title: C57BL6 LIVER S3 (9986350036_D)

description: Liver sox6_kd


title: MDA-Bone-Un_LASPKD_biological_rep1

status: Public on Jun 26 2015

type: RNA

city: Nashville

first: Dayanidhi

last: Raman

state: TN

address: PRB436, 23rd Ave S @ Pierce

department: Cancer Biology

country: USA

institute: Vanderbilt Universirty

description: Grown on Matrigel

hyb_protocol: Biotinylated reaction products were added to Hybridization mix and targets (final  ~25ng/ul) were hybridized in the hybridization cocktail for a total of 2.5ug of fragmented target.  The targets are heat denatured, centrifuged, and hybridized overnight to Human Gene 1.0 ST exon array, stained, washed and scanned.

scan_protocol: Affymetrix 7G plus  scanner using AGCC v. 3.2.4

data_processing: Analyzed on Affymetrix Expression Console v. 1.2 using a RMA normalization algorithm producing log base 2 results that forms the value for comparisons or for calcualting fold change.

label: Biotin-Streptavidin-Phycoerythrin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-Bone-Un-LASP1-KD cells

label_protocol: Ambion kit was used to synthesize the first and second strand RNA. IVT reactions were done overnight, cRNA productswas purified and quantified. Quantitated cRNA was used : random primer heat denaturation, 2nd cycle cDNA synthesis and cRNA hydrolysis with RNase H; cDNA was purified, fragmented and TdT-labeled with biotinylated nucleotides.

growth_protocol: MDA-MB-231S and MDA-Bone-Un breast cancer cells (Non-silencing and LASP-1 knock down) were cultured on growth factor reduced Matrigel for 3 days to form stellate clusters.

extract_protocol: Total RNA from MDA-MB-231S and MDA-Bone-Un stellate clusters was quantitated using the QuBit RNA assay and were run on the Agilent Bioanalyzer.

treatment_protocol: Not applicable

tag: cell line

value: MDA-Bone-Un

tag: cell type

value: Basal-like breast cells


title: C57BL6 EWAT S1 (9986350036_C)

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive

department: Growth Development Metabolism

country: Singapore

institute: Singapore Institute for Clinical Sciences

description: EWAT sox6_kd-S1 replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction was performed in GenomeStudio then data was exported. Probes were filtered for detection p-value <0.05 and NBEADS>3 in R. Data was then loaded into Arraystudio version 6 (Omicsoft). All expression values were log2 transformed and quantile normalised (lumi/R-bioconductor).

label: biotin

organism: Mus musculus

source_name: Epididymal White Adipose Tissue

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

growth_protocol: All animal procedures were performed according to the Institutional Animal Care and Use Committee of the Agency for Science, Technology and Research (A*STAR) of Singapore. All mice were male, of the C57BL/6J genetic background and housed in a 12-hour light-dark cycle with access ad libitum to water and a NCD (Harlan 2018 Teklab Global 18% Protein Rodent Diet).

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

treatment_protocol: Mice were injected intraperitoneal with either SOX6 specific or control antisense oligonucleotides and effects of the treatment studied after 48h.

tag: strain

tag: treatment

value: sox6 knockdown

tag: tissue

value: EWAT


title: C57BL6 EWAT C4 (9986350036_E)

description: EWAT control

value: control


title: MDA-231S_LASPKD_biological_rep1

description: Grown on Matrigel

source_name: MDA-MB-231S-LASP1-KD cells


title: jacks-00113: normal15

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: normal lung

value: normal lung

tag: Sex

value: female

tag: age

tag: genotype

value: F1 129svJae X C57/BL58

tag: phenotype

value: lung

value: Jacks lab/MIT CCR

value: adenocarcinoma

tag: histology


title: jacks-00113: normal18

scan_protocol: See mage-tab files linked to series entry for additional details

value: F1 129svJae X C57/BL61


title: jacks-00113: normal17

data_processing: See mage-tab files linked to series entry for additional details

value: F1 129svJae X C57/BL60


title: jacks-00113: normal8

label_protocol: See mage-tab files linked to series entry for additional details

value: male

value: F1 129svJae X C57/BL51


title: jacks-00113: normal19

extract_protocol: See mage-tab files linked to series entry for additional details

value: F1 129svJae X C57/BL62


title: jacks-00113: normal9

value: F1 129svJae X C57/BL52


title: MDA-231S_NS_biological_rep1

description: Grown on Matrigel

source_name: MDA-MB-231S-NS cells


title: jacks-00113: KT41

source_name: lung tumor

value: lung tumor

value: F1 129svJae X C57/BL24

value: lung cancer

value: mixed


title: C57BL6 LIVER C1 (9986350036_B)

description: Liver control-C1 replicate

source_name: Liver

value: control

value: Liver


title: C57BL6 LIVER C4 (9986350036_A)

description: Liver control-C4 replicate


title: jacks-00113: normal7

value: normal lung

value: F1 129svJae X C57/BL50


title: jacks-00113: normal20

value: female

value: F1 129svJae X C57/BL63

value: lung


title: jacks-00113: normal6

value: F1 129svJae X C57/BL49

value: Jacks lab/MIT CCR

value: adenocarcinoma


title: jacks-00113: normal1

value: male

value: F1 129svJae X C57/BL44


title: jacks-00113: normal11

value: F1 129svJae X C57/BL54


title: jacks-00113: normal10

value: F1 129svJae X C57/BL53


title: Populus_buds_February_rep1

city: Corvallis

first: Glenn

last: Howe

state: OR

address: 321 Richardson Hall

department: Forest Ecosystems and Society

institute: Oregon State University

description:
Axillary buds of Populus trichocarpa collected in February.  This is the first of two biological replicates collected from different trees of the same genotype.
FEB_1

hyb_protocol: Hybridization of biotin-labeled DNA was performed by NimbleGen Systems Inc. (Madison, WI; http:// www.nimblegen.com/) using their proprietary system.

scan_protocol: Scanning was performed by NimbleGen Systems Inc. (Madison, WI; http:// www.nimblegen.com/) using their proprietary system.

data_processing:
Raw data (.pair files) were log2 transformed, background corrected, and then normalized across all arrays using the Robust Multiple-array Average (RMA; Irizarry et al. 2003; Biostatistics 4:249) with quantile normalization (Bolstad et al. 2003; Bioinformatics 19:185) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
pair_report_settings = Design file: 2014_12_14_Howe_Populus_V3_60mer.ndf; Quant Border: 0; Locally align: false; Include controls: true
rma_settings = Quant Border: 0; Locally align: false; Design file: 2014_12_14_Howe_Populus_V3_60mer.ndf; Save expression values as log2: true; Background correction: true; Normalize: true; Container mode: Whole array

label: Biotin

organism: Populus trichocarpa

source_name: February_axillary buds

label_protocol: Total RNA was labeled with biotinylated-11-UTP using the Ambion MessageAmp™ II aRNA amplification kit according to the manufacturer’s protocol.  Labeled RNA was sent to NimbleGen Systems Inc. (Madison, WI; http:// www.nimblegen.com/) for fragmentation, hybridization, and array scanning.

growth_protocol: Field-grown trees

extract_protocol: Total RNA isolated using Qiagen RNeasy kit  using the Qiagen “on column” DNAse I treatment.

