title: 707_30 mg/kg bid GSK199

type: protein

city: Stanford

first: William

last: Robinson

address: 269 Campus Dr

institute: Stanford University

description: 1:250 dilution in PBS with 3% Fetal Bovine Serum

hyb_protocol: Synovial antigen arrays were produced using a robotic microarrayer to print peptides and proteins on SuperEpoxy2 microscope slides (ArrayIt Corporation, Sunnyvale, CA). On each slide, antigens were printed at 0.2 mg/ml in four replicates. Printed slides were first blocked overnight (PBS, 3% fetal bovine serum, 0.1% Tween 20) and then incubated for 1h at 4°C with individual mouse serum diluted 1:250 in PBS/3% fetal bovine serum.

scan_protocol: Slides were scanned to determine pixel intensities for each antigen feature at 532 nm to quantify IgG and IgM reactivity (Genepix 4400A, Molecular Devices, Sunnyvale, CA, USA). Images were saved as tiff files.

data_processing: GenePix Pro 7.0 software (Molecular Devices) was used to determine the net median pixel intensities for each antigen feature (each value is background-corrected by removing the background around each spotted protein). The median intensities for each protein were centered at 300 and log-scaled. A level of 10 digital fluorescence intensity units was set as a threshold for significant reactivity. The formula for values below 10 is log(10/300,2), and for all other values it is log(median pixel intensity/300,2).  Data analysis was performed using Significance Analysis for Microarrays (SAM) software (http://www-stat.stanford.edu/~tibs/SAM) to identify antigen features with statistically significant differences in reactivities between the experimental groups. Cluster software was then used to hierarchically group the samples and antigen features on the basis of a pairwise similarity function, and TreeView software was used to display the data as a heat map (http://rana.lbl.gov/EisenSoftware.htm).

molecule: protein

source_name: serum, 30 mg/kg bid GSK199

label_protocol: After washing with PBS/3% fetal bovine serum/0.1% Tween 20, reactive antibodies were detected using Cy3-conjugated goat-anti-mouse IgG/IgM secondary antibody (diluted 1:2,500 in PBS/3% fetal bovine serum; Jackson Immunoresearch). After incubating for 45 minutes at 4°C with the secondary antibody, the slides were washed with washing solution (PBS/3 % fetal bovine serum/0.1% Tween 20), then washed with PBS, water rinsed, and spun dry.

growth_protocol: Male DBA/1J mice were obtained from Jackson Laboratories and were between 6 and 8 weeks of age when experiments were initiated.

extract_protocol: All animals were sacrificed at day 35.

treatment_protocol: For induction of CIA, DBA/1J mice were injected intradermally with 100 µL of Incomplete Freund’s Adjuvant (IFA) containing 200 µg of bovine CII (Elastin Products) and 200 µg of inactivated Mycobacterium tuberculosis (H37Ra; Difco) on days 0 and 21. Each experimental group consisted of seven mice that were treated daily throughout the entire experiment, i.e. from day 0 of the first injection through to sacrifice on day 35, with one of three interventions: 0.9% NaCl (vehicle control), 30 mg/kg GSK199 qd, 30 mg/kg bid GSK199 (with a 6 hour interval between doses). All intervention injections were subcutaneous.

value: DBA (Jackson Laboratories)

tag: gender

value: male


title: 706_30 mg/kg bid GSK199

status: Public on Oct 08 2015

state: CA

country: USA

organism: Mus musculus

tag: strain


title: 705_30 mg/kg bid GSK199


title: 702_30 mg/kg bid GSK199


title: 701_30 mg/kg bid GSK199


title: 703_30 mg/kg bid GSK199


title: 709_30 mg/kg GSK199

source_name: serum, 30 mg/kg GSK199


title: 711_30 mg/kg GSK199


title: patient 32 with ALF - whole liver tissue mRNA - mRNA-ALF-32-3

type: RNA

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: specimen obtained from explanted liver of patient 32

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: tissue

value: whole liver

tag: phenotype

value: from OLT of HBV-associated acute liver failure


title: patient 31 with ALF - whole liver tissue mRNA - mRNA-ALF-31-3

source_name: specimen obtained from explanted liver of patient 31


title: patient 31 with ALF - whole liver tissue mRNA - mRNA-ALF-31-2


title: 727_Saline

source_name: serum, PBS vehicle control


title: patient 31 with ALF - whole liver tissue mRNA - mRNA-ALF-31-1


title: 726_Saline


title: patient 219 with ALF - whole liver tissue mRNA - mRNA-ALF-219-1

source_name: specimen obtained from explanted liver of patient 219


title: patient 219 with ALF - whole liver tissue mRNA - mRNA-ALF-219-4


title: patient 32 with ALF - whole liver tissue mRNA - mRNA-ALF-32-2


title: patient 241 with ALF - whole liver tissue mRNA - mRNA-ALF-241-2

source_name: specimen obtained from explanted liver of patient 241


title: patient 32 with ALF - whole liver tissue mRNA - mRNA-ALF-32-1


title: patient 219 with ALF - whole liver tissue mRNA - mRNA-ALF-219-3


title: 714_30 mg/kg GSK199


title: patient 241 with ALF - whole liver tissue mRNA - mRNA-ALF-241-1


title: 712_30 mg/kg GSK199


title: 708_30 mg/kg GSK199


title: 710_30 mg/kg GSK199


title: 704_30 mg/kg bid GSK199


title: patient 219 with ALF - whole liver tissue mRNA - mRNA-ALF-219-5


title: 724_Saline


title: 728_Saline


title: Input_1

type: genomic

city: Waltham

first: Michael

last: Marr

state: Massachusetts

address: 415 South St

department: Biology

institute: Brandeis University

description: Stable S2 cells sonicated

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner according to manufacturer's instruction.

data_processing: Data were processed using TAS software from Affymetrix

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Stable S2 cells sonicated

label_protocol: DNA was labeled as described (Sims HI, Chirn GW, Marr MT 2nd. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16516-21.)

growth_protocol: S2 cells containing stable dFOXO constitutive active construct were grown in schneiders media

extract_protocol: Chromatin was extracted as described (Puig O, Marr MT, Ruhf ML, Tjian R. Genes Dev. 2003 Aug 15;17(16):2006-20)

treatment_protocol: Copper Sulfate was added to 0.5mM to induce dFOXO, aftert 16 hours cells were crosslinked with formaldehyde.

tag: cell line

tag: antibody


title: FOXO IP_1

description: Stable S2 cells sonicated + IP

source_name: Stable S2 cells sonicated + IP

value: anti-dFOXO


title: 723_Saline


title: FOXO IP_2

description: Stable S2 cells sonicated + IP


title: patient 219 with ALF - whole liver tissue mRNA - mRNA-ALF-219-2


title: Fermentation_Xylose_ΔPHO13_run1

city: Kobe

first: Akihiko

last: Kondo

address: 1-1 Rokkodai, Nada

department: Chemical Science and Engineering

country: Japan

institute: Kobe University

description: 50 g/L xylose

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Yeast Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, R PMT is set to 100% and G PMT is set to 100%, XRD=0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 Apr08) and Grid: 015072_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ug RNA using the One-Color Low-input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer, and its quality checked by Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was obtained by following the protocol provided for the Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA, USA). RNA concentration and quality were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.

value: PHO13 deleted strain

tag: timepoint

value: after 9 hours of xylose fermentation


title: Fermentation_Xylose_ΔPHO13_run2

description: 50 g/L xylose


title: Fermentation_Xylose_Control_run2

description: 50 g/L xylose

value: Control strain


title: Fermentation_Xylose_Control_run1

description: 50 g/L xylose


title: Fermentation_Xylose_ΔPHO13_run3

description: 50 g/L xylose


title: Fermentation_Xylose_Control_run3

description: 50 g/L xylose


title: Input_3

description: Stable S2 cells sonicated


title: Input_2

description: Stable S2 cells sonicated


title: 722_Saline


title: rhl1a_Roots_TimePoint3_repl2

city: Katowice

first: Miroslaw

last: Kwasniewski

state: silesia district

address: Jagiellonska 28

country: Poland

institute: University of Silesia in Katowice

description: Gene expression in roots of rhl1.a mutant after 10 days of severe water stress

hyb_protocol: 55 µl of 2x the GE Hybridization mix (Agilent GE Hybridization Kit) was added to the fragmented cRNA and 110 was loaded onto the Agilent 4x44k Barley Array within a gasket array slide sandwich. Arrays were hybridised in a rotisserie hybridisation oven at 65°C for 17 hours (Agilent p/n G2545a Hybridization Oven). After 17 hours, the slides were removed from the oven and washed with Agilent Wash Buffers containing Triton X.

scan_protocol: After the wash, the slides were taken to be scanned on an Agilent High Resolution Scanner using the green dye channel at a resolution of a 5 µm single pass scan with no extended dynamic range.

data_processing: Scanned images were analysed using Agilent Feature extraction software version 10.7.3.1.

organism: Hordeum vulgare

source_name: rhl1.a, roots, after 10 days of severe water stress, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of RNA using the the Agilent Low Input Quick Amp Kit according to the manufacturer's instructions, followed by Qiagen RNeasy Mini Kit column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Water-deficiency stress experiment: seeds were sowed into Petri dishes that were filled with water-soaked vermiculite and were kept at 4°C in darkness for two days, and then were moved to 20°C in a greenhouse for another two days; germinated seeds were then placed in the pots filled with soil with known physicochemical properties, which was composed of clay and sand (7:2 ratio) and supplemented with a nutrient medium and plants were grown in the greenhouse conditions. Root hair formation transcriptome: seeds were surface sterilised with a 20% bleach solution (v/v) and germinated in sterile aeroponic conditions on a wet cotton wool plug, trapped between two glass tubes, which were linked with Parafilm M.

