissue


title: lung adenocarcinoma 6 rep2


title: sample215


title: CytD_exp|infected_5min_CytD|experiment_3|replicate_3

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: CytD_exp|infected_5min_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: FAT.SA03790

tag: age


title: sample245


title: FAT.SA81466


title: FAT.SA03737


title: lung adenocarcinoma 5 rep2

tag: tissue type

tag: pathologic stage

tag: microarray experiment


title: CytD_exp|infected_5min_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: lung adenocarcinoma 4 rep2


title: CytD_exp|infected_5min_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: lung adenocarcinoma 3 rep2


title: sample213

tag: disease


title: CytD_exp|infected_5min_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_5min_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: sample212


title: sample214


title: FAT.SA03785

tag: sample id

tag: gender

tag: bmi (kg/m2)


title: lung adenocarcinoma 2 rep2


title: FAT.SA03649

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: sample211


title: lung adenocarcinoma 1 rep2


title: FAT.SA03786

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: sample210


title: CytD_exp|infected_5min_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: lung adenocarcinoma 8 rep1


title: FAT.SA02962

tag: tissue

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: CytD_exp|infected_5min_CytD|experiment_1|replicate_2

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: sample209


title: FAT.SA02883

tag: age


title: CytD_exp|infected_5min_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: FAT.SA02729


title: CytD_exp|infected_5min_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: lung adenocarcinoma 6 rep1

tag: tissue type

tag: pathologic stage

tag: microarray experiment


title: sample208

tag: disease


title: FAT.SA02842

tag: sample id

tag: gender

tag: bmi (kg/m2)


title: sample207


title: lung adenocarcinoma 7 rep1


title: lung adenocarcinoma 5 rep1


title: FAT.SA02715

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: CytD_exp|infected_5min_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: FAT.SA02722

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: sample206


title: CytD_exp|infected_5min_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: lung adenocarcinoma 4 rep1


title: lung adenocarcinoma 3 rep1


title: FAT.SA02707

tag: tissue

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: sample205


title: lung adenocarcinoma 2 rep1


title: FAT.SA02603

tag: age


title: sample204


title: FAT.SA02498


title: FAT.SA02465


title: CytD_exp|infected_5min_CytD|experiment_2|replicate_1

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: CytD_exp|infected_5min_CytD|experiment_1|replicate_1

description: CytochalasinD experiment


title: sample203


title: lung adenocarcinoma 1 rep1

tag: tissue type

tag: pathologic stage

tag: microarray experiment


title: CytD_exp|infected_5min_w/o_CytD|experiment_6|replicate_3

description: CytochalasinD experiment


title: CytD_exp|infected_5min_w/o_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: FAT.SA02440

tag: sample id

tag: gender


title: CytD_exp|infected_5min_w/o_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: FAT.SA02439

tag: bmi (kg/m2)

tag: waist circumference (cm)


title: P114 Sca1+

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate of examined conditions: cancer cell lines grown with macrophages

hyb_protocol: The hybridization was performed with custom AMADID microarrays (Agilent, USA) using miRNA Complete Labeling and Hyb Kit (Agilent, USA) according to the manufacturer`s protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Sca1+ cells sorted from P114 cell line

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent, USA) was used according to manufacturer`s recommendations.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL–1), and fungizone (2.5 mg mL–1) (reagents obtained from Sigma Aldrich, USA), in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol.

treatment_protocol: Canine mammary cancer cell lines were stained using Stem Cell Antigen 1 antibodies and then sorted using FACS Aria II as Sca-1 positive (cancer stem cells) and Sca-1 negative (control). Then, total RNA was isolated and hybridized at miRNA microarrays.

tag: facs-sorted cell type


title: P114 Sca1-

source_name: Sca1- cells sorted from P114 cell line


title: sample201

tag: disease


title: sample202


title: CMT-U309 Sca1+

description: Biological replicate of control: cancer cell lines grown as mono-culture

source_name: Sca1+ cells sorted from CMT-U309 cell line


title: sample200


title: CytD_exp|infected_5min_w/o_CytD|experiment_3|replicate_3

description: CytochalasinD experiment


title: sample199


title: CytD_exp|infected_5min_w/o_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: CMT-U27 Sca1-

source_name: Sca1- cells sorted from CMT-U27 cell line


title: CMT-U309 Sca1-

source_name: Sca1- cells sorted from CMT-U309 cell line


title: CytD_exp|infected_5min_w/o_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: FAT.SA02329

