title: A02 P10-60adenine

description: This sample is of wild-type HFDPCs in passage 10 and add 60 microM adenine in culcural media.

tag: cell type

value: follicle dermal papilla cells

tag: passages

value: Passage 10

value: 60 microM Adenine


title: 546739A04 - 44B1.3-4h_BR2 vs 43A10.6-4h_BR2

status: Public on Nov 01 2014

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: To observe the effects of guanosine penta/tetraphosphate on gene expression

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Media=MS/2 hygrometry Temperature=21°C Light=80 µE

extract_protocol: 43A10.6-4h_BR2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Dex induction 4h - compound based treatment - flooding with a solution of dexomethasone  ,dexamethasone:time 4hour . Plants were treated at 10:30 in the morning (Time 0; 10:30 is 3 and a half hours after the onset of the light period) by flooding with 30uM dexamethasone (in aqueous solution with 0,3 % DMSO and 0,033 % Silwet L-77) for 5 minutes . Samples were taken at 4 hrs and 52 hrs after T0. Aerial parts of the seedlings were rapidly harvested and frozen in liquid nitrogen.

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

extract_protocol: 44B1.3-4h_BR2:5ug. (Qiagen_RNeasy.pdf)


title: CPC, CP150-TB

type: genomic

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
CP150-TB
Brain tumor

hyb_protocol: 20 tumor DNA samples were hybridized to Affymetrix OncoScan™ FFPE Express 2.0 arrays at St. Jude Children's Research Hospital.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Undertaken using the SNP-FASST2 Segmentation Algorithm within Nexus Copy number software (Discovery Edition 7.0, BioDiscovery, Hawthorne, CA) and NCBI genome build 37.
*probes.txt: Log2 ratio per probe generated by Nexus Copy Number Software.

molecule: genomic DNA

organism: Homo sapiens

source_name: choroid plexus tumor, CPC

extract_protocol: Tumor genomic DNA was extracted using standard phenol-chloroform extraction from fresh-frozen samples, and the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion, Carlsbad, USA) for FFPE samples.

treatment_protocol: DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=17) and an optimal cutting temperature compound (OCT)-embedded fresh frozen sample (n=1), and formalin-fixed paraffin-embedded (FFPE) samples (n=2).

tag: tissue

value: choroid plexus tumor

tag: subgroup

value: choroid plexus carcinoma

tag: p53 status

value: mut

tag: tissue type

value: frozen


title: Berry_pulp_23.2˚brix

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

country: USA

institute: University of Nevada, Reno

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry pulp. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 23.2˚Brixs.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berry pulp

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: A vineyard from a commercial winery (J. Lohr Vineyards & Wines) in Paso Robles, CA, planted with Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock), was dedicated to the study. Thirty-three vineyard rows, established as three separate blocks of 11 consecutive rows, were assigned to the project based on a completely randomized block design. The orientation of the vineyard was north-south.

extract_protocol: Skins were peeled from frozen berries with a razor blade for all berries on the clusters of each biological replicate. Separated skins and pulp of all the berries of each biological replicate were pooled (without seeds) and ground in a frozen mortar and pestle. Total RNA was extracted from the finely ground skins and pulp in liquid nitrogen using Qiagen RNeasy Plant MidiKit columns . The total RNA was further purified using a Qiagen RNeasy Plant Mini Kit according to the manufacturers’ instructions. RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).

treatment_protocol: IBMP concentrations of berries during maturation were determined. Twenty bunches per row were picked at each harvest date. Samples were collected from six assigned rows at each harvest date in the first five harvest dates and from three assigned rows in the last harvest. Two clusters per vine were sampled from the west arm on the cordon every ten plants (six biological replicates per harvest date). Clusters were carried in a cooler with dry ice to the laboratory and stored at -80 °C until analysis.

tag: cultivar

value: berry pulp

tag: brix level

tag: year

tag: vineyard name

value: J. Lohr Vineyards & Wines

tag: vineyard location

value: Paso Robles, CA, USA


title: Multiple Myeloma Patient 6 MSCs

city: Boston

first: Michaela

last: Reagan

state: MA

address: 77 Ave. Louis Pasteur

institute: Dana-Farber Cancer Institute

description: Total microRNA was analyzed with nanoString with 5 positive internal controls, five negative internal controls, 5 housekeeping genes, and 5 spike-in internal controls. A total of 800 human microRNAs were analyzed.

scan_protocol: 800 miRNAs were assessed using the nanoString miR analysis platform (nCounter human miRNA Expression Assay) following manufacturer’s protocol. Briefly, default settings for quality control on miRNA samples were used to assure high quality miRNA and accuracy of the experimental process for 4 parameters (Imaging, Binding Density, Positive Control Linearity, and Control Limit of Detection).

data_processing: The miRNAs were all normalized to the top 100 miRs per sample (by averaging the expression of the top 100 microRNAs per sample, and then dividing all microRNAs by this number).

label: nanoSting probe

source_name: primary bone marrow MSCs

label_protocol: A total of 100ng of mRNA and miRNA was used as input into the sample preparation reaction for the nanoString nCounter assay according to the procedures prescribed by nanoString.

extract_protocol: MSCs were isolated from bone marrow based on plastic adherence, expanded on tissue-culture plastic, and, for 3D culture, seeded onto silk scaffolds. After 2 weeks of co-culture in the 3D model, or after reaching P2 for Normal vs MM patient samples, miRNAs were isolated from cells using the miRNeasy isolation mini kit (Qiagen), quantified and tested for quality and contamination using a Nanodrop machine (ThermoScientific) and subjected to quality control minimum standards of 260/230>2 and 260/280>1.8 before further use for nanoString analysis.

tag: diagnosis

value: multiple myeloma

value: bone marrow

value: Menenchymal Stromal Cells (MSCs)


title: Multiple Myeloma Patient 5 MSCs


title: 546739A06 - 44B1.3-4h_BR3 vs 43A10.6-4h_BR3

extract_protocol: 43A10.6-4h_BR3:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 44B1.3-4h_BR3:5ug. (Qiagen_RNeasy.pdf)


title: CPC, CP157-T

description:
CP157-T
Brain tumor


title: Multiple Myeloma Patient 7 MSCs


title: Berry_skin_22.6˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skin. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 22.6˚Brixs.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berry skin

value: berry skin


title: Berry_pulp_22.6˚brix

description: This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry pulp. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 22.6˚Brixs.

value: Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock)


title: 546739A05 - 43A10.6-4h_BR3 vs 44B1.3-4h_BR3


title: 546739A03 - 43A10.6-4h_BR2 vs 44B1.3-4h_BR2


title: 546739A02 - 44B1.3-4h_BR1 vs 43A10.6-4h_BR1

extract_protocol: 43A10.6-4h_BR1:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 44B1.3-4h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: 546739A01 - 43A10.6-4h_BR1 vs 44B1.3-4h_BR1


title: 546738A11 - col0-52h_BR3 vs H1-P3.2-52h_BR3

treatment_protocol: Name:Dex induction 52h - compound based treatment - flooding with a solution of dexomethasone  ,dexamethasone:time 52hour . Plants were treated at 10:30 in the morning (Time 0; 10:30 is 3 and a half hours after the onset of the light period) by flooding with 30uM dexamethasone (in aqueous solution with 0,3 % DMSO and 0,033 % Silwet L-77) for 5 minutes . Samples were taken at 4 hrs and 52 hrs after T0. Aerial parts of the seedlings were rapidly harvested and frozen in liquid nitrogen.

extract_protocol: col0-52h_BR3:5ug. (Qiagen_RNeasy.pdf)


title: 546738A09 - col0-52h_BR2 vs H1-P3.2-52h_BR2

extract_protocol: col0-52h_BR2:5ug. (Qiagen_RNeasy.pdf)


title: CPC, CP147-TD

description:
CP147-TD
Brain tumor

value: wt


title: CPC, CP147-TA

description:
CP147-TA
Brain tumor

value: FFPE


title: aCPP, CP151-T

description:
CP151-T
Brain tumor

source_name: choroid plexus tumor, aCPP

value: atypical choroid plexus papilloma


title: aCPP, CP159-T

description:
CP159-T
Brain tumor


title: Multiple Myeloma Patient 4 MSCs


title: Multiple Myeloma Patient 2 MSCs


title: Multiple Myeloma Patient 3 MSCs


title: Normal Donor 3 MSCs

value: healthy (normal)


title: Multiple Myeloma Patient 1 MSCs


title: 546738A12 - H1-P3.2-52h_BR3 vs col0-52h_BR3


title: 546738A10 - H1-P3.2-52h_BR2 vs col0-52h_BR2


title: Normal Donor 2 MSCs


title: Normal Donor 1 MSCs


title: Normal Donor 6, MSCs cultured with MM1S


title: 546738A07 - col0-52h_BR1 vs H1-P3.2-52h_BR1

extract_protocol: col0-52h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: WILDTYPE_3h_ABA_rep2

city: Urumqi

first: Xiaoyu

last: Ji

address: Beijing road

country: China

institute: Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of AtbHLH112

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s  instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with R-software (The R Project for Statistical Computing, http:// www. r-project.org/) of SAS system statistics to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: WILDTYPE, 3h, ABA, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: ThbZIP1-overexpression plants and wild type of Columbia Arabidopsis thaliana seedlings grown in freshwater-irrigated pots filled with the artificial soil (Vermiculite: perlite: soil = 3:1:1, v/v) in a relative humidity of 55% under long-day conditions (16-h light/8-h dark)at 22°C (±2°C).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Four-week-old seedlings of T3 homozygous lines of the ThbZIP1-overexpression plants and wild type of Columbia Arabidopsis thaliana with or without 10 µM ABA treatment for 3 hours. The whole seedlings including root and shoot were harvested and pooled for each treatment before freezing in liquid nitrogen and storage at -80ºC for RNA isolation.

tag: genotype

value: wild type

tag: treatment

value: ABA

value: whole plant

tag: age

value: Four-week-old seedlings


title: 546738A08 - H1-P3.2-52h_BR1 vs col0-52h_BR1


title: ThbZIP1_3h_ABA_rep1

description: Gene expression after 3h in H2O-irrigated Arabidopsis seedlings of WILDTYPE

source_name: ThbZIP1, 3h, ABA, replicate 1

value: ThbZIP1 overexpression


title: 546738A06 - 44B1.3-52h_BR3 vs 43A10.6-52h_BR3

extract_protocol: 44B1.3-52h_BR3:5ug. (Qiagen_RNeasy.pdf)


title: 546738A01 - 43A10.6-52h_BR1 vs 44B1.3-52h_BR1

extract_protocol: 44B1.3-52h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: Normal Donor 6, MSCs cultured Alone


title: ThbZIP1_3h_ABA_rep2

source_name: ThbZIP1, 3h, ABA, replicate 2


title: TYR  treated rep3

city: Jaen

first: Francisco

middle: J.