treatment_protocol: No treatment

tag: month

value: February

value: axillary buds


title: Liver_12_wk_D_diet_ratD6

city: Anchorage

first: Jason

middle: Lee

last: Burkhead

state: AK

address: 3211 Providence Dr

department: Biological Sciences

institute: University of Alaska Anchorage

description:
20121213_D6
Gene expression after 12 weeks experimental diet

hyb_protocol: Fragmentation and hybridization were performed according to the manufacturer's instructions: http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf

scan_protocol: Scanning was performed with an Agilent scanner set to 8X60K using the GE1_107_Sep09 protocol.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE_107_Sep09) and Grid: 028279_D_F_20121204 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by silica column cRNA purification (Qiagen RNeasy kit), and fragmentation.

growth_protocol: Male Wistar rats were housed individually allowed ad libitum access to Mazuri Rodent Diet and water until six months of age.

extract_protocol: Hepatic RNA from was isolated from flash-frozen liver tissue by Trizol extraction followed by cleanup with the NucleoSpin RNA II kit (Machery-Nagel).

treatment_protocol: Mature (6 months old) male Wistar Rats that had been allowed ad libitum access to Mazuri rodent pellets were used in the study. Twenty-four rats were divided into four groups and fed for 12 weeks with diets based on the Purified AIN76A formulation, modified for target sucrose and Cu content (Custom Animal Diets, Bangor, NJ). Sucrose and copper content in diets were as follows: CuD/30%- Cu deficient (<0.3 mg Cu/kg)/30% sucrose, CuA/30%- Cu adequate (125 mg/kg)/30% sucrose, CuD/10%- <0.3 mg/kg Cu/10% sucrose, and D) CuA (125 mg/kg Cu)/10% sucrose (control). Starch and dextrin were used to equalize carbohydrates.

value: Wistar

tag: gender

value: 9 m

value: liver


title: Populus_buds_February_rep2

description:
Axillary buds of Populus trichocarpa collected in February.  This is the second of two biological replicates collected from different trees of the same genotype.
FEB_2


title: Transgenic_Ah24_OE

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

hyb_protocol: For pre-hybridization, the slide was re-hydrated with water vapor at 60ºC and fixed with two cycles of UV ligth. Then, the slide was submerged in boiling water for two minutes (92ºC) and washed with 95% ethanol for one minute. After that, the oligo array was prepared for hybridization in a buffer solution 5X SSC, 0.1% SDS and 1% BSA for one hour at 41ºC. Finally, the array was washed and dried for hybridization. Equal quantities of labeled cDNA were hybridized to the Arabidopsis array using hybridization solution UniHyb (TeleChem International INC) for 14 hr at 42ºC.

scan_protocol: Scanned on an ScanArray 4000 scanner with ScanArray 4000 software from Packard BioChips.

data_processing: The analysis of the microarray data: background correction, Lowess normalization, intensity filter and selection of differentially expressed genes, was performed with the software genArise (http://www.ifc.unam.mx/genarise/). The identification of differentially expressed genes was done by the calculation of a Z score using a sliding-window approach, where the algorithm calculates the mean and standard deviation (SD) within a window surrounding each data point to define a Z score, where Z is the number of SD a data point is from the window mean. To obtain the Z score, the next formula was applied, zi = (Ri - mean(R))/sd(R), where zi is the Z score for a given data point, Ri is the log ratio of signal intensity for each element, mean(R) and sd(R) are the mean and SD of the log ration of signal intensity of the surrounding window. Only the elements with an absolute Z score greater than 2 were considered differentially expressed (|Zscore| > 2) (Cheteleadle et al., 2003).

organism: Arabidopsis thaliana

source_name: Rossete leaves, 5-week old Wt plants

label_protocol: Total RNA were used for cDNA synthesis incorporating Alexa555 or Alexa647 making use of First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was tested by measuring the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Arabidospis plants were grown in controlled conditions of light (photosynthetic photon flux density (PPFD) of ≈ 200 µmol m-2 s-1), photoperiod (16 h light/ 8 h dark) and temperature (22 ± 1°C).

extract_protocol: Total RNA was extracted from 100–200 mg of frozen rosette tissue with the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, with modifications. These consisted of the addition of a salt solution (sodium citrate 0.8 M + 1.2 M NaCl) during precipitation in a 1:1 v/v ratio with isopropanol and further purification with LiCl (8 M) for one hour at 4°C. All RNA samples were analyzed by formaldehyde agarose gel electrophoresis and visual inspection of the ribosomal RNA bands upon ethidium bromide staining.

treatment_protocol: Plants were subjected to normal growing conditions

tag: ecotype

value: wild type

value: rossette leaves

source_name: Rossete leaves, 5-week old transgenic plants

value: Ah24 overexpression


title: Populus_buds_November_rep2

description:
Axillary buds of Populus trichocarpa collected in November.  This is the second of two biological replicates collected from different trees of the same genotype.
NOV_2

source_name: November_axillary buds

value: November


title: Populus_buds_March_rep1

description:
Axillary buds of Populus trichocarpa collected in March.  This is the first of two biological replicates collected from different trees of the same genotype.
MAR_1

source_name: March_axillary buds

value: March


title: jacks-00113: KT39

value: lung tumor

value: F1 129svJae X C57/BL22

value: lung cancer

value: lung


title: Populus_buds_December_rep2

description:
Axillary buds of Populus trichocarpa collected in December.  This is the second of two biological replicates collected from different trees of the same genotype.
DEC_2

source_name: December_axillary buds

value: December


title: Liver_12_wk_D_diet_ratD3

description:
20121213_D3
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D3

value: male


title: C57BL6 EWAT S4 (9996338116_E)

description: EWAT sox6_kd

value: sox6 knockdown

value: EWAT


title: Populus_buds_December_rep1

description:
Axillary buds of Populus trichocarpa collected in December.  This is the first of two biological replicates collected from different trees of the same genotype.
DEC_1

value: axillary buds


title: jacks-00113: KT35

value: F1 129svJae X C57/BL21

value: Jacks lab/MIT CCR

value: adenocarcinoma

value: mixed


title: Populus_buds_November_rep1

description:
Axillary buds of Populus trichocarpa collected in November.  This is the first of two biological replicates collected from different trees of the same genotype.
NOV_1


title: Populus_buds_March_rep2

description:
Axillary buds of Populus trichocarpa collected in March.  This is the second of two biological replicates collected from different trees of the same genotype.
MAR_2


title: Liver_12_wk_D_diet_ratD2

description:
20121213_D2
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D2

value: Wistar

value: 9 m

value: liver


title: Populus_buds_August_rep2

description:
Axillary buds of Populus trichocarpa collected in August.  This is the second of two biological replicates collected from different trees of the same genotype.
AUG_2

source_name: August_axillary buds

value: August


title: Liver_12_wk_C_diet_ratC6

description:
20121213_C6
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C6


title: Liver_12_wk_C_diet_ratC4

description:
20121213_C4
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C4


title: Liver_12_wk_C_diet_ratC5

description:
20121213_C5
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C5


title: Liver_12_wk_D_diet_ratD5

description:
20121213_D5
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D5


title: Liver_12_wk_C_diet_ratC3

description:
20121213_C3
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C3


title: Populus_buds_August_rep1

description:
Axillary buds of Populus trichocarpa collected in August.  This is the first of two biological replicates collected from different trees of the same genotype.
AUG_1