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)


title: CMT-U27 Sca1+

source_name: Sca1+ cells sorted from CMT-U27 cell line


title: sample198


title: FAT.SA02269

tag: tissue

tag: triacylglycerol (mg/dl)

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: CytD_exp|infected_5min_w/o_CytD|experiment_4|replicate_2

description: CytochalasinD experiment

tag: cell line

tag: infectious agent


title: CytD_exp|infected_5min_w/o_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: FAT.SA02235

tag: age


title: FAT.SA02387

tag: sample id


title: FAT.SA02335

tag: gender


title: sample196


title: FAT.SA02328

tag: bmi (kg/m2)


title: sample195

value: melanoma


title: FAT.SA02234

tag: waist circumference (cm)


title: sample197


title: CytD_exp|infected_5min_w/o_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: sample194


title: CytD_exp|infected_5min_w/o_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: sample192

value: sarcoidosis


title: sample193


title: FAT.SA02166


title: sample191


title: CytD_exp|infected_5min_w/o_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: CytD_exp|infected_5min_w/o_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: sample190


title: FAT.SA02224


title: CytD_exp|infected_5min_w/o_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_5min_w/o_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: Reference

description:
Sample 58.
Pool of all 54 RNAs of this study (samples 1-54).

hyb_protocol: Hybridizations and washes were performed according to the Exiqon® miRCURY™ LNA microRNA Array Instruction manual using an HS4800 hybridization station (Tecan®, Grödig, Austria). This work was performed as a commercial service by Exiqon®.

scan_protocol: Arrays were scanned using the G2565BA Microarray Scanner System (Agilent®), and image analysis was carried out using the ImaGene™ software (version 9; BioDiscovery®, Hawthorne, CA). This work was performed as a commercial service by Exiqon®.

data_processing:
Raw Hy3™ and Hy5™ signal data for all 58 arrays were processed together in R (version 2.15.1) using the limma Bioconductor package (version 3.12.3) on Mac OS X 10.6.8. Briefly, background signals were adjusted for using the 'normexp' method with 'offset' value of 10. Array data was then subjected to within-array global loess normalization with a 'span' value of 1/3. This was followed by between-array 'Rquantile' normalization. Probe-set summarization for Hy3™/Hy5™ ratio values (test RNA/reference RNA) was then performed, using the mean value from replicate probe-spots when the maximum was <1.5x minimum value, using the median value otherwise. All arrays appeared to have yielded data of good quality as assessed using criteria suggested by Exiqon®.

Raw data files:
1_Exiqon*: Hy3
0_Exiqon*: Hy5

label_protocol: The miRCURY™ LNA microRNA Hi-Power Labeling kit from Exiqon® was used to label 750 ng of test RNA with the Cy3-like Hy3™ dye. The reference RNA (750 ng) was similarly labeled with the Cy5-like Hy5™ dye. Artificial small RNAs were spiked in to test and reference RNA samples before labeling. This work was performed as a commercial service by Exiqon®.

growth_protocol: 3x10e5 NCI-H460 cells, at passage number 9 after procurement from ATCC® (Manassas, VA) and maintained in RPMI-1640 medium (Life Technologies®, Grand Island, NY) with 10% fetal bovine serum (Atlanta Biologicals®, Lawrenceville, GA) at 37 ºC under 5% carbon dioxide, were seeded per well of 6-well tissue culture dishes. After 24 hours, the culture medium was replaced with that without serum and cells were grown for another 24 hours.

extract_protocol: Total RNA was extracted from -80 ºC-frozen cell-pellets using the Total RNA Purification kit (catalog# 37500, Norgen-Biotek®, Thorold, ON, Canada) following the kit manufacturer's guidelines. The kit uses silicon carbide spin-columns. On-column DNase I treatment was performed to reduce contaminating genomic DNA. RNA eluted from the columns was treated on-column with DNase I again as per the manufacturer's guidelines provided with the RNase-free DNase I kit (Norgen-Biotek®). Absorbance at 260 nm and electrophoresis on Bioanalyzer™ 2100 (Agilent®, Austin, TX) was used to estimate RNA concentration and quality. The reference RNA was created by pooling all of the 54 unique RNA samples (at equal concentration).

treatment_protocol: Nictoine (5 uM; Sigma®, Saint Louis, MO) or cigarette smoke extract (5 uM nicotine-equivalent) was added to the culture media, and after 2 hours, cells were irradiated with one dose of 6 Gy ionizing radiation (cesium-137 source), or cisplatin (1 uM; Sigma®) was added to the culture medium. All treatments were performed concurrently using a total of nine 6-well cuture plates. After another 2 or 24 hours, cells were harvested by scraping into the culture medium, spun down, washed in 10 ml phosphate-buffered saline, and collected as cell-pellets after another round of centrifugation at room temperature. The total 54 cell-pellets were stored frozen at -80 ºC until RNA extraction.