extract_protocol: Total RNA was isolated using an RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. After isolation, RNA was purified using precipitation in 1M lithium chloride. Each RNA precipitate was dissolved in nuclease-free H2O. The yield and purity of the RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Water-deficiency stress treatment: germinated seeds were inserted into pots evenly (15 per pot) and grown in the greenhouse at 20°C/18°C, 16/8 h photoperiod and 200 µEm-2s-1 light intensity that was provided by fluorescent lamps; during the control growth, the soil water content was maintained at 12% volumetric water content (vwc) by supplying water on daily basis (time point 1, control conditions); the water stress treatment was performed as follows: starting from the 11th day after sowing (DAS) the moisture was gradually decreased by limiting the irrigation in order to achieve 3% vwc on the 15th DAS (time point 2, onset of water stress); then the plants were transferred into a growth chamber with controlled conditions, where the temperature regime was set at 25°C/20°C day/night, 16/8 h photoperiod, 200 µEm-2s-1 light intensity; the soil moisture was maintained at 1.5% vwc; water stress treatment was applied for 10 days until the 25th DAS (time point 3, after 10 days of severe water stress); detached tissue samples were snap-frozen in liquid nitrogen and were stored at -80°C until RNA isolation.  Root hair formation transcriptome: six-day-old seedlings grown in aeroponic conditions were used for RNA isolation.

tag: cultivar

value: Karat

tag: genotype

value: Roots

tag: water stress time point

value: 3 (after 10 days of severe water stress)


title: WT_Roots_aeroponic_repl4

description: Gene expression in roots of wild-type barley in aeroponic conditions

source_name: wild-type, roots, aeroponic conditions, replicate 4

value: wildtype

value: aeroponic conditions


title: rhl1a_Roots_aeroponic_repl2

description: Gene expression in roots of rhl1.a mutant in aeroponic conditions

source_name: rhl1.a, roots, aeroponic conditions, replicate 2


title: WT_Roots_aeroponic_repl3

source_name: wild-type, roots, aeroponic conditions, replicate 3


title: rhl1a_Roots_TimePoint3_repl1

source_name: rhl1.a, roots, after 10 days of severe water stress, replicate 1


title: WT_Roots_TimePoint3_repl1

description: Gene expression in roots of wild-type barley after 10 days of severe water stress

source_name: wild-type, roots, after 10 days of severe water stress, replicate 1


title: rhl1a_Roots_aeroponic_repl3

source_name: rhl1.a, roots, aeroponic conditions, replicate 3


title: rhl1a_Roots_aeroponic_repl1

source_name: rhl1.a, roots, aeroponic conditions, replicate 1


title: WT_Roots_aeroponic_repl1

source_name: wild-type, roots, aeroponic conditions, replicate 1


title: rhl1a_Roots_TimePoint2_repl3

description: Gene expression in roots of rhl1.a mutant at onset of water stress

source_name: rhl1.a, roots, onset of water stress, replicate 3

value: 2 (onset of water stress)


title: WT_Roots_aeroponic_repl2

source_name: wild-type, roots, aeroponic conditions, replicate 2


title: rhl1a_Leaf_timePoint3_repl3

description: Gene expression in leaf of rhl1.a mutant after 10 days of severe water stress

source_name: rhl1.a, leaf no.2, after 10 days of severe water stress, replicate 3

value: Leaf no. 2


title: WT_Leaf_TimePoint3_repl3

description: Gene expression in leaf of wild-type barley after 10 days of severe water stress

source_name: wild-type, leaf no.2, after 10 days of severe water stress, replicate 3


title: rhl1a_Roots_aeroponic_repl4

source_name: rhl1.a, roots, aeroponic conditions, replicate 4


title: WT_Roots_TimePoint3_repl3

source_name: wild-type, roots, after 10 days of severe water stress, replicate 3


title: rhl1a_Roots_TimePoint3_repl3

source_name: rhl1.a, roots, after 10 days of severe water stress, replicate 3


title: rhl1a_Leaf_timePoint2_repl2

description: Gene expression in leaf of rhl1.a mutant at onset of water stress

source_name: rhl1.a, leaf no.2, onset of water stress, replicate 2


title: WT_Roots_TimePoint3_repl2

source_name: wild-type, roots, after 10 days of severe water stress, replicate 2


title: rhl1a_Roots_TimePoint2_repl1

source_name: rhl1.a, roots, onset of water stress, replicate 1


title: WT_Roots_TimePoint2_repl2

description: Gene expression in roots of wild-type barley at onset of water stress

source_name: wild-type, roots, onset of water stress, replicate 2


title: WT_Leaf_TimePoint3_repl2

source_name: wild-type, leaf no.2, after 10 days of severe water stress, replicate 2


title: WT_Leaf_TimePoint3_repl1

source_name: wild-type, leaf no.2, after 10 days of severe water stress, replicate 1


title: rhl1a_Roots_TimePoint2_repl2

source_name: rhl1.a, roots, onset of water stress, replicate 2


title: rhl1a_Leaf_timePoint2_repl3

source_name: rhl1.a, leaf no.2, onset of water stress, replicate 3


title: WT_Roots_TimePoint2_repl3

source_name: wild-type, roots, onset of water stress, replicate 3


title: 725_Saline

source_name: serum, PBS vehicle control


title: rhl1a_Leaf_timePoint2_repl1

source_name: rhl1.a, leaf no.2, onset of water stress, replicate 1


title: WT_Leaf_TimePoint2_repl1

description: Gene expression in leaf of wild-type barley at onset of water stress

source_name: wild-type, leaf no.2, onset of water stress, replicate 1


title: WT_Roots_TimePoint2_repl1

source_name: wild-type, roots, onset of water stress, replicate 1


title: 823 treated with MYCOII,biological rep1

city: beijing

first: shi

middle: qin

last: yuan

state: beijing

address: fucheng road 52#

department: tumor cancer research

country: China

institute: peking university

description: Gene expression data from BGC823cell treated with MYCOII for 24 hr

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 640 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Raw data were normalized with the RMA algorithm by Gene Spring Software 12.5 (Agilent technologies, Santa Clara, CA, US).

label: biotin

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: AGS and BGC823 cells (1x10^6/10 cm^2 plate) were treated with A2PP, CIP, MYCO I and MYCO II for 24 hr

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: AGS and BGC823 cells were treated with A2PP, CIP, MYCO I and MYCO II in a concentration of 10μM ,4 μg/ml,5 μg/ml and10 μg/ml.

tag: treatment

value: MYCOII for 24 hr


title: WT_Leaf_TimePoint2_repl2

source_name: wild-type, leaf no.2, onset of water stress, replicate 2


title: AGS treated with MYCOI,biological rep1

description: Gene expression data from AGScell treated with MYCOI for 24 hr

source_name: AGScell treated with MYCOI for 24 hr

value: AGS

value: MYCOI for 24 hr


title: AGS treated with CIP,biological rep1

description: Gene expression data from AGS cell treated with CIP for 24 hr

source_name: AGS cell treated with CIP for 24 hr

value: CIP for 24 hr


title: Ifnb+/+ +IFN-b sample 3

city: Lund

first: Robert

last: Carlsson

address: Sölvegatan 17

department: IKVL

country: Sweden

institute: Lund University

hyb_protocol: Fifteen micrograms of the biotin labeled cRNA was fragmented to strands between 35 and 200 bases in length, 10 micrograms of which was hybridised onto the GeneChip® Mouse genome 430 2.0 array (Affymetrix, Inc, Santa Clara, CA, USA) overnight in the GeneChip® Hybridisation oven 6400 using standard procedures.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: Affymetrix analysis and data sets were quantile normalized and processed by the RMA algorithm in Arraystar 3.0

source_name: CGN Ifnb+/+, IFN-b-treated, 3 days in culture

label_protocol: RNA quality and concentration was measured using an Agilent 2100 bioanalyzer and Nanodrop ND-1000 respectively. Total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as a template to generate biotin-targeted cRNA following manufacturer’s specifications.

growth_protocol: 7 day-old pups from wt (Ifnb+/+) and Ifnb–/– mice and were decapitated and cerebellum dissected. Neurons were proceessed to a single cell suspension and subsequently cultured poly-Dlysine coated culture dishes for 3 days in neurobasal medium containing P/S (1%), GlutaMax (1:1200), and B27 (1.5%).

extract_protocol: Trizol with DNAse cleanup

treatment_protocol: The CGNs were treated with IFN-beta (100U/ml) for 24 hours or left untreated before cell lysis on the 3rd day of culture.

value: Ifnb+/+

value: IFN-b

tag: cell type

value: Cerebellar granular neurons

tag: age

value: 3 days in culture


title: rhl1a_Roots_TimePoint1_repl1

description: Gene expression in roots of rhl1.a mutant in control conditions

source_name: rhl1.a, roots, control conditions, replicate 1

value: 1 (control conditions)


title: rhl1a_Roots_TimePoint1_repl3

source_name: rhl1.a, roots, control conditions, replicate 3


title: 713_30 mg/kg GSK199

source_name: serum, 30 mg/kg GSK199

value: DBA (Jackson Laboratories)

value: male


title: rhl1a_Leaf_timePoint1_repl2

description: Gene expression in leaf of rhl1.a mutant in control conditions

source_name: rhl1.a, leaf no.2, control conditions, replicate 2

value: Karat


title: WT_Leaf_TimePoint2_repl3

source_name: wild-type, leaf no.2, onset of water stress, replicate 3


title: AGS treated with A2PP,biological rep1

description: Gene expression data from AGScell treated with A2PP for 24 hr

source_name: AGScell treated with A2PP for 24 hr

value: A2PP for 24 hr


title: AGS treated with MYCOII,biological rep1

description: Gene expression data from AGScell treated with MYCOII for 24 hr

source_name: AGScell treated with MYCOII for 24 hr


title: rhl1a_Leaf_timePoint1_repl3

source_name: rhl1.a, leaf no.2, control conditions, replicate 3


title: Ifnb+/+ +IFN-b sample 1


title: Ifnb+/+ sample 3

source_name: CGN Ifnb+/+, untreated, 3 days in culture

value: untreated


title: 823 treated with A2PP,biological rep1

description: Gene expression data from BGC823cell treated with A2PP for 24 hr

source_name: BGC823cell treated with A2PP for 24 hr


title: Ifnb+/+ +IFN-b sample 2


title: rhl1a_Leaf_timePoint3_repl2

source_name: rhl1.a, leaf no.2, after 10 days of severe water stress, replicate 2

value: 3 (after 10 days of severe water stress)


title: rhl1a_Roots_TimePoint1_repl2

source_name: rhl1.a, roots, control conditions, replicate 2

value: Roots


title: rhl1a_Leaf_timePoint1_repl1

source_name: rhl1.a, leaf no.2, control conditions, replicate 1

value: Leaf no. 2


title: Ifnb+/+ sample 1


title: Ifnb+/+ sample 2


title: egr1-1egr2-1 at -1.2 MPa, biological rep 3_stress

city: Taipei

first: Bhaskara

last: Goivnal Badiger

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

department: Institue of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression data of egr1-1egr1-2 at control condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: egr1-1egr2-1 at stress condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seedlings were grown on agar plates containing half-strength MS salts and 2 mM MES buffer.  No sugar was added to the media.  Plates were positioned vertically for seeding growth along the surface of the agar and were kept in a growth chamber at 25 C, continuous light at 85-100 micromol photons m-2 sec-1 and high (80-90%) relative humidity.