title: Liver_12_wk_D_diet_ratD1

description:
20121213_D1
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D1


title: Liver_12_wk_D_diet_ratD4

description:
20121213_D4
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/10% sucrose, Rat D4


title: jacks-00113: KT33

source_name: lung tumor

value: lung tumor

value: F1 129svJae X C57/BL20

value: mixed/epithelioid


title: Liver_12_wk_C_diet_ratC1

description:
20121213_C1
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C1


title: Liver_12_wk_B_diet_ratB6

description:
20121213_B6
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B6


title: Liver_12_wk_C_diet_ratC2

description:
20121213_C2
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/10% sucrose, Rat C2


title: jacks-00113: KT32

value: F1 129svJae X C57/BL19

value: lung cancer

value: lung


title: jacks-00113: KT25

value: female

value: F1 129svJae X C57/BL17

value: inflammation


title: jacks-00113: KT24

value: F1 129svJae X C57/BL16


title: jacks-00113: normal5

source_name: normal lung

value: normal lung

value: male

value: F1 129svJae X C57/BL48

value: Jacks lab/MIT CCR


title: jacks-00113: KT21

value: F1 129svJae X C57/BL15

value: adenocarcinoma

value: mixed


title: jacks-00113: normal13

value: F1 129svJae X C57/BL56


title: jacks-00113: normal2

value: F1 129svJae X C57/BL45


title: jacks-00113: normal12

value: F1 129svJae X C57/BL55


title: Liver_12_wk_B_diet_ratB1

description:
20121213_B1
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B1

value: Wistar

value: 9 m

value: liver


title: jacks-00113: KT10

value: lung tumor

value: F1 129svJae X C57/BL7

value: lung cancer

value: lung


title: Liver_12_wk_B_diet_ratB5

description:
20121213_B5
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B5


title: jacks-00113: KT11

value: F1 129svJae X C57/BL8

value: columnar


title: Liver_12_wk_A_diet_ratA5

description:
20121213_A5
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A5

value: male


title: Liver_12_wk_A_diet_ratA2

description:
20121213_A2
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A2


title: Liver_12_wk_A_diet_ratA4

description:
20121213_A4
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A4


title: Liver_12_wk_A_diet_ratA3

description:
20121213_A3
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A3


title: jacks-00113: KT7

value: F1 129svJae X C57/BL29

value: Jacks lab/MIT CCR


title: Liver_12_wk_B_diet_ratB4

description:
20121213_B4
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B4


title: Liver_12_wk_A_diet_ratA6

description:
20121213_A6
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A6


title: Liver_98d.p.e._Rep1

city: Freising

first: Ralph

last: Kuehn

address: Hans-Carl-von-Carlowitz-Platz 2

department: Chair of Zoology

country: Germany

institute: Technical University of Munich

description:
Liver 98  days post exposure. Biological replicate 1 of 3.
98d.p.e.-Rep1

hyb_protocol: The microarray hybridization process was performed according to the Genisphere Array 50 Protocol (revised version 5; http://web.uvic.ca/cbr/grasp/microarray/array.html) with minor adjustments. Briefly, cDNA was synthesized from 20 μg of total liver RNA using Invitrogen's SuperScript Indirect cDNA labeling system (Invitrogen, Life Technologies GmbH, Darmstadt, Germany). The Microcon Spin Columns YM-30 (Millipore, Schwalbach, Germany) was then employed to purify and concentrate the cDNA. The microarray slides were postprint processed by placing them twice in 0.2% SDS for 5 minutes followed by five rinses using HPLC water and subsequently dried. The microarray slides were then pre-hybridized for 45min at 49°C in 5× SSC with 0.1% SDS and 0.2% BSA, washed twice with HPLC water and stored at 49°C until cDNA hybridization was performed. The cDNA was combined with 2× formamide buffer and LNA dT blocker (Genisphere, Hatfield, PA, U.S.A.) to a total volume of 55 μl and heated to 80°C for 10 minutes. The hybridization solution was loaded onto the slides, covered with the LifterSlips™ (Implen GmbH, Schatzbogen, Germany) and incubated for 16 h at 49°C in a hybridization oven (Peqlab). After this a series of post-cDNA-hybridization washes were performed in the following order: one 2X SSC with 0.1% SDS wash for 10 minutes at 49°C, two 2X SSC with 0.1% SDS washes for 5 minutes at room temperature, two 1X SSC washes for 5 minutes at room temperature and one 0.1X SSC wash for 5 minutes at room temperature followed by drying and storage at 49°C. The 3DNA capture reagents for Cy3 and Cy5 from the Array 50 Kit (Genisphere, Version 2, Hatfield, PA, U.S.A.) were then hybridized to the cDNA-hybridized microarrays at 49°C for a duration of 2 hours in the hybridization oven (Peqlab) and washed in the following manner; one 2X SSC with 0.1% SDS wash for 10 minutes at 49°C, two 2X SSC with 0.1% SDS washes for 5 minutes at room temperature, two 1X SSC washes for 5 minutes at room temperature and one 0.1X SSC wash for 5 minutes at room temperature. The microarrays were then dried and scanned.

scan_protocol: After drying, the microarrays were scanned for Cy3 and Cy 5 using a GenePix® 4000 Microarray Scanner (Axon Instruments, Molecular devices GmbH, Biberach, Germany)

data_processing: Spot identification, intensity quantification and quality control were carried out with the GenePix® Pro 6 software (Molecular Devices GmbH, Biberach, Germany). For each microarray slide features with weak signal intensities in one or both channels or showing substantial overlap in the distributions of the intensities of the foreground and background pixels were flagged and filtered out in subsequent processes. The red and green intensities (RGlists) from the 3 biological replicates microarrays from each the 14 time points were background adjusted using the Kooperberg model-based background correction for GenePix® data. The background-corrected RGlists from the 3 biological replicates microarrays were then normalized within arrays by the Loess method followed by normalization between arrays using the scale method.

organism: Salmo trutta fario

source_name: Liver_treatment station_98d.p.e.

label_protocol: The 3DNA capture reagents for Cy3 and Cy5 from the Array 50 Kit (Genisphere, Version 2, Hatfield, PA, U.S.A.) were used following the protocol at http://web.uvic.ca/cbr/grasp/microarray/array.html (Genisphere Array 50 Protocol Revised version 5).

growth_protocol: Over the course of the experiment brown trout were fed twice a week with Ecolife 16, 3mm (BioMar, Brande, Denmark) using an amount corresponding to 1% of bodyweight.

extract_protocol: Liver tissue was homogenized in Qiazol (Qiagen GmbH, Hilden, Germany) using the MagN lyser (Roche Applied Science, Penzberg, Germany), and total RNA was extracted following the manufacturer’s directions. After precipitation the RNA pellet was resuspended in RNase-free water (Qiagen GmbH, Hilden, Germany)

tag: experimental station

value: treatment station

tag: sampling time point

value: Liver

tag: replicate

value: replicate 1

source_name: Liver_control station_98d.p.e.