tag: cell type

value: human lung large cell carcinoma cells

tag: sample type

value: reference


title: sample189

tag: disease


title: CytD_exp|infected_5min_w/o_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: FAT.SA01908

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: FAT.SA01977

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)


title: CytD_exp|infected_5min_w/o_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: CytD_exp|infected_5min_w/o_CytD|experiment_2|replicate_1

description: CytochalasinD experiment


title: FAT.SA01687

tag: tissue

tag: triacylglycerol (mg/dl)


title: FAT.SA01841

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: sample188


title: Control_24h_rep1_technical_duplicate

description:
Sample 57.
Technical duplicate for sample 28.

source_name: NCI-H460, control, 24 hr

tag: cell line

tag: treatment

value: control (none)

tag: timepoint

value: 24 hours

source_name: Pool of all 54 RNAs of this study (samples 1-54)


title: Cigarette_smoke_extract_2h_rep1_technical_duplicate

description:
Sample 56.
Technical duplicate for sample 7.

source_name: NCI-H460, cigarette smoke extract, 2 hr

value: cigarette smoke extract

value: 2 hours


title: sample187

value: ductal adenocarcinoma


title: FAT.SA01682

tag: sample id

tag: gender

tag: age


title: Cisplatin+cigarette_smoke_extract_24h_rep3

description:
Sample 54.
Biological replicate 3.

source_name: NCI-H460, cisplatin and cigarette smoke extract, 24 hr

tag: cell type

value: cisplatin and cigarette smoke extract


title: Nicotine_2h_rep2_technical_duplicate

description:
Sample 55.
Technical duplicate for sample 5.

source_name: NCI-H460, nicotine, 2 hr

value: nicotine

tag: sample type


title: CytD_exp|infected_5min_w/o_CytD|experiment_1|replicate_1

description: CytochalasinD experiment

tag: infectious agent

value: Mycobacterium tuberculosis (Mtb)


title: sample186

tag: disease


title: Cisplatin+cigarette_smoke_extract_24h_rep2

description:
Sample 53.
Biological replicate 2.


title: CytD_exp|uninfected_90min_CytD|experiment_6|replicate_3

description: CytochalasinD experiment


title: sample185

value: others


title: FAT.SA01685

value: abdominal subcutaneous adipose tissue, fasted

tag: bmi (kg/m2)

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: sample184

value: pancreatitis


title: Cisplatin+nicotine_24h_rep3

description:
Sample 51.
Biological replicate 3.

source_name: NCI-H460, cisplatin and nicotine, 24 hr

value: cisplatin and nicotine


title: Cisplatin+cigarette_smoke_extract_24h_rep1

description:
Sample 52.
Biological replicate 1.


title: CytD_exp|uninfected_90min_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: FAT.SA01658

tag: tissue

value: F

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: sample183

value: melanoma


title: Cisplatin+nicotine_24h_rep2

description:
Sample 50.
Biological replicate 2.

tag: cell line

tag: treatment


title: sample182


title: FAT.SA01477

tag: sample id

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: FAT.SA01664

tag: gender

value: M

tag: age


title: Cisplatin+nicotine_24h_rep1

description:
Sample 49.
Biological replicate 1.

tag: cell type

value: human lung large cell carcinoma cells

tag: timepoint

tag: sample type


title: Cisplatin_24h_rep3

description:
Sample 48.
Biological replicate 3.

source_name: NCI-H460, cisplatin, 24 hr

value: cisplatin

value: reference


title: FAT.SA01467

tag: bmi (kg/m2)

tag: waist circumference (cm)


title: CytD_exp|uninfected_90min_CytD|experiment_3|replicate_3

description: CytochalasinD experiment

tag: infectious agent


title: CytD_exp|uninfected_90min_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: FAT.SA01280

tag: tissue

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)


title: FAT.SA01283

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: sample179

source_name: RNA from blood

tag: disease


title: sample180


title: CytD_exp|uninfected_90min_CytD|experiment_6|replicate_2

description: CytochalasinD experiment

tag: cell line


title: FAT.SA01254

tag: sample id

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: Radiation+cigarette_smoke_extract_24h_rep3

description:
Sample 45.
Biological replicate 3.

