title: Normal adrenal cortex sample 6

city: NSW

first: Anthony

middle: R

last: Glover

state: St Leonards, Sydney

address: Level 9, Kolling Institute of Medical Research, Royal North Shore Hospital

institute: University of Sydney

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 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 G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 15 out of 23 samples. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: NAC patient sample 6

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 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 RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from approximately 30 mg of fresh frozen tissue using a Qiazol protocol (RNeasy Mini Kit, Qiagen, Hilden, Germany) in accordance with the manufacturer’s instructions.  RNA quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Englewood, CO, USA) with a minimum RNA integrity number (RIN) of seven required.

treatment_protocol: Samples were obtained during surgery and snap frozen in liquid nitrogen and stored at -80 C.

value: Normal adrenal cortex

tag: source

value: Anonymous patient sample


title: Brain_CON:NT2_None

status: Public on Jan 01 2015

type: RNA

city: San Francisco

first: Derek

last: Pappas

state: CA

address: 675 Nelson Rising Lane, RM 240

department: Neurology

country: USA

institute: University of California, San Francisco

description:
4060001023_A
CON_NT2
Mock control replicate 2 of 5.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were background subtracted and normalized (cubic spline) using the Illumina BeadStudio Gene Expression module v3.1.

molecule: total RNA

organism: Mus musculus

source_name: Cortical neurons, none, NMDA

label_protocol: Standard Illumina labeling protocol.

growth_protocol: Dissociated cortical neurons were cultured on poly-ornithine/poly-lysine coated plates in neurobasal A medium supplemented with B-27 and penicillin/streptomycin. Neurons were cultured for seven days before experimental conditions were introduced.

extract_protocol: RNA was extracted with clean-up using the QIAGEN RNeasy mini kit in accordance with the manufacturer's protocol.

treatment_protocol: Media was replaced with fresh media containing neuroprotective molecules or controls and incubated for one hour. Neurons were then exposed to NDMA in excitotoxic media (hypotonic salt solution) for one hour. Media was replaced with fresh media containing molecule or controls, respectively, and incubated for a further 16hr.

tag: cell type

value: cortical neurons from whole brain

tag: neuroprotective molecule

tag: solvent

value: water

tag: mechanism

value: control

tag: ratio protection

tag: class

value: non-protective


title: Brain_4PB_4-PPBP

description:
4060001023_B
4PB
Non-control single sample.

source_name: Cortical neurons, 4-PPBP, NMDA

value: ethanol

value: receptor agonist


title: P01287 Non-failing Left Ventricle

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
P01287
PolyA mRNA

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.1 ST Array GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

label: biotin

organism: Homo sapiens

source_name: heart left ventricle, non-failing

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

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

treatment_protocol: Explanted myocardium snap frozen in liquid nitrogen.

tag: tissue

value: heart left ventricle

tag: heart failure

value: no

tag: disease status

value: non-failing

tag: gender

value: female

tag: age


title: C00117 Non-failing Left Ventricle

description:
C00117
PolyA mRNA

value: male


title: C00154 Non-failing Left Ventricle

description:
C00154
PolyA mRNA


title: Brain_PRO_Propranolol

description:
4060001018_F
PRO
Non-control single sample.

source_name: Cortical neurons, Propranolol, NMDA

value: Propranolol

value: not used


title: L_ANEU_2.3N

type: genomic

city: Scottsdale

first: Mitesh

last: Borad

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic in Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol

scan_protocol: The arrays were scanned using an Agilent Technologies G2656C Scanner and default setting according to manufacturer's recommendation.

data_processing: Data was extracted from the TIFF files using default settings in Agilent FE 7.5.  The data quality was assessed using the QC reports in FE 7.5.

molecule: genomic DNA

source_name: liposarcoma

label_protocol: DNA was digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to manufacturer's protocol.

growth_protocol: Tumor sample from a liposarcoma was flash frozen and stored at -80 C until processed for flow sorting

extract_protocol: Tumor was chipped from flash frozen samples. Nuclei were extracted then resuspended in the presence of 10mg/ml DAPI in NST buffer prior to sorting with an Influx flow cytometer equipped with a UV laser. The DNA from each flow sorted sample was extracted with QIAGEN QIAamp DNA Micro Kit according to the manufacturer's protocol.

tag: disease state

value: Well differentiated liposarcoma

source_name: Reference pooled 46XX

value: Normal female genome


title: C00155 Non-failing Left Ventricle

description:
C00155
PolyA mRNA


title: PCB_50 - Aa26, liver

city: Arcachon

first: lucie

last: baillon

address: place du docteur Peyneau

country: France

institute: université de Bordeaux UMR ePOC

description: SAMPLE 17

hyb_protocol: For cDNA hybridization, microarray was pre-hybridized in 5X SSC buffer; 0.1% SDS; 0.1 g.L-1 BSA during 45 min at 55°C. Microarray was washed twice 5 min in 0.1X SSC at RT followed by 30s in purified water under continuous agitation. Microarray was then centrifuged 2 min for drying.   800ng of cDNA sample was pooled with 800ng of cDNA reference and hybridized on microarray in 2X hybridization buffer (8X SSC; 0.4% SDS; 0.1g.L-1 calf thymus DNA) and incubated at 55°C in Agilent chamber overnight. Hybridized microarray was washed at 55°C in 2X SSC; 0.1% SDS buffer, washed, twice 5 min in 2X SSC; 0.1% SDS buffer under agitation at RT; twice 5 min in 0.1X SSC; 0.1% SDS buffer and finally 4 times in 0.1X SSC buffer and dried by centrifugation (2 min).

scan_protocol: Microarray data were generated by the Innoscan 710 microarray scanner using Mapix software.

data_processing:
the filtering of raw data was done for both green and red channels. The median foreground (F635median and F532median) and median background (B635median and B532median) was chosen for the data normalization. If the ratio Fmedian/Bmedian was lower than 1.5, data were removed from the analysis. For each channel, the background was removed of the foreground data and the mean of triplicates (three spots for each gene) was then calculated and both green and red channels were used for data normalization. Normalization and statistical analysis was done by using the BRB-arrayTools version 4.4.0 software package (http://linus.nci.nih.gov/BRB-ArrayTools.html). Each array was median normalized over entire arrays and genes were excluded if 50% of values were missing in the complete set of arrays.
Data normalized by median-centering log-ratios in each array,  based on the average of the red and green log-intensities

organism: Anguilla anguilla

source_name: Fish from laboratory PCBs experiment

label_protocol: For the first step of reverse-transcription procedure, 10µg of RNA was mixed with 3µg of random primer and 2µg of oligodT. Water was added for 20µl qs. Mix was incubated 5 min at 70°C followed by10 min at 18°C and finally stored at 4°C. 20µl of the RT mix (GoScript™ 5X Reaction Buffer: 8µl; DTT [0.1M]: 4µl; MgCl2 [25mM]: 4.8µl; 50X aa-dNTP mix (25mM each): 1µl; dUTP: 1µl; GoScript™ RT: 2µl) was added to the RNA mix. The mix was incubated during 12h at 42°C followed by 5 min at 18 °C and stored at 4°C. RNAs were then hydrolyzed with 4µl of EDTA [0.2M] pH 8 and 6µl of NaOH [1M] during 10 min at 70°C.  To re-adjust the pH, 6µl of HCL [1M] was then added. cDNA purification was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol. cDNA was eluted in 60µl of sodium bicarbonate [0.1M] pH 9 and placed at -20°C before labeling.   In order to normalize microarray data, we used a common reference design. This was composed by a pool of 30 wild eels of Certes (15 fishes collected in 2011 and 15 in 2012). This reference was combined in equal amounts with each sample before to be hybridized on the microarray slide. . Reference and sample cDNAs were labeled with CyDye™ Post-Labelling Reactive Dye Pack (Amersham). Each cDNA sample and reference was mix with 1 vial of CyDye (Cy3 for sample and Cy5 for reference) and incubated at RT in the dark during 90 min. Reaction was stopped by adding 15µl of hydroxylamine hydrochloride [4M] and incubated during 15 min in the dark. Purification of labeled cDNA was carried out with the Qiagen PCR purification kit following the manufacturer’s protocol and eluted in 60µl of water. Amount of labeled cDNA  as well as the frequency of incorporation (FOI) were determined spectrophotometrically (Epoch, Biotek).

extract_protocol: RNA extraction was carried out by means of the SV total RNA islotaion Kit, promega). Sampleswere placed in 450 µl of RNA lysis (Promega) buffer in sterile microtube and were homogenized by means of two metal beads and tissue homogenizer (Retsch). After 2 min of centrifugation at 10,000 rpm, 400 µl of the lysate was recovered.  One volume of Phenol:Chloroform:Isoamyl Alcohol 25:24:1 was then added. The homogenate was vortexed 10s and centrifuged 10 min at RT. The upper phase was recovered. One volume of 75% EtOH was adeed. After homogenization by vortexing, the mix was transferred to a spin column and the standard manufacturer’s procedures were followed (including DNAseI treatment).. Quality and integrity of the total RNA were controlled by electrophoresis on a 1% agarose gel.

value: Liver

tag: treatment

value: PCB [50ng/g dw]_trophic_route

source_name: reference pool

tag: reference composition

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Brain_MPBrep1_MitoPBN

description:
4060001018_E
MPBrep1
Non-control single sample.

source_name: Cortical neurons, MitoPBN, NMDA

value: cortical neurons from whole brain

value: MitoPBN

value: DMSO

value: free radical scavenger


title: Normal adrenal cortex sample 4

country: Australia

source_name: NAC patient sample 4

value: Normal adrenal cortex

value: Anonymous patient sample


title: PCB_50 - Aa27, liver

description: SAMPLE 18


title: PCB_50 - Aa28, liver

description: SAMPLE 19


title: Normal adrenal cortex sample 2

source_name: NAC patient sample 2


title: Normal adrenal cortex sample 3

source_name: NAC patient sample 3


title: PCB_50 - Aa25, liver

description: SAMPLE 16


title: C00089 Non-failing Left Ventricle

description:
C00089
PolyA mRNA

value: heart left ventricle

value: no

value: non-failing


title: Salinity - Aa24, liver

description: SAMPLE 15

source_name: Fish from laboratory high salinity experiment

value: High salinity [water at 18‰ ]


title: C00093 Non-failing Left Ventricle

description:
C00093
PolyA mRNA

value: female


title: Normal adrenal cortex sample 1

source_name: NAC patient sample 1


title: C00088 Non-failing Left Ventricle

description:
C00088
PolyA mRNA


title: Brain_CLO_Clofibric Acid

description:
4060001018_C
CLO
Non-control single sample.

source_name: Cortical neurons, Clofibric acid, NMDA

value: Clofibric acid

value: ethanol

value: enzyme inhibitor

value: not used


title: Brain_CON:ND5_Vehicle

description:
4060001018_B
CON_ND5
Vehicle control replicate 5 of 5.