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

treatment_protocol: Seven-day-old seedlings were transferred from agar plates of control media to agar plates of fresh control media (water potential -0.25 MPa) or low water potential agar plates (-1.2 MPa).  Low water potential plates were prepared by overlaying a solution of polyethylene glycol (molecular weight 8000) on the control agar plates and equilibrating overnight.  Details of PEG-agar plate preparation can be found in Verslues et al., Plant J 45:523-539 2006.  After transfer to treatment plates, seedlings were returned to growth chamber for 96 h before sample collection.

value: seedlings

value: 7 days


title: 823 treated with MYCOI,biological rep1

description: Gene expression data from BGC823cell treated with MYCOI for 24 hr

source_name: BGC823cell treated with MYCOI for 24 hr

value: MYCOI for 24 hr


title: 823 treated with CIP,biological rep1

description: Gene expression data from BGC823 cell treated with CIP for 24 hr

source_name: BGC823 cell treated with CIP for 24 hr

value: CIP for 24 hr


title: Ifnb-/- +IFN-b sample 3

source_name: CGN Ifnb–/–, IFN-b-treated, 3 days in culture

value: Ifnb-/-


title: WT_Roots_TimePoint1_repl3

description: Gene expression in roots of wild-type barley in control conditions

source_name: wild-type, roots, control conditions, replicate 3

value: wildtype


title: NCI-H1963

status: Public on Oct 07 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a HiScan Reader (Illumina).

data_processing:
Genomic DNA extracted from cancer cell lines was genotyped using Infinium HumanOmni5-quad-v1 Genotyping BeadChips (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

label_protocol: 400ng of genomic DNA was whole-genome amplified in an overnight reaction at 37ºC using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cultured cell lines was performed using proteinase K and repeated phenol-chloroform extraction.

value: small cell lung cancer


title: WT_Leaf_TimePoint1_repl3

description: Gene expression in leaf of wild-type barley in control conditions

source_name: wild-type, leaf no.2, control conditions, replicate 3


title: WT_Leaf_TimePoint1_repl2

source_name: wild-type, leaf no.2, control conditions, replicate 2


title: Ifnb-/- +IFN-b sample 1

value: IFN-b

value: Cerebellar granular neurons

value: 3 days in culture


title: WT_Roots_TimePoint1_repl2

source_name: wild-type, roots, control conditions, replicate 2

value: 1 (control conditions)


title: Ifnb-/- sample 2

source_name: CGN Ifnb–/–, untreated, 3 days in culture


title: DMS-114

description: Genomic DNA extracted from cancer cell lines was genotyped using Infinium HumanOmni5-quad-v1 Genotyping BeadChips (Illumina).


title: Ifnb-/- sample 3


title: HCC-33


title: egr1-1egr2-1 at  -0.25 MPa, biological rep 3_control

source_name: egr1-1egr2-1 at control condition


title: WT_Leaf_TimePoint1_repl1

source_name: wild-type, leaf no.2, control conditions, replicate 1

value: Karat


title: NCI-N417


title: egr1-1egr2-1 at  -0.25 MPa, biological rep 2_control


title: NCI-H1048


title: Ifnb-/- +IFN-b sample 2


title: NCI-H740


title: Ifnb-/- sample 1


title: egr1-1egr2-1 at  -0.25 MPa, biological rep 1_control


title: egr1-1egr2-1 at  -1.2 MPa, biological rep 2_stress


title: DMS-273


title: NCI-H2171


title: rhl1a_Leaf_timePoint3_repl1

description: Gene expression in leaf of rhl1.a mutant after 10 days of severe water stress

source_name: rhl1.a, leaf no.2, after 10 days of severe water stress, replicate 1


title: NCI-H1672


title: WT_Roots_TimePoint1_repl1

source_name: wild-type, roots, control conditions, replicate 1


title: NCI-H2029


title: egr1-1egr2-1 at  -1.2 MPa, biological rep 1_stress


title: wild type rep 2 lung

city: Tampere

first: Maarit

middle: Susanna

last: Patrikainen

address: Medisiinarinkatu 3

department: School of Medicine/Anatomy

country: Finland

institute: University of Tampere

description: SAMPLE 30

hyb_protocol: Each sample were hybridized onto Illumina’s Sentrix® Mouse Ref-8 v2 Bead Chips (Illumina, Inc., San Diego, CA) and hybridization was carried out using Illumina Whole-Genome Gene Expession Direct Hybridization Assay (Illumina, Inc.) by Gen-Probe Life Sciences Ltd.

scan_protocol: Scanning was carried out using Illumina Iscan (Illumina, Inc.). Samples were analyzed using GenomeStudio (2010.3) Gene Expression Module (1.8.0) software by Gen-Probe Life Sciences Ltd.

data_processing: Trachea and Lung array data were normalized separately with Chipster version 2.9.0 using the quantile normalization method.

source_name: mouse lung

label_protocol: 150 ng total RNA from each sample was converted to double-stranded cDNA, and amplified using Biotin-label protocol from Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Inc., TX, USA) by Gen-Probe Life Sciences Ltd. at Oak Business Park in Manchester, UK.

extract_protocol: Total RNAs were purified using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). On-column DNase digestion was performed during RNA purification process. RNA concentrations, A260/280, and A260/230 ratios were determined using the ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, USA).

value: male

value: 2 months

tag: genotype/variation

value: wild-type


title: knockout rep 1 lung

description: SAMPLE 29


title: wild type 7 trachea

description: SAMPLE 27

source_name: mouse trachea


title: knockout rep 5 trachea

description: SAMPLE 31


title: wild type rep 2 trachea

description: SAMPLE 32


title: wild type 5 trachea

description: SAMPLE 25


title: wild type 6 trachea

description: SAMPLE 26


title: wild type 4 trachea

description: SAMPLE 24


title: wild type 3 trachea

description: SAMPLE 23


title: wild type 1 trachea

description: SAMPLE 21


title: knockout 7 trachea

description: SAMPLE 20


title: wild type 8 trachea

description: SAMPLE 28


title: knockout 5 trachea

description: SAMPLE 18


title: Ovarian Sample JB 4160

city: New York

first: Douglas

last: Levine

state: NY

address: 1275 York Ave.

department: Surgery

institute: MSKCC

description: ST

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

source_name: short time OVCA survivor

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Tissue were collected according to standard conditions.

tag: disease state

value: OVCA

tag: survival

value: ST

value: Tube


title: wild type 2 trachea

description: SAMPLE 22


title: knockout 1 trachea

description: SAMPLE 15


title: Ovarian Sample JB 4387

description: ST

value: Ovary


title: Ovarian Sample JB 4757

description: ST


title: knockout 2 trachea

description: SAMPLE 16


title: knockout 6 trachea

description: SAMPLE 19


title: Ovarian Sample JB 1989

description: ST


title: wild type 8 lung

description: SAMPLE 14


title: Ovarian Sample JB 4079

description: ST

value: Peritoneum


title: wild type 5 lung

description: SAMPLE 11


title: wild type 7 lung

description: SAMPLE 13


title: wild type 3 lung

description: SAMPLE 9


title: Ovarian Sample GL 5113

description: ST


title: Ovarian Sample JB 1045

description: LT

source_name: long time OVCA survivor

value: LT


title: Ovarian Sample JB 3025

description: ST


title: Ovarian Sample GL 3793

description: ST


title: Ovarian Sample JB 4900

description: ST


title: wild type 2 lung

description: SAMPLE 8


title: Ovarian Sample JB 1412

description: LT


title: wild type 4 lung

description: SAMPLE 10


title: Ovarian Sample JB 1738

description: LT


title: knockout 6 lung

description: SAMPLE 5


title: Ovarian Sample JB 5223

description: ST


title: Ovarian Sample JB 1001

description: LT


title: knockout 5 lung

description: SAMPLE 4


title: knockout 7 lung

description: SAMPLE 6


title: Ovarian Sample JB 1209

description: LT


title: Ovarian Sample JB 3838

description: ST


title: Ovarian Sample JB 1796

description: LT


title: Ovarian Sample JB 4860

description: ST


title: Ovarian Sample JB 2011

description: LT


title: knockout 1 lung

description: SAMPLE 1


title: Ovarian Sample JB 126

description: LT


title: Ovarian Sample JB 2063

description: LT


title: Ovarian Sample JB 1843

description: LT


title: knockout 4 lung

description: SAMPLE 3


title: knockout 4 trachea

description: SAMPLE 17


title: knockout 2 lung

description: SAMPLE 2


title: wild type 6 lung

description: SAMPLE 12


title: wild type 1 lung

description: SAMPLE 7


title: Ovarian Sample JB 337

description: LT


title: Ovarian Sample JB 471

description: LT


title: Primary AML patient 1183

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

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

data_processing: Genome Studio V2011.2. Unmethylated and methylated signal intensities included in signals_AML.txt file.