last: Esteban

state: Jaen

address: Campus Las Lagunillas s/n

department: Experimental Biology

country: Spain

institute: University of Jaen

hyb_protocol: A total of 15 µg of biotin-labeled aRNA was fragmented following the instructions described  in the Affymetrix  manual (P/N 702646 Rev.8) and  hybridized to C. elegans GeneChip® Genome Arrays (Affymetrix, 900383).

scan_protocol: Arrays were processed and scanned using Affymetrix instrumentation and with hybridization, washing and scanning parameters provided by the manufacturer.

data_processing: Computational and statistical analyses were carried out using the R software (http://www.r-project.org/) and the appropriate Bioconductor packages (http://www.bioconductor.org/) run under R. In order to remove all the possible sources of variation of a non-biological origin between arrays, densitometry values between arrays were normalized using the RMA (robust multiarray) normalization function implemented in the Bioconductor affylmGUI package. Statistically significant differences between groups were identified using the rank product non-parametric test implemented in the Bioconductor Rank-Prod package. Those genes showing a corrected (PFP) p-value < 0.05 were selected as significant.

label: biotin

organism: Caenorhabditis elegans

source_name: TYR  treated

label_protocol: A total amount of 50 ng of RNA was used as the template for cDNA synthesis and in vitro transcription to synthesized biotin-modified aRNA using the GeneChip® 3’ IVT Express Kit (Affymetrix, 901228). aRNA was purified from unincorporated  nucleotides and other  reaction components using the RNeasy Mini Kit (Qiagen).

growth_protocol: The Caenorhabditis elegans strain fer-15(b26) was obtained from the Caenorhabditis Genetics Center (Minneapolis, MN) which is supported by NIH funding. Worms were propagated at 20°C on solid nematode growth media (NGM) seeded with the E. coli strain OP50. To prepare TYR treatment, TYR (2-(4-Hydroxyphenyl) ethylalcohol; Extrasynthese, France) was dissolved in ethanol and added to the liquid NGM medium previously autoclaved and cooled to 50°C to a final concentration of 250 μM. The medium was immediately dispensed into Petri dishes that were kept protected from light and stored at 4°C until use. A final ethanol concentration of 0.1% (v/v) was maintained in both, control and TYR containing plates. Nematodes were exposed to the treatment starting from the egg stage until their collection for the experiments.

extract_protocol: At the fourth day of adulthood, nematodes were collected from the plates in M9 buffer, washed 3 times and pelleted by centrifugation for RNA isolation. After centrifugation, worms were resuspended in 350 μl of RLT/BME buffer, flash frozen in liquid nitrogen and thawed at 37 °C three times for disruption and total RNA was extracted using the RNeasy Mini Kit (Qiagen, CA, USA) following the manufacturer recommended protocol. Final volume of isolated RNA was 50 μl per biological sample. RNA quality was analyzed with the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 nano kit. All RNA samples were of sufficient quality for gene array analysis with RNA Integrity Number (RIN)>7.

treatment_protocol: C. elegans were maintained on Nematode Growth Medium (NGM) and E. coli OP50 as described [21]. For microarray experiments, fer15(b26) nematodes were synchronized by hypochlorite treatment and raised at 25°C on NGM plates containing either 250 μM TYR (n=3) or vehicle (control; n=3).

tag: developmental stage

value: adult day 4

value: tyrosol

tag: strain


title: 546738A02 - 44B1.3-52h_BR1 vs 43A10.6-52h_BR1


title: Normal Donor 5, MSCs cultured Alone

tag: cell type


title: Normal Donor 5, MSCs cultured with MM1S


title: TYR  treated rep2


title: ThbZIP1_3h_H2O_rep1

description: Gene expression after 3h in H2O-irrigated Arabidopsis seedlings of AtbHLH112

source_name: ThbZIP1, 3h, H2O, replicate 1


title: WILDTYPE_3h_H2O_rep1

description: Gene expression after 3h in H2O-treatmented Arabidopsis seedlings of SALK_033618C

source_name: WILDTYPE, 3h, H2O, replicate 1


title: ThbZIP1_3h_H2O_rep2

source_name: ThbZIP1, 3h, H2O, replicate 2


title: Normal Donor 4, MSCs cultured with MM1S


title: control rep3

source_name: control

value: control


title: TYR  treated rep1


title: Normal Donor 4, MSCs cultured Alone


title: Normal Donor 3, MSCs cultured with MM1S


title: CPC, CP10-T

description:
CP10-T
Brain tumor

value: choroid plexus tumor

value: choroid plexus carcinoma

value: mut

value: frozen


title: WILDTYPE_3h_ABA_rep1

source_name: WILDTYPE, 3h, ABA, replicate 1


title: Normal Donor 2, MSCs cultured with MM1S

value: bone marrow

value: Menenchymal Stromal Cells (MSCs)


title: naiveTcells_3h_donor4

city: Muenchen

first: Kathrin

last: Suttner

address: Biedersteiner Str. 29

department: Helmholtz Zentrum und TU Muenchen

country: Germany

institute: ZAUM-Center for Allergy and Environment

description: Gene expression of 3h aCD3/aCD28 stimulated (naive) CD4+ T cells

hyb_protocol: Hybridisation to microarray was done by using the Hybridisation Kit (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the microarray scanner system Iscan (Agilent Technologies) using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3µm).

data_processing: The Agilent Feature Extraction software was used to read and process the microarray image files. GeneSpring software GX 12.5 (Agilent Technologies) was used for data analysis.

source_name: naive CD4 T cells, unstimulated, replicate 4

label_protocol: 25µg of total RNA (RIN ≥ 9) was amplified and Cy3-labeled using the 1-color Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA), according to manufacturer's protocol.

growth_protocol: Naive CD4+ T cells were isolated from human whole blood. PBMCs were first obtained via standard Lymphoprep density centrifugation, naive CD4+ T cells were isolated via Naive CD4+ T cell kit II (Miltenyi Biotech, Bergisch Gladbach, Germany), followed by the depletion of CD45RO+ cells via CD45RO microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany).

extract_protocol: Quiagen RNeasy Mini Kit was used for isolation of RNA and afterwards RNA quality (RIN = RNA integrity number) was assesed using Agilent 2100 Bioanalyzer together with the RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNA from naive CD4+ T cells was directly extracted after the isolation or naive T cells were stimulated with aCD3 (0,75µg, plate-bound) and aCD28 (0,75 µg) in AIMV medium for 3h and then RNA was isolated.

value: blood

value: naive CD4+ T cells

tag: atopy status

value: non-atopic


title: Normal Donor 2, MSCs cultured Alone

value: healthy (normal)

tag: tissue


title: control rep2


title: naiveTcells_0h_donor3

description: Gene expression of freshly isolated naive CD4+ T cells

source_name: naive CD4 T cells, unstimulated, replicate 3


title: naiveTcells_0h_donor2

source_name: naive CD4 T cells, unstimulated, replicate 2


title: control rep1


title: Normal Donor 1, MSCs cultured with MM1S


title: 4B  Tg/+ 9758

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Samples were hybridized onto the Illumina Sentrix BeadChip Array MouseRef-8 v2 for 18 hours at 58°C (protocol available at http://www.illumina.com/products/mouseref-8_expression_beadchip_kits_v2.ilmn).

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

organism: Mus musculus

label_protocol: Standard Illumina biotin-labeling protocol

extract_protocol: RNA  from gastrocnemius skeletal muscle was extracted using RNAeasy mini kit (Qiagen) with DNase I treatment to eliminate genomic DNA contamination

tag: genotype/variation

value: Tg

value: gastrocnemius skeletal muscle


title: 4B wt 9756

value: wt


title: naiveTcells_3h_donor2

source_name: naive CD4 T cells, 3h stimulated, replicate 2


title: naiveTcells_3h_donor3

source_name: naive CD4 T cells, 3h stimulated, replicate 3


title: naiveTcells_0h_donor4


title: naiveTcells_3h_donor1

source_name: naive CD4 T cells, 3h stimulated, replicate 1


title: Normal Donor 1, MSCs cultured Alone

source_name: primary bone marrow MSCs


title: 4B wt 9768


title: Veh  Tg/+ 9788

value: Veh


title: Veh  Tg/+ 9777


title: Veh wt 9757

source_name: Veh wt 9757


title: 4B wt 9769


title: 521T  tumor unmatched

city: Sao Paulo

first: mateus

middle: camargo

last: barros filho

state: SP

address: Tagua Street 440

country: Brazil

institute: AC Camargo Cancer Center

description: target sample Cy3-labeled mixed with reference sample Cy5-labeled

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

scan_protocol: Images were capture in Microarray Scanner System (Agilent), with Scan Control Software 8.1 (Agilent). Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: Numeric data was generated and normalized by intensity-dependent global normalization (LOWESS) with Feature Extraction v10.1 software (Agilent)

source_name: thyroid carcinoma labeled with Cyanine-3 (green)

label_protocol: Tumor and reference samples (300ng) were differentially labeled using Low Input Quick Amp Labeling (Agilent) (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Not applicable

extract_protocol: Total RNA from 61 PTC and 13 adjacent normal thyroid tissue from total thyroidectomy was isolated by the standard Rneasy or Trizol-based method.

value: papillary thyroid carcinoma

tag: gender

value: male

tag: histological variant

value: classic

tag: multifocality

value: multifocal

tag: primary tumor dimension (cm)

source_name: pool of 9 adjacent normal thyroid tissue labeled with Cyanine-5 (red)

value: pool of 9 adjacent normal thyroid tissues


title: Motile strain of Sphingomonas sp. A1 grown on alginate medium

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA according to their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, according to their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Sphingomonas sp. A1

source_name: motile strain of Sphingomonas sp. A1 grown on alginate medium

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Wild-type and motile strains of Sphingomonas sp. A1 were grown to mid-log phase (O.D.600nm 0.5 to 0.6) at 30°C in 0.5% alginate medium (0.1% (NH4)2SO4, 0.1% KH2PO4, 0.1% Na2HPO4, 0.01% MgSO4•7H2O, 0.01% yeast extract, and 0.5% sodium alginate (pH 7.2)) .