source_name: Cortical neurons, vehicle, NMDA

value: vehicle

value: control

value: non-protective


title: Adrenocortical adenoma clincal sample 5

source_name: ACA patient sample 5

value: Adrenocortical adenoma


title: Salinity - Aa23, liver

description: SAMPLE 14

value: Liver

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Salinity - Aa22, liver

description: SAMPLE 13


title: Salinity - Aa21, liver

description: SAMPLE 12


title: Adrenocortical adenoma clincal sample 3

source_name: ACA patient sample 3

value: Anonymous patient sample


title: Adrenocortical adenoma clincal sample 4

source_name: ACA patient sample 4


title: Brain_CON:NT5_None

description:
4060001018_A
CON_NT5
Mock control replicate 5 of 5.

source_name: Cortical neurons, none, NMDA

value: cortical neurons from whole brain

value: water


title: C00084 Non-failing Left Ventricle

description:
C00084
PolyA mRNA

source_name: heart left ventricle, non-failing

value: heart left ventricle

value: no

value: non-failing

value: male


title: Brain_PHE_Phenytoin

description:
4060001017_F
PHE
Non-control single sample.

source_name: Cortical neurons, Phenytoin, NMDA

value: Phenytoin

value: ethanol

value: ion channel blocker


title: C00070 Non-failing Left Ventricle

description:
C00070
PolyA mRNA


title: C00069 Non-failing Left Ventricle

description:
C00069
PolyA mRNA

value: female


title: Brain_CIT_Citicoline

description:
4060001017_C
CIT
Non-control single sample.

source_name: Cortical neurons, Citicoline, NMDA

value: Citicoline

value: free radical scavenger


title: Brain_FLE_Flecainide

description:
4060001017_D
FLE
Non-control single sample.

source_name: Cortical neurons, Flecainide, NMDA

value: Flecainide

value: non-protective


title: Brain_IDO_Indomethacin

description:
4060001018_D
IDO
Non-control single sample.

source_name: Cortical neurons, Indomethacin, NMDA

value: Indomethacin

value: enzyme inhibitor

value: protective


title: Adrenocortical adenoma clincal sample 2

source_name: ACA patient sample 2

value: Adrenocortical adenoma

value: Anonymous patient sample


title: C00067 Non-failing Left Ventricle

description:
C00067
PolyA mRNA

value: heart left ventricle


title: C00058 Non-failing Left Ventricle

description:
C00058
PolyA mRNA

value: no


title: Brain_MIN_Minocycline

description:
4060001017_E
MIN
Non-control single sample.

source_name: Cortical neurons, Minocycline, NMDA

value: cortical neurons from whole brain

value: Minocycline

value: water

value: antibiotic

value: not used


title: Salinity - Aa20, liver

description: SAMPLE 11

value: Liver

value: High salinity [water at 18‰ ]

source_name: reference pool

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: C00082 Non-failing Left Ventricle

description:
C00082
PolyA mRNA

value: non-failing

value: male


title: Adrenocortical carcinoma clincal sample 10

source_name: ACC patient sample 10

value: Adrenocortical carcinoma


title: Diet - Aa17, liver

description: SAMPLE 10

source_name: Fish from laboratory restrictive diet experiment

value: Restrictive diet [food at 2.5 % of total animal weight]


title: Diet - Aa14, liver

description: SAMPLE 8


title: Adrenocortical adenoma clincal sample 1

source_name: ACA patient sample 1

value: Adrenocortical adenoma


title: Diet - Aa16, liver

description: SAMPLE 9


title: Diet - Aa13, liver

description: SAMPLE 7


title: Diet - Aa12, liver

description: SAMPLE 6


title: C00057 Non-failing Left Ventricle

description:
C00057
PolyA mRNA

value: female


title: Adrenocortical carcinoma clincal sample 8

source_name: ACC patient sample 8

value: Anonymous patient sample


title: Brain_CON:ND4_Vehicle

description:
4060001017_B
CON_ND4
Vehicle control replicate 4 of 5.

source_name: Cortical neurons, vehicle, NMDA

value: vehicle

value: DMSO

value: control

value: non-protective


title: Control - Aa10, liver

description: SAMPLE 5

source_name: Fish from laboratory control experiment

value: Control


title: C00047 Non-failing Left Ventricle

description:
C00047
PolyA mRNA

value: heart left ventricle

value: no


title: Adrenocortical carcinoma clincal sample 6

source_name: ACC patient sample 6


title: Adrenocortical carcinoma clincal sample 9

source_name: ACC patient sample 9


title: Brain_CON:NT1_None

description:
4060001017_A
CON_NT1
Mock control replicate 1 of 5.

source_name: Cortical neurons, none, NMDA

value: cortical neurons from whole brain

value: water


title: Adrenocortical carcinoma clincal sample 5

source_name: ACC patient sample 5


title: Adrenocortical carcinoma clincal sample 7

source_name: ACC patient sample 7


title: C00111 Non-failing Left Ventricle

description:
C00111
PolyA mRNA

source_name: heart left ventricle, non-failing


title: Adrenocortical carcinoma clincal sample 3

source_name: ACC patient sample 3


title: C00114 Non-failing Left Ventricle

description:
C00114
PolyA mRNA


title: C00049 Non-failing Left Ventricle

description:
C00049
PolyA mRNA


title: Adrenocortical carcinoma clincal sample 4

source_name: ACC patient sample 4


title: Adrenocortical carcinoma clincal sample 2

source_name: ACC patient sample 2


title: C00137 Non-failing Left Ventricle

description:
C00137
PolyA mRNA


title: C00142 Non-failing Left Ventricle

description:
C00142
PolyA mRNA


title: Control - Aa8, liver

description: SAMPLE 3

value: Liver

value: 30 samples from reference site (Certes, France) collected in spring 2011 and 2012

value: liver


title: Control - Aa9, liver

description: SAMPLE 4


title: Control - Aa6, liver

description: SAMPLE 1


title: Control - Aa7, liver

description: SAMPLE 2


title: Brain_CYC_Cyclophosphamide

description:
4060001023_C
CYC
Non-control single sample.

source_name: Cortical neurons, Cyclophosphamide, NMDA

value: Cyclophosphamide

value: immunomodulator

value: protective


title: Normal adrenal cortex sample 5

source_name: NAC patient sample 5

value: Normal adrenal cortex


title: P01085 Non-failing Left Ventricle

description:
P01085
PolyA mRNA

value: non-failing

value: female


title: C00112 Non-failing Left Ventricle

description:
C00112
PolyA mRNA


title: m2_2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: This sample is of Fusarium graminearum deleted for MAT1-2. It is the second of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days

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

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

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

organism: Fusarium graminearum

source_name: F. graminearum deleted for the MAT1-2 locus at 48 h on carrot agar

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

growth_protocol: All F. graminearum strains were maintained on carrot agar (PDA) at 25°C with 12 h light–dark cycle. For sexual induction, freshly grown aerial mycelia on carrot agar grown for 7 days were removed and incubated at 25°C for additional 48 hrs in the same condition. Perithecia and/or hyphae were collected by scraping the agar plate, and frozen at -80°C.

extract_protocol: Frozen mycelia were pulverized with mortar and pestle using liquid nitrogen for nucleic acid extraction. Total RNAs were extracted by TRI Reagent. Extracted total RNA was treated with DNase I (Takara, Japan) to remove genomic DNA according to instructions provided by the manufacturer. The total RNA sample were precipitated with ethanol and resuspended in DEPC-treated water finally.

tag: genotype/variation

value: deleted for MAT1-2 (self-sterile)


title: m2_3

description: This sample is of Fusarium graminearum deleted for MAT1-2. It is the third of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: m1m2_1

description: This sample is of Fusarium graminearum deleted for both MAT1-1 & MAT1-2. It is the first of two biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days

source_name: F. graminearum deleted for both the MAT1-1 & MAT1-2 loci at 48 h on carrot agar

value: deleted for both MAT1-1 & MAT1-2 (self-sterile)


title: P00166 Idiopathic Dilated CMP Left Ventricle

description:
P00166
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

value: idiopathic dilated CMP

value: male


title: m1_3

description: This sample is of Fusarium graminearum deleted for MAT1-1. It is the third of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days

source_name: F. graminearum deleted for the MAT1-1 locus at 48 h on carrot agar

value: deleted for MAT1-1 (self-sterile)


title: m1m2_2

description: This sample is of Fusarium graminearum deleted for both MAT1-1 & MAT1-2. It is the second of two biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: P01070 Non-failing Left Ventricle

description:
P01070
PolyA mRNA

value: heart left ventricle

value: no


title: C00113 Non-failing Left Ventricle

description:
C00113
PolyA mRNA


title: Adrenocortical carcinoma clincal sample 1

source_name: ACC patient sample 1

value: Adrenocortical carcinoma

value: Anonymous patient sample


title: m1_2

description: This sample is of Fusarium graminearum deleted for MAT1-1. It is the second of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: P00176 Ischemic Left Ventricle

description:
P00176
PolyA mRNA

source_name: heart left ventricle, ischemic

value: ischemic


title: m2_1

description: This sample is of Fusarium graminearum deleted for MAT1-2. It is the first of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: m1_1

description: This sample is of Fusarium graminearum deleted for MAT1-1. It is the first of three biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: P00026 Ischemic Left Ventricle

description:
P00026
PolyA mRNA


title: P00038 Ischemic Left Ventricle

description:
P00038
PolyA mRNA


title: OM4_2

description: This sample is of Fusarium graminearum overexpressing MAT1-2-1. It is the second of two biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days

source_name: Fusarium graminearum overexpressing MAT1-2-1 at 48 h on carrot agar

value: overexpressing MAT1-2-1 (self-fertile)


title: OM4_1

description: This sample is of Fusarium graminearum overexpressing MAT1-2-1. It is the first of two biological replicates used in this experiment and is harvested together with the other transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: P00460 Non-failing Left Ventricle

description:
P00460
PolyA mRNA


title: WT_2

description: This sample is of wild-type Fusarium graminearum. It is the second of two wild-type biological replicates used in this experiment and is harvested together with the transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days

source_name: Fusarium graminearum WT 3643 at 48 h on carrot agar

value: wild-type strain (self-fertile)


title: P00025 Ischemic Left Ventricle

description:
P00025
PolyA mRNA


title: P00343 Idiopathic Dilated CMP Left Ventricle

description:
P00343
PolyA mRNA


title: WT_1

description: This sample is of wild-type Fusarium graminearum. It is the first of two wild-type biological replicates used in this experiment and is harvested together with the transgenic strains at 48h after the removal of aerial mycelia grown on carrot agar for 7 days


title: P01163 Idiopathic Dilated CMP Left Ventricle

description:
P01163
PolyA mRNA


title: P01082 Idiopathic Dilated CMP Left Ventricle

description:
P01082
PolyA mRNA


title: 833KE fe [exon-level]

city: Oslo

first: Sharmini

last: Alagaratnam

address: Radiumhospitalet, Montebello

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
H27 [exon-level]
H27_HuEx.CEL (see Series record)
H27_HuEx.rma-exon-core-dabg.chp