value: control station


title: Liver_12_wk_B_diet_ratB2

description:
20121213_B2
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B2


title: Liver_12_wk_B_diet_ratB3

description:
20121213_B3
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding High Cu/30% sucrose, Rat B3


title: Liver_98d.p.e._Rep3

description:
Liver 98  days post exposure. Biological replicate 3 of 3.
98d.p.e.-Rep3

value: replicate 3


title: Liver_98d.p.e._Rep2

description:
Liver 98  days post exposure. Biological replicate 2 of 3.
98d.p.e.-Rep2

value: replicate 2


title: Liver_91d.p.e._Rep2

description:
Liver 91  days post exposure. Biological replicate 2 of 3.
91d.p.e.-Rep2

source_name: Liver_control station_91d.p.e.

source_name: Liver_treatment station_91d.p.e.


title: Liver_91d.p.e._Rep3

description:
Liver 91  days post exposure. Biological replicate 3 of 3.
91d.p.e.-Rep3


title: Liver_91d.p.e._Rep1

description:
Liver 91  days post exposure. Biological replicate 1 of 3.
91d.p.e.-Rep1


title: Liver_84d.p.e._Rep3

description:
Liver 84  days post exposure. Biological replicate 3 of 3.
84d.p.e.-Rep3

source_name: Liver_treatment station_84d.p.e.

source_name: Liver_control station_84d.p.e.


title: Liver_84d.p.e._Rep2

description:
Liver 84  days post exposure. Biological replicate 2 of 3.
84d.p.e.-Rep2


title: Liver_77d.p.e._Rep2

description:
Liver 77  days post exposure. Biological replicate 2 of 3.
77d.p.e.-Rep2

source_name: Liver_control station_77d.p.e.

source_name: Liver_treatment station_77d.p.e.


title: Liver_84d.p.e._Rep1

description:
Liver 84  days post exposure. Biological replicate 1 of 3.
84d.p.e.-Rep1


title: Liver_77d.p.e._Rep1

description:
Liver 77  days post exposure. Biological replicate 1 of 3.
77d.p.e.-Rep1


title: Liver_12_wk_A_diet_ratA1

description:
20121213_A1
Gene expression after 12 weeks experimental diet

source_name: Liver, 12 weeks feeding Low Cu/30% sucrose, Rat A1

value: Wistar

value: 9 m


title: Liver_77d.p.e._Rep3

description:
Liver 77  days post exposure. Biological replicate 3 of 3.
77d.p.e.-Rep3

value: liver


title: jacks-00113: KT14

source_name: lung tumor

value: lung tumor

value: F1 129svJae X C57/BL11

value: adenocarcinoma

value: mixed


title: Liver_70d.p.e._Rep3

description:
Liver 70  days post exposure. Biological replicate 3 of 3.
70d.p.e.-Rep3

source_name: Liver_treatment station_70d.p.e.

source_name: Liver_control station_70d.p.e.


title: jacks-00113: KT15

value: F1 129svJae X C57/BL12

value: lung cancer

value: lung


title: Liver_70d.p.e._Rep2

description:
Liver 70  days post exposure. Biological replicate 2 of 3.
70d.p.e.-Rep2


title: jacks-00113: KT1

value: male

value: F1 129svJae X C57/BL6

value: Jacks lab/MIT CCR


title: jacks-00113: KT6

value: F1 129svJae X C57/BL28


title: Liver_70d.p.e._Rep1

description:
Liver 70  days post exposure. Biological replicate 1 of 3.
70d.p.e.-Rep1

value: treatment station

value: Liver

value: replicate 1

value: control station


title: Liver_63d.p.e._Rep2

description:
Liver 63  days post exposure. Biological replicate 2 of 3.
63d.p.e.-Rep2

source_name: Liver_control station_63d.p.e.

value: replicate 2

source_name: Liver_treatment station_63d.p.e.


title: WGP-treated MDSC

city: zhenjiang

first: Jie

last: Tian

state: Jiangsu

address: Xuefu Road 301

department: School of Medicine

country: China

institute: Jiangsu University

description: Experimental animals were male and commercially-available C57BL/6 mice (Yangzhou University, Jiangsu,China ).

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: myeloid derived suppressor cells

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: myeloid derived suppressor cells isolated from Lewis lung carcinoma mice splenocytes were treated with WGP or not

value: spleen

value: myeloid-derived suppressor cells

value: 100 µg/ml WGP for 24 h


title: Non-treated MDSC

description: Experimental animals were male and commercially-available C57BL/6 mice (Yangzhou Univesity, Jiangsu, China).


title: Liver_63d.p.e._Rep3

description:
Liver 63  days post exposure. Biological replicate 3 of 3.
63d.p.e.-Rep3

value: replicate 3

value: liver


title: jacks-00113: KT9

value: lung tumor

value: F1 129svJae X C57/BL31

value: adenocarcinoma

value: mixed


title: Liver_63d.p.e._Rep1

description:
Liver 63  days post exposure. Biological replicate 1 of 3.
63d.p.e.-Rep1


title: Liver_56d.p.e._Rep2

description:
Liver 56  days post exposure. Biological replicate 2 of 3.
56d.p.e.-Rep2

source_name: Liver_control station_56d.p.e.

source_name: Liver_treatment station_56d.p.e.


title: jacks-00113: KT17

value: female

value: F1 129svJae X C57/BL14

value: lung cancer

value: lung

value: columnar


title: jacks-00113: KT8

value: F1 129svJae X C57/BL30

value: Jacks lab/MIT CCR


title: jacks-00113: KT4

value: F1 129svJae X C57/BL23


title: krahe-00060: cd34_8

source_name: Normal mononuclear cells

value: Bone Marrow

value: Myeloid cell

value: normal


title: krahe-00060: cd34_9


title: jacks-00113: KT12

value: F1 129svJae X C57/BL9


title: Liver_56d.p.e._Rep1

description:
Liver 56  days post exposure. Biological replicate 1 of 3.
56d.p.e.-Rep1

value: treatment station

value: Liver

value: replicate 1

value: control station

value: liver


title: krahe-00060: cd34_7


title: jacks-00113: KT5

value: lung tumor

value: male

value: F1 129svJae X C57/BL26

value: adenocarcinoma

value: mixed


title: Liver_49d.p.e._Rep3

description:
Liver 49  days post exposure. Biological replicate 3 of 3.
49d.p.e.-Rep3

source_name: Liver_control station_49d.p.e.

value: replicate 3

source_name: Liver_treatment station_49d.p.e.


title: jacks-00113: KT3

value: F1 129svJae X C57/BL18

value: lung cancer

value: lung

value: Jacks lab/MIT CCR

value: columnar


title: Liver_49d.p.e._Rep2

description:
Liver 49  days post exposure. Biological replicate 2 of 3.
49d.p.e.-Rep2

value: replicate 2


title: jacks-00113: KT13

value: female

value: F1 129svJae X C57/BL10


title: krahe-00060: cd34_5

value: Bone Marrow

value: Myeloid cell

value: normal


title: Liver_42d.p.e._Rep1

description:
Liver 42  days post exposure. Biological replicate 1 of 3.
42d.p.e.-Rep1

source_name: Liver_treatment station_42d.p.e.

value: treatment station

value: Liver

value: replicate 1

source_name: Liver_control station_42d.p.e.