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Bacterial cells were treated with RNA Protect Bacteria Reagent (Quiagen Inc., Valencia, CA, USA)

value: motile


title: 520T  tumor unmatched


title: 522T  tumor unmatched

value: female


title: Veh wt 9770

source_name: Veh wt 9770


title: 4B  Tg/+ 9753


title: naiveTcells_0h_donor1

source_name: naive CD4 T cells, unstimulated, replicate 1


title: 546738A05 - 43A10.6-52h_BR3 vs 44B1.3-52h_BR3

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)


title: 10nM Iso rep2

city: San Francisco

first: Nikoleta

last: Tsvetanova

address: 600 16th street

institute: University of California, San Francisco

description: Sample 3

hyb_protocol: Cy5- and Cy3-labeled aRNA were combined in 3× SSC, 50 mM Hepes (pH 7.0), 20 µg of poly(A) RNA, 20 µg Cot-1 DNA, 20 µg tRNA, and 0.3% SDS to a total volume of 50uL. Samples were then heated to 70°C for 5 min, spun at 14,000rpm at room temperature in a microfuge for 5 min, then hybridized at 65°C using the MAUI hybridization system (BioMicro) for 12–16 hrs

scan_protocol: Microarrays were scanned using AxonScanner 4000B (Molecular Devices), and PMTs were manually adjusted for every slide scanned to maximize signal without saturation

data_processing: GenePix was used to extract data from scanned microarray images. Log2(Treated/Untreated) from duplicate sports were averaged and all log2 ratios were median-centered on an array-by-array basis

source_name: HEK293_10nM Iso

label_protocol: Amersham Cy dye kit

growth_protocol: HEK293 cells were grown in a CO2 incubator at 37C in DMEM+FBS medium; before treatment with drug, cells were washed once in DMEM without serum, then DMEM without serum was added together with drug for 2 hrs

extract_protocol: RNeasy Mini Kit

treatment_protocol:
10nM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium

tag: cell line

tag: treated with

value: 10uM isoproterenol for 2hrs

tag: sample group

value: Agonist response

source_name: HEK293_untreated cells

value: none (untreated control)

value: reference


title: Dyngo/1uM Iso rep2

description: Sample 2

source_name: HEK293_Dyngo_1uM Iso

treatment_protocol:
Cells were pre-treated with Dyngo for 15 min, then 1uM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium

tag: pre-treated with

value: Dyngo for 15 min

value: 1uM isoproterenol for 2hrs


title: Dyngo/10nM Iso rep2

description: Sample 1

source_name: HEK293_Dyngo_10nM Iso

treatment_protocol:
Cells were pre-treated with Dyngo for 15 min, then 10nM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium


title: 1uM Iso rep2

description: Sample 4

source_name: HEK293_1uM Iso

treatment_protocol:
1uM isoproterenol was added without changing medium for 2 hrs
Agonist added at indicated concentration for 2 hrs directly to medium


title: 516T  tumor unmatched

value: unique


title: 4B wt 391

tag: treatment

value: gastrocnemius skeletal muscle


title: 395T  tumor unmatched

tag: age

value: follicular


title: Veh  Tg/+ 9752

value: Tg

value: Veh


title: 467T  tumor unmatched

value: papillary thyroid carcinoma


title: 518T  tumor unmatched

value: male


title: Veh wt 393

source_name: Veh wt 393

value: wt


title: 429T  tumor unmatched

value: classic

value: pool of 9 adjacent normal thyroid tissues


title: 4B wt 9766


title: 4B  Tg/+ 9786


title: 462T  tumor unmatched

value: female


title: Veh wt 9771

source_name: Veh wt 9771


title: rNCSC-2-rep3

city: Innsbruck

first: Galina

last: Apostolova

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

description: DRG-derived NCSCs are reprogrammed in neurosphere cultures to rNCSCs that can give rise to CNS progeny including Olig2+ cells with oligodendrocyte morphology and markers O4, CNPase and Sox10.

hyb_protocol: Following fragmentation, 20 µg of cRNA were hybridized on GeneChip Mouse 430_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Fluorescence signals were recorded by an  Affymetrix scanner 3000.

data_processing: All further analysis was performed in R (http://www.r-project.org) using packages from the Bioconductor project. Functions from the affyPLM package were used for quality assessments of the microarrays and only good quality arrays were further analysed. GeneChip raw expression values were normalized and summarized using the GC-RMA method.

source_name: Neurosphere cultures from embryonic DRG

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: DRG were isolated from C57BL/6J mice at embryonic day 12.5; palatal tissue was dissected from 3 to 5 C57BL/6J mice of the age of 6 to 8 weeks. Tissue was dissociated enzymatically, followed by mechanical trituration. Dissociated cells were cultured in proliferation medium. After 5–7 d in vitro, primary neurospheres were collected, incubated in accutase for 30 min, dissociated into single cells and plated for secondary sphere formation. For microarray  analysis, passage 3 neurospheres were used.

extract_protocol: Total RNA was extracted and purified by using a combination of TRIzol reagent (Life Technologies) and RNeasy MinElute Spin Columns (Quiagen) according to the manufacturers’ instructions.

treatment_protocol: rNCSCs and pNCSCs were cultured in serum-free proliferation medium: DMEM/F12, bFGF (20 or 40ng/ml), EGF (20 ng/ml), heparin (0.5 U/m)l,  N2 (1%), B27 (1% or 3% ), Glutamine (1%) and Penicillin/Streptomycin (1%).

value: embryonic day E12.5 DRG


title: Veh  Tg/+ 9763


title: pNCSC-rep3

description: Palate neural crest-derived stem cells (pNCSCs) in neurosphere cultures with heparin-enhanced FGF signaling downregulate the PNS markers Sox10 and p75 but, in contrast to rNCSCs, do not induce any of the CNS progenitor markers.

source_name: Neurosphere cultures from adult palate

value: adult mouse palate


title: Spleen naïve - germ free [GF-S1142]

city: Turku

first: Tiina

middle: Kelkka

last: Ilona

address: Tykistökatu 6A

department: Medicity

country: Finland

institute: University of Turku

hyb_protocol: 750 ng each cRNA sample was hybridized to Illumina’s Sentrix BeadChip Array MouseRef-8 v2

scan_protocol: Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%) and the numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction.

data_processing: Quantile normalized and log2 transformed using Bioconductors LIMMA packages in R. Germ free samples were normalized separately from the other (SPF) samples, similarly blood and spleen samples were normalized separately.

source_name: Spleen naïve - germ free

label_protocol: from 250 ng total RNA with Ambion's Illumina Total Prep RNA Amplification kit (cat # AMIL1791). cRNA concentrations where checked with Nanodrop ND-1000 and the quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: whole blood and total spleen samples were used without ex vivo culture or any ex vivo treatment

extract_protocol: In experiment I: total RNA from the spleen samples was isolated using Ambion’s Ribo Pure Kit (cat# 1924) and from the blood samples by using Ambion’s Mouse RiboPure™-Blood RNA Isolation Kit (cat# AM1951). In experiment I blood samples were purified using LiCl precipitation (Ambion, AM9480). In experiment II spleen samples were collected in RNALater (Ambion, AM7020 ) and 50 – 100 mg total RNA was isolated using Qiagen’s RNeasy mini kit (cat# 74104) with the optional DNase-treatment step (RNase-Free DNase Set, Qiagen, 79254). In experiment II blood samples were collected in RNAprotect Animal Blood Tubes (Qiagen, 76544) and RNA was isolated using Qiagen’s RNeasy Protect Animal Blood Kit (cat# 73224). All samples were treated with with Ambion’s GLOBINclear™–Mouse/Rat Kit (cat# AM1981) using 1-2 ug of blood RNA as starting material.

treatment_protocol: Samples were not treated after collection

tag: Sex

value: Male

tag: experiment

value: Germ-free


title: Spleen naïve - germ free [GF-S1143]

tag: strain


title: 410T  tumor unmatched

value: multifocal


title: pNCSC-rep2


title: 393T  tumor unmatched


title: pNCSC-rep1


title: 381T  tumor unmatched


title: Spleen naïve - germ free [GF-S504]


title: rNCSC-2-rep2


title: rNCSC-2-rep1


title: 384T  tumor unmatched


title: BMP NCSC-rep3

description: BMP4-treated DRG-derived NCSCs do not undergo CNS reprogramming, contain progenitors of PNS neurons and glia and MSCs .

scan_protocol: Fluorescence signals were recorded by an  Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: All further analysis was performed in R (http://www.r-project.org) using packages from the Bioconductor project. Functions from the affyPLM package were used for quality assessments of the microarrays and only good quality arrays were further analysed. GeneChip raw expression values were normalized and summarized using the GCRMA method.

source_name: Neurosphere cultures from embryonic DRG cultured in 10 ng/ml BMP4

growth_protocol: Spinal cord and DRG were isolated from C57BL/6J mice at embryonic day 12.5. Tissue was dissociated enzymatically, followed by mechanical trituration. Dissociated cells were cultured in proliferation medium. After 5–7 d in vitro, primary neurospheres were collected, incubated in accutase for 30 min, dissociated into single cells and plated for secondary sphere formation. For microarray  analysis, passage 3 neurospheres were used.

treatment_protocol: rNCSC and SCSCs were cultured in serum-free proliferation medium: DMEM/F12, 20 ng/ml bFGF (basic fibroblast growth factor), 20 ng/ml epidermal growth factor (EGF), 0.5 U/ml heparin, 1% N2, 1% B27, and 1% Penicillin/Streptomycin. For BMP NCSCs, proliferation medium  was supplemented with 10 ng/ml BMP4.

tag: growth factors in the culture medium

value: bFGF, EGF, BMP4


title: 382T  tumor unmatched

tag: tissue

value: unique


title: BMP NCSC-rep1


title: 377T  tumor unmatched


title: SCSC-rep3

description: SCSCs represent a homogenous Olig2+ CNS stem cell population.

source_name: Neurosphere cultures from embryonic spinal cord

value: embryonic day E12.5 spinal cord

value: bFGF, EGF


title: 379T  tumor unmatched

source_name: thyroid carcinoma labeled with Cyanine-3 (green)


title: 369T  tumor unmatched

source_name: pool of 9 adjacent normal thyroid tissue labeled with Cyanine-5 (red)


title: Spleen naïve - germ free [GF-S463]

tag: genotype/variation

value: BQ wildtype


title: Spleen naïve - germ free [GF-S462]


title: Germany-Hamm-F sample

city: East Lansing

first: Kevin

middle: Jensen

last: Liu

state: MI

address: 428 S. Shaw Lane

department: Computer Science and Engineering

institute: Michigan State University

description: Wild derived house mice presumed to be M. m. domesticus but known to contain an unknown genomic fraction of M. spretus

hyb_protocol: as done by the Jackson Laboratory, Bar Harbour, Maine, USA JAX Genome Scanning Services.