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned in-house.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; core-gene and core-exon analyses
CHP files were generated from raw CEL files by Expression Console software. Both CEL and CHP files were used as input for data analysis, specifically PCA in Qlucore (CHP), gene- and exon-level expression differences by XRAY (CEL files) and limma (CHP files), and two-class pair-wise Significance of Microarrays (CHP files).

source_name: EC cell line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA after rRNA reduction with the WT cDNA Synthesis and Amplification Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All ES lines and the three EC lines marked 'fe' were grown on mitomycin C-inactivated mouse embryo fibroblasts in knock-out DMEM with 10% Serum Replacement and 4 ng/ml FGF. All EC cells were grown in plastic flasks in high-glucose DMEM with 10% FCS.

extract_protocol: Total RNA was isolated from the cell lines using the AllPrep DNA/RNA Mini kit (Qiagen).

treatment_protocol: All cells were FACS sorted for the surface marker SSEA3 before storage in RNAlater (Qiagen).

tag: cell line

value: EC cell line

tag: growth protocol

value: feeder-grown (fe)


title: C02177 Idiopathic Dilated CMP Left Ventricle

description:
C02177
PolyA mRNA


title: C02131 Ischemic Left Ventricle

description:
C02131
PolyA mRNA


title: U-BRCA1-20

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: U2OS cells transfected with BRCA1-targeting siRNA and treated with bortezomib

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Affymetrix Human Gene 2.0 ST array. GeneChips were washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned on a GeneChip® Scanner with Affymetrix Command Console.

data_processing: probe re-annotation according to the Ensembl Gene database (brainarray alternative CDF v. 16), preprocessing by RMA

source_name: U2OS, siBRCA1, bortezomib

label_protocol: sense-strand cDNA (ss-cDNA) was prepared from 100 ng total RNA using the Ambion WT Expression Kit, Part Number 4425209. 15 ug of cRNA was used for ss-cDNA synthesis. A total of 5,5 ug of sscDNA was fragmented and labelled using the Applied Biosystems GeneChip® WT Terminal Labeling and Hybridization Kit, P/N 702808

growth_protocol: Cells were grown in Dulbecco’s modiﬁed Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), L-Glutamine (2 mM) and 1×Penicillin-Streptomycin (Life Technologies) at 37 °C in a 5% CO2 atmosphere.

extract_protocol: Total RNAs was extracted with the Nucleospin RNA II kit (Macherey-Nagel) according to manufacturer's instructions. RNA quality was tested using Agilent 2100 Bioanalyzer.

treatment_protocol: 80-90% confluent HeLa and U2OS cells grown in 6 cm dishes were transfected with siRNA at 20 nM final concentration. 24 h later, cells were treated (or not) with 20 nM bortezomib for 8 h, after which a total RNAs was extracted.

tag: sirna

tag: bortezomib treatment

value: 20 nM


title: H-BRCA1-20

description: HeLa cells transfected with BRCA1-targeting siRNA and treated with bortezomib

source_name: HeLa, siBRCA1, bortezomib

value: HeLa


title: H9 [exon-level]

description:
H23 [exon-level]
H23_HuEx.CEL (see Series record)
H23_HuEx.rma-exon-core-dabg.chp

source_name: ES cell line

value: ES cell line

value: feeder-grown


title: Shef7 [exon-level]

description:
H24 [exon-level]
H24_HuEx.CEL (see Series record)
H24_HuEx.rma-exon-core-dabg.chp


title: TERA1 [exon-level]

description:
H22 [exon-level]
H22_HuEx.CEL (see Series record)
H22_HuEx.rma-exon-core-dabg.chp

value: plastic-grown


title: Shef3 [exon-level]

description:
H20 [exon-level]
H20_HuEx.CEL (see Series record)
H20_HuEx.rma-exon-core-dabg.chp


title: 833KE pl [exon-level]

description:
H21 [exon-level]
H21_HuEx.CEL (see Series record)
H21_HuEx.rma-exon-core-dabg.chp


title: 2102Ep pl [exon-level]

description:
H19 [exon-level]
H19_HuEx.CEL (see Series record)
H19_HuEx.rma-exon-core-dabg.chp


title: Shef 6 [exon-level]

description:
H17 [exon-level]
H17_HuEx.CEL (see Series record)
H17_HuEx.rma-exon-core-dabg.chp


title: MDA-MB-231 Calcitriol 1

city: Bornova

first: Hikmet

middle: Hakan

last: Aydin

state: Izmir

department: Department of Medical Biochemistry

country: Turkey

institute: Ege University School of Medicine

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Ege University School of Medicine AREL Microarray Core Facility.

data_processing:
Raw data were processed with Partek Genomic Suite  (Partek) for background correction and normalization. Data analysis and statistical evaluations were performed with Partek Genomic Suite (Partek) (version 6.6.2, http://www.partek.com).
RMA expression value derived from Expression Console software (v.1.3.1.187); core-exon analysis

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Expression Kit (Ambion) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: All cells were grown in DMEM medium (Lonza) with 10% fetal bovine serum and %1 penicillin/streptomycin supplement and maintained in a CO2 incubator with standard incubation conditions.

extract_protocol: RNA was isolated from the cells with RNAeasy mini kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: MCF-7 cells were treated with 40 μM calcitriol or 0.20% DMSO; MDA-MB-231 cells were treated with 50 μM calcitriol or 0.25% DMSO for 24 hours.

tag: cell type

value: ER- breast cancer cells

tag: treated with

value: 50 μM calcitriol for 24 hrs


title: MDA-MB-231 Calcitriol 2


title: MDA-MB-231 DMSO 3

value: 0.25% DMSO for 24 hrs


title: C02130 Ischemic Left Ventricle

description:
C02130
PolyA mRNA

value: heart left ventricle

value: yes

value: male


title: H-Ctrl-0

description: HeLa cells transfected with non-targeting siRNA

source_name: HeLa, siCtrl, untreated

value: non-targeting control


title: MDA-MB-231 Calcitriol 3


title: C02114 Ischemic Left Ventricle

description:
C02114
PolyA mRNA

value: ischemic


title: NTERA2 pl [exon-level]

description:
H25 [exon-level]
H25_HuEx.CEL (see Series record)
H25_HuEx.rma-exon-core-dabg.chp


title: MDA-MB-231 DMSO 2


title: H-Ctrl-20

description: HeLa cells transfected with non-targeting siRNA and treated with bortezomib

source_name: HeLa, siCtrl, bortezomib


title: MCF-7 DMSO 3

value: ER+ breast cancer cells

value: 0.20% DMSO for 24 hrs


title: U-BRCA1-0

description: U2OS cells transfected with BRCA1-targeting siRNA

source_name: U2OS, siBRCA1, untreated


title: C02083 Ischemic Left Ventricle

description:
C02083
PolyA mRNA

value: female


title: C02058 Idiopathic Dilated CMP Left Ventricle

description:
C02058
PolyA mRNA

value: idiopathic dilated CMP


title: C02116 Idiopathic Dilated CMP Left Ventricle

description:
C02116
PolyA mRNA


title: C02123 Ischemic Left Ventricle

description:
C02123
PolyA mRNA


title: MDA-MB-231 DMSO 1


title: IFNGR KO L.pneu vs. IFNGR KO PBS

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: whole lung

label_protocol: RNA labeling was performed with the Quick Amp Kit (Agilent Technologies) according supplier's instructions.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Anaesthetized mice were intranasally infected with 1e6 L. pneumophila JR32 in 40 µl of PBS (Archer et al., 2009). Determination of bacterial counts, pulmonary leukocytes and blood leukocytes have been described elsewhere (Lippmann et al., 2011).

value: IFNGR KO

tag: strain

tag: infection

value: L.pneumophila infected

value: PBS mock infected


title: MCF-7 DMSO 1


title: NTERA2 fe [exon-level]

description:
H11 [exon-level]
H11_HuEx.CEL (see Series record)
H11_HuEx.rma-exon-core-dabg.chp

value: EC cell line

value: feeder-grown (fe)


title: C02061 Ischemic Left Ventricle

description:
C02061
PolyA mRNA

tag: tissue


title: C02057 Ischemic Left Ventricle

description:
C02057
PolyA mRNA

tag: heart failure


title: IFN dKO L.pneu vs. IFN dKO PBS

value: IFN dKO


title: H-BRCA1-0

description: HeLa cells transfected with BRCA1-targeting siRNA

source_name: HeLa, siBRCA1, untreated

value: HeLa


title: IFN dKO PBS vs. IFN dKO L.pneu


title: 2102Ep fe [exon-level]

description:
H13 [exon-level]
H13_HuEx.CEL (see Series record)
H13_HuEx.rma-exon-core-dabg.chp


title: C02045 Idiopathic Dilated CMP Left Ventricle

description:
C02045
PolyA mRNA

tag: disease status


title: C02031 Ischemic Left Ventricle

description:
C02031
PolyA mRNA

tag: gender


title: IFNGR KO PBS vs. IFNGR KO L.pneu


title: MCF-7 DMSO 2


title: MCF-7 Calcitriol 1

value: 40 μM calcitriol for 24 hrs


title: C01997 Idiopathic Dilated CMP Left Ventricle

description:
C01997
PolyA mRNA

value: heart left ventricle

tag: age


title: IFNAR KO PBS vs. IFNAR KO L.pneu

value: IFNAR KO


title: MCF-7 Calcitriol 3


title: NCCIT [exon-level]

description:
H18 [exon-level]
H18_HuEx.CEL (see Series record)
H18_HuEx.rma-exon-core-dabg.chp

value: plastic-grown


title: IFNAR KO L.pneu vs. IFNAR KO PBS


title: H14 [exon-level]

description:
H4 [exon-level]
H4_HuEx.CEL (see Series record)
H4_HuEx.rma-exon-core-dabg.chp

value: ES cell line

value: feeder-grown


title: WT PBS vs. WT L.pneu

value: WT


title: C01960 Idiopathic Dilated CMP Left Ventricle

description:
C01960
PolyA mRNA

value: yes

value: male


title: C01990 Idiopathic Dilated CMP Left Ventricle

description:
C01990
PolyA mRNA

value: idiopathic dilated CMP


title: MCF-7 Calcitriol 2

value: ER+ breast cancer cells


title: Shef5 [exon-level]

description:
H7 [exon-level]
H7_HuEx.CEL (see Series record)
H7_HuEx.rma-exon-core-dabg.chp


title: WT L.pneu vs. WT PBS

value: L.pneumophila infected


title: C01954 Idiopathic Dilated CMP Left Ventricle

description:
C01954
PolyA mRNA


title: BALB/c HBV transgenic  vs. BALB/c wild-type

description: HBV transgenic mice expressed in the liver Hepatitis B virus envelope polypeptides under the control of Albumin promoter

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies).