source_name: Primary AML patient

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: blood

tag: dnmt3a mutation status

value: Wildtype


title: H2030-BrM3 PARP1 targeting shRNA-2

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

country: South Korea

institute: KAIST

description:
SAMPLE 3
9477874112_L_Grn.idat

hyb_protocol: Biotin labeled cRNA are hybridized withIllumina Human HT-12 v4 chip using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScan scanner

data_processing: The data is analyzed using Illumina GenomeStudio software. Framwork version: v2011.1, Gene Expression module version: 1.9.0. There are 14 probes for which there is no raw data available.

source_name: H2030-BrM3 PARP1 targeting shRNA-2

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

growth_protocol: H2030-BrM3 cells were cultured in RPMI 1640 (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 1 days.

extract_protocol: Total RNAs were isolated using Rneasy Mini Kit  (Qiagen, Valencia, CA) according to manufacturer's protocol.

value: Lung adenocarcinoma


title: Primary AML patient 1302


title: H2030-BrM3 PARP1 targeting shRNA-1

description:
SAMPLE 2
9477874112_K_Grn.idat

source_name: H2030-BrM3 PARP1 targeting shRNA-1


title: Primary AML patient 1180


title: Primary AML patient 1554


title: Primary AML patient 1166


title: Primary AML patient 1274


title: Primary AML patient 919


title: Primary AML patient 933


title: Primary AML patient 1557


title: Primary AML patient 595


title: Primary AML patient 1328


title: Primary AML patient 1082


title: Primary AML patient 1621


title: Primary AML patient 589


title: H2030-BrM3 non-targeting shRNA

description:
SAMPLE 1
9477874112_J_Grn.idat

source_name: H2030-BrM3 non-targeting shRNA


title: Primary AML patient 1085


title: Primary AML patient 1497


title: Primary AML patient 1496


title: Primary AML patient 1301


title: Primary AML patient 922


title: Primary AML patient 1035


title: Primary AML patient 1615


title: Primary AML patient 1488


title: Primary AML patient 1515


title: Primary AML patient 1011


title: Primary AML patient 1464


title: Primary AML patient 1514


title: Primary AML patient 1384


title: Primary AML patient 1456


title: Primary AML patient 1495


title: Primary AML patient 1479


title: Primary AML patient 1530


title: Primary AML patient 1478


title: Primary AML patient 1449


title: Primary AML patient 1480


title: Primary AML patient 1383


title: Primary AML patient 1361


title: Primary AML patient 1155


title: Primary AML patient 1306


title: FLS RA patient + TNFa

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: The slides were washed and stained on a GeneChip® Fluidics Station (Affymetrix) and scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing: Fluorescence intensity data were normalized by robust multiarray analysis (RMA) using GeneSpring® (Agilent Technologies, Santa Clara, CA).

source_name: Fibroblast-like synovial cells, cultured overnight, stimulated overnight with 10 ng/ml recombinant human TNFa

label_protocol: RNA was labeled using a One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Minced synovial fragments were digested in 1 mg/ml hyaluronidase solution (Sigma-Aldrich) for 15 minutes at 37°C and 6 mg/ml collagenase type IV (Invitrogen) for 2 hours at 37°C. Next, cells were washed, resuspended in high-glucose Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 1% antibiotics-antimycotics (Invitrogen), 1% minimum essential medium sodium pyruvate (Invitrogen) and 10% foetal calf serum, and seeded at 10,000 cells per square centimeter in six-well plates. When the cells reached confluence, adherent cells were detached using sterile 0.5% trypsin-ethylenediaminetetraacetic acid (EDTA; Invitrogen).

extract_protocol: Total RNA was extracted using the Nucleospin RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integriti number (RIN) > 7

treatment_protocol: Cells were used between passages 7 and 9, seeded at 25,000/well in 24-well plates, and cultured overnight with or without 10 ng/ml recombinant human TNFα (R&D Systems).

tag: disease

value: rheumatoid arthritis

tag: gender

value: Female


title: Primary AML patient 1341

tag: tissue


title: U-2OS CDK11 siRNA

city: Boston

first: Yong

last: Feng

state: MA

address: 100 Fruit St

institute: Massachusetts General Hospital

hyb_protocol: Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu)

scan_protocol: The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide

data_processing: GeneSifter and Qlucore were used to analyze the microarray data (http://www.genesifter.net/web/; http://www.qlucore.com). Fold change in expression between CDK11 siRNA treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

source_name: osteosarcoma cell line with CDK11 siRNA

label_protocol: To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis

growth_protocol: The U-2OS and KHOS osteosarcoma cell lines where seeded onto the 100mm cell culture plate

extract_protocol: Total RNA was collected from these cells using TRIzol® Reagent (GIBCO Grand Island, NY) according to the manufacturer’s instructions

treatment_protocol: Cell were treated with CDK11 siRNA (40nM) or nonspecificsiRNA (40nM)

tag: transfection

value: CDK11 siRNA


title: U-2OS nonspecific siRNA

source_name: osteosarcoma cell line with nonspecific siRNA

tag: cell line

value: nonspecific siRNA


title: Primary AML patient 1305


title: FLS OA patient

source_name: Fibroblast-like synovial cells, cultured overnight, no stimulation

value: osteoarthritis

value: Male


title: Primary AML patient 1154


title: FLS OA patient + TNFa


title: Primary AML patient 1429


title: Primary AML patient 1448


title: Primary AML patient 1333


title: KHOS CDK11 siRNA

value: KHOS


title: Primary AML patient 1362


title: Primary AML patient 1319


title: U-2OS control

source_name: osteosarcoma cell line


title: Primary AML patient 587


title: KHOS nonspecific siRNA


title: Primary AML patient 1156


title: Primary AML patient 1182

value: Mutant


title: Primary AML patient 1300


title: Primary AML patient 1044


title: Primary AML patient 1635


title: Primary AML patient 1304


title: Primary AML patient 1627


title: Primary AML patient 577


title: Primary AML patient 1552


title: Primary AML patient 1486


title: FLS RA patient


title: SW403 mirZIP429 A

status: Public on Oct 06 2015

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description:
9423641054_I
Replicate A

hyb_protocol: Hybridization of aRNAs (750 ng) was carried out using Illumina Human 48k gene chips (Human HT-12 V4 BeadChip). Array washing was performed using Illumina High-stringency wash buffer for 10 min at 55°C.

scan_protocol: Hybridized BeadChips were stained according to standard Illumina protocols and scanned with the Illumina BeadArray Reader.

data_processing:
Non-normalized data were generated by the Illumina GenomeStudio software version V2011.1. Data were Loess normalized with the Lumi R package.
GSE59883_non-normalized.txt: Signal values and detection p-values as provided by the Illumina Genome Studio software.
Sample data table: Normalized signal values as provided by the Lumi R package.

source_name: SW403 cells transduced with miRZIP-429

label_protocol: Synthesis of cDNA and biotinylated aRNA was performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500ng of total RNA. Quality assessment and quantification of cRNAs were performed on Bioanalyzer 2100.

growth_protocol: HT29, NCI-H508 and SW403 colon cancer cell lines were obtained from American Type Culture Collection (ATCC). All cells were regularly authenticated by the Promega Cell ID system, which is based on sequencing known STRs (short-tandem repeats). HT29 and NCI-H508 cell lines were cultured in RPMI-1640 medium (Gibco). SW403 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Gibco). The medium was supplemented with 10% FBS (Gibco) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen), according to the manufacturer's protocol. The quantification and quality analysis of RNA were performed on a Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were transduced with a 1:3 dilution of supernatants containing miRZip Lentiviral vectors (System Biosciences). Transduction was followed by selection with puromycin (2 ng/ml). The miRZip vectors were used to downregulate mir-194 (cat. n. SBMZIP194PA1), miR-200b (cat. n. SBMZIP200bPA1), miR-203 (cat. n. SBMZIP203PA1) and miR-429 (cat. n. SBMZIP429PA1); pGreenPuro Scramble Harpin Control Vector (cat. n. SBMZIP000PA1) was used as negative control. All lentiviral supernatants were produced by Lipofectamine (Invitrogen) transfection of HEK293T cells.

value: colorectal cancer (CRC) cell line

tag: mirzip


title: SW403 WT A

description:
9423641054_D
Replicate A

source_name: SW403 cells wild-type


title: KHOS control


title: SW403 mirZIP429 B

description:
9423641058_I
Replicate B


title: SW403 Scramble B

description:
9423641058_D
Replicate B

source_name: SW403 cells transduced with Scramble Vector

value: scramble vector


title: HT29 mirZIP429 B

description:
9445264071_G
Replicate B

source_name: HT29 cells transduced with miRZIP-429


title: HT29 mirZIP429 A

description:
9445264082_G
Replicate A


title: Blastocysts from complete in vitro culture vs. in vivo blastocysts-replicate 4

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

country: Germany

institute: University of Bonn

description: The DNA methylation pattern of blastocysts derived from complete in vitro  culture were determined with reference to the complete vivo blastocysts

hyb_protocol: Non incorporated ULS-Cy3/5 was removed using  QIAquick PCR Purification Kit and hybridizations were performed by mixing  labeled gDNA with of hybridization master mix containing bovine Cot-1 DNA, Agilent 100x Blocking Agent and  Agilent 2x HI-RPM, Hybridization Buffer (Agilent Technologies). The samples were incubated at 95°C for 3 min and at 37°C for 30 min and then 65 μL of Agilent-CGHBlock was added. The samples were loaded onto the microarray and hybridization was performed for 40 h at 65°C and 20 rpm.

scan_protocol: Slides were scanned using Agilent’s High-Resolution Scanner (Agilent Technologies, CA, and USA

data_processing: Agilent Feature Extraction Software was used quantify the array images. Loess normalization, quantile inter-array scale normalization was performed and fitted to a linear model and  Bayesian statistics of differential expression were obtained. Differentially methylated probes were identified using linear models for microarray data (limma).

organism: Bos taurus

label_protocol: Two micrograms of  amplified gDNA was labelled using with either Cy-3 or Cy-5 dyes using ULS Fluorescent gDNA labelling kit (Kreatech Biotechnology) according to the manufacturer's protocol

growth_protocol: Embryos were cultured partially under in vitro condition followed by in vivo condition.or under complete in vitro or in vivo condition.