value: control station

value: liver


title: Liver_42d.p.e._Rep3

description:
Liver 42  days post exposure. Biological replicate 3 of 3.
42d.p.e.-Rep3

value: replicate 3


title: Liver_35d.p.e._Rep3

description:
Liver 35  days post exposure. Biological replicate 3 of 3.
35d.p.e.-Rep3

source_name: Liver_control station_35d.p.e.

source_name: Liver_treatment station_35d.p.e.


title: krahe-00060: cd34_4


title: Liver_35d.p.e._Rep2

description:
Liver 35  days post exposure. Biological replicate 2 of 3.
35d.p.e.-Rep2


title: krahe-00060: cd34_1


title: Liver_56d.p.e._Rep3

description:
Liver 56  days post exposure. Biological replicate 3 of 3.
56d.p.e.-Rep3


title: Liver_49d.p.e._Rep1

description:
Liver 49  days post exposure. Biological replicate 1 of 3.
49d.p.e.-Rep1


title: Liver_42d.p.e._Rep2

description:
Liver 42  days post exposure. Biological replicate 2 of 3.
42d.p.e.-Rep2


title: krahe-00060: aml_883

source_name: AML normal cytogenetics

value: AML


title: krahe-00060: aml_830


title: Liver_28d.p.e._Rep2

description:
Liver 28  days post exposure. Biological replicate 2 of 3.
28d.p.e.-Rep2

source_name: Liver_control station_28d.p.e.

source_name: Liver_treatment station_28d.p.e.


title: Liver_28d.p.e._Rep1

description:
Liver 28 days post exposure. Biological replicate 1 of 3.
28d.p.e.-Rep1


title: Liver_28d.p.e._Rep3

description:
Liver 28  days post exposure. Biological replicate 3 of 3.
28d.p.e.-Rep3


title: Liver_21d.p.e._Rep3

description:
Liver 21 days post exposure. Biological replicate 3 of 3.
21d.p.e.-Rep3

source_name: Liver_control station_21d.p.e.

source_name: Liver_treatment station_21d.p.e.


title: Serum-Control-R7

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: Total RNA isolated from serum

data_processing:
Matrix non-normalized contains raw Ct-values, derived from second derivative maximum method
Matrix normalized contains delta Ct values: Normalization was performed based on the average of miRNAs detected in all samples. In the present study, this included 114 miRNAs. Using Normfinder it was shown that the stability of the average of the 114 miRNAs is higher than any single miRNA in the data set as measured . Normalized Cp values (dCp) were calculating using the follow formula:  Normalized Cp = average Cp (n=114 assays) – assay Cp (sample)  Where a higher value indicates that a determined miRNA is more abundant in the analyzed sample.
For the fold change data, delta Ct values were averaged for each groups, fractur and control, respectively. Delta-delta Ct values (log2 fold change) were calculated: fracture - control
Fold Change: delta-delta Ct-values (log2 fold change)
miRBase version 19 microRNA ID

label: SYBR Green

source_name: Serum

label_protocol: miRNA expression profiling was performed by Exiqon Inc., Denmark using an LNA qPCR Array platform and the commercially available serum/plasma miRNA focus panel in 384-well format.  In order to evaluate the reverse transcription efficiency, prior to the reverse transcription step synthetic RNA oligonucleotides (RNA spike-in, UniSp6) were added to all samples (Supplemental figure 1b). Then, 15 µl RNA were reverse transcribed in 75 µl volume reactions using the miRCURY LNA™ Universal RT miRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon). At this step, a synthetic DNA spike-in (UniSp3) was added to all the cDNA samples (Supplemental figure 1b). Subsequently, cDNA was diluted and assayed in 10 µl PCR reactions according to the protocol for miRCURY LNA™ Universal RT miRNA PCR Human serum/plasma focus panel. Negative controls excluding template from the reverse transcription reaction were performed and profiled similar to the samples. qPCR amplifications were performed in 384-well plates, in a LightCycler® 480 Real-Time PCR System (Roche). The determination of Crossing point (Cp) and melting curve analysis were done using the Roche LC software and the 2nd derivative method.

growth_protocol: not relevant

extract_protocol: Serum samples were collected by centrifugation at room temperature at 2000xg for 15 minutes after incubation at room temperature for 30 minutes, and frozen at -80°C for long term storage. Upon RNA isolation, serum was thawed at 37°C, centrifuged at 12000xg for 5 minutes and 200 µl supernating serum were homogenized in 750 µl Qiazol containing 35 fmol synthetic cel-miR-39-3p spike-in control. RNA isolation was performed using chloroform extraction and ethanol precipitation following by purification using the miRNeasy isolation kit (Qiagen, Germany) with the following deviations from the standard protocol: 200 µl plasma were homogenized in 750 µl Qiazol. Exactly 500 µl aqueous phase were taken and Glycogen (Ambion, TX) was added to a final concentration of 50 µg/ml and precipitated with 750 µl 100% Ethanol. Columns were washed three times with RPE buffer and plasma-RNA was eluted once in 30 µl nuclease-free water and stored at -80°C.

treatment_protocol: not relevant


title: Liver_21d.p.e._Rep2

description:
Liver 21 days post exposure. Biological replicate 2 of 3.
21d.p.e.-Rep2


title: krahe-00060: aml_679


title: Liver_21d.p.e._Rep1

description:
Liver 21 days post exposure. Biological replicate 1 of 3.
21d.p.e.-Rep1


title: krahe-00060: aml_645


title: Liver_14d.p.e._Rep3

description:
Liver 14 days post exposure. Biological replicate 3 of 3.
14d.p.e.-Rep3

source_name: Liver_treatment station_14d.p.e.

source_name: Liver_control station_14d.p.e.


title: Serum-Control-R6

description: Total RNA isolated from serum


title: ZR_donor50

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Human Genome U133 Plus 2.0 Arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the affy package implemented in the R-statistical environment version 2.15.1. The Robust Multi-array Average (RMA) algorithm was used to estimate log2 transformed expression values for each probe-set.

source_name: Adrenal gland from kidney donor 50

label_protocol: 1-10 ng total RNA was reverse-transcribed and amplified with the Ovation Pico WTA System V2 (NuGEN Technologies, San Carlos, CA).  cDNA was purified using QIAquick PCR Purification Kit (Qiagen, Hilden, Germany) and biotin-labeled using Encore Biotin Module (NuGEN Technologies, San Carlos, CA).

extract_protocol: Total RNA was extracted using PicoRule RNA isolation kits (Molecular Devices, Sunnyvale, CA).

value: zona reticularis

value: male


title: krahe-00060: cd34_3


title: krahe-00060: aml_644


title: Liver_35d.p.e._Rep1

description:
Liver 35  days post exposure. Biological replicate 1 of 3.
35d.p.e.-Rep1


title: krahe-00060: aml_430


title: Serum-Control-R5

description: Total RNA isolated from serum


title: Serum-Control-R4

description: Total RNA isolated from serum


title: krahe-00060: aml_183


title: krahe-00060: aml_1029


title: Serum-Control-R3

description: Total RNA isolated from serum


title: krahe-00060: aml_1028


title: Liver_14d.p.e._Rep2

description:
Liver 14 days post exposure. Biological replicate 2 of 3.
14d.p.e.-Rep2


title: Serum-Control-R2

description: Total RNA isolated from serum


title: krahe-00060: aml8_c3

source_name: AML trisomy 8


title: Serum-Control-R1

description: Total RNA isolated from serum


title: Serum-Fracture-R7

description: Total RNA isolated from serum


title: krahe-00060: aml8_c2


title: ZR_donor45

source_name: Adrenal gland from kidney donor 45


title: Serum-Fracture-R6

description: Total RNA isolated from serum


title: ZR_donor46

source_name: Adrenal gland from kidney donor 46


title: ZR_donor48

source_name: Adrenal gland from kidney donor 48


title: Serum-Fracture-R5

description: Total RNA isolated from serum


title: Liver_7d.p.e._Rep2

description:
Liver 7 days post exposure. Biological replicate 1 of 3.
7d.p.e.-Rep2

source_name: Liver_control station_7d.p.e.