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

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed on reporter and sequence level with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: H-HBV

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

growth_protocol: Generation and characteristics of transgenic C57BL/6 lineages Tg(Alb-1HBV), internal designation (HBVTg/6) have been described previously  in PMID: 2598264 and http://jaxmice.jax.org/strain/002226.html; these mice were backcrossed to fibrosis susceptible Balb/c genetic background for at least 6 generations

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

treatment_protocol: At age of 12 weeks mice were killed by CO2-inhalation. Liver samples were collected andhomogenized in TRIzol.

tag: strain background

value: BALB/c

value: HBV transgenic

value: 12 wks

value: liver

source_name: LM ctrl

value: wild-type


title: IFNGR KO L.pneu vs. IFN dKO L.pneu

value: IFNGR KO

value: IFN dKO


title: C02111 Ischemic Left Ventricle

description:
C02111
PolyA mRNA

value: heart left ventricle

value: ischemic


title: BALB/c wild-type vs. BALB/c HBV transgenic


title: C02109 Idiopathic Dilated CMP Left Ventricle

description:
C02109
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP


title: C02097 Idiopathic Dilated CMP Left Ventricle

description:
C02097
PolyA mRNA


title: C02094 Idiopathic Dilated CMP Left Ventricle

description:
C02094
PolyA mRNA

value: female


title: IFN dKO L.pneu vs. IFNAR KO L.pneu

value: IFNAR KO


title: IFNGR KO L.pneu vs. IFNAR KO L.pneu


title: SC_D5_C-Level_control

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

description: pool of 3 animals

hyb_protocol: The obtained labeled copy RNA samples were hybridized 17 h at 65°C to a SurePrint G3 Rat GE 8x60K (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Slides were scanned using an Agilent C Scanner

data_processing: The raw data were processed using Feature Extraction software version 10.5. The initial analysis and normalization to the median were performed using GeneSpring GX software (Agilent). Differentially expressed mRNAs with signal intensities higher than two-fold over the background standard deviation were filtered by t-test with p<0.05. Only the statistically significant data (p<0.05) were used to calculate gene expression ratios in the samples.

organism: Rattus norvegicus

source_name: Spinal cord, C-level contol, 5 days post-injection

label_protocol: Samples of total RNA (50 ng) were labeled using a LowInput QuickAmp Labeling Kit and Cy3-CTP (Agilent Technologies).

extract_protocol: Total RNA was extracted using TRIzol reagent and purified using the RNeasy columns (Qiagen). The RNA purity was estimated by measuring the OD260/280 and the 260/230 ratios. The integrity of the RNA samples was validated using an Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: Adult female Sprague-Dawley rats (200-225 g; Harlan) were housed under the regular 22 ± 1°C temperature and 12:12 h light-dark cycle conditions. Animals had access to food and water ad libitum. Anesthesia was induced by a 5% isoflurane/air mixture (5% Forene) and maintained using a 2.5% isoflurane/air mixture. The common sciatic nerve was exposed unilaterally at the mid-thigh level and transected using surgical scissors. At day 1 and week 1 after injury, the proximal, distal and contralateral nerve segments were collected for subsequent analysis. Spinal cord sections were collected from animals after 5 days post-injury. In accordance with both the NIH Guidelines for the Care and Use of Laboratory Animals and protocols approved by the Institutional Animal Care and Use Committee at the VA San Diego Healthcare System, animals were sacrificed using an overdose of a rodent anesthesia cocktail [50 mg/ml Nembutal (Abbott Labs) and 5 mg/ml diazepam (Steris Labs) in 0.9% PBS (Steris Labs)], followed by i.p. injection of Beuthanasia (100-150 mg/ml; Schering-Plough Animal Health). Stimulation of cultured Schwann cells using S100A8/A9. S100A8/A9 proteins were a kind gift from Dr. Thomas Vogl, Institute of Immunology, University of Muenster, Muenster, Germany.  Primary Schwann cells were isolated from sciatic nerves of postnatal day 1-3 Sprague-Dawley rats, further purified from fibroblasts, using AraC, an anti-fibronectin Thy1.1 antibody, and rabbit complement. According to the S100 staining, the purity of the isolated Schwann cell samples was over 99%.  Schwann cells were then plated in 75 cm2 flasks coated with 50 µg/ml poly-D-lysine (Chemicon) in DMEM containing 10% fetal bovine serum (FBS), 50 µg/ml poly-D-lysine (Chemicon), 100 units/ml penicillin and 100 μg/ml streptomycin, 21 μg/ml bovine pituitary extract (Life Technologies) and 4 μM forskolin (Calbiotech) at 37°C and 5.0% CO2. Cells were passaged until they reached confluence and used in experiments at passages 3-7. For stimulation, Schwann cells were plated in wells of a 6-well plate and allowed to reach a 75% confluence level. Purified S100A8/A9 (5 µg/ml) was added to the cells for either 1 h or 24 h. Cells were then harvested and washed.

value: Sprague-Dawley

value: Spinal cord, C-level


title: Schwann cell 24h stimulation by S100A8/9 at 5 µg/ml conc

description: Schwann cells, 24h post-stimulation

source_name: primary Schwann cells, S100A8/A9 stimulation, 24 h post-stimulation

value: primary Schwann cells


title: IFN dKO L.pneu vs. WT L.pneu

value: WT


title: IFNAR KO L.pneu vs. IFNGR KO L.pneu


title: C02092 Ischemic Left Ventricle

description:
C02092
PolyA mRNA

source_name: heart left ventricle, ischemic

value: yes

value: male


title: C02095 Idiopathic Dilated CMP Left Ventricle

description:
C02095
PolyA mRNA

value: idiopathic dilated CMP


title: Schwann cell 24h control

description: Schwann cells control

source_name: primary Schwann cells, no stimulation control, 24 h post-stimulation


title: IFNAR KO L.pneu vs. IFN dKO L.pneu

value: L.pneumophila infected


title: Schwann cell 1h stimulation by S100A8/9 at 5 µg/ml conc

description: Schwann cells, 1h post-stimulation

source_name: primary Schwann cells, S100A8/A9 stimulation, 1 h post-stimulation


title: SC_D5_Dorsal_hemisection

description: pool of 3 animals

source_name: Spinal cord dorsal hemisection, 5 days post-injection

value: Spinal cord dorsal hemisection


title: WT L.pneu vs. IFN dKO L.pneu


title: C02081 Idiopathic Dilated CMP Left Ventricle

description:
C02081
PolyA mRNA


title: IFNGR KO L.pneu vs. WT L.pneu


title: C02080 Idiopathic Dilated CMP Left Ventricle

description:
C02080
PolyA mRNA


title: LND_D1

description: pool of 3 animals

source_name: Left sciatic nerve, distal nerve segment, day 1 post-injury

value: left sciatic nerve


title: LNP_D1

description: pool of 3 animals

source_name: Left sciatic nerve, proximal nerve segment, day 1 post-injury


title: C02077 Ischemic Left Ventricle

description:
C02077
PolyA mRNA


title: WT L.pneu vs. IFNGR KO L.pneu


title: RN_D1

description: pool of 3 animals

source_name: Right sciatic nerve control (PBS injection site), day 1 post-injury

value: right sciatic nerve


title: C02069 Idiopathic Dilated CMP Left Ventricle

description:
C02069
PolyA mRNA


title: WT L.pneu vs. IFNAR KO L.pneu


title: C02068 Ischemic Left Ventricle

description:
C02068
PolyA mRNA


title: IFNAR KO L.pneu vs. WT L.pneu


title: C00083 Non-failing Left Ventricle

description:
C00083
PolyA mRNA

source_name: heart left ventricle, non-failing

value: no

value: non-failing


title: C00107 Non-failing Left Ventricle

description:
C00107
PolyA mRNA

value: heart left ventricle


title: C00076 Non-failing Left Ventricle

description:
C00076
PolyA mRNA


title: MALIGNANT PHYLLODES TUMOR [20130227_205635330814_01-11752-A3_09.RCC]

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: The data were normalized using 5 HK genes.  Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: Tumor

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO´s Translational Genomics Group

extract_protocol: Total RNA was isolated from macrodissected FFPE tissue using ROCHE High Pure FFPE Kit

tag: tumor size

tag: rfs event

tag: rfs time

value: Normal

tag: ror-s score

tag: ror-s groups

value: med


title: MALIGNANT PHYLLODES TUMOR [20130227_205635330814_99-6240-F10_07.RCC]

value: Basal

value: high


title: MALIGNANT PHYLLODES TUMOR [20130123_205611630814_06-13456-A2_10.RCC]


title: C00096 Non-failing Left Ventricle

description:
C00096
PolyA mRNA


title: MALIGNANT PHYLLODES TUMOR [20130123_205611630814_06-18382-A5_09.RCC]


title: C57BL/6 HBV transgenic  vs. C57BL/6 wild-type

source_name: HBV Tr

tag: genotype/variation

value: HBV transgenic

value: 12 wks

value: liver

source_name: HBV LM

value: wild-type


title: C00098 Non-failing Left Ventricle

description:
C00098
PolyA mRNA

value: male


title: C57BL/6 wild-type vs. C57BL/6 HBV transgenic


title: MALIGNANT PHYLLODES TUMOR [20130419_205635520814_13-7292_04.RCC]

value: Claudin


title: C00097 Non-failing Left Ventricle

description:
C00097
PolyA mRNA

value: female


title: C00044 Non-failing Left Ventricle

description:
C00044
PolyA mRNA


title: C00045 Non-failing Left Ventricle

description:
C00045
PolyA mRNA


title: C00042 Non-failing Left Ventricle

description:
C00042
PolyA mRNA


title: MALIGNANT PHYLLODES TUMOR [20130305_205635410814_10-342-A5_10.RCC]


title: Sample 55, replicate 3

city: Thiverval-Grignon

first: Nicolas

last: Morin

address: Av. Lucien Bretignières

department: UMR 1319 Micalis

institute: INRA

description: Sample 55, replicate 3

hyb_protocol: Hybridization was performed according to Agilent's general protocol (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf)

scan_protocol: Scanning was performed using an Agilent scanner (Agilent, USA). Images were further treated using Feature Extraction v10.0 (Agilent, USA).

data_processing: Raw transcriptomic data were filtered and normalized using the R software and the Limma package of the Bioconductor library. Local background estimates were corrected using the “normexp + offset” method, using an offset value of 10. A « scale » normalization method was applied to normalize background substracted data between arrays.

organism: Yarrowia lipolytica

source_name: Sample 55, replicate 3

label_protocol: Samples were treated with the Low Input Quick Amp  labelling kit (Agilent, USA), according to manufacturer's protocol.