extract_protocol: Genomic DNA was isolated from all blastocyst groups using the Allprep DNA/RNA micro kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Blastocysts were categorized according to the culture source of the early preimplantation embryos

value: Blastocyst

value: day 7 embryo

source_name: Blastocysts from complete in vivo  culture


title: Blastocysts from complete in vitro culture vs. in vivo blastocysts-replicate 2


title: HT29 mirZIP200b B

description:
9445264071_F
Replicate B

source_name: HT29 cells transduced with miRZIP-200b


title: SW403 WT B

description:
9423641058_C
Replicate B


title: HT29 mirZIP200b A

description:
9445264082_F
Replicate A


title: Primary AML patient 1299


title: Primary AML patient 1452


title: Blastocysts from in vitro zygote transfer vs. in vivo blastocysts-replicate 3

description: The DNA methylation pattern of blastocysts derived from in vitro zygotes transferred to the recipients were determined with reference to the complete vivo blastocysts


title: Blastocysts from in vitro 16 cell transfer vs. in vivo blastocysts- replicate 1

description: The DNA methylation pattern of blastocysts derived from in vitro 16 cell embryos transferred to the recipients were determined with reference to the complete vivo blastocysts


title: Blastocysts from in vitro 16 cell transfer vs. in vivo blastocysts- replicate 3


title: HT29 Scramble B

description:
9445264082_D
Replicate B

source_name: HT29 cells transduced with Scramble Vector


title: NCIH508 mirZIP429 B

description:
9445264095_K
Replicate B

source_name: NCI-H508 cells transduced with miRZIP-429


title: SW403 Scramble A

description:
9423641054_E
Replicate A


title: HT29 WT A

description:
9445264071_A
Replicate A

source_name: HT29 cells wild-type


title: HT29 mirZIP194 B

description:
9445264071_E
Replicate B

source_name: HT29 cells transduced with miRZIP-194


title: Blastocysts from complete in vitro culture vs. in vivo blastocysts-replicate 1


title: Blastocysts from in vitro 4 cell transfer vs. in vivo blastocysts-replicate 1

description: The DNA methylation pattern of blastocysts derived from in vitro 4 cell embryos transferred to the recipients were determined with reference to the complete vivo blastocysts


title: NCIH508 mirZIP200b A

description:
9445264085_J
Replicate A

source_name: NCI-H508 cells transduced with miRZIP-200b


title: NCIH508 mirZIP200b B

description:
9445264095_I
Replicate B


title: HT29 mirZIP194 A

description:
9445264082_E
Replicate A


title: Blastocysts from in vitro 16 cell transfer vs. in vivo blastocysts- replicate 4


title: Blastocysts from complete in vitro culture vs. in vivo blastocysts-replicate 3


title: HT29 Scramble A

description:
9445264071_D
Replicate A


title: NCIH508 mirZIP203 B

description:
9445264095_B
Replicate B

source_name: NCI-H508 cells transduced with miRZIP-203


title: NCIH508 mirZIP429 A

description:
9445264085_F
Replicate A


title: NCIH508 mirZIP194 B

description:
9445264095_A
Replicate B

source_name: NCI-H508 cells transduced with miRZIP-194


title: Blastocysts from in vitro 16 cell transfer vs. in vivo blastocysts- replicate 2


title: Blastocysts from in vitro zygote transfer vs. in vivo blastocysts-replicate 4


title: Blastocysts from in vitro zygote transfer vs. in vivo blastocysts-replicate 1


title: HT29 WT B

description:
9445264082_A
Replicate B


title: NCIH508 mirZIP203 A

description:
9445264085_C
Replicate A


title: NCIH508 Scramble B

description:
9445264095_G
Replicate B

source_name: NCI-H508 cells transduced with Scramble Vector


title: Blastocysts from in vitro zygote transfer vs. in vivo blastocysts-replicate 2


title: Blastocysts from in vitro 4 cell transfer vs. in vivo blastocysts-replicate 2


title: 992RMS RRMS treated with IFNb

city: Ramat-Gan

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

description: RRMS treated with IFNb

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization)

source_name: PBMC from IFNb treated RRMS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: PBMC were purified from Ficoll hypaque gradient (Invitrogen, USA)

value: male

tag: age (years)

tag: edss

value: IFNb


title: Blastocysts from in vitro 4 cell transfer vs. in vivo blastocysts-replicate 3


title: Blastocysts from in vitro 4 cell transfer vs. in vivo blastocysts-replicate 4


title: NCIH508 Scramble A

description:
9445264085_G
Replicate A


title: 1032RMS RRMS treated with IFNb

description: RRMS treated with IFNb


title: NCIH508 WT A

description:
9445264085_I
Replicate A

source_name: NCI-H508 cells wild-type


title: 997RMS RRMS treated with IFNb

description: RRMS treated with IFNb


title: NCIH508 mirZIP194 A

description:
9445264085_A
Replicate A


title: 1048RMS RRMS treated with IFNb

description: RRMS treated with IFNb


title: NCIH508 WT B

description:
9445264095_F
Replicate B


title: 781RMS RRMS untreated

description: RRMS untreated

source_name: PBMC from untreated RRMS

value: untreated


title: Inactivated RSV and human serum donor 4

city: Nijmegen

first: Marloes

last: Vissers

address: Geert Grooteplein Zuid 10

department: Department of Pediatrics

country: Netherlands

institute: Radboud university medical center

hyb_protocol: Hybridization was performed following Nimblegen's standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed following Nimblegen's standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA quantile normalization in Arraystar.

source_name: PBMC

label_protocol: Labeling was performed following Nimblegen's standard operating protocol. See www.nimblegen.com.

growth_protocol: PBMCs isolated according to protocol of Vissers et al. Journal of Visualized Experiments 2013.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed with Turbo DNase (DNA-free kit, Ambion).

treatment_protocol: PBMCs were treated according to protocol of Vissers et al.

tag: sample type

value: Inactivated RSV and human serum donor


title: 8766RR164 RRMS treated with IFNb

description: RRMS treated with IFNb


title: Inactivated RSV and antibody depleted human serum donor 2


title: 670RMS RRMS untreated

description: RRMS untreated

value: female


title: 840RMS RRMS treated with IFNb

description: RRMS treated with IFNb


title: Inactivated RSV and antibody depleted human serum donor 3


title: 518RMS RRMS untreated

description: RRMS untreated


title: 807RMS RRMS untreated

description: RRMS untreated


title: 679RMS RRMS untreated

description: RRMS untreated


title: Inactivated RSV and antibody depleted human serum donor 4


title: 1850REB51 RRMS treated with IFNb

description: RRMS treated with IFNb


title: 568RMS RRMS untreated

description: RRMS untreated


title: 1950REB50 RRMS treated with IFNb

description: RRMS treated with IFNb


title: Inactivated RSV and human serum donor 3


title: 1412REB50 RRMS treated with IFNb

description: RRMS treated with IFNb


title: Inactivated RSV and antibody depleted human serum donor 1


title: 1378REB50 RRMS treated with IFNb

description: RRMS treated with IFNb


title: Inactivated RSV and human serum donor 2


title: Set982111OUT98 RRMS untreated

description: RRMS untreated


title: MiceLungTissue_Control_12d

city: Nanjing

first: HAO

last: SUN

state: Jiangsu

address: Guangzhou Road 300

department: Department of Emergency

institute: The first affiliated hospital with Nanjing Medical University

description: lncRNA expression after 12d in control mice lung tissues

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B). Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology Agilent p/n 5190-0442) with minor modifications. Briefly, mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mice were housed on a constant 12 h light/12 h dark cycle in a temperature (22.2℃)-controlled room and given ad libitum access to ordinary chow.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Mice in the model group were administered 10mg/kg paraquat (SIGMA Chemical Co., St. Louis, MO, USA) dissolved in sterile saline via intraperitoneal injection (once per day for 5 days). The normal control group were administered an equal volume of saline at the same time. Mice were examined daily, body weights and survival rates were recorded daily. Lung tissues were harvested on the 12st day following the first treatment.

tag: strain

value: BALB/c

value: lower lobe right lung

value: 8 weeks

value: control


title: MiceLungTissue_PQ_12d

description: lncRNA expression after 12d in paraquat treated mice lung tissues

tag: treatment

value: paraquat


title: 341REB51 RRMS untreated

description: RRMS untreated

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


title: Inactivated RSV and human serum donor 1


title: Inactivated RSV donor 3

value: Inactivated RSV donor


title: 8509RR162 RRMS untreated

description: RRMS untreated


title: 8500RR162 RRMS untreated

description: RRMS untreated


title: 8477RR162 RRMS untreated

description: RRMS untreated


title: Inactivated RSV donor 4


title: RSV and antibody depleted human serum donor 3


title: 6107REM128 RRMS untreated

description: RRMS untreated


title: 8164RR163 RRMS untreated

description: RRMS untreated


title: RSV and antibody depleted human serum donor 4


title: 8579RR164 RRMS untreated

description: RRMS untreated


title: 1772REL128 RRMS untreated

description: RRMS untreated


title: RSV and antibody depleted human serum donor 2


title: 2122REB51 RRMS untreated

description: RRMS untreated


title: RSV and antibody depleted human serum donor 1


title: RSV and human serum donor 4

value: RSV and human serum donor


title: 1631REB50 RRMS untreated

description: RRMS untreated


title: Inactivated RSV donor 1


title: RSV and human serum donor 3


title: 1857REB51 RRMS untreated

description: RRMS untreated


title: Inactivated RSV donor 2


title: Set98235OUT98 RRMS untreated

description: RRMS untreated


title: OA chondrocytes OA-4935

city: Montreal

first: Johanne

last: Martel-Pelletier

state: Quebec

address: 900 rue St-Denis

country: Canada

institute: CRCHUM

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization,  the housekeeping gene RPLPO was used.
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RPLPO)]
The raw data were analyzed by the deltadeltaCt based fold-change calculations.
Fold Change worksheet reports test/control  i.e. the average of three OA specimens/average of three normal specimens

label: SYBR Green

source_name: cartilage-derived Osteoarthritic (OA)  chondrocytes

label_protocol: PCR assays were performed using the UPR PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed on an ABI 7900HT qPCR instrument (Applied Biosystems, Foster City, CA) equipped with SDS 2.3 software.