data_processing: We used MouseDivGeno version 1.0.4 to genotype raw sequence reads, following the procedure of Didion et al. BMC Genomics 2012.

organism: Mus musculus domesticus

source_name: Michael,H,Kohn Lab

growth_protocol: N/A Liver Tissue was received

tag: gender

value: liver


title: 373T  tumor unmatched

value: papillary thyroid carcinoma

tag: histological variant


title: Spleen naïve - germ free [GF-S461]


title: Germany-Hamm-C sample

scan_protocol: as done by the Jackson Laboratory, Bar Harbour, Maine, USA JAX Genome Scanning Services.


title: Spleen naïve - germ free [GF-S1141]


title: Germany-Hamm-D sample

label_protocol: as done by the Jackson Laboratory, Bar Harbour, Maine, USA JAX Genome Scanning Services.

value: male


title: SCSC-rep2


title: BMP NCSC-rep2


title: 376T  tumor unmatched

tag: multifocality


title: Spleen naïve - germ free [GF-S503]


title: Germany-Hamm-B sample

extract_protocol: as done by the Jackson Laboratory, Bar Harbour, Maine, USA JAX Genome Scanning Services.


title: Germany-Hamm-E sample


title: Time 6 Replication 4. Dye Swap

city: Columbia

first: David

middle: W

last: Emerich

state: MO

address: 117 Schweitzer Hall

department: Biochemistry

institute: University of Missouri-Columbia

description: Sample:Control=Bacteria:Bacteroids

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined, averaged, and subsequently subjected to significance analysis of microarray (SAM) data using the SAM package (Tusher et al. 2001). Significant genes were selected based on a 1.5- or 2-fold cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: Bacteria

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: cell

value: 4-week-old Free-living cells grown in HM-Arabinose

source_name: Bacteroids

value: bacteroids harvested from 95-day-old soybean root nodules.


title: 366T  tumor unmatched

value: tall cells

tag: primary tumor dimension (cm)

value: pool of 9 adjacent normal thyroid tissues


title: rNCSC-rep3

value: embryonic day E12.5 DRG


title: Germany-Hamm-A sample


title: Spleen naïve - germ free [GF-S3]


title: Time 6 Replication 4.

description: Sample:Control=Bacteroids:Bacteria


title: 365T  tumor unmatched

value: female

value: classic


title: Spleen naïve - germ free [GF-S5]

value: Male

value: Germ-free


title: WILDTYPE_3h_H2O_rep2

source_name: WILDTYPE, 3h, H2O, replicate 2

tag: genotype

value: wild type

value: whole plant

value: Four-week-old seedlings


title: SCSC-rep1

value: embryonic day E12.5 spinal cord

value: bFGF, EGF


title: Time 6 Replication 3.

description: Sample:Control=Bacteroids:Bacteria


title: rNCSC-rep2


title: 361T  tumor unmatched

value: unique


title: rNCSC-rep1


title: Normal Donor 3, MSCs cultured Alone

source_name: primary bone marrow MSCs

extract_protocol: MSCs were isolated from bone marrow based on plastic adherence, expanded on tissue-culture plastic, and, for 3D culture, seeded onto silk scaffolds. After 2 weeks of co-culture in the 3D model, or after reaching P2 for Normal vs MM patient samples, miRNAs were isolated from cells using the miRNeasy isolation mini kit (Qiagen), quantified and tested for quality and contamination using a Nanodrop machine (ThermoScientific) and subjected to quality control minimum standards of 260/230>2 and 260/280>1.8 before further use for nanoString analysis.

tag: diagnosis

value: healthy (normal)

value: bone marrow

tag: cell type

value: Menenchymal Stromal Cells (MSCs)


title: MAP_P2_PMT750_rep3

city: Corvallis

first: Luiz

middle: E

last: Bermudez

state: Oregon

address: 105 Dryden Hall

department: Biomedical Sciences

institute: Oregon State University

description: Total RNA amplified using biotinylated nucleotides to make amplified RNA (aRNA); aRNA serve as hybridization probe

hyb_protocol: The MAP K10 specific DNA oligo spotted arrays were designed and printed at the National Animal Disease Center (USDA-ARS, Ames, IA) and were post-processed, blocked, and hybridized prior to use as per standard protocol (http://derisilab.ucsf.edu/microarray/protocols.html).  For hybridization total RNA was fragmented to 200 base pair fragments by incubation for 30 minutes at 94°C in fragmentation buffer (100 mM potassium acetate, 30 mM magnesium acetate, and 40 mM tris-acetate).  Array chips were hybridized with 6 µg of biotinylated RNA for 16 hours using an InSlide Hybridization Oven (Thomas Scientific, Swedesboro, NJ) in a humidified chamber at 45°C.  Chips were washed for 5 minutes in 5x SSC, 0.01% SDS buffer, 3 minutes in 0.5x SSC buffer, and 30 seconds in 0.1x SSC buffer, stained with streptavidin-Cy3 (Life Technologies, Grand Island, NY) in 10% bovine serum albumin in HBSS for 1 hour, and washed again in 5x SSC/0.01% SDS buffer for 5 minutes, 0.5x SSC for 1 minute, 0.01x SSC for 10 seconds, and slides were centrifuged to dry.

scan_protocol: Array chip fluorescence was measured using the Axon4000 slide reader at the Center for Genome Resources and Bioinformatics at Oregon State University.  Hybridization fluorescence was analyzed using Axon4000 software and spots containing bubbles, scratches, or inconsistency in fluorescence across the circle were censored from the data.  Triplicate spots on each array were averaged and each slide was normalized to hybridization buffer only control spots.  Triplicate biological replicates were averaged and the ratio of the fluorescence values of secondary MAP/primary MAP was determined.  Fluorescence values were normalized to hybridization buffer spots within each individual array chip.

data_processing: Spots that did not hybridize, had flaws in staining, located within bubbles, or exhibited inconsistant staining throughout the spot were tagged as errors and removed from the study.  All replicate values of fluorescence intensities from a single slide were averaged.  Values for each oligo were divided by the average value of spotting buffer to normalize staining across all slides.

organism: Mycobacterium avium subsp. paratuberculosis

source_name: bacterial RNA, inflammatory phenotype (P2)

growth_protocol: P0 RNA samples were extracted after 24 hours of intracellular growth within bovine MDBK epithelial cells; P2 RNA samples were extracted after serial culture of 24 hours in MDBK epithelial cells, 72 hours in macrophages, and another 24 hours in MDBK cells

extract_protocol: Infected cell monolayers were lysed with guanidine thiocyanate (GTC) buffer (4M guanidine thiocyanate, 0.5% N-Lauryl sarcosine, 30mM sodium citrate, pH 7.0) with 0.1M B-mercaptoethanol, and lysates were pelleted at 2,700 × g at 4°C.  Pellet was washed twice with GTC buffer and pelleted at 2,700 × g at 4°C.  Intact bacterial pellet was lysed in Trizol (Life Technologies, Carlsbad, CA) with 0.5 ml of 0.1 mm glass beads by bead beating in a reciprocal bead beater for 20 seconds each, incubated on ice for 1 minute, and repeated 3 times.  Chloroform:isoamyl alcohol (24:1; Ambion; Carlsbad, CA) was added and mixture was centrifuged at 9,500 × g at 4°C.  Aqueous layer was collected, equal volume chloroform added, mixed, and centrifuged at 9,500 × g at 4°C.  Aqueous layer was collected and nucleic acids were precipitated with 0.7 volume isopropanol and 15 µg of linear polyacrylamide overnight at -20°C.  Nucleic acids were pelleted at 9,500 × g at 4 °C for 30 minutes, washed with 70% ethanol, and suspended in nuclease-free water.  DNase treatment and RNA clean-up were performed using the RNeasy Mini Kit (Qiagen; Valencia, CA) as per manufacturer's instructions.  RNA preparation was verified for absence of DNA contamination and quantified.  For each sample, 100 ng of RNA was amplified using the Message AmpII-Bacteria RNA Amplification Kit (Ambion, Grand Island, NY) as per manufacturer's instructions.  Amplified RNA (aRNA) was synthesized using biotin-labeled UTP nucleotides (Ambion) and analyzed for quality on an Agilent Bioanalyzer 2100 at the Center for Genome Research and Biocomputing at Oregon State University.  Samples were aliquoted and stored at -80°C prior to microarray analysis.

tag: phenotype

value: inflammatory phenotype (P2)


title: Blood naïve - germ free [GF-B114]

source_name: Blood naïve - germ free


title: Time 6 Replication 3. Dye Swap

description: Sample:Control=Bacteria:Bacteroids

value: 4-week-old Free-living cells grown in HM-Arabinose

value: bacteroids harvested from 95-day-old soybean root nodules.


title: MAP_P2_PMT600_rep3

label_protocol: Amplified RNA (aRNA) was synthesized using biotin-labeled UTP nucleotides (Ambion)


title: Time 6 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Spleen naïve - germ free [GF-S1]

value: BQ wildtype


title: 355T  tumor unmatched

value: papillary thyroid carcinoma

value: female

value: pool of 9 adjacent normal thyroid tissues


title: 354T  tumor unmatched

value: classic

value: multifocal


title: Blood naïve - germ free [GF-B1]

value: Male

value: Germ-free


title: Time 6 Replication 2.

description: Sample:Control=Bacteroids:Bacteria


title: 350T  tumor unmatched


title: Blood naïve - germ free [GF-B3]


title: Blood naïve [II-B3]

source_name: Blood naïve

value: II


title: Time 6 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Blood naïve [II-B5]


title: Time 6 Replication 1.

description: Sample:Control=Bacteroids:Bacteria


title: MAP_P2_PMT750_rep2


title: MAP_P2_PMT600_rep2


title: MAP_P2_PMT400_rep3


title: MAP_P2_PMT400_rep2


title: 349T  tumor unmatched


title: Time 5 Replication 4. Dye Swap

description: Sample:Control=Bacteria:Bacteroids

value: bacteroids harvested from 71-day-old soybean root nodules.


title: 347T  tumor unmatched

value: oncocytic


title: Time 5 Replication 4.