growth_protocol: Precultivations for chemostat were carried out on a 5-ml tube of YPD medium at 28 °C for 16 h at 100 rpm. The culture in growth phase was transferred into a 1-l Erlenmeyer flask containing 170 ml of mineral medium at pH 5.6 prepared as follows (all compounds are expressed in gl-1): (NH4)2SO4, 3.5; KH2PO4, 6; MgSO4, 2; EDTA, 0.0375; ZnSO4∙7H2O, 0.0281; MnCl2∙4H2O, 0.0025; CoCl2∙6H2O, 0.00075; CuSO4∙5H2O, 0.00075;  Na2MoSO4∙2H2O, 0.00005; CaCl2∙2H2O, 0.0125; FeSO4∙7H2O, 0.00875; H3BO3, 0.0025; D-biotin, 0.00025; D-L-panthotenic acid, 0.001; nicotinic acid, 0.001; my0-inositol, 0.00625; thiamin, 0.001; pyridoxine, 0.001; para-aminobenzoic acid, 0.0002. Glucose was added to a final concentration of 18 gl-1 with chloramphenicol at 10 mgl-1. After 16 h of growth at 28°C and 100 rpm, 170 ml of the broth were used to inoculate 1.7 l of the same mineral medium in a 3-l bioreactor.  Chemostat and D-Stat experiments were performed in a 3-l stirred tank bioreactor with a working volume of 1.5 l using the Biostat B. Braun Biotech International (Sartorius AG , Germany) with the acquisition software MFCS/win 2.0. The temperature was regulated at 28°C and the pH at 5.6 by the in-line addition of 5 M NaOH. The fermentation started in batch under full aerobic conditions. The Dissolved Oxygen was maintained above 20% of saturation by modulating the air flow rate or the stirring rate in order to avoid oxygen limitation. 11 h after inoculation, when the glucose was totally consumed, continuous cultivation was started. For chemostat cultivation, the bioreactor was continuously fed with the mineral medium (except (NH4)2SO4) supplemented with 23 gl-1 glucose at 0.108 lh-1. The bioreactor was fed with a second reservoir containing 60 gl-1 (NH4)2SO4 at 0.0117 lh-1 corresponding to a N/C ratio of 0.129 molN.Cmol-1. The working dilution rate was 0.08 h-1. When the steady state was reached after 5 residence times (ד= 1/D), the D-Stat was set up. The feeding rate of the mineral medium supplemented with glucose was maintained constant at 0.120 lh-1 while the (NH4)2SO4 feeding rate followed a linear and smooth decrease from 0.0117 lh-1 to 0.0003 lh-1 for 50 h (deceleration factor : 0.00015 h-2) corresponding  to a decrease in the N/C ratio from 0.129 to 0.0028 molNCmol-1. All other parameters were maintained unchanged.

extract_protocol: Frozen samples were treated by mechanical disruption, using a bead beater (Microdismenbrator, Braun, Germany) and a tungsten bead (Ø ~ 7 mm), for 2 min at 2600 rpm. After disruption, the resulting cell powder was recovered and further processed for RNA purification using the RNEasy Midi Kit (Qiagen, The Netherlands), according to the manufacturer's instruction.

treatment_protocol: Samples have been collected from the bioreactor directly through the sampling septum. For each time point, a volume equivalent to ca. 300 mg dry cell weight was harvested, frozen in liquid nitrogen, and further stored at -80°C until extraction.

tag: sampling time (h)

tag: n/c  ratio (moln / cmol)


title: Sample 55, replicate 2

description: Sample 55, replicate 2

source_name: Sample 55, replicate 2


title: MALIGNANT PHYLLODES TUMOR [20130227_205635330814_01-13114-A_10.RCC]


title: MALIGNANT PHYLLODES TUMOR [20130305_205635410814_01-8178-A4_04.RCC]


title: Sample 56, replicate 3

description: Sample 56, replicate 3

source_name: Sample 56, replicate 3


title: Sample 56, replicate 2

description: Sample 56, replicate 2

source_name: Sample 56, replicate 2


title: Sample 56, replicate 1

description: Sample 56, replicate 1

source_name: Sample 56, replicate 1


title: Sample 55, replicate 1

description: Sample 55, replicate 1

source_name: Sample 55, replicate 1


title: IFN dKO L.pneu vs. IFNGR KO L.pneu

source_name: whole lung

value: IFN dKO

value: L.pneumophila infected

value: IFNGR KO


title: Hemolymph from healthy clams - replicate 6

city: Stony Brook

first: Bassem

last: Allam

state: NY

address: School of Marine and Atmospheric Sciences

institute: Stony Brook University

description:
48
raw data file: 36-48.gpr

hyb_protocol: All arrays were hybridized with the same amount of cRNA (300 ng of each Cy3- and Cy5-labeled cRNA).

scan_protocol: Arrays were scanned with a GenePix 4000B scanner using the suggested Agilent scan settings.

data_processing:
Generated fluorescence intensities were normalized to remove within-array and between-array variations using the LIMMA package in R software.
After normalization, probes with intensities less than two-fold background intensities (in all biological replicates) were eliminated from further analysis.

organism: Ruditapes philippinarum

source_name: Hemolymph from healthy clams

label_protocol: Labeled (Cy3 or Cy5) complementary RNA (cRNA) was synthesized from 150 ng of RNA purified from different tissues of healthy and diseased clams using the Two-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp Labeling) following manufacturer’s protocol

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

treatment_protocol: Disease diagnostic was performed on shells and clams ranked as either diseased (animals showing signs of brown ring disease) or healthy.

value: Adult

tag: origin

value: Aquacultured

tag: clam condition

value: Healthy

value: Hemocytes from Hemolymph


title: P01039 Idiopathic Dilated CMP Left Ventricle

description:
P01039
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: heart left ventricle

value: yes

value: idiopathic dilated CMP


title: MALIGNANT PHYLLODES TUMOR [20130227_205635330814_00-22198-R_08.RCC]

value: Basal

value: high


title: Hemolymph from healthy clams - replicate 5

description:
47
raw data file: 35-47.gpr


title: C00041 Non-failing Left Ventricle

description:
C00041
PolyA mRNA

value: no

value: non-failing


title: Hemolymph from diseased clams - replicate 6

description:
45
raw data file: 33-45.gpr

source_name: Hemolymph from diseased clams

value: Diseased


title: C00165 Non-failing Left Ventricle

description:
C00165
PolyA mRNA


title: MALIGNANT PHYLLODES TUMOR [20130227_205635330814_99-13734_06.RCC]

value: Claudin


title: Sample 54, replicate 1

description: Sample 54, replicate 1

source_name: Sample 54, replicate 1


title: P01036 Idiopathic Dilated CMP Left Ventricle

description:
P01036
PolyA mRNA

value: male


title: MALIGNANT PHYLLODES TUMOR [20130220_205635320814_09-501241-A10_03.RCC]

value: med


title: Hemolymph from diseased clams - replicate 5

description:
44
raw data file: 32-44.gpr


title: Hemolymph from diseased clams - replicate 4

description:
43
raw data file: 31-43.gpr


title: Sample 53, replicate 3

description: Sample 53, replicate 3

source_name: Sample 53, replicate 3


title: C00162 Non-failing Left Ventricle

description:
C00162
PolyA mRNA

value: female


title: Sample 54, replicate 3

description: Sample 54, replicate 3

source_name: Sample 54, replicate 3


title: BENIGN PHYLLODES TUMOR [20131010_205635340814_04-8830-A2_12.RCC]

value: Normal

value: low


title: Sample 54, replicate 2

description: Sample 54, replicate 2

source_name: Sample 54, replicate 2


title: BENIGN PHYLLODES TUMOR [20131010_205635340814_03-11474_11.RCC]

source_name: Tumor


title: C00163 Non-failing Left Ventricle

description:
C00163
PolyA mRNA

source_name: heart left ventricle, non-failing


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_02-8828-R_10.RCC]


title: Hemolymph from diseased clams - replicate 3

description:
42
raw data file: 30-42.gpr

value: Adult

value: Aquacultured


title: Sample 52, replicate 3

description: Sample 52, replicate 3

source_name: Sample 52, replicate 3


title: C00157 Non-failing Left Ventricle

description:
C00157
PolyA mRNA


title: Sample 51, replicate 3

description: Sample 51, replicate 3

source_name: Sample 51, replicate 3


title: Sample 52, replicate 2

description: Sample 52, replicate 2

source_name: Sample 52, replicate 2


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_02-2623-R6_09.RCC]


title: Hemolymph from diseased clams - replicate 2

description:
41
raw data file: 29-41.gpr

value: Hemocytes from Hemolymph


title: C00153 Non-failing Left Ventricle

description:
C00153
PolyA mRNA

value: heart left ventricle


title: Hemolymph from healthy clams - replicate 4

description:
46
raw data file: 34-46.gpr

value: Healthy


title: Sample 52, replicate 1

description: Sample 52, replicate 1

source_name: Sample 52, replicate 1


title: Sample 51, replicate 2

description: Sample 51, replicate 2

source_name: Sample 51, replicate 2


title: C00151 Non-failing Left Ventricle

description:
C00151
PolyA mRNA


title: C00119 Non-failing Left Ventricle

description:
C00119
PolyA mRNA


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_02-3817-R_07.RCC]


title: Hemolymph from healthy clams - replicate 3

description:
39
raw data file: 27-39.gpr


title: Sample 53, replicate 2

description: Sample 53, replicate 2

source_name: Sample 53, replicate 2


title: Hemolymph from healthy clams - replicate 2

description:
38
raw data file: 26-38.gpr


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_01-10017-A1_05.RCC]


title: Hemolymph from healthy clams - replicate 1

description:
37
raw data file: 25-37.gpr


title: C00150 Non-failing Left Ventricle

description:
C00150
PolyA mRNA


title: Extrapallial fluid from healthy clams - replicate 6

description:
36
raw data file: 36-48.gpr

source_name: Extrapallial fluid from healthy clams

value: Hemocytes from extrapallial fluid


title: Sample 53, replicate 1

description: Sample 53, replicate 1

source_name: Sample 53, replicate 1


title: Hemolymph from diseased clams - replicate 1

description:
40
raw data file: 28.40.gpr


title: Sample 51, replicate 1

description: Sample 51, replicate 1

source_name: Sample 51, replicate 1


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_99-2757-B_02.RCC]

value: LumA


title: Sample 50, replicate 3

description: Sample 50, replicate 3

source_name: Sample 50, replicate 3


title: Ma-Mel-100a

city: Essen

first: Klaus

middle: Georg

last: Griewank

address: Hufelandstr. 55

department: Dermatology

institute: University of Duisburg-Essen

description: CytoScanHD-Array

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

scan_protocol: According to manufacturers instructions.