source_name: NCI-H460, radiation and cigarette smoke extract, 24 hr

tag: cell type

tag: treatment

value: radiation and cigarette smoke extract

value: 24 hours


title: Cisplatin_24h_rep1

description:
Sample 46.
Biological replicate 1.

tag: timepoint

tag: sample type


title: CytD_exp|uninfected_90min_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: sample178


title: Cisplatin_24h_rep2

description:
Sample 47.
Biological replicate 2.


title: sample181


title: CytD_exp|uninfected_90min_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: sample177


title: Radiation+cigarette_smoke_extract_24h_rep2

description:
Sample 44.
Biological replicate 2.


title: FAT.SA01179

tag: gender

tag: age

tag: bmi (kg/m2)

tag: waist circumference (cm)


title: sample176


title: Radiation+cigarette_smoke_extract_24h_rep1

description:
Sample 43.
Biological replicate 1.


title: CytD_exp|uninfected_90min_CytD|experiment_3|replicate_2

description: CytochalasinD experiment

tag: infectious agent


title: Radiation+nicotine_24h_rep3

description:
Sample 42.
Biological replicate 3.

source_name: NCI-H460, radiation and nicotine, 24 hr

value: radiation and nicotine


title: CytD_exp|uninfected_90min_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: FAT.SA01281

tag: tissue

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)


title: sample175

tag: disease


title: FAT.SA01064

tag: sample id

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)


title: Radiation+nicotine_24h_rep2

description:
Sample 41.
Biological replicate 2.

tag: cell line

tag: cell type


title: sample174


title: sample173


title: FAT.SA01036

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: FAT.SA00986

tag: gender


title: sample172


title: CytD_exp|uninfected_90min_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: Radiation+nicotine_24h_rep1

description:
Sample 40.
Biological replicate 1.

tag: treatment

tag: timepoint

tag: sample type


title: CytD_exp|uninfected_90min_CytD|experiment_5|replicate_1

description: CytochalasinD experiment

tag: infectious agent


title: Radiation_24h_rep2

description:
Sample 38.
Biological replicate 2.

source_name: NCI-H460, radiation, 24 hr

value: radiation


title: FAT.SA01065

tag: tissue

tag: age

tag: bmi (kg/m2)

tag: waist circumference (cm)


title: Radiation_24h_rep3

description:
Sample 39.
Biological replicate 3.


title: sample171

tag: disease


title: FAT.SA00722

tag: sample id

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)


title: CytD_exp|uninfected_90min_CytD|experiment_4|replicate_1

description: CytochalasinD experiment

tag: cell line


title: Radiation_24h_rep1

description:
Sample 37.
Biological replicate 1.

tag: cell type


title: Cigarette_smoke_extract_24h_rep3

description:
Sample 36.
Biological replicate 3.

source_name: NCI-H460, cigarette smoke extract, 24 hr

value: cigarette smoke extract


title: FAT.SA00904

tag: high density lipoprotein cholesterol (mg/dl)

tag: triacylglycerol (mg/dl)

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: sample170


title: CytD_exp|uninfected_90min_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: sample169


title: FAT.SA00427

tag: gender


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_6|replicate_3

description: CytochalasinD experiment

tag: infectious agent


title: CytD_exp|uninfected_90min_CytD|experiment_1|replicate_1

description: CytochalasinD experiment


title: FAT.SA00429

tag: tissue


title: CytD_exp|uninfected_90min_CytD|experiment_2|replicate_1

description: CytochalasinD experiment


title: FAT.SA00678

tag: age


title: Cigarette_smoke_extract_24h_rep1

description:
Sample 34.
Biological replicate 1.

tag: treatment

tag: timepoint

tag: sample type


title: Cigarette_smoke_extract_24h_rep2

description:
Sample 35.
Biological replicate 2.


title: FAT.SA00298

tag: sample id

tag: bmi (kg/m2)

tag: waist circumference (cm)


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: Nicotine_24h_rep3

description:
Sample 33.
Biological replicate 3.

source_name: NCI-H460, nicotine, 24 hr

value: nicotine


title: sample166

tag: disease

value: tumor of stomach


title: Nicotine_24h_rep2

description:
Sample 32.
Biological replicate 2.

tag: cell line


title: sample165


title: sample168


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: Nicotine_24h_rep1

description:
Sample 31.
Biological replicate 1.

tag: cell type


title: FAT.SA00254

tag: systolic blood pressure (mm hg)