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

tag: cell type

value: human chondrocytes


title: Set981431OUT98 RRMS untreated

first: Michael

description: RRMS untreated


title: RSV donor 4

value: RSV donor


title: 7001RR163 RRMS untreated

description: RRMS untreated


title: RSV and human serum donor 1


title: RSV and human serum donor 2


title: 1174REB50 RRMS untreated

description: RRMS untreated


title: antibody depleted human serum donor 4

value: antibody depleted human serum donor


title: 1640REB51 RRMS untreated

description: RRMS untreated


title: RSV donor 1


title: antibody depleted human serum donor 2


title: 9239SP162 SPMS treated with IFNb

description: SPMS treated with IFNb

source_name: PBMC from IFNb treated SPMS


title: OA chondrocytes OA-4912

description: Test


title: 9772SP164 SPMS treated with IFNb

description: SPMS treated with IFNb


title: RSV donor 2


title: 4842SP111 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 8779RR164 RRMS untreated

description: RRMS untreated


title: 7087SP143 SPMS treated with IFNb

description: SPMS treated with IFNb


title: Normal chondrocytes N-5174

description: Control

source_name: cartilage-derived Normal chondrocytes


title: antibody depleted human serum donor 1


title: antibody depleted human serum donor 3


title: OA chondrocytes OA-5164

description: Test


title: human serum donor 4

value: human serum donor


title: Normal chondrocytes N-4905

description: Control


title: 9130SP164 SPMS treated with IFNb

description: SPMS treated with IFNb


title: RSV donor 3


title: human serum donor 3


title: human serum donor 2


title: 9693SP163 SPMS treated with IFNb

description: SPMS treated with IFNb


title: Normal chondrocytes N-4084

description: Control


title: OA chondrocytes C-6501 Tm treated

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization,  the housekeeping gene RPLPO was used.
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RPLPO)]
The raw data were analyzed by the deltadeltaCt based fold-change calculations.
Fold Change worksheet reports test/control ratio  i.e. the average of three treated specimens/average of three control or untreated.

source_name: cartilage-derived OA chondrocytes

tag: activation agent

value: Tunicamycin 500ng/ml

tag: time

value: 4 days (including a 20 hours treatment)


title: OA chondrocytes C-6499 Tm treated

description: Test


title: OA chondrocytes C-6501 Tg treated

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization,  the housekeeping gene RPLPO was used.
The raw data were analyzed by the deltadeltaCt based fold-change calculations.
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RPLPO)]
Fold Change worksheet reports test/control ratio  i.e. the average of three treated specimens/average of three control or untreated.

value: Thapsigargin 50nM


title: OA chondrocytes C-6499 Tg treated

description: Test


title: OA chondrocytes C-6500 Tg treated

description: Test


title: 1746REB51 RRMS untreated

description: RRMS untreated

value: untreated


title: 9233SP164 SPMS treated with IFNb

description: SPMS treated with IFNb

value: male

value: IFNb


title: 1826SP162 SPMS treated with IFNb

description: SPMS treated with IFNb

value: female


title: medium donor 4

value: medium donor


title: OA chondrocytes C-6500 Tm treated

description: Test


title: OA chondrocytes C-6500

description: Control

value: Control

value: 4 days


title: human serum donor 1


title: medium donor 1


title: medium donor 2


title: 4725SP111 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 9226SP162 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 6996SP163 SPMS treated with IFNb

description: SPMS treated with IFNb


title: medium donor 3


title: 7648SP164 SPMS treated with IFNb

description: SPMS treated with IFNb


title: OA chondrocytes C-6501

description: Control


title: 9786SP164 SPMS treated with IFNb

description: SPMS treated with IFNb


title: OA chondrocytes C-6499

description: Control


title: 754SP111 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 9166SP163 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 7327RR144 SPMS treated with IFNb

description: SPMS treated with IFNb


title: PT Day 1 YNG r5

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Gene expression data from BAL from mice.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA). For bone marrow SK cells, 7.5ug cDNA were hybridized onto mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized using RMA. Analyzed using BRB array tools.

source_name: Bronchoalveolar lavage, young, polytrauma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. Biotinylated cDNA for bone marrow LSK samples were prepared using Nugen Ovation Pico WTA V2 kit and labeled and fragmented with the Encore® Biotin Module from total RNA.

growth_protocol: Mus musculus 6 to 12 weeks (young), and 20 to 24 weeks (old).

extract_protocol: Extraction of total RNA was performed with QIAGEN RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Murine polytrauma (PT) model: mice undergo hemorrhagic shock, long bone fracture, and cecectomy.

tag: strain/background

value: bronchoalveolar lavage

tag: age

value: young

value: polytrauma (PT)


title: PT Day 1 OLD r4

source_name: Bronchoalveolar lavage, old, polytrauma

value: 20-24 months


title: 9816SP164 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 9227SP163 SPMS treated with IFNb

description: SPMS treated with IFNb


title: PT Day 1 OLD r3


title: PT Day 1 OLD r2


title: PT Day 1 YNG r4


title: PT Day 1 OLD r1


title: PT Day 1 YNG r3


title: 3520-SYH avrE hopM1 strain inoculated

city: East Lansing

first: Sheng Yang

last: He

state: Michigan

address: 612 Wilson Rd, Rm106

institute: Michigan State University

description: Gene expression data of Arabidopsis leaf inoculated with Pst DC3000 avrE hopM1 strain

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on the Arabidopsis ATH1 GeneChip . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Bioconductor-Limma.

source_name: Arabidopsis leaf tissue inoculated with avrE hopM1 strain

label_protocol: Biotinylated cRNA was prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturers instructions.

growth_protocol: Arabidopsis was grown in an environmentally-controlled chamber under a 12-hour-day/12-hour-night cycle (120 µE cool-white fluorescent light, 22 ºC). 5-week-old plants were used for experiments.

extract_protocol: Tissue samples were collected by snap-freezing plant leaf tissue in liquid nitrogen 7 h after bacterial infiltration, and total RNA was extracted using RNeasy plant mini kits (Qiagen), following manufacturer's protocols.

treatment_protocol: Leaves of 5-week-old Arabidopsis Col-0 plants were vacuum-infiltrated with Pst DC3000, the avrE mutant, the hopM1 mutant or the avrE hopM1 double mutant at 1x108 cfu/ml.

value: leaf


title: 9229SP162 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 8651SP164 SPMS

description: SPMS untreated

source_name: PBMC from untreated SPMS


title: 3525-SYH avrE hopM1 strain inoculated

value: inoculated with Pst DC3000 avrE hopM1 strain


title: Naive OLD r4

source_name: Bronchoalveolar lavage, old, naive control

value: naive control


title: 3517-SYH hopM1 strain inoculated

description: Gene expression data of Arabidopsis leaf inoculated with Pst DC3000 hopM1 strain

source_name: Arabidopsis leaf tissue inoculated with hopM1 strain

value: inoculated with Pst DC3000 hopM1 strain


title: 3530-SYH avrE hopM1 strain inoculated


title: PT Day 1 YNG r1


title: 6942RR144 SPMS

description: SPMS untreated


title: PT Day 1 YNG r2


title: 7100SP128 SPMS

description: SPMS untreated


title: 3628SP72 SPMS

description: SPMS untreated


title: 3528-SYH avrE strain inoculated

description: Gene expression data of Arabidopsis leaf inoculated with Pst DC3000 avrE strain

source_name: Arabidopsis leaf tissue inoculated with avrE strain

value: inoculated with Pst DC3000 avrE strain


title: 9225SP162 SPMS treated with IFNb

description: SPMS treated with IFNb


title: 3527-SYH hopM1 strain inoculated


title: 3522-SYH hopM1 strain inoculated


title: 4096SP117 SPMS

description: SPMS untreated


title: Naive OLD r3


title: 3523-SYH avrE strain inoculated


title: 4246SP117 SPMS

description: SPMS untreated


title: Naive OLD r2


title: 7027SP128 SPMS

description: SPMS untreated


title: Naive YNG r3

source_name: Bronchoalveolar lavage, young, naive control


title: 3531-SYH DC3000 strain inoculated

description: Gene expression data of Arabidopsis leaf inoculated with DC3000

source_name: Arabidopsis leaf tissue inoculated with DC3000

value: inoculated with DC3000


title: Naive OLD r1


title: 3518-SYH avrE strain inoculated


title: Naive YNG r2


title: 8612SP163 SPMS

description: SPMS untreated

value: untreated


title: Naive YNG r4

value: male


title: 3526-SYH DC3000 strain inoculated


title: 8591SP163 SPMS

description: SPMS untreated


title: 3972SP72 SPMS

description: SPMS untreated


title: Naive YNG r1


title: PT_Neutro_Naive r4

description: Gene expression data from neutrophils from mice.

source_name: Bone marrow LSK cells, naive control

value: bone marrow LSK cells


title: 3529-SYH H2O inoculated; control

description: Gene expression data of Arabidopsis leaf inoculated with H2O (as control)

source_name: Arabidopsis leaf tissue inoculated with H2O

value: inoculated with H2O (as control)


title: PT_Neutro_Naive r3


title: PT_Neutro_Naive r1


title: 3521-SYH DC3000 strain inoculated


title: 8646SP164 SPMS

description: SPMS untreated

value: female


title: 3519-SYH H2O inoculated; control


title: PT_Neutro_Naive r2


title: 3649SP72 SPMS

description: SPMS untreated


title: 3524-SYH H2O inoculated; control


title: PT_Neutro_3day r2

source_name: Bone marrow LSK cells, polytrauma


title: LF32

city: Berlin

first: Liang

last: Fang

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

description: SAMPLE 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genomestudio (v.2010.1) with Modules  Gene Expression 1.6.0 and Illumina Genome Viewer 1.6.1

source_name: salivary gland_LF3

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

growth_protocol: Mouse salivary cancer stem cells were primarily isolated and cultured in in DMEM/F12 (Invitrogen) supplemented with 20% KSR, nonessential minimal amino acids, penicillin, streptomycin, L-glutamine and β-mercaptoethanol.