data_processing:
The array image was acquired using Affymetrix® Chromosome Analysis Suite (ChAS) Software
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.1
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = apt-copynumber-cyto.exe
program-version = 1.15.1
program-company = Affymetrix
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from celllines using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and PicoGreen

tag: patient id

tag: cell line

value: melanoma cell line from 1st LN metastasis


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_98-18163-A_01.RCC]


title: Extrapallial fluid from healthy clams - replicate 4

description:
34
raw data file: 34-46.gpr

tag: tissue


title: Sample 50, replicate 2

description: Sample 50, replicate 2

source_name: Sample 50, replicate 2


title: C00127 Non-failing Left Ventricle

description:
C00127
PolyA mRNA

tag: heart failure

value: no

tag: disease status


title: C00170 Non-failing Left Ventricle

description:
C00170
PolyA mRNA

value: non-failing

tag: gender

tag: age


title: Sample 50, replicate 1

description: Sample 50, replicate 1

source_name: Sample 50, replicate 1


title: Extrapallial fluid from healthy clams - replicate 5

description:
35
raw data file: 35-47.gpr


title: C00122 Non-failing Left Ventricle

description:
C00122
PolyA mRNA


title: BENIGN PHYLLODES TUMOR [20130514_205635530814_02-15624_03.RCC]

tag: tumor size


title: Ma-Mel-48c

description: CytoScanHD-Array

value: melanoma cell line from 2nd LN metastasis


title: Extrapallial fluid from diseased clams - replicate 5

description:
32
raw data file: 32-44.gpr

source_name: Extrapallial fluid from diseased clams

value: Diseased


title: C00118 Non-failing Left Ventricle

description:
C00118
PolyA mRNA


title: Extrapallial fluid from diseased clams - replicate 6

description:
33
raw data file: 33-45.gpr


title: Sample 49, replicate 3

description: Sample 49, replicate 3

source_name: Sample 49, replicate 3


title: Ma-Mel-48a

description: CytoScanHD-Array

value: melanoma cell line from skin metastasis


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_06-19327-A1_05.RCC]

tag: rfs event


title: Ma-Mel-100b

description: CytoScanHD-Array


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_06-10607-A1_06.RCC]

tag: rfs time


title: Extrapallial fluid from diseased clams - replicate 4

description:
31
raw data file: 31-43.gpr


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_05-25800-A1_04.RCC]

tag: ror-s score

value: med


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_05-15311-A3_02.RCC]

tag: ror-s groups


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_05-13657-A1_03.RCC]


title: C00121 Non-failing Left Ventricle

description:
C00121
PolyA mRNA

value: male


title: BENIGN PHYLLODES TUMOR [20130319_205635510814_02-4617-R_01.RCC]

value: Normal


title: Sample 49, replicate 1

description: Sample 49, replicate 1

source_name: Sample 49, replicate 1


title: Extrapallial fluid from diseased clams - replicate 3

description:
30
raw data file: 30-42.gpr


title: C00120 Non-failing Left Ventricle

description:
C00120
PolyA mRNA


title: Germline Ma-Mel-48

description: CytoScanHD-Array

source_name: Germline Ma-Mel-48

value: germline DNA of Ma-Mel-48 Celllines


title: C00104 Non-failing Left Ventricle

description:
C00104
PolyA mRNA

source_name: heart left ventricle, non-failing


title: Sample 48, replicate 3

description: Sample 48, replicate 3

source_name: Sample 48, replicate 3


title: Extrapallial fluid from diseased clams - replicate 1

description:
28
raw data file: 28.40.gpr

value: Adult


title: BENIGN PHYLLODES TUMOR [20130220_205635320814_03-19607-R_07.RCC]

source_name: Tumor

value: low


title: Sample 49, replicate 2

description: Sample 49, replicate 2

source_name: Sample 49, replicate 2


title: Sample 48, replicate 2

description: Sample 48, replicate 2

source_name: Sample 48, replicate 2


title: Sample 48, replicate 1

description: Sample 48, replicate 1

source_name: Sample 48, replicate 1


title: C00102 Non-failing Left Ventricle

description:
C00102
PolyA mRNA

value: female


title: C00101 Non-failing Left Ventricle

description:
C00101
PolyA mRNA

value: heart left ventricle


title: BENIGN PHYLLODES TUMOR [20130305_205635410814_01-14818_05.RCC]


title: C00064 Non-failing Left Ventricle

description:
C00064
PolyA mRNA


title: Extrapallial fluid from diseased clams - replicate 2

description:
29
raw data file: 29-41.gpr

value: Aquacultured


title: Sample 47, replicate 3

description: Sample 47, replicate 3

source_name: Sample 47, replicate 3


title: Extrapallial fluid from healthy clams - replicate 3

description:
27
raw data file: 27-39.gpr

source_name: Extrapallial fluid from healthy clams

value: Healthy

value: Hemocytes from extrapallial fluid


title: C00060 Non-failing Left Ventricle

description:
C00060
PolyA mRNA


title: C00115 Non-failing Left Ventricle

description:
C00115
PolyA mRNA


title: Ma-Mel-48b

description: CytoScanHD-Array

value: melanoma cell line from 1st LN metastasis


title: Sample 47, replicate 2

description: Sample 47, replicate 2

source_name: Sample 47, replicate 2


title: Extrapallial fluid from healthy clams - replicate 2

description:
26
raw data file: 26-38.gpr


title: BENIGN PHYLLODES TUMOR [20130220_205635320814_04-862-A7_02.RCC]


title: C00109 Non-failing Left Ventricle

description:
C00109
PolyA mRNA

value: no


title: Sample 32, replicate 3

description: Sample 32, replicate 3

source_name: Sample 32, replicate 3


title: Sample 47, replicate 1

description: Sample 47, replicate 1

source_name: Sample 47, replicate 1


title: Extrapallial fluid from healthy clams - replicate 1

description:
25
raw data file: 25-37.gpr


title: BORDERLINE PHYLLODES TUMOR [20130227_205635330814_06-22116-A1_03.RCC]


title: Sample 32, replicate 2

description: Sample 32, replicate 2

source_name: Sample 32, replicate 2


title: BORDERLINE PHYLLODES TUMOR [20130227_205635330814_00-10421-R_01.RCC]


title: Mantle from healthy clams - replicate 5

source_name: Mantle from healthy clams

value: Mantle


title: BENIGN PHYLLODES TUMOR [20130220_205635320814_03-20155_04.RCC]


title: BENIGN PHYLLODES TUMOR [20130220_205635320814_03-19609-R_01.RCC]


title: Mantle from healthy clams - replicate 4


title: C00077 Non-failing Left Ventricle

description:
C00077
PolyA mRNA

value: non-failing


title: Mantle from healthy clams - replicate 6


title: C00133 Non-failing Left Ventricle

description:
C00133
PolyA mRNA


title: Mantle from diseased clams - replicate 5

source_name: Mantle from diseased clams

value: Diseased


title: Mantle from diseased clams - replicate 6


title: BORDERLINE PHYLLODES TUMOR [20130123_205611630814_05-13123-A9_08.RCC]


title: Sample 30, replicate 3

description: Sample 30, replicate 3

source_name: Sample 30, replicate 3


title: Sample 30, replicate 2

description: Sample 30, replicate 2

source_name: Sample 30, replicate 2


title: BORDERLINE PHYLLODES TUMOR [20130123_205611630814_07-23055-A10_11.RCC]


title: BORDERLINE PHYLLODES TUMOR [20130123_205611630814_07-13312-A5_12.RCC]


title: Sample 30, replicate 1

description: Sample 30, replicate 1

source_name: Sample 30, replicate 1


title: Reduction Mammoplasty [20130313_205635470814_13-4228-A4_11.RCC]

source_name: Reduction Mammoplasty


title: C00043 Non-failing Left Ventricle

description:
C00043
PolyA mRNA

source_name: heart left ventricle, non-failing


title: Reduction Mammoplasty [20130313_205635470814_13-2659-A1_10.RCC]


title: Mantle from diseased clams - replicate 2


title: C00062 Non-failing Left Ventricle

description:
C00062
PolyA mRNA


title: Sample 26, replicate 3

description: Sample 26, replicate 3

source_name: Sample 26, replicate 3


title: C00164 Non-failing Left Ventricle

description:
C00164
PolyA mRNA


title: Reduction Mammoplasty [20130313_205635470814_12-25819-B2_09.RCC]


title: Sample 32, replicate 1

description: Sample 32, replicate 1

source_name: Sample 32, replicate 1


title: Sample 26, replicate 2

description: Sample 26, replicate 2

source_name: Sample 26, replicate 2


title: Reduction Mammoplasty [20130313_205635470814_12-21075-B1_07.RCC]


title: C00160 Non-failing Left Ventricle

description:
C00160
PolyA mRNA


title: Reduction Mammoplasty [20130313_205635470814_12-21633-A2_08.RCC]


title: Mantle from diseased clams - replicate 1


title: Mantle from diseased clams - replicate 3


title: Mantle from diseased clams - replicate 4


title: Sample 45, replicate 2

description: Sample 45, replicate 2

scan_protocol: Scanning was performed using a INNOSCAN 900 Microarray Scanner (INNOPSYS, France). Images were further treated using Mapix v5.5.0 (Innopsys, France).

source_name: Sample 45, replicate 2


title: C00138 Non-failing Left Ventricle

description:
C00138
PolyA mRNA


title: Reduction Mammoplasty [20130313_205635470814_12-20288-A1_06.RCC]


title: Sample 26, replicate 1

description: Sample 26, replicate 1

source_name: Sample 26, replicate 1


title: C00099 Non-failing Left Ventricle

description:
C00099
PolyA mRNA


title: C00078 Non-failing Left Ventricle

description:
C00078
PolyA mRNA


title: Sample 45, replicate 3

description: Sample 45, replicate 3

source_name: Sample 45, replicate 3


title: C00080 Non-failing Left Ventricle

description:
C00080
PolyA mRNA


title: C00116 Non-failing Left Ventricle

description:
C00116
PolyA mRNA


title: Sample 45, replicate 1

description: Sample 45, replicate 1

source_name: Sample 45, replicate 1


title: Reduction Mammoplasty [20130313_205635470814_12-19079-A3_05.RCC]


title: C00081 Non-failing Left Ventricle

description:
C00081
PolyA mRNA


title: Mantle from healthy clams - replicate 2


title: Reduction Mammoplasty [20130313_205635470814_12-18889-B3_04.RCC]


title: Sample 26, replicate 1 (technical replicate of 26_r1)


title: Mantle from healthy clams - replicate 3


title: C00040 Non-failing Left Ventricle

description:
C00040
PolyA mRNA


title: Reduction Mammoplasty [20130313_205635470814_12-15974-A5_03.RCC]

tag: age (years)

tag: tumor size (mm)

tag: relapse-free survival event (0=no recurrence; 1=recurrence)

tag: relapse-free survival time (months)


title: Mantle from healthy clams - replicate 1

tag: origin

tag: clam condition


title: Reduction Mammoplasty [20130313_205635470814_12-15561-A2_02.RCC]


title: Reduction Mammoplasty [20130109_205611930814_12-8927-A3_02.RCC]


title: C00048 Non-failing Left Ventricle

description:
C00048
PolyA mRNA


title: Sample 44, replicate 1

description: Sample 44, replicate 1

source_name: Sample 44, replicate 1

tag: sampling time (h)

tag: n/c  ratio (moln / cmol)


title: Reduction Mammoplasty [20130109_205611930814_12-7740-A5_03.RCC]


title: Sample 44, replicate 3

description: Sample 44, replicate 3

source_name: Sample 44, replicate 3


title: Reduction Mammoplasty [20130109_205611930814_12-7732-A2_01.RCC]


title: Sample 43, replicate 3

description: Sample 43, replicate 3

source_name: Sample 43, replicate 3


title: C00171 Non-failing Left Ventricle

description:
C00171
PolyA mRNA

tag: tissue

tag: heart failure


title: Sample 44, replicate 2

description: Sample 44, replicate 2

source_name: Sample 44, replicate 2


title: Reduction Mammoplasty [20130109_205611930814_12-11244-A2_04.RCC]


title: P00368 Idiopathic Dilated CMP Left Ventricle

description:
P00368
PolyA mRNA

source_name: heart left ventricle, idiopathic dilated CMP

value: yes

tag: disease status

value: idiopathic dilated CMP

tag: gender


title: C00108 Non-failing Left Ventricle

description:
C00108
PolyA mRNA

value: male

tag: age


title: P01165 Non-failing Left Ventricle

description:
P01165
PolyA mRNA


title: Thyroidectomized Side Population cells 6

city: Bethesda

first: Tsutomu

last: Matsubara

state: MD

address: 9000 Rockville Pike

institute: NCI

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Side population cells of mouse thyroid after partial thyroidectomy

label_protocol: Antisense RNAs were amplified with the Amino Allyl MessageAmp™ II aRNA Kit and labelled with the MonoReactive Dye Pack.