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)


title: sample164


title: FAT.SA00236

tag: gender

tag: triacylglycerol (mg/dl)

tag: fasting plasma glucose (mg/dl)

tag: fasting plasma insulin (μu/ml)


title: sample167

value: lung cancer


title: FAT.SA00228

tag: tissue

value: abdominal subcutaneous adipose tissue, fasted

tag: age


title: Control_24h_rep3

description:
Sample 30.
Biological replicate 3.

tag: treatment

value: control (none)

tag: timepoint

tag: sample type


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_2|replicate_3

description: CytochalasinD experiment

tag: infectious agent


title: sample162

tag: disease

value: normal


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_3|replicate_3

description: CytochalasinD experiment

tag: cell line


title: Control_24h_rep2

description:
Sample 29.
Biological replicate 2.

tag: cell type


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: Control_24h_rep1

description:
Sample 28.
Biological replicate 1.


title: FAT.SA00204

tag: sample id

tag: bmi (kg/m2)

tag: waist circumference (cm)

tag: systolic blood pressure (mm hg)


title: sample160


title: sample161


title: FAT.SA00093

tag: gender

tag: diastolic blood pressure (mm hg)

tag: total cholesterol (mg/dl)

tag: high density lipoprotein cholesterol (mg/dl)


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: Cisplatin+cigarette_smoke_extract_2h_rep3

description:
Sample 27.
Biological replicate 3.

source_name: NCI-H460, cisplatin and cigarette smoke extract, 2 hr

value: cisplatin and cigarette smoke extract

value: 2 hours


title: sample163


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: Cisplatin+cigarette_smoke_extract_2h_rep2

description:
Sample 26.
Biological replicate 2.


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: sh95 9-17, P5

first: Daphne

middle: C.

last: Thijssen-Timmer

address: Plesmanlaan 125

department: Hematopoiesis

institute: Sanquin Blood Supply

description: polysomal RNA

hyb_protocol: According to Illumina protocol Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Scanning was performed using the Illumina iScan array scanner

data_processing: R version 2.15 and Bioconductor 2.11 were used for  quality control and normalization. VSN normalization was used.

source_name: Meg01 cell line_ATXN2_sh95_polysomal

label_protocol: Illumina TotalPrep 96 Amplification Kit was used to generate biotin-labeled cRNA

growth_protocol: RPMI medium supplemented with 10% fetal calf serum and penicillin / streptomycin

extract_protocol: In three independent experiments, 7x10^6 transduced Meg01 cells were lysed and loaded on a 7-46% sucrose gradient. RNA was isolated from all fractions using an adjusted phenol-chloroform extraction and RNA from fraction 1-8 was pooled as subpolysomal, RNA from fraction 9-17 pooled as polysomal RNA.

treatment_protocol: Lentiviral transduction using a MOI (multiplicity of infection) of 10

value: megakaryocyte


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: sh95 9-17, P4

description: polysomal RNA


title: sample159

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..


title: sh95 9-17, P2

description: polysomal RNA


title: shc002 9-17, P4

description: polysomal RNA

source_name: Meg01 cell line_control_shc_polysomal


title: shc002 9-17, P5

description: polysomal RNA


title: sample158

value: pancreatitis


title: sample157

value: long-lived individuals


title: sample156

value: others


title: sample155


title: Cisplatin+nicotine_2h_rep2

description:
Sample 23.
Biological replicate 2.

source_name: NCI-H460, cisplatin and nicotine, 2 hr

value: human lung large cell carcinoma cells

value: cisplatin and nicotine

value: reference


title: Cisplatin+cigarette_smoke_extract_2h_rep1

description:
Sample 25.
Biological replicate 1.


title: Cisplatin+nicotine_2h_rep3

description:
Sample 24.
Biological replicate 3.


title: sample153


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: sample152

value: ductal adenocarcinoma


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_1|replicate_1

description: CytochalasinD experiment


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_3|replicate_1

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_CytDC|experiment_6|replicate_3

description: CytochalasinD experiment


title: sh95 1-8, P3

description: subpolysomal RNA

source_name: Meg01 cell line_ATXN2_sh95_subpolysomal


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: sample154


title: sh95 1-8, P1

description: subpolysomal RNA


title: shc002 1-8, P1

description: subpolysomal RNA


title: CytD_exp|uninfected_90min_w/o_CytD|experiment_2|replicate_1

description: CytochalasinD experiment


title: Dox1000 rep4

city: Seattle

first: Andrew

last: Strand

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scan protocol.

data_processing: The complete set of microarray data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi

source_name: Dox1000 cell line

label_protocol: RNA was converted to cDNA and biotin labeled using Ambion's Illumina TotalPrep RNA Amplification kit.