description: Sample:Control=Bacteroids:Bacteria


title: Blood naïve [II-B33]


title: Spleen naïve [II-S3]

source_name: Spleen naïve


title: Spleen naïve [II-S39]


title: Time 5 Replication 3. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: MAP_P2_PMT750_rep1


title: 348T  tumor unmatched

value: unique


title: MAP_P2_PMT400_rep1


title: MAP_P2_PMT600_rep1


title: Time 5 Replication 3.

description: Sample:Control=Bacteroids:Bacteria


title: Time 5 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: MAP_P0_PMT750_rep3

source_name: bacterial RNA, non-inflammatory phenotype (P0)

value: non-inflammatory phenotype (P0)


title: 346T  tumor unmatched

value: follicular


title: Spleen naïve [II-S38]


title: 344T  tumor unmatched


title: 345T  tumor unmatched

value: male


title: Spleen naïve [II-S33]


title: Time 5 Replication 2.

description: Sample:Control=Bacteroids:Bacteria

value: 4-week-old Free-living cells grown in HM-Arabinose


title: MAP_P0_PMT400_rep3


title: Spleen naïve [II-S1]


title: 343T  tumor unmatched


title: MAP_P0_PMT600_rep3


title: 342T  tumor unmatched


title: Time 5 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Blood naïve [II-B37]


title: Blood naïve [II-B32]


title: Blood naïve [II-B1]


title: MAP_P0_PMT750_rep2


title: Time 5 Replication 1.

description: Sample:Control=Bacteroids:Bacteria


title: MAP_P0_PMT600_rep2


title: MAP_P0_PMT400_rep2


title: Time 4 Replication 4.

description: Sample:Control=Bacteroids:Bacteria

value: bacteroids harvested from 55-day-old soybean root nodules.


title: Time 4 Replication 3.

description: Sample:Control=Bacteroids:Bacteria


title: 337T  tumor unmatched


title: Blood naïve [II-B38]

value: BQ wildtype


title: 340T  tumor unmatched

value: papillary thyroid carcinoma


title: 339T  tumor unmatched

value: female


title: 334T  tumor unmatched

value: pool of 9 adjacent normal thyroid tissues


title: Blood naïve [II-B34]


title: Time 4 Replication 4. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Ctrl_s2_1

first: Andrew

last: Emili

address: 160 College St #602

department: Donnelly Centre

institute: University of Toronto

description: interanl control

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol

scan_protocol: Slides were scanned on Agilent Microarray Scanner (G2505B)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent)

source_name: Internal control

label_protocol: See Agilent Technologies website for miRNA label protocol

extract_protocol: not provided

value: Ventricle

value: Internal Control


title: MAP_P0_PMT400_rep1


title: Time 4 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 333T  tumor unmatched

value: multifocal


title: Blood naïve [II-B7]

value: Male


title: MAP_P0_PMT600_rep1


title: 358T  tumor unmatched

value: classic


title: Time 4 Replication 2.

description: Sample:Control=Bacteroids:Bacteria


title: Spleen naïve [II-S32]

value: II


title: 329T  tumor unmatched


title: Time 4 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Spleen naïve [II-S5]


title: R9C_s2_3

description: miRNA expression in PLN 08w mice heart ventricle tissue

source_name: Phospholamaban mutant mouse heart, 8w, rep3

value: PLN


title: Spleen naïve [II-S37]


title: R9C_s2_2

source_name: Phospholamaban mutant mouse heart, 8w, rep2


title: MAP_P0_PMT750_rep1


title: Ctrl_s2_2

description: interanl control


title: Time 4 Replication 1.

description: Sample:Control=Bacteroids:Bacteria


title: Time 3 Replication 4. Dye Swap

description: Sample:Control=Bacteria:Bacteroids

value: bacteroids harvested from 49-day-old soybean root nodules.


title: WT_s2_2

description: miRNA expression in healthy littermate control mice heart ventricle tissue

source_name: Control mouse heart, 8w, rep2

value: FVB/N


title: 328T  tumor unmatched

value: follicular

value: unique


title: R9C_s2_1

source_name: Phospholamaban mutant mouse heart, 8w, rep1


title: Time 3 Replication 4.

description: Sample:Control=Bacteroids:Bacteria

value: 4-week-old Free-living cells grown in HM-Arabinose


title: Ctrl_s1_2

description: interanl control


title: Time 3 Replication 3. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Time 3 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 332T  tumor unmatched

source_name: thyroid carcinoma labeled with Cyanine-3 (green)


title: 326T  tumor unmatched

source_name: pool of 9 adjacent normal thyroid tissue labeled with Cyanine-5 (red)


title: Time 3 Replication 3.

description: Sample:Control=Bacteroids:Bacteria


title: Time 3 Replication 2.

description: Sample:Control=Bacteroids:Bacteria


title: Spleen naïve [II-S34]


title: R9C_s1_3


title: WT_s2_1

source_name: Control mouse heart, 8w, rep1


title: Blood naïve [II-B2]


title: 323T  tumor unmatched

value: male


title: Blood naïve [II-B39]

value: BQ wildtype


title: Spleen naïve [II-S8]


title: 318T  tumor unmatched

value: papillary thyroid carcinoma


title: Spleen naïve [II-S2]


title: 325T  tumor unmatched

value: female


title: 321T  tumor unmatched

value: pool of 9 adjacent normal thyroid tissues


title: 320T  tumor unmatched

value: sclerosing


title: 315T  tumor unmatched


title: Ctrl_s1_1

description: interanl control

value: Ventricle

value: Internal Control


title: Time 3 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids

source_name: Bacteria


title: Blood naïve [II-B8]

value: Male


title: Blood naïve [I-B31]

value: I


title: 16866  tumor unmatched

value: solid


title: Spleen naïve [II-S7]

value: II


title: Time 2 Replication 4. Dye Swap

description: Sample:Control=Bacteria:Bacteroids

source_name: Bacteroids

value: bacteroids harvested from 43-day-old soybean root nodules.


title: Blood naïve [I-B6]


title: 16805  tumor unmatched

value: classic


title: Spleen naïve [I-S7]


title: WT_s1_2

value: FVB/N


title: WT_s1_1


title: Time 3 Replication 1.

description: Sample:Control=Bacteroids:Bacteria

value: bacteroids harvested from 49-day-old soybean root nodules.


title: R9C_s1_1

value: PLN


title: Time 2 Replication 3.

description: Sample:Control=Bacteroids:Bacteria

value: 4-week-old Free-living cells grown in HM-Arabinose


title: Time 2 Replication 4.

description: Sample:Control=Bacteroids:Bacteria


title: Time 2 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Time 2 Replication 3. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 16776  tumor unmatched

value: unique


title: 4368  tumor unmatched

value: papillary thyroid carcinoma

value: male

value: follicular

value: multifocal


title: Blood naïve [I-B5]

value: BQ wildtype


title: Time 2 Replication 2.

description: Sample:Control=Bacteroids:Bacteria


title: Spleen naïve [I-S5]


title: Blood naïve [I-B30]


title: Time 2 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 4247  tumor unmatched

value: female

value: pool of 9 adjacent normal thyroid tissues


title: Blood naïve [I-B27]

value: Male

value: I


title: Spleen naïve [I-S27]


title: 4369  tumor unmatched


title: 4190  tumor unmatched


title: R9C_s1_2

value: Ventricle


title: Blood naïve [I-B7]


title: Time 2 Replication 1.

description: Sample:Control=Bacteroids:Bacteria

value: bacteroids harvested from 43-day-old soybean root nodules.


title: Spleen naïve [I-S25]


title: 507N non-tumor matched with 507T

source_name: adjacent normal thyroid labeled with Cyanine-3 (green)

value: adjacent normal thyroid tissue

value: Not applicable


title: Time 1 Replication 3.

description: Sample:Control=Bacteroids:Bacteria

value: bacteroids harvested from 34-day-old soybean root nodules.


title: Time 1 Replication 2. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 4209  tumor unmatched

value: classic


title: Time 1 Replication 2.

description: Sample:Control=Bacteroids:Bacteria

value: 4-week-old Free-living cells grown in HM-Arabinose


title: 407T  tumor matched with 407N

value: unique


title: Time 1 Replication 4. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Time 1 Replication 3. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: Spleen naïve [I-S3]


title: Spleen naïve [I-S31]


title: Time 1 Replication 1. Dye Swap

description: Sample:Control=Bacteria:Bacteroids


title: 386N non-tumor matched with 386T


title: 407N non-tumor matched with 407T


title: Blood naïve [I-B25]


title: Blood naïve [I-B1]


title: Time 1 Replication 1.

description: Sample:Control=Bacteroids:Bacteria


title: planktonic culture, mid-log phase I, rep 1

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from mid-exponential phase S. aureus strain COL cells

hyb_protocol: 1.0 ug of RNA were hybrized for 16 hr at 45C on an S. aureus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

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

label: Biotin

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

label_protocol: 10 ng were amplified using ExpressArt Nanokits (Amsbio) according to the manufacturer's recommendation for bacterial mRNA amplification except that the final transcription and labeling step was performed using Enzo BioArray Highyield RNA Transcript Labeling kits to incorporate biotinylated ribonucleotides into final RNA products.

growth_protocol: S. aureus strain COL (MRSA) was grown to mid-exponential phase (Optical Density 600nm of 0.4-0.5) in BHI broth at 37C with aeration (225 rpm in a rotary shaker).  Cells were then used to inoculate: 1. catherterized Sprague-Dawley rats, 2. Rats pretreated (48 hr; 60 mg/kg) with streptoxotocin to induce diabetic state, or 3. Fresh BHI medium and grown to either exponential phase or stationary phase growth.

extract_protocol: Rat homogenate was treated with proteinase K (4 mg/ml) for 30 min to liberate bacteria and cells were then mechanically disrupted.  Planktonic culture samples were mechanically disrupted.  Following disruption, total bacterial RNA was isolated using RNeasy Mini kits (Qiagen).

treatment_protocol: Rats were euthanized 3 days post inoculation and aortic valve vegatations were homogenzied and then suspended in RNA protect (Qiagen); Planktonic cells were pelleted and suspended in equal volume of RNA protect.

value: Whole cell

value: Wild type (strain COL)

tag: growth phase

value: Mid-exponential


title: 316T  tumor matched with 316N

value: papillary thyroid carcinoma

tag: age

value: mucinous

value: multifocal


title: Bacteroids and free-living cells Replication 4.