extract_protocol: Total RNAs were extracted using the miRNeasy Mini Kit following the manufacturer's instructions.

treatment_protocol: Mouse thyroids with and without partial thyroidectomy were digested with collagenase and dispase 1, and the resulting cells were cultured for 2 days.  Cells were collected and treated with Hoechst 33342 fluorescence dye in the presence and absence of verapamil, which were then subjected to FACS analysis. SP and non-SP (main population: MP) cells were separately collected.

value: male/female

tag: strain

value: thyroid

tag: cell population

value: side

tag: treatment

value: partial thyroidectomy

source_name: Ambion Mouse Assorted Total RNA

value: Swiss Webster

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: Thyroidectomized Main Population cells 1

source_name: Main population cells of mouse thyroid after partial thyroidectomy

value: main


title: C00079 Non-failing Left Ventricle

description:
C00079
PolyA mRNA

value: heart left ventricle

value: female


title: Thyroidectomized Side Population cells 5


title: Sample 43, replicate 1

description: Sample 43, replicate 1

source_name: Sample 43, replicate 1


title: Sample 42, replicate 2

description: Sample 42, replicate 2

source_name: Sample 42, replicate 2


title: Thyroidectomized Main Population cells 3


title: P01152 Non-failing Left Ventricle

description:
P01152
PolyA mRNA

source_name: heart left ventricle, non-failing


title: Thyroidectomized Main Population cells 2


title: Thyroidectomized Side Population cells 4


title: Thyroidectomized Side Population cells 3


title: Sample 43, replicate 2

description: Sample 43, replicate 2

source_name: Sample 43, replicate 2


title: Thyroidectomized Side Population cells 2


title: IDC Breast Cancer [20130115_205611740814_09-557-A2_01.RCC]

source_name: Tumor

tag: ror-s score

tag: ror-s groups

value: high


title: P01101 Non-failing Left Ventricle

description:
P01101
PolyA mRNA

value: no


title: IDC Breast Cancer [20130115_205611740814_09-3703-A1_07.RCC]

tag: age (years)

tag: tumor size (mm)

value: LumA

value: low


title: IDC Breast Cancer [20130115_205611740814_09-160-A1_12.RCC]

tag: relapse-free survival event (0=no recurrence; 1=recurrence)

tag: relapse-free survival time (months)

value: med


title: IDC Breast Cancer [20130115_205611740814_09-31-A1_10.RCC]


title: Thyroidectomized Side Population cells 1


title: IDC Breast Cancer [20130115_205611740814_09-1420-A1_06.RCC]

value: LumB


title: Sample 41, replicate 3

description: Sample 41, replicate 3

source_name: Sample 41, replicate 3


title: Sample 42, replicate 3

description: Sample 42, replicate 3

source_name: Sample 42, replicate 3


title: P01183 Non-failing Left Ventricle

description:
P01183
PolyA mRNA

value: non-failing


title: IDC Breast Cancer [20130115_205611740814_09-3460-A6_11.RCC]


title: Sample 41, replicate 2

description: Sample 41, replicate 2

source_name: Sample 41, replicate 2


title: Sample 42, replicate 1

description: Sample 42, replicate 1

source_name: Sample 42, replicate 1


title: Control Main Population cells 2

source_name: Main population cells of mouse thyroid w/o partial thyroidectomy

value: no partial thyroidectomy


title: Sample 41, replicate 1

description: Sample 41, replicate 1

source_name: Sample 41, replicate 1


title: IDC Breast Cancer [20130115_205611740814_09-3383-A1_09.RCC]


title: P01184 Non-failing Left Ventricle

description:
P01184
PolyA mRNA


title: Sample 40, replicate 3

description: Sample 40, replicate 3

source_name: Sample 40, replicate 3


title: P01100 Non-failing Left Ventricle

description:
P01100
PolyA mRNA

value: male


title: P01067 Non-failing Left Ventricle

description:
P01067
PolyA mRNA


title: P01140 Non-failing Left Ventricle

description:
P01140
PolyA mRNA


title: Control Side Population cells 6

source_name: Side population cells of mouse thyroid w/o partial thyroidectomy

value: male/female

value: thyroid


title: Sample 40, replicate 2

description: Sample 40, replicate 2

source_name: Sample 40, replicate 2


title: Control Main Population cells 1


title: Sample 40, replicate 1

description: Sample 40, replicate 1

source_name: Sample 40, replicate 1


title: Control Side Population cells 3

value: side

source_name: Ambion Mouse Assorted Total RNA


title: P01252 Non-failing Left Ventricle

description:
P01252
PolyA mRNA


title: Control Side Population cells 4

value: Swiss Webster


title: IDC Breast Cancer [20130115_205611740814_09-1255-A8_08.RCC]


title: Sample 39, replicate 3

description: Sample 39, replicate 3

source_name: Sample 39, replicate 3


title: Control Side Population cells 5

value: brain, embryo (10–12 days), heart, kidney, liver, lung, ovary, spleen, testicle, and thymus


title: Control Main Population cells 3

value: main


title: P01138 Non-failing Left Ventricle

description:
P01138
PolyA mRNA

value: heart left ventricle


title: IDC Breast Cancer [20130115_205611740814_08-1156-A5_03.RCC]


title: IDC Breast Cancer [20130115_205611740814_08-2882-A3_04.RCC]

value: Basal


title: IDC Breast Cancer [20130115_205611730814_08-3859-A5_10.RCC]


title: P01136 Non-failing Left Ventricle

description:
P01136
PolyA mRNA

value: female


title: IDC Breast Cancer [20130115_205611730814_08-2842-A3_09.RCC]


title: HeLa_heat-shock_vs_control_rep2_dye-swap

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

country: India

institute: CSIR-Institute Of Genomics and Integrative Biology

description: Dye-swap of replicate 2

hyb_protocol: Samples were incubated for 16-18 hrs. in a water bath. Post-incubation, slides were washed rigorously and scanned.

scan_protocol: After drying, chips were scanned using Perkin Elmer scanner at 10µM resolution and PMT of 60.

data_processing: The .gpr files were obtained from Perkin Elmer scanner. The arrays were dye-swapped and gene-specific dye-bias correction was applied using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009)) implemented in the “dyebias” BioConductor package. For normalization, Lowess method is used. The uploaded processed data files contain Lowess normalized log2 test/control ratios.

label_protocol: 1µg of total RNA was used for 5'-dephosphorylation of miRNAs using calf intestinal phosphatase (CIP). Spike-in miRNAs were also added for experimental control. Subsequently, samples were fluorescently labeled with Hy3 or Hy5 to the 3'-end of the miRNAs. The complementary samples labeled with Hy3 or Hy5 were combined on ice and added onto the slide placed in the slide chamber for hybridization.

growth_protocol: HeLa cell line was used which was procured from National Center for Cell Science, Pune, India. Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with heat inactivated 10% fetal bovine serum (FBS) from GIBCO and 1% antibiotic antimycotic solution from HiMedia, at 37°C in 5% CO2 and 95% atmosphere incubator.

extract_protocol: Total RNA used for the whole-genome expression profiling of miRNA was isolated using Trizol (Invitrogen), according to the manufacturer’s instructions. Further, RNA was purified using RNeasy purification kit from Qiagen to remove residual aromatic compounds that may hinder with microarray expression.

treatment_protocol: Heat shock stress was induced by subjecting the cells to the temperature of 45°C for 30 minutes, in water bath. Cells were subsequently transferred to the incubator for two hours. Before subjecting to heat shock, cells were washed with 1X PBS twice and then fresh media was added for proper quantization of heat shock response.

tag: cell line

value: HeLa cell

value: control RNA

value: HeLa

value: heat-shock treated RNA


title: HeLa_heat-shock_vs_control_rep3_dye-swap

description: Dye-swap of replicate 3


title: P01176 Non-failing Left Ventricle

description:
P01176
PolyA mRNA

value: no


title: Sample 39, replicate 1

description: Sample 39, replicate 1

source_name: Sample 39, replicate 1

tag: sampling time (h)


title: Sample 39, replicate 2

description: Sample 39, replicate 2

source_name: Sample 39, replicate 2

tag: n/c  ratio (moln / cmol)


title: HeLa_heat-shock_vs_control_rep1_dye-swap

description: Dye-swap of replicate 1


title: IDC Breast Cancer [20130115_205611730814_08-27434-A4_03.RCC]

value: high


title: Control Side Population cells 2

tag: tissue

value: no partial thyroidectomy


title: HeLa_heat-shock_vs_control_rep3

description: Replicate 3


title: P01232 Non-failing Left Ventricle

description:
P01232
PolyA mRNA

source_name: heart left ventricle, non-failing

tag: heart failure

value: non-failing

value: male


title: C00075 Non-failing Left Ventricle

description:
C00075
PolyA mRNA

tag: disease status


title: Control Side Population cells 1

tag: gender

value: male/female

value: thyroid


title: HeLa_heat-shock_vs_control_rep2

description: Replicate 2


title: Sample 38, replicate 2

description: Sample 38, replicate 2

source_name: Sample 38, replicate 2


title: IDC Breast Cancer [20130115_205611730814_08-1113-A9_05.RCC]

source_name: Tumor

value: LumA

value: low


title: C00091 Non-failing Left Ventricle

description:
C00091
PolyA mRNA

tag: age


title: C00146 Non-failing Left Ventricle

description:
C00146
PolyA mRNA


title: IDC Breast Cancer [20130115_205611730814_08-2765-A3_08.RCC]

value: LumB

value: med


title: HeLa_heat-shock_vs_control_rep1

description: Replicate 1


title: P01279 Non-failing Left Ventricle

description:
P01279
PolyA mRNA

value: heart left ventricle


title: Sample 38, replicate 3

description: Sample 38, replicate 3

source_name: Sample 38, replicate 3


title: Sample 38, replicate 1

description: Sample 38, replicate 1

source_name: Sample 38, replicate 1


title: Sample 37, replicate 3

description: Sample 37, replicate 3

source_name: Sample 37, replicate 3


title: C00134 Non-failing Left Ventricle

description:
C00134
PolyA mRNA


title: IDC Breast Cancer [20130115_205611640814_09-3889-A3_06.RCC]