source_name: Liver_treatment station_7d.p.e.


title: krahe-00060: aml8_965


title: Liver_7d.p.e._Rep1

description:
Liver 7 days post exposure. Biological replicate 1 of 3.
7d.p.e.-Rep1


title: krahe-00060: aml8_924


title: ZF_donor45

value: zona fasciculata


title: Serum-Fracture-R4

description: Total RNA isolated from serum


title: Serum-Fracture-R3

description: Total RNA isolated from serum


title: krahe-00060: aml8_832


title: krahe-00060: aml8_549


title: Liver_7d.p.e._Rep3

description:
Liver 7 days post exposure. Biological replicate 1 of 3.
7d.p.e.-Rep3


title: ZF_donor50


title: Serum-Fracture-R2

description: Total RNA isolated from serum


title: Serum-Fracture-R1

description: Total RNA isolated from serum


title: krahe-00060: aml8_546


title: ZG_donor48

value: zona glomerulosa


title: krahe-00060: aml8_294


title: krahe-00060: aml8_221


title: krahe-00060: cd34_6

source_name: Normal mononuclear cells


title: krahe-00060: aml8_112


title: ZG_donor46


title: Liver_14d.p.e._Rep1

description:
Liver 14 days post exposure. Biological replicate 1 of 3.
14d.p.e.-Rep1


title: krahe-00060: aml8_#5


title: krahe-00060: aml8_416


title: APCC_donor50

value: Aldosterone producing cell clusters


title: ZG_donor45

value: female


title: krahe-00060: aml8_#6


title: krahe-00060: aml8_#3


title: ZG_donor50


title: APCC_donor48


title: APCC_donor46


title: Liver_Lpcat3fl/fl Albumin-Cre_wd

city: los angeles

first: Xin

last: Rong

state: California

address: 675 Charles E Young Dr. South

department: Pathology and Laboratory Medicine

institute: UCLA

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix 430.2 mouse GeneChips and the arrays were washed and stained according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

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

source_name: liver from Lpcat3fl/fl Albumin-Cre mice on western diet

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2008, Affymetrix).

growth_protocol: Mice were housed under pathogen-free conditions in a temperature-controlled room with a 12-h light/dark cycle. Mice were fed a western diet for 9 weeks since 7 weeks old.

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

treatment_protocol: Livers were harvested from mice after 6 hr fasting.

value: Lpcat3fl/fl Albumin-Cre


title: jacks-00113: KT16

source_name: lung tumor

value: lung tumor

value: F1 129svJae X C57/BL13

value: lung cancer

value: lung

value: Jacks lab/MIT CCR

value: adenocarcinoma

value: mixed


title: Liver_Lpcat3fl/fl _wd

source_name: liver from Lpcat3fl/fl mice on western diet

value: liver


title: Liver_Lpcat3fl/fl Albumin-Cre_chow

source_name: liver from Lpcat3fl/fl Albumin-Cre mice on chow diet

growth_protocol: Mice were housed under pathogen-free conditions in a temperature-controlled room with a 12-h light/dark cycle. Mice were fed a chow diet.


title: human melanoma, primary, rep2

city: Shinanomachi Shinjuku-ku

first: Keitaro

last: Fukuda

state: Tokyo

department: Dermatology

country: Japan

institute: Keio University School of Medicine

description: blue black patch on the sole

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

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

data_processing: The data were analyzed with GeneChip Operation Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: primary lesion

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And RNA was prepared using the RNAeasy. mini(QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease

value: melanoma

tag: type of melanoma

value: acral lentiginous melanoma

value: skin

tag: lesion

value: primary


title: APCC_donor45


title: human melanoma, primary, rep3

description: blue black patch on the sole

value: male


title: splenic pDC rep2

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

description: Gene expression data from lung of uninfected control mice

hyb_protocol: Biotinylated cRNA was hybridized on MOE430 2.0 GeneChips, that were stained and washed following Affymetrix standard procedures.

scan_protocol: Scanned following Affymetrix standard procedures.

data_processing: The probe level data (CEL files) were processed for global normalization and generation of expression values using the robust multi-array average algorithm (RMA) of the “affy package” in the R software environment (http://www.R-project.org).

source_name: splenic pDC rep2

label_protocol: Per sample, 1 µg total RNA was processed according to the manufacturer’s instructions.

growth_protocol: To increase the number of DC in vivo, C57BL/6 mice were injected with recombinant Flt3L to induce DC differentiation. On day 12 after injection, spleens were harvested, and following DC enrichment by centrifugation over OptiPrep™ gradient and MACS separation (using beads for isolation of PDCA-1+ and CD11c+ pDC and cDC, respectively), cells were stained for CD11c and B220 and purified by MoFlo cell sort.

extract_protocol: total RNA was extracted using Trizol.

tag: background mouse strain

tag: isolation beads


title: human melanoma, wound metastasis, rep1

description: ulcerated black plaque on the heel

source_name: wound metastatic lesion

tag: tissue

value: wound metastasis


title: splenic pDC rep1

source_name: splenic pDC rep1


title: human melanoma, primary, rep1

description: blue black patch on the sole


title: Liver_Lpcat3fl/fl _chow

source_name: liver from Lpcat3fl/fl mice on chow diet

tag: Sex


title: human melanoma, wound metastasis, rep2

description: ulcerated black plaque on the heel


title: Mhc7, biological replicate 1

status: Public on Jun 25 2015

city: Bangalore

first: Aditi

last: Madan

state: Karnataka

address: GB-03,Dept. of MRDG,New BioSciences Bldg, IISc

department: Dept. of MRDG

country: India

institute: Indian Institute of Science

description:
Gene expression data from IFMs of 1-2 day old adult male flies
Mhc7_01

hyb_protocol: Labeled samples were hybridized for 16h at 45deg C on Affymetrix GeneChip Drosophila Genome 2.0 Array. The arrays were washed using Affymetrix Fluidics Station.

scan_protocol: Array scanning and image analysis was performed with the Affymetrix GeneChip Operating Software.

data_processing: Data normalization was done using the Robust Multi-array Analysis (RMA) method using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Drosophila melanogaster

source_name: Drosophila IFM from 1-2 day old adult male flies

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

growth_protocol: Flies of the 3 genotypes (Canton-S, Act88FKM88, Mhc7) were reared under controlled temperature (25deg C) and circadian cycles (12h light/12h dark); and 1-2 day old adult males were collected for IFM dissections.