description: Sample:Control=Bacteria:Bacteroids

value: Free-living cells grown in HM-Arabinose

value: Four-week-old bacteroids harvested from soybean root nodules.


title: Bacteroids and free-living cells Replication 4. Dye swap

description: Sample:Control=Bacteroids:Bacteria


title: Spleen naïve [I-S30]

value: BQ wildtype

tag: Sex

value: Male

value: I


title: 386T  tumor matched with 386N

value: female

value: pool of 9 adjacent normal thyroid tissues


title: 507T  tumor matched with 507N


title: planktonic culture, mid-log phase III, rep 2


title: Spleen naïve [I-S6]

tag: experiment


title: Blood naïve [I-B4]

tag: strain


title: Blood naïve [I-B3]


title: Spleen naïve [I-S4]


title: Bacteroids and free-living cells Replication 3. Dye swap

description: Sample:Control=Bacteroids:Bacteria


title: Bacteroids and free-living cells Replication 3.

description: Sample:Control=Bacteria:Bacteroids


title: Bacteroids and free-living cells Replication 2. Dye swap

description: Sample:Control=Bacteroids:Bacteria


title: 316N non-tumor matched with 316T

value: adjacent normal thyroid tissue

value: Not applicable


title: planktonic culture, stationary phase I, rep 1

description: Gene expression data from stationary phase S. aureus strain COL cells

value: Stationary


title: Blood naïve [I-B29]


title: planktonic culture, stationary phase II, rep 2


title: Bacteroids and free-living cells Replication 2.

description: Sample:Control=Bacteria:Bacteroids


title: rat endocarditis vegetation, diabetic sample, rep 3

description: Gene expression data from S. aureus strain COL isolated from diabetic rat endocarditis vegetation

value: Diabetic vegetation


title: rat endocarditis vegetation, diabetic sample, rep 1

value: Whole cell


title: Blood naïve [I-B28]


title: Spleen naïve [I-S28]


title: Spleen naïve [I-S29]


title: Spleen naïve [I-S1]


title: rat endocarditis vegetation, diabetic sample, rep 2

value: Wild type (strain COL)


title: Bacteroids and free-living cells Replication 1. Dye swap

description: Sample:Control=Bacteroids:Bacteria


title: rat endocarditis vegetation, non-diabetic sample, rep 2

description: Gene expression data from S. aureus strain COL isolated from non-diabetic rat endocarditis vegetation

value: Non-diabetic vegetation


title: rat endocarditis vegetation, non-diabetic sample, rep 1


title: Bacteroids and free-living cells Replication 1.

description: Sample:Control=Bacteria:Bacteroids


title: CP65-T

first: Diana

last: Merino

address: 686 Bay St.

institute: The Hospital for Sick Children

description: cpp

hyb_protocol: Hybridization of total RNA to GeneChip® Human Exon 1.0ST gene expression microarrays took place at the Toronto Centre of Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Canada, according to manufacturer's instructions.

scan_protocol: not provided

data_processing:
Gene expression analysis was conducted in Partek GS6.5 with the following uploading parameters: Probes to import: Interrogating Probes and Control Probes. Probe filtering: Include Core Meta-Probeset: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps. Pre-background Adjustment: Adjust for GC Content. Background correction: RMA Background correction. Normalization: one-way anova normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish. ANOVA statistical test was used to identify gene expression differences between subgroups.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: brain tumor

label_protocol: not provided

growth_protocol: Total RNA was isolated from fresh-frozen tumor soon after tumor resection

extract_protocol: Total RNA was isolated using the TRIzol method (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions.

treatment_protocol: Fresh-frozen samples (snapped frozen in liquid nitrogen).

tag: tissue type

value: choroid plexus papillomas

tag: p53 status

value: wt


title: CP58-T

description: cpc

value: choroid plexus carcinomas


title: BoNT-A_1yr_168

city: La Jolla

first: Kavitha

last: Mukund

state: California

address: 9500 Gilman Drive #0412

institute: University of California, San Diego

description: Gene expression data from injected TA muscle of BoNT-A treated rats, extracted 52 weeks after treatment

hyb_protocol: Following fragmentation, 250 ng of cDNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GS FLX System (Roche Diagnostic Corporation, Basel, Switzerland).

data_processing: Raw data was GCRMA normalized using the GCRMA package in R/Bioconductor

organism: Rattus norvegicus

source_name: Tibialis anterior muscle, botox injected, extracted at 12 months/52 weeks after treatment

label_protocol: RNA was reverse-transcribed into cDNA using the SuperScript First-Strand Synthesis System (Life Technologies, Grand Island, NY, USA)

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

tag: tissue

value: Tibialis anterior


title: CP56-T

city: Toronto

description: cpc


title: BoNT-A_1wk_77

description: Gene expression data from injected TA muscle of BoNT-A treated rats, extracted 1 week after treatment

source_name: Tibialis anterior muscle, botox injected, extracted at 1 week


title: CP51-T

description: cpc

value: mut


title: BoNT-A_1yr_171


title: BoNT-A_1yr_170


title: CP55-T

description: acpp

value: atypical choroid plexus papillomas


title: BoNT-A_1yr_166


title: CP57-T

description: cpp


title: BoNT-A_1wk_79


title: BoNT-A_1wk_78


title: CP62-T

description: cpp


title: CP5-TB

description: cpc


title: CP52-T

description: cpc


title: CP47-T

description: cpp


title: BoNT-A_1wk_76


title: Saline_3mnth_32

description: Gene expression data from contralateral TA muscle of saline treated rats, extracted 12 weeks after treatment

source_name: Tibialis anterior muscle, contralateral, saline injected, extracted at 3 months/12 weeks after treatment


title: CP43-T

description: cpc


title: CP46-T

description: cpc


title: CP4-T

description: acpp


title: Saline_3mnth_31


title: Saline_3mnth_30


title: Saline_3mnth_29


title: CP148-T

description: cpp


title: BoNT-A_1mnth_22

description: Gene expression data from injected TA muscle of BoNT-A treated rats, extracted 4 week after treatment

source_name: Tibialis anterior muscle, botox injected, extracted at 1 months/4 weeks after treatment


title: CP3-T

description: cpc


title: BoNT-A_1mnth_23


title: BoNT-A_1mnth_17


title: BoNT-A_1mnth_24


title: CP41-T

description: cpc


title: CP142-TB

description: cpp


title: CP141-TB

description: cpc


title: BoNT-A_3mnth_15

description: Gene expression data from injected TA muscle of BoNT-A treated rats, extracted 12 weeks after treatment

source_name: Tibialis anterior muscle, botox injected, extracted at 3 months/12 weeks after treatment


title: CP146-T

description: cpc


title: BoNT-A_3mnth_16


title: BoNT-A_3mnth_9


title: BoNT-A_3mnth_7


title: CP62-T

description: cpp

hyb_protocol: Hybridization of genomic DNA to Genome-Wide Human SNP Array 6.0 genotyping microarrays took place at the Toronto Centre of Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Canada, according to manufacturer's instructions.

data_processing:
Partek® Genomics Suite™ 6.5 (PGS) (Partek Inc. St. Louis, USA) was used for initial copy number analysis. Inferred copy number states (regions of deletion or duplication) were derived from Partek's genomic segmentation algorithm (Partek, St Louis,MO) such that segmented regions were significantly different from neighbouring regions (p<0.001) and contained 10 or more probes, with a signal to noise ratio of 0.3. Diploid samples were those with a copy number between 1.75-2.25. Segmentation assumed all somatic chromosomes were diploid. Annotation file: GenomeWideSNP_6.na33.annot.csv
Copy number (by Genomic Segmentation algorithm) and allele ratio data provided.

growth_protocol: DNA was isolated from fresh-frozen tumor soon after tumor resection

extract_protocol: Tumor genomic DNA was extracted using standard phenol-chloroform extraction from fresh-frozen samples, and the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion, Carlsbad, USA) from FFPE samples.

treatment_protocol: DNA was isolated from fresh-frozen samples (snapped frozen in liquid nitrogen) (n=46) and optimal cutting temperature compound (OCT)-embedded fresh frozen (n=8),  and formalin-fixed paraffin embedded (FFPE) (1) samples.

tag: tissue source

value: frozen


title: CP139-TB

description: cpc


title: CP138-T

description: acpp


title: CP65-T

description: cpp


title: CP56-T

description: cpc


title: Control PC-3 cells

city: Indianapolis

first: Pierrick

middle: GJ

last: Fournier

state: IN

address: 980 West Walnut Street

department: Medicine

institute: Indiana University

description: PC3 C

hyb_protocol: 8µg of biotin-labeled cRNA were hybridized to Affymetrix HG-U133A probe array (GPL96) for 16h and washed using an Affymetrix GeneChip Fluidics station.

scan_protocol: GeneChips were scanned with a 2.5μm resolution HP Microarray Scanner.

data_processing: The scanned image files were analyzed using Affymetrix Microarray Analysis Suite 5.0 (MAS 5.0). The significance criterion matrix consisted of: 1) P≤0.05; 2) fold change≥1.5; and 3) signal differential ≥ Min (100, 10X  10% mean signal intensity of absent probe sets).

source_name: PC-3 cells treated with vehicle (48h)

label_protocol: cDNA and labelled cRNA were synthesized according to standard Affymetrix protocols.

growth_protocol: PC-3 cells (ATCC # CRL-1435) were grown in RPMI supplemented with 10% heat-inactivated fetal bovine serum at 37°C in humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Near-confluent cells were serum starved overnight in basal RPMI media. PC-3 cells were further grown in RPMI with 1% FBS supplemented with recombinant human TGF-β1 (5ng/mL) or its vehicle (PBS-BSA 0.1%) for 48h.

tag: cell line

value: prostate cancer cell line

tag: treatment

value: vehicle (PBS-BSA 0.1%)

tag: treatment duration


title: CP55-T

description: acpp


title: CP60-T

description: cpp

value: OCT


title: CP133-T

description: cpp


title: CP66-T

description: cpc


title: CP136-T

description: acpp


title: CP57-T

description: cpp


title: CP132-T

description: acpp


title: TGF-β-treated PC-3 cells

description: PC3 T

source_name: PC-3 cells treated with TGF-β (5ng/mL, 48h)

value: TGF-β

tag: treatment dosage


title: cortex, SPAK KO 4

city: Baltimore

middle: R

last: Grimm

state: MD

address: 660 West Redwood Street

department: Physiology

institute: University of Maryland School of Medicine

description: Tissue comprising the renal cortex was disected from the rest of the kindey. Total RNA was subsequently extracted from the cortex tissue and used for the array.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Exon Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Mouse Gene 1.0 ST Exon Array were scanned using the AffyMetrix GeneChip Scanner 3000 7G.