title: IDC Breast Cancer [20130115_205611640814_09-2308-A25_02.RCC]


title: Sample 37, replicate 2

description: Sample 37, replicate 2

source_name: Sample 37, replicate 2


title: C00094 Non-failing Left Ventricle

description:
C00094
PolyA mRNA


title: IDC Breast Cancer [20130115_205611640814_09-1795-A2_03.RCC]

value: Basal


title: IDC Breast Cancer [20130115_205611640814_09-2068-A2_04.RCC]

value: Normal


title: IDC Breast Cancer [20130115_205611640814_09-5736-A3_10.RCC]


title: YP20 replicate 1

city: Burjassot (Valencia)

first: Marcel·lí

last: del Olmo

address: Dr Moliner, 50

department: Bioquímica i Biologia Molecular

institute: Universitat de València

description: Biological replicate 1/2

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

organism: Saccharomyces cerevisiae

source_name: YPD yeast cells_no_stress

label_protocol: 10 µg of total RNA reversed transcribed with SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: yeast cultures were kept in the exponential growth phase for 16h. OD600=0,8 cells were exposed to the osmotic stress conditions considered 20% (w/v) glucose (YP20), 1M sorbitol (YPS) or YPD (no stress conditions) during 30 min

extract_protocol: total RNA isolation using the protocol described in Carrasco et al., 2003

treatment_protocol: Stress caused by 20% (w/v) glucose or 1M Sorbitol during 30 minutes

tag: strain

source_name: YP20 yeast cells_20%glucose


title: YP20 replicate 2

description: Biological replicate 2/2


title: IDC Breast Cancer [20130111_205611680814_08-8906-A3_04.RCC]


title: IDC Breast Cancer [20130115_205611640814_09-1349-A1_09.RCC]


title: IDC Breast Cancer [20130115_205611640814_09-1189-A5_01.RCC]


title: IDC Breast Cancer [20130111_205611680814_08-5802-A1_02.RCC]


title: C00145 Non-failing Left Ventricle

description:
C00145
PolyA mRNA

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.1 ST Array GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

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


title: YPS replicate 2

description: Biological replicate 2/2

source_name: YPS yeast cells_1M_sorbital


title: IDC Breast Cancer [20130111_205611680814_08-2801-A1_01.RCC]


title: Sample 35, replicate 3

description: Sample 35, replicate 3

source_name: Sample 35, replicate 3


title: IDC Breast Cancer [20130111_205611680814_08-27373-A2_11.RCC]


title: Sample 36, replicate 3

description: Sample 36, replicate 3

source_name: Sample 36, replicate 3


title: YPS replicate 1

description: Biological replicate 1/2

source_name: YPS yeast cells_1M_sorbitol


title: P01259 Non-failing Left Ventricle

description:
P01259
PolyA mRNA


title: Sample 34, replicate 1

description: Sample 34, replicate 1

source_name: Sample 34, replicate 1


title: P01257 Non-failing Left Ventricle

description:
P01257
PolyA mRNA

value: female


title: Sample 36, replicate 2

description: Sample 36, replicate 2

source_name: Sample 36, replicate 2


title: Reference sample, replicate 4 (pool of sample 22, 23 and 24)


title: P01171 Non-failing Left Ventricle

description:
P01171
PolyA mRNA


title: Sample 35, replicate 2

description: Sample 35, replicate 2

source_name: Sample 35, replicate 2


title: Hoxa9 and Meis1 2

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from myeloid cells without 4-hydroxy tamoxifen treatment

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

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.

source_name: Hoxa9 Meis1 AML control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were grown in Iscove's modified DMEM supplemented with 10% FBS and 5 ng/ml IL-3.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: For conditional knock-out of exogenous Meis1, 2 μM of 4-hydroxytamoxifen (Sigma) was added to the medium and Meis1 deletion was confirmed by genomic PCR.

tag: cell type

value: immortalized myeloid cell


title: IDC Breast Cancer [20130111_205611680814_08-25056-A1_12.RCC]


title: Reference sample, replicate 3 (pool of sample 22, 23 and 24)


title: IDC Breast Cancer [20130111_205611680814_08-17058-A3_08.RCC]


title: Sample 34, replicate 2

description: Sample 34, replicate 2

source_name: Sample 34, replicate 2


title: Hoxa9 4

description: Gene expression data from myeloid cells treated with 4-hydroxy tamoxifen

source_name: Hoxa9/Meis1 AML with Meis deletion


title: IDC Breast Cancer [20130111_205611680814_08-16256-A7_07.RCC]

source_name: Tumor


title: Hoxa9 and Meis1 3


title: P01197 Non-failing Left Ventricle

city: Philadelphia

first: Michael

last: Morley

institute: Perelman School of Medicine at the University of Pennsylvania

description:
P01197
PolyA mRNA

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Microarray Processing batch were controlled for using the R package Combat. Differential gene expression was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates.

source_name: heart left ventricle, non-failing


title: Sample 36, replicate 1

description: Sample 36, replicate 1

source_name: Sample 36, replicate 1


title: Reference sample, replicate 2 (pool of sample 22, 23 and 24)


title: Hoxa9 1


title: P01226 Non-failing Left Ventricle

description:
P01226
PolyA mRNA


title: P01256 Non-failing Left Ventricle

description:
P01256
PolyA mRNA


title: P01237 Non-failing Left Ventricle

description:
P01237
PolyA mRNA


title: Sample 34, replicate 3

description: Sample 34, replicate 3

source_name: Sample 34, replicate 3


title: IDC Breast Cancer [20130110_205611690814_12-5811 A1 S_07.RCC]


title: P01200 Non-failing Left Ventricle

description:
P01200
PolyA mRNA


title: P01273 Non-failing Left Ventricle

description:
P01273
PolyA mRNA


title: Sample 37, replicate 1

description: Sample 37, replicate 1

source_name: Sample 37, replicate 1


title: IDC Breast Cancer [20130110_205611690814_12-17072 A1 S_09.RCC]


title: uninfected vs. flu infected

description: Quantification of RNA and quality control was done using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA) and a Nan drop photometer (Kisker, Steinfurt, Germany). Dual color hybridizations with 0.25-0.75 µg RNA per Cy-dye were performed with SlideHyb Glass Array Hybridization Buffer #3 (Ambion) and LifterSlips (Erie Scientific, Portsmouth, USA).

hyb_protocol: Dual color hybridizations with 0.25-0.75 µg RNA were performed for 16 h at 60°C (Exiqon) with SlideHyb Glass Array Hybridization Buffer #3 (Ambion) and LifterSlips (Erie Scientific, Portsmouth, USA). LNA microarrays were washed with 1x SSC + 0.5% SDS for 1 min at 65°C, followed by 1x SSC + 0.5% SDS for 10 min at 65°C, 1x SSC + 0.5% SDS for 10 min at 60°C, 0.25x SSC + 0.5% SDS for 10 min at 55°C and finally with 0.025x SSC for 3 min at 42°C.

scan_protocol: Scanning of all microarrays was performed with 5µm resolution using a DNA microarray laser scanner (DNA Microarray Scanner BA, Agilent Technologies) according the manufacturer's instructions.

data_processing: Raw microarray images were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.7.5, Agilent Technologies) using almost default settings for miRNA microarrays loaded with a grid file or standard setting. Non-uniformity outlier flagging was done with a 5x default value of the constant coefficient of variation for features ((CV)2 Term (A) = 0.55 ) and background ((CV)2 Term (A) = 0.45 ). Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

source_name: uninfected

label_protocol: Labeling of miRNAs in the mirCURY LNA miRNA array analysis was done with 1-2 μg of total RNA per labeling reaction per slide hybridization according the manufacturer’s instruction (Exiqon) without subsequent purification of the labeling reaction.

extract_protocol: For miRNA profiling total RNA from influenza A infected (A/WSN/33, MOI 1) or non-infected A549 cells was extracted 24 h p.i. and purified using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen, Hilden, Germany), followed by the enrichment of small miRNAs with the RNeasy MinElute Cleanup Kit using the user-developed protocol "Purifying miRNA from cells and soft tissues (RY20 Jan-05)" formerly published by Qiagen in the internet. Quality control and quantification of samples was done using an Agilent 2100 bioanalyzer (Agilent Technologies) and a Nan drop photometer (Kisker, Steinfurt, Germany).

treatment_protocol: Cell line was grown in DMEM media (Invitrogen, Karlsruhe, Germany) with 4 mM L-glutamine, 4 mM sodium pyruvate, 100 U/ml penicillin/streptomycin and 10% fetal calf serum (FCS) at 37°C and 5% CO2. Phoenix-ECO packaging cells (G.P. Nolan, Stanford University, USA), 293T (CRL-11268, ATCC-LGC) and MDCK (CCL-34, ATCC-LGC) cells were grown in DMEM supplemented with 4 mM L-glutamine, 100 U/ml penicillin/streptomycin and 10% FCS. Cells were regularly checked for mycoplasma contamination.

value: The A549 human lung epithelial cell line (CCL-185, ATCC-LGC, Wesel, Germany)

source_name: flu infected

treatment_protocol:
Cells were washed with PBS and then infected at the indicated MOIs in PBS (PBS supplemented with 0.2% bovine serum albumin) for 45 min at room temperature (RT). Cells were washed again (in PBS) and incubated for the indicated time periods at 37°C in DMEM containing 0.2% bovine serum albumin, 4 mM L-glutamine and antibiotics, unless otherwise stated.
Numbers of infected versus noninfected cells were determined using automated microscopy (Olympus, Hamburg, Germany).

tag: influenza strains


title: Hoxa9 3


title: Hoxa9 and Meis1 4


title: P01281 Non-failing Left Ventricle

description:
P01281
PolyA mRNA

value: no


title: Hoxa9 and Meis1 1


title: Sample 35, replicate 1

description: Sample 35, replicate 1

source_name: Sample 35, replicate 1


title: Reference sample, replicate 1 (pool of sample 22, 23 and 24)


title: IDC Breast Cancer [20130110_205611690814_11-25229 A3 S_05.RCC]

tag: ror-s score


title: Hoxa9 2


title: P01122 Non-failing Left Ventricle

description:
P01122
PolyA mRNA


title: IDC Breast Cancer [20130110_205611690814_11-23162 A4 S_03.RCC]

tag: ror-s groups

value: high


title: IDC Breast Cancer [20130110_205611690814_11-16721 A9 S_01.RCC]

tag: age (years)


title: C00086 Non-failing Left Ventricle

description:
C00086
PolyA mRNA


title: P01202 Non-failing Left Ventricle

description:
P01202
PolyA mRNA


title: IDC Breast Cancer [20130110_205611690814_08-5238-A4_12.RCC]

tag: tumor size (mm)


title: flu infected vs. uninfected