growth_protocol: RPMI media plus 10% fetal bovine serum

extract_protocol: Qiagen RNeasy RNA preparation kit with Qiashredder step.

treatment_protocol: growth in media containing doxorubin equal to the cell line's particular maximum tolerance, i.e., 100nM doxorubin for Dox100 cells, 250nM doxorubicin for Dox250 cells, etc.

value: Dox1000, a derivative of Dox750 that grows in 1000nM doxorubicin


title: Dox1000 rep3


title: shc002 9-17, P2

description: polysomal RNA


title: shc002 1-8, P3

description: subpolysomal RNA


title: Radiation+cigarette_smoke_extract_2h_rep3

description:
Sample 18.
Biological replicate 3.

source_name: NCI-H460, radiation and cigarette smoke extract, 2 hr

value: radiation and cigarette smoke extract

source_name: Pool of all 54 RNAs of this study (samples 1-54)


title: Cisplatin_2h_rep1

description:
Sample 19.
Biological replicate 1.

source_name: NCI-H460, cisplatin, 2 hr

value: cisplatin


title: Cisplatin_2h_rep2

description:
Sample 20.
Biological replicate 2.


title: sample151


title: Cisplatin+nicotine_2h_rep1

description:
Sample 22.
Biological replicate 1.


title: Dox1000 rep2


title: Cisplatin_2h_rep3

description:
Sample 21.
Biological replicate 3.


title: Radiation+cigarette_smoke_extract_2h_rep2

description:
Sample 17.
Biological replicate 2.


title: CytD_exp|uninfected_5min_CytDC|experiment_5|replicate_3

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_CytDC|experiment_4|replicate_3

description: CytochalasinD experiment


title: Radiation+cigarette_smoke_extract_2h_rep1

description:
Sample 16.
Biological replicate 1.


title: sample150

value: prostate cancer


title: Radiation+nicotine_2h_rep3

description:
Sample 15.
Biological replicate 3.

source_name: NCI-H460, radiation and nicotine, 2 hr

value: radiation and nicotine


title: sample149


title: Dox1000 rep1


title: sample147


title: sample148


title: CytD_exp|uninfected_5min_CytDC|experiment_3|replicate_3

description: CytochalasinD experiment


title: sample146


title: sample145


title: Radiation_2h_rep3

description:
Sample 12.
Biological replicate 3.

source_name: NCI-H460, radiation, 2 hr

value: radiation


title: Radiation+nicotine_2h_rep1

description:
Sample 13.
Biological replicate 1.


title: Radiation_2h_rep2

description:
Sample 11.
Biological replicate 2.


title: sample144

source_name: RNA from blood


title: CytD_exp|uninfected_5min_CytDC|experiment_2|replicate_3

description: CytochalasinD experiment


title: Radiation_2h_rep1

description:
Sample 10.
Biological replicate 1.


title: CytD_exp|uninfected_5min_CytDC|experiment_1|replicate_3

description: CytochalasinD experiment


title: sample143


title: Dox750 rep3

source_name: Dox750 cell line

value: Dox750, a derivative of Dox500 that grows in 750nM doxorubicin


title: CytD_exp|uninfected_5min_CytDC|experiment_6|replicate_2

description: CytochalasinD experiment


title: sample142

value: multiple sclerosis


title: Dox750 rep4


title: Radiation+nicotine_2h_rep2

description:
Sample 14.
Biological replicate 2.

value: 2 hours


title: Cigarette_smoke_extract_2h_rep2

description:
Sample 8.
Biological replicate 2.

source_name: NCI-H460, cigarette smoke extract, 2 hr

value: cigarette smoke extract


title: CytD_exp|uninfected_5min_CytDC|experiment_2|replicate_2

description: CytochalasinD experiment


title: Dox750 rep2


title: CytD_exp|uninfected_5min_CytDC|experiment_4|replicate_2

description: CytochalasinD experiment


title: Dox250 rep4

source_name: Dox250 cell line

value: Dox250, a derivative of Dox100 that grows in 250nM doxorubicin


title: Dox500 rep2

source_name: Dox500 cell line

value: Dox500, a derivative of Dox250 that grows in 500nM doxorubicin


title: Cigarette_smoke_extract_2h_rep3

description:
Sample 9.
Biological replicate 3.


title: Cigarette_smoke_extract_2h_rep1

description:
Sample 7.
Biological replicate 1.