treatment_protocol: Thoraces were separated from heads and abdomens, and transferred immediately to ice-cold 70% ethanol and allowed to dehydrate overnight at -20deg C. IFM dissections were done by cutting thoraces along the midline and separating the hemi-thoraces. The muscles were then detached, isolated and transferred to TRIzol (Sigma).

value: Indirect Flight Muscles (IFMs)

value: Male

tag: age

value: 1-2 day old adults


title: Act88FKM88, biological replicate 3

description:
Gene expression data from IFMs of 1-2 day old adult male flies
KM88_03

tag: genotype


title: Act88FKM88, biological replicate 2

description:
Gene expression data from IFMs of 1-2 day old adult male flies
KM88_02


title: splenic cDC rep2

source_name: splenic cDC rep2


title: Act88FKM88, biological replicate 1

description:
Gene expression data from IFMs of 1-2 day old adult male flies
KM88_01


title: Mhc7, biological replicate 3

description:
Gene expression data from IFMs of 1-2 day old adult male flies
Mhc7_03


title: splenic cDC rep1

source_name: splenic cDC rep1


title: Mhc7, biological replicate 2

description:
Gene expression data from IFMs of 1-2 day old adult male flies
Mhc7_02


title: Canton-S, biological replicate 2

description:
Gene expression data from IFMs of 1-2 day old adult male flies
CS_02

value: Canton-S


title: BjΔntrC low nitrogen:BjΔntrC high nitrogen rep 1

city: Arlington

first: Woo-Suk

last: Chang

state: TX

address: 501 S. Nedderman Dr. , Life Science Building 216

department: Biology

institute: University of Texas at Arlington

description: Sample:Control=BjΔntrC low nitrogen:BjΔntrC high nitrogen

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

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

data_processing: Signal intensities were normalized for spot and slide abnormalities using spatial lowess. Lowess adjusted data were subsequently analyzed by mixed effect microarray analysis of variance (MAANOVA) (Kerr et al. 2000). The resulting variety-by-gene interaction (VG) values were combined with the residual noise from each spot to obtain the filtered and adjusted expression values (Kerr et al. 2000; Kerr and Churchill 2001). Both lowess and MAANOVA are part of the R/maanova microarray statistical analysis package (http://www.jax.org/staff/churchill/labsite/). Expression values from two technical replicates in each array were combined and averaged. Significant genes were selected based on a 2.0-cut off threshold with a false discovery rate lower than 5%.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: BjΔntrC

label_protocol: 10 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, DE). Four micrograms of cDNA were used for labeling with either cy3 or cy5 (Armersham) and unincorporated dyes were removed using a Qiaquick PCR purification Kit (Qiagen).

extract_protocol: Standard hot-phenol method

tag: treatment

value: Free-living cells grown in low nitrogen

value: Free-living cells grown in high nitrogen


title: BjΔntrC high nitrogen:BjΔntrC low nitrogen rep 2 Dye swap

description: Sample:Control=BjΔntrC high nitrogen:BjΔntrC low nitrogen


title: BjΔntrC low nitrogen:BjΔntrC high nitrogen rep 3


title: BjΔntrC high nitrogen:BjΔntrC low nitrogen rep 3 Dye swap


title: BjΔntrC low nitrogen:BjΔntrC high nitrogen rep 2


title: Canton-S, biological replicate 1

description:
Gene expression data from IFMs of 1-2 day old adult male flies
CS_01


title: BjΔntrC high nitrogen:BjΔntrC low nitrogen rep 1 Dye swap


title: BjΔntrC low nitrogen:Bj110  low nitrogen rep 3

description: Sample:Control=BjΔntrC low nitrogen:Bj110  low nitrogen


title: Canton-S, biological replicate 3

description:
Gene expression data from IFMs of 1-2 day old adult male flies
CS_03


title: replicate2 Drug MPS1 inhibitor treated for 24h U87

type: protein

city: Bethesda

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

description:
protein lysate
NMS2uM 24hr U87-b

hyb_protocol: 5 serial dilutions of lysates were arrayed on nitrocellulose‐coated slides, probed with (172 phosphorylated and non- phosphorylated) antibodies. Samples were probed with antibodies by a tyramide amplification approach (Dako CSA) and visualized by DAB colorimetric reaction.

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images.  Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer software.

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve antibody slide. All the data points were normalized for protein loading and transformed to a linear value. Linear values were transformed to Log2 value and then median‐centered for hierarchical cluster analysis.

label: DAB

molecule: protein

source_name: U87-GBM cell line

label_protocol: visualized by DAB colorimetric reaction

growth_protocol: U251, U87  (National Cancer Institute Frederick Tumor Repository) human GBM cell lines were grown in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (FBS), and maintained at 37°C, 5% CO2.

extract_protocol: Treated GBM cell (U251,U87)  lysates were prepared  in  RPPA lysis buffer [1% Triton X-100, 50 nmol/L Hepes (pH 7.4), 150 nmol/L NaCl, 1.5 nmol/L MgCl2, 1 mmol/L EGTA, 100 nmol/L NaF, 10 nmol/L NaPPi, 10% glycerol, 1 nmol/L phenylmethylsulfonyl fluoride, 1 nmol/L Na3VO4, and aprotinin 10 μg/mL) as described elsewhere, and sent to RPPA Core Facility, MD Andersen Cancer Center, Houston, TX for RPPA analysis.

treatment_protocol: siRNA transfections, 2-pmol siMPS1, (5’ TTGGACTGTTATACTCTTGAA3’, SI00071624, siMiR21 (GeneSolution siRNA cat: 1027416 (mix of 4 validated anti Hs_MiR21)) (Qiagen Inc., Germantown, MD) was complexed with RNAi Max lipid transfection reagent (Invitrogen) in DMEM media for 15 minutes at ambient temperature.For NMS-P715 mediated inhibition of MPS1, cells were plated Overnight prior to drug treatment and treated with NMS-P715 at the concentrations indicated in each experiment.Proteins for RPPAt analysis was harvested 24 and  48 hours post siRNA transfection or Drug treatments