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

treatment_protocol: Cells were treated with LF3 and ICG-001 for 24 h

value: salivary gland cancer stem cells

tag: treated with

value: LF3 for 24 h


title: 7620SP141 SPMS

description: SPMS untreated


title: PT_Neutro_3day r3


title: 4443SP72 SPMS

description: SPMS untreated


title: PT_Neutro_3day r1


title: ICG3

description: SAMPLE 6

source_name: salivary gland_ICG

value: ICG-001 for 24 h


title: LF33

description: SAMPLE 9


title: ICG1

description: SAMPLE 4


title: LF31

description: SAMPLE 7


title: PT_Neutro_1day r2


title: 4474SP117 SPMS

description: SPMS untreated


title: PT_Neutro_1day r4


title: 7583RR144 SPMS

description: SPMS untreated


title: ICG2

description: SAMPLE 5


title: DMSO3

description: SAMPLE 3

source_name: salivary gland_DMSO

value: DMSO for 24 h


title: 4384SP117 SPMS

description: SPMS untreated


title: DMSO2

description: SAMPLE 2


title: DMSO1

description: SAMPLE 1


title: PT_Neutro_2hr r4

value: polytrauma (PT)


title: PT_Neutro_1day r3


title: 7166SP143 SPMS

description: SPMS untreated


title: 7488SP162 SPMS

description: SPMS untreated


title: 8716SP164 SPMS

description: SPMS untreated


title: PT_Neutro_1day r1


title: 6898SP128 SPMS

description: SPMS untreated


title: PT_Neutro_2hr r3


title: PT_Neutro_3day r4


title: 3774SP72 SPMS

description: SPMS untreated


title: 8617SP163 SPMS

description: SPMS untreated


title: 7289RR144 SPMS

description: SPMS untreated


title: PT OLD 2hr r5

description: Gene expression data from WBC from mice.

source_name: Whole blood cells, old, polytrauma

value: whole blood cells

value: 20-24 months


title: 7125RR144 SPMS

description: SPMS untreated


title: PT_Neutro_2hr r2


title: 7008RR144 SPMS

description: SPMS untreated


title: 8480SP162 SPMS

description: SPMS untreated


title: 7937SP141 SPMS

description: SPMS untreated


title: PT_Neutro_2hr r1


title: PT OLD Day3 r3


title: PT OLD 2hr r4


title: 8488SP162 SPMS

description: SPMS untreated


title: PT OLD Day3 r2-


title: 8677SP164 SPMS

description: SPMS untreated


title: PT OLD Day3 r2


title: PT OLD Day3 r1


title: PT OLD Day3 r4


title: PT OLD Day1 r4


title: C3H, Liver, 21 days HFD, rep6

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

institute: Hemholtz Center Munich

description: Gene expression data from liver of radnom fed C3H mice, 21 days HFD

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.1) including median polish and Sketch-Quantile normalisation

source_name: C3H, Liver, 21 days HFD

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix)

growth_protocol: Single housed animals

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, mice were fed with a HFD (21 days) or LFD (≤ 21 days) and gene transcription analyses in liver was performed.

value: 17 weeks

tag: genotype

value: WT

value: 21 days HFD


title: PT OLD Day1 r3

tag: gender


title: C3H, Liver, 21 days HFD, rep7

scan_protocol: According to the Affymetrix expression protocol


title: C3H, Liver, 21 days HFD, rep5


title: C3H, Liver, 21 days HFD, rep8


title: PT OLD Day1 r2

tag: tissue


title: PT OLD 2hr r3


title: C3H, Liver, 21 days HFD, rep4


title: C3H, Liver, 21 days HFD, rep2


title: PT OLD Day1 r1


title: PT OLD 2hr r2


title: C3H, Liver, 21 days HFD, rep3


title: C3H, Liver, control, rep17

description: Gene expression data from liver of random fed C3H mice, control

source_name: C3H, Liver, control

value: 15-17 weeks


title: C3H, Liver, control, rep18


title: C3H, Liver, 21 days HFD, rep1


title: PT YNG Day 1 r6

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

source_name: PT YNG Day 1 r6

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

growth_protocol: Mus musculus 6 to 12 weeks

treatment_protocol: Used the Cecal Ligation and Puncture (CLP), and Polytrauma (PT), and Polytrauma plus Pseudomonas Infections (PT + Pp) models

value: white blood cells

value: 6-12 weeks


title: PT YNG Day 1 r5

source_name: PT YNG Day 1 r5


title: C3H, Liver, control, rep16

value: male


title: PT OLD 2hr r1


title: PT YNG Day 1 r4

source_name: PT YNG Day 1 r4


title: PT YNG Day 1 r3

source_name: PT YNG Day 1 r3


title: C3H, Liver, control, rep14


title: PT YNG Day 1 r2

source_name: PT YNG Day 1 r2


title: PT YNG Day 1 r1

source_name: PT YNG Day 1 r1


title: C3H, Liver, control, rep13


title: C3H, Liver, control, rep15


title: sample_12-DB-007 [copy number]

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

hyb_protocol: Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 (manufacturer's protocol).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G (manufacturer's protocol).

data_processing: Affymetrix® Genotyping Console.

source_name: Breast cancer, CHER-LOB Arm B, pre-treated

label_protocol: Affymetrix (manufacturer's protocol).

extract_protocol: Qiagen DNeasy Blood & Tissue Kit (manufacturer's protocol).

treatment_protocol: CHER-LOB is a phase II, randomized, multicenter, trial in which 121 patients with primary HER2-positive breast cancer were randomized to receive preoperative chemotherapy with weekly paclitaxel times 12 followed by 4 courses of 3-weekly FEC (fluorouracil, epirubicin and cyclophosphamide) plus either trastuzumab (Arm A), lapatinib (Arm B) or the combination of trastuzumab and lapatinib (Arm C). The trial design, eligibility criteria, statistical analysis, and clinical results including response, surgery outcomes and treatment safety are described in details elsewhere.

tag: disease state

value: HER2-positive breast cancer

value: breast cancer

tag: cher-lob arm

value: B

tag: arm description

value: chemotherapy+lapatinib

tag: pcr (1=yes)


title: C3H, Liver, control, rep12


title: C3H, Liver, control, rep11


title: sample_11-RG-005 [copy number]


title: C3H, Liver, control, rep10


title: sample_11-VB-001 [copy number]


title: PT YNG 2hr r4

source_name: PT YNG 2hr r4


title: PT YNG 2hr r2

source_name: PT YNG 2hr r2


title: sample_11-LT-009 [copy number]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

value: C

value: chemotherapy+trastuzumab+lapatinib


title: sample_11-IS-004 [copy number]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: A

value: chemotherapy+trastuzumab


title: sample_08-KA-004 [copy number]


title: sample_11-EV-003 [copy number]


title: PT YNG 2hr r1

source_name: PT YNG 2hr r1

value: polytrauma (PT)


title: PT YNG 2hr r3

source_name: PT YNG 2hr r3


title: sample_08-NC-008 [copy number]


title: C3H, Liver, control, rep9


title: C3H, Liver, control, rep7


title: PT YNG Day 3 r3

source_name: PT YNG Day 3 r3


title: sample_08-GZ-010 [copy number]


title: sample_08-OS-013 [copy number]


title: sample_08-EM-014 [copy number]


title: sample_08-MS-016 [copy number]


title: C3H, Liver, control, rep6


title: C3H, Liver, control, rep8


title: sample_08-GL-002 [copy number]


title: sample_08-CM-05 [copy number]


title: sample_08-GC-001 [copy number]


title: sample_08-MR-009 [copy number]


title: Control rep4

source_name: Control r4

value: naive control


title: C3H, Liver, control, rep5


title: PT YNG Day 3 r1

source_name: PT YNG Day 3 r1


title: PT YNG Day 3 r4

source_name: PT YNG Day 3 r4


title: sample_08-ZMT-006 [copy number]


title: Control rep3

source_name: Control r3


title: sample_08-BS-012 [copy number]


title: UC-MSCs-IGF-1

city: Guangzhou

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

description: gene expression in human umbilical cord-derived mesenchymal stem cells after infected with retrovirus containing pMX-IGF-1 vector for 48 hours

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human umbilical cord-derived mesenchymal stem cells infected with retrovirus containing pMX-IGF-1 vector

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The protocol includes Phase Separation, RNA Precipitation, RNA Wash, and Redissolving the RNA.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The collected umbilical cords were washed in phosphate-buffered saline for 3 times, and further minced and incubated with collagenase IV (1 mg/ml, Gibco) for 4 hours, then DNase I (1 mg/ml, Gibco) for 15 min, and 0.25% trypsin (Gibco) for 15 min at 37℃. After filtration through a 40-μm cell strainer, the cells were then collected by centrifugation, and cultured in DMEM/F12 (Hyclone), containing 10% fetal bovine serum (FBS; Gibco), penicillin/streptomycin (100 U/mL to 0.1 mg/mL; Hyclone), and 2 mM L-glutamine (Gibco), in a humidified incubator with 5% CO2 at 37℃.

value: umbilical cord

value: female

value: mesenchymal stem cells (MSCs)


title: C3H, Liver, control, rep2

source_name: C3H, Liver, control

value: 15-17 weeks

value: WT


title: sample_08-AT-015 [copy number]


title: C3H, Liver, control, rep1


title: C3H, Liver, control, rep3


title: C3H, Liver, control, rep4


title: UC-MSCs-vector

description: gene expression in human umbilical cord-derived mesenchymal stem cells after infected with retrovirus containing blank pMX vector for 48 hours

source_name: human umbilical cord-derived mesenchymal stem cells infected with retrovirus containing blank pMX vector


title: Control rep1

source_name: Control r1

value: white blood cells

value: 6-12 weeks


title: sample_06-NP-002 [copy number]

value: HER2-positive breast cancer


title: sample_06-SF-003 [copy number]

value: breast cancer


title: sample_08-FP-003 [copy number]


title: sample_06-LN-005 [copy number]


title: sample_08-BMC-017 [copy number]

value: B


title: B6N, Liver, 21 days HFD, rep7

description: Gene expression data from liver of random fed B6N mice, 21 days HFD

source_name: B6N, Liver, 21 days HFD

value: 17 weeks

value: male

value: 21 days HFD


title: Whole larvae_RA-PHdiet_fish8

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air.   For each array, 3 μg Cy5-labeled aRNA from an individual larva was combined with 3 μg Cy3-labeled aRNA from the common reference. Labeled aRNA was then fragmented using Ambion Fragmentation Reagents (Ambion). Fragmented aRNA and 2 μL of LNA blocker (Genisphere, Hatfield, Pennsylvania, USA) were combined in formamide-based hybridization buffer (Genisphere), applied to the array and hybridized overnight (∼16 h) at 42°C.  After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