title: CytD_exp|uninfected_5min_CytDC|experiment_5|replicate_2

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_CytDC|experiment_6|replicate_1

description: CytochalasinD experiment


title: Dox500 rep3


title: CytD_exp|uninfected_5min_CytDC|experiment_1|replicate_2

description: CytochalasinD experiment


title: Dox750 rep1


title: Nicotine_2h_rep3

description:
Sample 6.
Biological replicate 3.

source_name: NCI-H460, nicotine, 2 hr

value: nicotine


title: Dox500 rep4


title: sample140

value: others


title: CytD_exp|uninfected_5min_CytDC|experiment_3|replicate_2

description: CytochalasinD experiment


title: sample139


title: sample141

value: lung cancer


title: CytD_exp|uninfected_5min_CytDC|experiment_5|replicate_1

description: CytochalasinD experiment


title: sample137


title: sample138


title: Nicotine_2h_rep1

description:
Sample 4.
Biological replicate 1.

value: human lung large cell carcinoma cells

value: reference


title: Control_2h_rep3

description:
Sample 3.
Biological replicate 3.

source_name: NCI-H460, control, 2 hr

value: control (none)


title: Dox250 rep3


title: Dox250 rep1


title: Nicotine_2h_rep2

description:
Sample 5.
Biological replicate 2.


title: CytD_exp|uninfected_5min_CytDC|experiment_4|replicate_1

description: CytochalasinD experiment


title: sample135

value: ductal adenocarcinoma


title: Dox250 rep2


title: Control_2h_rep2

description:
Sample 2.
Biological replicate 2.


title: Dox100 rep4

source_name: Dox100 cell line

value: Dox100, a derivative of the Ramos cells that grows in media plus 100nM doxorubicin


title: Dox100 rep2


title: sample136


title: CytD_exp|uninfected_5min_CytDC|experiment_3|replicate_1

description: CytochalasinD experiment


title: Ramos rep4

source_name: Ramos

value: Ramos

value: human Burkitt's lymphoma cells


title: sample132


title: sample134

value: pancreatitis


title: CytD_exp|uninfected_5min_CytDC|experiment_2|replicate_1

description: CytochalasinD experiment


title: sample131

value: melanoma


title: Dox100 rep3


title: CytD_exp|uninfected_5min_CytDC|experiment_1|replicate_1

description: CytochalasinD experiment


title: Control_2h_rep1

description:
Sample 1.
Biological replicate 1.


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_5|replicate_3

description: CytochalasinD experiment


title: sample133


title: Ramos rep3


title: FFPE metastatic tumor match to fresh frozen 13-03

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

hyb_protocol: Genome-wide copy number variation was measured by a 2-color microarray approach using Agilent SurePrint G3 ISCA Human Cancer CGH+SNP 180K x 4 arrays

scan_protocol: CytoCGH_0205_Oct12 protocol and Agilent G4900DA SureScan Microarray Scanner System

data_processing: Raw data files were acquired using software: Agilent Feature Extraction for Cytogenomics 2.5.1.0. Sample Tables contain the log10 Cy5/Cy3 from the Feature Extraction File.  Log2 ratios for genome (hg19) coordinates and genes showing copy number variation (CNV) were acquired using Agilent CytoGenomics Edition 2.5.8.1 using the CGH_v2 default, the ADM2 threshold set at 6 and an 8 probe minimum. An additional absolute log2 ratio threshold was set at 0.4 for analysis of reoccurring lesions or 0.8 to study high amplitude copy number aberrations. The sample supplementary files named "IntervalBasedReport*.txt" contain the genomic coordinates and genes displaying CNV.

label_protocol: Cancer and reference DNA (500ng each) were labeled with fluorescent dyes, Cy5 and Cy3 respectively, using the SureTag Complete DNA Labeling Kit (Agilent Technologies) or Universal Linkage System labeling kit for DNA from FFPE specimens

extract_protocol: DNA was isolated using the EZ1 Advanced XL magnetic bead technology, the EZ1 DNA de-paraffinization method (where appropriate) and the EZ1 DNA Tissue kit (Qiagen, Valencia, CA). DNA was analyzed for quantity by nanodrop 3000 () and quality using the TapeStation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: tumor specimens were either FFPE or fresh frozen as indicated in the sample list