data_processing: The data were normalized by Affymetrix Expression Console software using RMA method.

source_name: cortex from WTSPAK KO mouse 4

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix GeneChip WT Terminal Labeling and Hybridiazation User Manual from 6 ug total RNA.

growth_protocol: At weening tail snips were taken and used for PCR-based geneotyping to identify SPAK KO and littermate WT animals. Animals were sacrificed at 10 weeks of age.

treatment_protocol: Animals were given free access to water and feed. The diet fed to both groups contained 0.32% NaCl and 1% KCl.

tag: gender

value: male

value: kidney cortex

value: 10 weeks

tag: genotype

value: littermate SPAK (Stk39) KO


title: CP59-T

description: cpc


title: CP52-T

description: cpc


title: CP125-T

description: cpp


title: CP53-T

description: cpp


title: CP51-T

description: cpc


title: CP54-T

description: cpc


title: CP63-T

description: cpc


title: CP122-TB

description: acpp


title: CP122-TA

description: acpp


title: CP50-T

description: cpc


title: CP127-T

description: cpc


title: CP121-T

description: acpp


title: CP118-T

description: cpp


title: cortex, SPAK KO 2

source_name: cortex from WTSPAK KO mouse 2


title: cortex, WT 1

source_name: cortex from WT mouse 1

value: littermate wild type


title: CP43-T

description: cpc


title: CP45-T

description: cpp


title: cortex, WT 4

source_name: cortex from WT mouse 4


title: CP46-T

description: cpc


title: cortex, SPAK KO 3

source_name: cortex from WTSPAK KO mouse 3


title: cortex, WT 2

source_name: cortex from WT mouse 2


title: CP117-T

description: cpp


title: CP4-T

description: acpp

value: DNA


title: MEF+mHSF1-KD-HS_3

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45˚C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affimetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: DMEM containing 10% fetal bovine serum at 37˚C.

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Immortalized MEF cells (ICR background) were infected with and adenovirus expressing each shRNA (1 x 108 pfu/ml) for 2 h, and maintained with normal medium for 70 h. Cells were untreated or treated with heat shock at 42˚C for 1 h in water bath and then recovered at 37˚C for 6h.

tag: cell type

value: immortalized MEF cells

tag: shRNA

value: HSF1 knockdown

value: heat shock at 42˚C for 1 h and then recovered at 37˚C for 6 h


title: cortex, WT 3

source_name: cortex from WT mouse 3


title: CP115-T

description: cpc

value: choroid plexus carcinomas


title: cortex, SPAK KO 1

source_name: cortex from WTSPAK KO mouse 1


title: MEF+mHSF1-KD-HS_2


title: CP144-TB

description: cpc

value: mut


title: CP113-T

description: cpc

value: wt


title: CP146-T

description: cpc

value: frozen


title: CP41-TA

description: cpc


title: CP148-T

description: cpp

value: choroid plexus papillomas


title: MEF+mHSF1-KD-HS_1


title: CP114-T

description: cpp


title: CP143-TB

description: cpc


title: CP3-T

description: cpc


title: CP47-T

description: cpp


title: MEF+scr-HS_3

value: control


title: MEF+scr-HS_1


title: CP108-T

description: cpp


title: MEF+scr-HS_2


title: CP107-TA

description: cpp


title: CP104-T

description: cpp


title: MEF+scr-Cont_3


title: MEF+mHSF1-KD-Cont_2


title: CP103-T

description: cpp


title: MEF+mHSF1-KD-Cont_1


title: MEF+mHSF1-KD-Cont_3


title: CP141-TB

description: cpc


title: CP110-T

description: cpp


title: FACS isolated CNS surface glia 9.137-GFP, rep5

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

description:
sg_5
FACS isolated surface glia from 10-15 brains - both males and females used

hyb_protocol: The entire fragmented, labeled cDNA fraction was placed into a hyb cocktail volume of 150uL; 130uL were hybridized for 18-20 hr at 45C on GeneChip Drosophila Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: All microarray data analysis was performed using R/Bioconductor packages. CEL files were read and raw data normalized using RMA in the affy package. Prior to statistical analysis, probes were filtered if the Present sum was less than 4 for all genotypes; in other words, a probe needed to be expressed in at least one genotype to be included. This metric was shown to significantly reduce false positives. 7090 probes were filtered according to this criterion. The remaining probes were used for statistical analyses in the limma package. Pairwise comparisons were performed for all possible combinations, and fold changes and standard errors were estimated by fitting a linear model for each gene. Empirical Bayes smoothing to the standard errors was applied and differentially expressed genes were chosen according to an FDR-adjusted P < 0.05. Lists of differentially expressed genes were trimmed to ensure that genes were indeed expressed in the enriched genotype (expression > 100 AND Present sum ≥ 4).

organism: Drosophila melanogaster

source_name: Drosophila adult

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module kit from 3.5ug amplified RNA.

growth_protocol: All flies were raised and maintained on standard cornmeal molasses agar at 16˚C or room temperature.

extract_protocol: RNA was isolated using Ambion RNAqueous Micro columns and amplified using the NuGEN Ovation FFPE WTA System V3.

treatment_protocol: Brains were dissected under Schneider’s media (SM) and transferred directly to a chilled tube containing SM. Each tube contained 10-15 brains. Brains were washed with 1mL SM and resuspended in 220uL SM. Collagenase A (Roche No. 10103586001) and DNase I were added to final concentrations of 2mg/mL and 20 units, respectively. Brains were dissociated at 37˚C in a Thermomixer according to following conditions: 1000rpm for 20min (Elav/neurons), 500pm for 20min (Repo/all glia), and 500pm for 5min (9-137/surface glia). EDTA (pH 7) was added to a final concentration of 5mM to inactivate the collagenase. Dissociated tissue was filtered through a 70 or 100um filter and immediately sorted using a BD FACSAria at the Laboratory for Cell Analysis at UCSF.

value: brain

value: surface glia


title: FACS isolated CNS surface glia 9.137-GFP, rep4

description:
sg_4
FACS isolated surface glia from 10-15 brains - both males and females used


title: CP140-TB

description: cpc

source_name: brain tumor


title: MEF+scr-Cont_1


title: CP1-T

description: cpc


title: MEF+scr-Cont_2


title: CP139-TB

description: cpc


title: CP138-T

description: acpp

value: atypical choroid plexus papillomas


title: FACS isolated CNS surface glia 9.137-GFP, rep3

description:
sg_3
FACS isolated surface glia from 10-15 brains - both males and females used


title: FACS isolated CNS surface glia 9.137-GFP, rep2

description:
sg_2
FACS isolated surface glia from 10-15 brains - both males and females used


title: FACS isolated CNS surface glia 9.137-GFP, rep1

description:
sg_1
FACS isolated surface glia from 10-15 brains - both males and females used


title: CP142-TB

description: cpp


title: FACS isolated CNS glia REPO-GFP, rep5

description:
Repo_5
FACS isolated glia from 10-15 brains - both males and females used

value: all glia


title: 9322863087_D: Organoids

city: Groningen

first: lalitha

middle: sy

last: nanduri

state: Groningen

address: Antonius deusinglaan 1

department: cell biology

country: Netherlands

institute: university medical center groningen

description: replicate 3 out of 3

hyb_protocol: standard illumina hybridisation protocol

scan_protocol: standard illumina scanning protocol

data_processing: The data were normalised using the neqc function of the R/BioConductor library Limma (normalized expression by control background correction, quantile normalization and log2 transformation).

source_name: salivary gland

label_protocol: biotinylated cRNA was prepared for labeling

extract_protocol: RNA was extracted with Qiagen RNAeasy micro kit, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: female

value: salivary gland

tag: developmental stage

value: adult

tag: cell population

value: Organoids


title: 9322863087_A: Primary spheres

description: replicate 2 out of 2

value: Primary spheres


title: 9322863087_B: Organoids

description: replicate 2 out of 3


title: ATDC5 overexpressing GFP

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

description: SAMPLE 1

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: ATDC5 overexpressing GFP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Two stable DOX-inducible ATDC5 cell lines were seeded onto 60 mm dishes. They were cultured with 2 ug/mL DOX for 2 days, and differentiated with ITS for 3 weeks.

value: mouse chondrocyte cell line

tag: genotype/variation

value: overexpressing GFP


title: 9322863060_C: CD24hi/CD29hi_Passage-10 cells

description: replicate 2 out of 2


title: CP137-T

department: Genetics and Genome Biology

description: acpp


title: ATDC5 overexpressing A-CEBP

description: SAMPLE 2

source_name: ATDC5 overexpressing A-CEBP

value: overexpressing A-CEBP


title: CP136-T

description: acpp


title: CP128-T

description: cpc

value: choroid plexus carcinomas

value: mut

value: DNA


title: FACS isolated CNS glia REPO-GFP, rep4

description:
Repo_4
FACS isolated glia from 10-15 brains - both males and females used


title: BAB3277

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

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

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

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

source_name: patient genomic DNA

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: mutation

value: 0.241 Mb deletion spanning 17p13.1

tag: disease

value: 17p13.1 microdeletion syndrome [MIM 613776]

value: whole blood

source_name: Reference sample


title: FACS isolated CNS glia REPO-GFP, rep3

description:
Repo_3
FACS isolated glia from 10-15 brains - both males and females used

value: brain


title: 9322863022_D: CD24hi/CD29hi_Passage-0 cells

description: replicate 2 out of 2

tag: strain


title: BAB3302

value: 0.940 Mb deletion spanning 17p13.1


title: DECIPHER4155

value: 1.17 Mb deletion spanning 17p13.1


title: 9322863022_F: CD24hi/CD29hi_Passage-10 cells

description: replicate 1 out of 2

value: female


title: BAB3036

value: 0.157 Mb deletion spanning 17p13.1


title: CP122-TB

description: acpp

tag: tissue type

value: atypical choroid plexus papillomas

tag: p53 status

value: wt

value: OCT


title: CP132-T

description: acpp

tag: tissue source

value: frozen


title: CP119-T

description: cpp

value: choroid plexus papillomas


title: FACS isolated CNS glia REPO-GFP, rep2

description:
Repo_2
FACS isolated glia from 10-15 brains - both males and females used

tag: tissue

value: all glia


title: FACS isolated CNS glia REPO-GFP, rep1

description:
Repo_1
FACS isolated glia from 10-15 brains - both males and females used


title: BAB3045

value: 1.25 Mb triplication spanning 17p13.1

value: Phenotype includes absolute microcephaly, global development delay.