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

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 3 * SD) for each channel on each array.  Logratios of duplicate spots were averaged.

organism: Gadus morhua

source_name: Whole larvae, RA-PH diet, individual fish

label_protocol: Individual DNAse-treated, column-purified total RNA samples from 8 fish per group (9 mm RA, 9 mm RA-PH and 9 mm RA-Zoo larvae) were used for microarray analysis using the Atlantic cod 20K oligonucleotide microarray platform (Booman et al. 2011) and a common reference experimental design.  On each array, RNA from an individual fish was hybridized together with a common reference RNA.  For each larva, 1 μg of RNA was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion/Life Technologies) according to the manufacturer's protocol.  To generate the common reference pool, 10 μg of aRNA from each of the twenty-four 9 mm individuals was pooled.  Twenty μg of each individual sample aRNA was labeled with Cy5, and 20 μg aliquots of the common reference aRNA were labeled with Cy3 (CyDye Post-Labeling Reactive Dye Packs, GE Healthcare Life Sciences) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion/Life Technologies) according to the manufacturer's protocol.

growth_protocol: Eggs for this study were collected from communally spawning broodstock, disinfected with ozone and distributed into two 0.3 m^3 cone-shaped incubators with flow-through seawater (32 ppt) at 6.0-7.0°C until 100% hatch. The eggs had an average diameter of 1.6 mm, a 95% fertilization rate and 91% symmetrical cleavage. At 100% hatch (93.4 degree days) the larvae were transferred to 16, 400 L flow-through tanks at a density of 50 larvae L^-1. These tanks were then divided randomly into 3 different treatments based on feeding regime/diet. The experiment consisted of three different feeding regimes/diets as follows: Treatment 1 (RA), Treatment 2 (RA-Zoo), and Treatment 3 (RA-PH).  Potters clay (400 ml) was added to all the larval rearing tanks, twice a day, to increase tank turbidity and to reduce bacterial numbers within the tanks.  Rearing temperature was increased from 6.0-7.0°C (incubation temperature) to 10.5°C over a period of 10 days, and water flow rate was gradually increased from 0.8 l min^-1 (at 0 dph) to 4.5 l min^-1 at 35 dph. Dissolved oxygen levels in the tanks were measured daily (YSI, ProODO, OH, USA) and kept at an average value of 117% saturation to alleviate any possible issues with nitrogen super-saturation. Whole larvae from each feeding regimes/diets were sampled when fish in particular treatment reached an average length of   ~ 9 mm. The sampled larvae were anaesthetized in MS-222, rinsed in UV-treated filtered seawater on a mesh strainer, patted dry on a Kimwipe, transferred to RNase/DNase-free 1.5 mL microcentrifuge tubes, flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

extract_protocol: Larval samples were homogenized in 300 µL of TRIzol Reagent (Invitrogen/Life Technologies) using a motorized Kontes RNase-Free Pellet Pestle Grinder (Kimble Chase, Vineland, NJ).  An additional 450 µL of TRIzol Reagent (Invitrogen/Life Technologies) was added, mixed by pipetting, and the homogenates frozen on dry ice and stored at -80°C.  Frozen homogenates were further processed by slowly thawing on ice and then passing through a QIAshredder (QIAGEN, Mississauga, ON) spin column following the manufacturer’s instructions.  Two-hundred and fifty µL of TRIzol (Invitrogen/Life Technologies) was then added to each sample to make a total homogenate volume of approximately 1 mL, and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions.  Individual total RNA samples were treated with 6.8 Kunitz units of DNaseI (RNase-Free DNase Set, QIAGEN) with the manufacturer’s buffer (1X final concentration) at room temperature for 10 min to degrade any residual genomic DNA.  DNase-treated RNA samples were column purified using the RNeasy MinElute Cleanup Kit (QIAGEN) following the manufacturer’s methods.

value: Whole larvae

tag: life stage

value: Larvae

source_name: pool of RNAs from whole larvae, all three dietary treatments (RA, RA-Zoo, RA-PH).


title: Control rep2

source_name: Control r2


title: B6N, Liver, 21 days HFD, rep8


title: I-012R1

city: Seoul

first: Jinkuk

address: 50 Irwon-dong, Gangnam-gu

institute: Samsung Medical Center

description: copy number profile

hyb_protocol: Conducted according  to manufacturer's instructions.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  All 36 FE files were loaded simultaneously into Agilent Genomic Workbench v7 for normalization (using default parameters).

source_name: Human glioblastoma tissue I-012R1

growth_protocol: Not applicable.

extract_protocol: gDNA extraction was done using DNeasy kit (QIAgen), according to manufacturer's instructions.

tag: tumor histology

value: GBM

value: TMZ, radiation

source_name: Random normal human tissue


title: PT YNG Day 3 r2

source_name: PT YNG Day 3 r2

value: polytrauma (PT)


title: Whole larvae_RA-PHdiet_fish6


title: B6N, Liver, 21 days HFD, rep6

tag: strain


title: UC-MSCs

description: gene expression in normal human umbilical cord-derived mesenchymal stem cells

value: umbilical cord

value: female


title: B6N, Liver, 21 days HFD, rep5

tag: treatment


title: Whole larvae_RA-PHdiet_fish7


title: Whole larvae_RA-PHdiet_fish5


title: 768I

description: copy number profile

scan_protocol: Conducted according  to manufacturer's instructions.

source_name: Human glioblastoma tissue 768I


title: B6N, Liver, 21 days HFD, rep4


title: Whole larvae_RA-PHdiet_fish4


title: 671I

description: copy number profile

source_name: Human glioblastoma tissue 671I

label_protocol: Conducted according  to manufacturer's instructions.


title: 740R1

description: copy number profile

source_name: Human glioblastoma tissue 740R1


title: Whole larvae_RA-PHdiet_fish3


title: B6N, Liver, 21 days HFD, rep2


title: sample_05-LA-003 [copy number]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

value: C

value: chemotherapy+trastuzumab+lapatinib


title: sample_05-LR-004 [copy number]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: A

value: chemotherapy+trastuzumab


title: 660R1

description: copy number profile

source_name: Human glioblastoma tissue 660R1


title: Whole larvae_RA-PHdiet_fish2


title: sample_05-GS-007 [copy number]

value: HER2-positive breast cancer


title: 602R1

description: copy number profile

source_name: Human glioblastoma tissue 602R1


title: B6N, Liver, 21 days HFD, rep1

value: WT


title: 520I

description: copy number profile

source_name: Human glioblastoma tissue 520I


title: B6N, Liver, control, rep8

description: Gene expression data from liver of random fed B6N mice, control

source_name: B6N, Liver, control

value: 15-17 weeks


title: Whole larvae_RA-PHdiet_fish1


title: B6N, Liver, 21 days HFD, rep3

value: 17 weeks


title: 592I

description: copy number profile

source_name: Human glioblastoma tissue 592I

value: male


title: sample_06-AD-001 [copy number]

value: breast cancer


title: sample_05-LF-002 [copy number]

source_name: Breast cancer, CHER-LOB Arm B, pre-treated

value: B

value: chemotherapy+lapatinib


title: sample_05-MP-006 [copy number]


title: Whole larvae_RA-Zoodiet_fish8

source_name: Whole larvae, RA-Zoo diet, individual fish

value: Whole larvae

value: Larvae


title: Whole larvae_RA-Zoodiet_fish7

source_name: pool of RNAs from whole larvae, all three dietary treatments (RA, RA-Zoo, RA-PH).


title: sample_03-ECC-003 [copy number]


title: B6N, Liver, control, rep7


title: sample_05-IL-001 [copy number]


title: B6N, Liver, control, rep5


title: B6N, Liver, control, rep6


title: 640I

description: copy number profile

source_name: Human glioblastoma tissue 640I

value: GBM


title: sample_03-AM-010 [copy number]


title: 788R1

description: copy number profile

source_name: Human glioblastoma tissue 788R1

value: TMZ, radiation


title: I-025R1

description: copy number profile

source_name: Human glioblastoma tissue I-025R1

source_name: Random normal human tissue


title: B6N, Liver, control, rep4


title: Whole larvae_RA-Zoodiet_fish5


title: 780I

description: copy number profile

source_name: Human glioblastoma tissue 780I


title: B6N, Liver, control, rep3


title: Whole larvae_RA-Zoodiet_fish4


title: Whole larvae_RA-Zoodiet_fish6


title: sample_05-CB-005 [copy number]


title: B6N, Liver, control, rep2


title: 572I

description: copy number profile

source_name: Human glioblastoma tissue 572I


title: Whole larvae_RA-Zoodiet_fish2


title: 618R1

description: copy number profile

source_name: Human glioblastoma tissue 618R1


title: sample_03-MAM-008 [copy number]


title: B6N, Liver, control, rep1


title: sample_02-MF-009 [copy number]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated


title: Whole larvae_RAdiet_fish8

source_name: Whole larvae, RA diet, individual fish


title: Whole larvae_RA-Zoodiet_fish1


title: B6J, Liver, 21 days HFD, rep6

description: Gene expression data from liver of random fed B6J mice, 21 days HFD

source_name: B6J, Liver, 21 days HFD

value: 21 days HFD


title: sample_02-SC-012 [copy number]


title: sample_02-IR-008 [copy number]


title: B6J, Liver, 21 days HFD, rep7