tag: tissue

value: breast cancer metastasis brain tumor

source_name: Female Reference DNA

tag: reference tissue

value: Agilent Female European DNA


title: Dox100 rep1


title: Ramos rep2


title: sample130

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_6|replicate_3

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_4|replicate_3

description: CytochalasinD experiment


title: sample129

value: prostate cancer


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_3|replicate_3

description: CytochalasinD experiment


title: sample128


title: FFPE metastatic tumor match to fresh frozen 13-19


title: FFPE metastatic tumor match to fresh frozen 13-02


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_2|replicate_3

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_1|replicate_3

description: CytochalasinD experiment


title: Ramos rep1


title: FFPE metastatic tumor match to fresh frozen 09-34


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_6|replicate_2

description: CytochalasinD experiment


title: sample127


title: sample126


title: rep3-GBZ 50µM

city: Singapore

first: Wei

last: Zhou

address: 8 College Road

department: Signature Program in Cardiovascular and Metabolic Disorders

country: Singapore

institute: DUKE-NUS Graduate Medical School

description:
84B
Sample 8

label: Biotin

source_name: RPMI8226_GBZ 50µM

label_protocol: Biotin-labelled cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) from 500ng of total RNA

growth_protocol: Multiple myeloma (MM) cells RPMI8266 were maintained on RPMI1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone) to the exponential growth stage.

extract_protocol: Cells were spun down 200 × g for 5 min. Total RNA were extracted using RNeasy Kit (Qiagen), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit Quality and quantity of RNA was determined by Agilent Bioanalyzer.

treatment_protocol: Cells were treated with Guanabenz (GBZ) 50µM, Sal003 20µM or no treatment for 24 hr

value: Multiple myeloma (MM) cells

tag: treated with

value: Guanabenz (GBZ) 50µM for 24hrs


title: rep3-Sal003 20µM

description:
84C
Sample 9

value: Sal003 20µM for 24hrs


title: rep2-Sal003 20µM

description:
83C
Sample 6


title: FFPE original breast cancer match to 13-877-A FFPE metastatic tumor and 13-19 fresh frozen metastatic tumor


title: rep3-control

description:
84A
Sample 7

value: none (untreated control)


title: FFPE original breast cancer match to 13-96A FFPE metastatic tumor and 13-03 fresh frozen metastatic tumor


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_5|replicate_2

description: CytochalasinD experiment


title: FFPE original breast cancer match to 13-64A FFPE metastatic tumor and 13-02 fresh frozen metastatic tumor


title: sample125


title: FFPE original breast cancer match to 09-3469A FFPE metastatic tumor and 09-34 fresh frozen metastatic tumor


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_2|replicate_2

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_4|replicate_2

description: CytochalasinD experiment


title: sample123


title: sample124


title: fresh frozen metastatic tumor_10


title: rep2-GBZ 50µM

description:
83B
Sample 5


title: sample122


title: sample121


title: rep2-control

description:
83A
Sample 4


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_3|replicate_2

description: CytochalasinD experiment


title: sample120


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_1|replicate_2

description: CytochalasinD experiment


title: rep1-GBZ 50µM

description:
82B
Sample 2


title: fresh frozen metastatic tumor_9


title: Dox500 rep1

value: Dox500, a derivative of Dox250 that grows in 500nM doxorubicin


title: rep1-Sal003 20µM

description:
82C
Sample 3


title: sample119


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_5|replicate_1

description: CytochalasinD experiment


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_6|replicate_1

description: CytochalasinD experiment


title: fresh frozen metastatic tumor_8


title: sample118


title: fresh frozen metastatic tumor_4


title: fresh frozen metastatic tumor_7


title: fresh frozen metastatic tumor_6


title: CytD_exp|uninfected_5min_w/o_CytD|experiment_4|replicate_1

description: CytochalasinD experiment


title: fresh frozen metastatic tumor_5


title: sample117


title: sample116


title: P47

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

hyb_protocol: According to manufacturer (Illumina) specifications.

data_processing: Data was back+B51ground-corrected using the Illumina BeadStudio median background substraction algorithm, a constant 11 was added to every expression value, genes with missing values in >10% of samples were excluded; otherwise missing values were imputed using k-nearest neighbors implemented in the impute R package. Quantile normalization was performed using the preprocessCore R package and values were log2 transformed. Each gene was median centered across the 49 primary data sets. Subtyping was performed on the normalized expression matrix using the genefu R package and the published gene lists PAM50, Sorlie and Hu.

source_name: Primary breast tumor

extract_protocol: QIAGEN AllPrep

value: primary breast tumor

tag: ht12 subtype pam50

value: Normal

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: P48

scan_protocol: According to manufacturer (Illumina) specifications.

value: LumA


title: sample115

city: Homburg

tag: disease

value: Wilms Tumor


title: fresh frozen metastatic tumor_3


title: fresh frozen metastatic tumor_2