tag: cell line


title: CP133-T

description: cpp


title: 9322863022_B: Primary Spheres

description: replicate 1 out of 2

value: salivary gland

value: adult

value: Primary Spheres


title: CP122-TA

description: acpp


title: CP121-T

description: acpp


title: FACS isolated CNS neurons, ELAV-GFP, rep5

description:
Elav_5
FACS isolated neurons from 10-15 brains - both males and females used

value: neurons


title: 9322863015_F: Organoids

description: replicate 1 out of 3

value: Organoids


title: FACS isolated CNS neurons, ELAV-GFP, rep4

description:
Elav_4
FACS isolated neurons from 10-15 brains - both males and females used

value: brain


title: rdo5-1 at 14 days after pollination, biological rep2

city: koeln

first: Yong

last: Xiang

address: Carl-von-Linne-Weg 10

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Normalization, processing and statistical analysis of the raw data were performed using RankProd in R programming. Background correction, normalization, and summarization of probe sets were based on the Affymetrix AGRONOMICS Tiling Array [CDF: agronomics1attairg version 13.0.0] and RMA implemented in the Aroma.Affymetrix package.

source_name: rdo5-1 at 14 days after pollination

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip HT 3' IVT Express Kit Manual, Affymetrix).

growth_protocol: All plants were sown on soil and grown in a growth chamber with a 16-h-light/8-h-dark cycle (22°C/16°C)

extract_protocol: Total RNA was extracted from developing Arabidopsis siliques or imbibed seeds using RNAqueous columns and RNA isolation aid (Ambion) as described previously (Kushiro et al., 2004)

treatment_protocol: No treament

tag: genotype/varation


title: CP114-T

description: cpp


title: 9322863015_C: CD24hi/CD29hi_Passage-0 cells

description: replicate 1 out of 2


title: rdo5-1 at 14 days after pollination, biological rep3


title: CP118-T

description: cpp


title: Mouse tumor cells transduced with 18 ul STC1 shRNA virus_B2-18

city: Westmead

first: Andy

middle: C-M

last: Chang

state: New South Wales

address: 214 Hawkesbury Rd

department: Cancer Unit

country: Australia

institute: Children's Medical Research Institute

description:
B2_18
STC1(18 ul virus) replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization was performed using the normalization function in R/Bioconductor package called beadarray 2.10.0

source_name: 4T1ch9 cells

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

extract_protocol: RNA was extracted with  QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with agilent Bioanalyser.

value: Balb/c

value: 4T1ch9 cells

value: STC1 down-regulation

tag: transduction

value: 18 ul STC1 shRNA virus


title: FACS isolated CNS neurons, ELAV-GFP, rep3

city: San Francisco

description:
Elav_3
FACS isolated neurons from 10-15 brains - both males and females used


title: CP116-T

state: Ontario

description: cpp

value: wt


title: FACS isolated CNS neurons, ELAV-GFP, rep2

description:
Elav_2
FACS isolated neurons from 10-15 brains - both males and females used


title: rdo5-1 at 6 hours imbibed seeds, biological rep3

source_name: rdo5-1 at 6 hours imbibed seeds


title: Mouse tumor cells transduced with 18 ul STC1 shRNA virus_B1-18

description:
B1_18
STC1(18 ul virus) replicate 1


title: FACS isolated CNS neurons, ELAV-GFP, rep1

description:
Elav_1
FACS isolated neurons from 10-15 brains - both males and females used


title: AD8_DC_D4

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
4625016057_F
AD8_DC

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V3 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at CGC.

scan_protocol: The arrays were scanned using an Illumina BeadArray scanner and quantified using Genome Studio software (Illumina).

data_processing: Analysis of the iScan output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center (CGC) at http://www.vgtifl.org. Missing values were imputed using the KNN algorithm from the impute R package. Expression intensity filtering was performed keeping probe sets that have expression higher than log2(40) in at least 2 samples,  Expression variability  filtering was performed using the Inter Quartile Range (IQR) across the samples on the log2 is at least 0.3.  Quantile normalization was applied, followed by a log2 transformation and differential gene expression testing using Limma from Bioconductor.

source_name: CD4+ Tcell

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: SNARF labelled resting CD4+ T cells were cultured with or without syngeneic DC in the presence or absence of NL(AD8)-nef/EGFP (MOI 5) for 5 days, at which time SNARFhiEGFP- CD4+ T cells were sorted for gene expression analysis.

extract_protocol: totalRNA using Qiagen RNeasy Micro Kit  by the Laboratory of Dr. Sekaly at University of Montreal

treatment_protocol: Sorted SNARFhiEGFP- CD4+ T cells were lysed in RLT buffer and stored at -80oC prior to RNA extraction

tag: donor

tag: treatment

value: DC

tag: coculture

value: NL(AD8)-nef/EGFP (MOI 5)

tag: sorted population

value: SNARFhiEGFP- CD4+ Tcell


title: rdo5-1 at 14 days after pollination, biological rep1


title: CP115-T

description: cpc

value: choroid plexus carcinomas

value: mut

value: frozen


title: AD8_CCL19_D4

description:
4625016057_E
AD8_CCL19


title: rdo5-1 at 6 hours imbibed seeds, biological rep2


title: Canton S, wildtype, whole brain, rep5

description:
Brain5
5 brains total containing both male and female flies

tag: cell type

value: all CNS cells


title: CP110-T

description: cpp

value: choroid plexus papillomas


title: Mouse tumor cells transduced with 6 ul STC1 shRNA virus_A1-6

description:
A1_6
STC1(6 ul virus) replicate 1

value: 6 ul STC1 shRNA virus


title: AD8_ctrl_D4

description:
4625016057_D
AD8_ctrl

value: control


title: rdo5-1 at 6 hours imbibed seeds, biological rep1


title: Mock_DC_D4

description:
4625016057_C
Mock_DC

value: Mock


title: CP112-T

description: cpc


title: Mouse tumor cells transduced with 6 ul STC1 shRNA virus_A2-6

description:
A2_6
STC1(6 ul virus) replicate 2


title: Canton S, wildtype, whole brain, rep4

description:
Brain4
5 brains total containing both male and female flies

value: brain


title: rdo5-1 at dry seeds, biological rep2

source_name: rdo5-1 at dry seeds


title: rdo5-1 at dry seeds, biological rep3


title: Mock_CCL19_D4

description:
4625016057_B
Mock_CCL19


title: rdo5-1 at dry seeds, biological rep1


title: AD8_DC_D3

description:
4625016057_A
AD8_DC


title: Canton S, wildtype, whole brain, rep2

description:
Brain2
5 brains total containing both male and female flies


title: Canton S, wildtype, whole brain, rep3

description:
Brain3
5 brains total containing both male and female flies


title: CP113-T

description: cpc


title: NIL-DOG1 at 14 days after pollination, biological rep3

source_name: NIL-DOG1 at 14 days after pollination

value: wildtype


title: Mouse tumor cells transduced with 6 ul non-targeting shRNA virus_NTA

description:
NTA
control 1

value: Balb/c

value: 4T1ch9 cells

value: 6 ul non-targeting shRNA virus


title: Canton S, wildtype, whole brain, rep1

description:
Brain1
5 brains total containing both male and female flies


title: AD8_ctrl_D3

description:
4625016055_H
AD8_ctrl


title: KTS+ rep3

city: Parkville

last: Ekert

state: Vic

address: 1G Royal Parade

department: Cell Signalling and Cell Death

institute: Walter and Eliza Hall Institute of Medical Research

description: MEF

data_processing: Data was norm-exp background corrected, quantile normalized and log2 transformed, generated using the Bioconductor package limma

source_name: Murine embryonic fibroblasts infected with tetracycline repressible EWS/WT1+KTS

label_protocol: Standard Illumina labelling protocol

growth_protocol: Primary freshly generated MEFs, infected tetracycline repressible lentivrial vector expressing EWS/WT1-KTS, EWS/WT1+KTS or eGFP control

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen Sciences, MD, USA Cat number:74104).

treatment_protocol: No tetracycline

value: murine embryonic fibroblasts

tag: transgene

tag: genetic background


title: NIL-DOG1 at 14 days after pollination, biological rep2


title: KTS- rep3

description: MEF

source_name: Murine embryonic fibroblasts infected with tetracycline repressible EWS/WT1-KTS


title: CP109-T

description: cpp


title: GFP-rep4

description: MEF

source_name: Murine embryonic fibroblasts infected with GFP

value: GFP


title: CP107-TA

description: cpp

value: OCT


title: Mock_DC_D3

description:
4625016055_G
Mock_DC

value: DC

value: SNARFhiEGFP- CD4+ Tcell


title: CP108-T

description: cpp

value: wt


title: Mock_ctrl E4_D3

description:
4625016055_E
Mock_ctrl


title: CP107-T

description: cpp

value: mut

value: frozen


title: NIL-DOG1 at 14 days after pollination, biological rep1


title: Mock_CCL19_D3

description:
4625016055_F
Mock_CCL19


title: CGD-24

city: Turku

first: Tiina

last: Ilona

address: Tykistökatu 6A

institute: University of Turku

hyb_protocol: 750 ng each cRNA sample was hybridized to Illumina’s HumanHT-12 v3 Expression BeadChip at 58 C overnight (18 h) according to manufacturer's instructions.

scan_protocol: Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%) and the numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction.

data_processing: Quantile normalized and log2 transformed using Bioconductors LIMMA packages in R.

source_name: Whole blood

label_protocol: from 250 ng total RNA with Ambion's Illumina Total Prep RNA Amplification kit (cat # AMIL1791).cRNA concentrations where checked with Nanodrop ND-1000 and the quality was controlled by BioRad’s Experion electrophoresis station.

growth_protocol: Whole blood was used as sample material without any ex vivo treatment

extract_protocol: Blood was stored and RNA isolated using reagents in PAXgene Blood RNA Kit (Qiagen, cat# 762174) according to the manufacturer's instructions. Globin was removed using Ambion’s GLOBINclear™–Human Kit (cat# AM1980) using 1-2 ug of blood RNA as starting material.

tag: group

value: Healthy control

tag: mutation

value: No mutation

tag: age

value: Adult

tag: Sex

value: Male

tag: chip number

tag: chip position

value: J