tag: cell line

value: Drug MPS1 inhibitor treated for 24h


title: replicate2 siTTK gene at 48h U87

description:
protein lysate
siTTK 48hr U87-b

value: siTTK gene at 48h


title: Bj110 low nitrogen:BjΔntrC  low nitrogen rep 2 Dye swap

description: Sample:Control=Bj110 low nitrogen:BjΔntrC  low nitrogen


title: replicate2 Control U87

description:
protein lysate
Ctrl U87-b

value: Control


title: replicate2 siTTK gene at 24h U87

description:
protein lysate
siTTK 24hr U87-b

value: siTTK gene at 24h


title: replicate1 siNegative control U87

description:
protein lysate
siNeg U87-a

value: siNegative control


title: replicate1 siTTK gene at 24h U87

description:
protein lysate
siTTK 24hr U87-a


title: replicate1 Drug MPS1 inhibitor treated for 24h U87

description:
protein lysate
NMS2uM 24hr U87-a


title: Bj110 low nitrogen:Bj110 high nitrogen rep 1

description: Sample:Control=Bj110 low nitrogen:Bj110 high nitrogen


title: replicate1 Control U87

description:
protein lysate
Ctrl U87-a


title: replicate2 Drug MPS1 inhibitor treated for 48h U251

description:
protein lysate
NMS2uM 48hr U251-b

source_name: U251-GBM cell line

value: Drug MPS1 inhibitor treated for 48h


title: BjΔntrC low nitrogen:Bj110  low nitrogen rep 2


title: replicate2 Drug MPS1 inhibitor treated for 48h U87

description:
protein lysate
NMS2uM 48hr U87-b


title: Bj110 low nitrogen:Bj110 high nitrogen rep 3


title: Bj110 high nitrogen:Bj110 low nitrogen rep 3 Dye swap

description: Sample:Control=Bj110 high nitrogen:Bj110 low nitrogen


title: Bj110 low nitrogen:BjΔntrC  low nitrogen rep 1 Dye swap


title: Bj110 low nitrogen:BjΔntrC  low nitrogen rep 3 Dye swap


title: BjΔntrC low nitrogen:Bj110  low nitrogen rep 1


title: Bj110 high nitrogen:Bj110 low nitrogen rep 2 Dye swap


title: replicate2 Drug MPS1 inhibitor treated for 24h U251

description:
protein lysate
NMS2uM 24hr U251-b


title: Bj110 high nitrogen:BjΔntrC  high nitrogen rep 2 Dye swap

description: Sample:Control=Bj110 high nitrogen:BjΔntrC  high nitrogen


title: BjΔntrC high nitrogen:Bj110  high nitrogen rep 3

description: Sample:Control=BjΔntrC high nitrogen:Bj110  high nitrogen


title: Bj110 high nitrogen:BjΔntrC  high nitrogen rep 3 Dye swap


title: replicate2 siTTK gene at 48h U251

description:
protein lysate
siTTK 48hr U251-b


title: replicate1 siTTK gene at 48h U87

description:
protein lysate
siTTK 48hr U87-a


title: Bj110 high nitrogen:Bj110 low nitrogen rep 1 Dye swap


title: Bj110 low nitrogen:Bj110 high nitrogen rep 2


title: Bj110 high nitrogen:BjΔntrC  high nitrogen rep 1 Dye swap


title: replicate2 siTTK gene at 24h U251

description:
protein lysate
siTTK 24hr U251-b


title: harri-00137: 680-1

source_name: Preoperative core biopsy

value: Female

tag: diagnosis

value: human epidermal growth factor receptor 2 (HER2)-positive breast cancer

value: tumor

tag: path cr

value: B

tag: clin resp

tag: clin prog

value: G

tag: t stage

tag: er

value: P

tag: pr

tag: FISH


title: replicate2 siNegative control U251

description:
protein lysate
siNeg U251-b


title: harri-00137: 652-1

tag: gender


title: harri-00137: 641-1

value: N


title: harri-00137: 662-1


title: harri-00137: 637-1


title: harri-00137: 600-1


title: replicate1 Drug MPS1 inhibitor treated for 48h U87

description:
protein lysate
NMS2uM 48hr U87-a


title: replicate2 siNegative control U87

description:
protein lysate
siNeg U87-b


title: replicate2 Control U251

description:
protein lysate
Ctrl U251-b


title: BjΔntrC high nitrogen:Bj110  high nitrogen rep 1


title: harri-00137: 611-1


title: harri-00137: 514-1


title: replicate1 Drug MPS1 inhibitor treated for 24h U251

description:
protein lysate
NMS2uM 24hr U251-a


title: harri-00137: 568-1

value: R


title: replicate1 siTTK gene at 48h U251

description:
protein lysate
siTTK 48hr U251-a


title: replicate1 Control U251

description:
protein lysate
Ctrl U251-a


title: replicate1 siTTK gene at 24h U251

description:
protein lysate
siTTK 24hr U251-a


title: replicate1 Drug MPS1 inhibitor treated for 48h U251

description:
protein lysate
NMS2uM 48hr U251-a


title: harri-00137: 513-2


title: BjΔntrC high nitrogen:Bj110  high nitrogen rep 2


title: replicate1 siNegative control U251

description:
protein lysate
siNeg U251-a


title: ZF_donor48

source_name: Adrenal gland from kidney donor 48

value: zona fasciculata

value: male


title: harri-00137: 512-2


title: harri-00137: 483-1-2


title: harri-00137: 483-1-1


title: harri-00137: 441-1

value: L


title: ZF_donor46

source_name: Adrenal gland from kidney donor 46

value: female


title: freshly isolated hepatocytes without culturing 2

city: Saitama

first: Ryosuke

last: Takahashi

address: 2520 Hatoyama

department: Central Research Laboratory

institute: Hitachi, Ltd.

description: Gene expression in freshly isolated hepatocytes

hyb_protocol: 1.65 ug of Cy3-labeled cRNA was fragmented and hybridized at 65ºto the Agilent Whole Rat Genome Microarrays 4× 014879).

scan_protocol: Microarrays were scanned using an Agilent DNA microarray scanner.

data_processing:
The microarray data were analyzed by using the GeneSpring GX 10.0.2. (Agilent Technologies)
Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software version 10.5.1.1, which performs background subtractions.

source_name: freshly isolated hepatocytes without culturing extracted from rat #2

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using an Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions. Briefly, 100 ng of total RNA was reverse-transcribed to double-strand cDNA by using a poly dT-T7 promoter primer. Primer, template RNA, and quality-control transcripts of known concentration and quality were first denatured at 65ºC for 10 min and incubated for two hours at 40ºC with 5X first-strand buffer, 0.1-M DTT, 10-mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70ºC for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and incubated at 40ºC for two hours. The labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted in 30 μl of nuclease-free water. Subsequently, amplified cRNA quantity and labeled cyanine incorporation were determined using a Nanodrop ND-1000 spectrophometer and an Agilent bioanalyzer.

extract_protocol: Total RNA was extracted from the four kinds of samples mentioned above using an RNeasy Plus Micro Kit (Qiagen GmbH, Germany) according to the manufacturer’s instructions. Quantity and quality of RNA were determined by a Nanodrop ND-1000 spectrophometer (Thermo Fisher Scientific Inc., Waltham, MA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), as recommended.

value: freshly isolated

tag: cell type

value: primary hepatocyte

tag: genetic background


title: harri-00137: 422-1

tag: tissue


title: harri-00137: 405-1


title: harri-00137: 438-1


title: harri-00137: 408-1


title: harri-00137: 334-2


title: harri-00137: 381-2


title: Sandwich-cultured hepatocytes 3

description: Gene expression in sandwich-cultured hepatocytes

source_name: Sandwich-cultured hepatocytes extracted from rat #3

value: Sandwich-cultured


title: harri-00137: 278253


title: freshly isolated hepatocytes without culturing 3

source_name: freshly isolated hepatocytes without culturing extracted from rat #3


title: Sandwich-cultured hepatocytes 2

source_name: Sandwich-cultured hepatocytes extracted from rat #2


title: p53-/-_GAP940_Signal

city: Cardiff

first: Karen

middle: Ruth

last: Reed

address: Maindy Road

country: United Kingdom

institute: ECSCRI, Cardiff University

description: P53 null (5 Days post Cre induction)

hyb_protocol: PICR Standard 11uM feature-1 protocol - carried out in the Affymetrix Hybridization Oven 640 according to the manufacturer’s instructions

scan_protocol: PICR Standard 11uM feature-1 protocol - using the Affymetrix GeneChip Scanner 3000 system with Autoloader

data_processing:
Raw signal intensities were initially screened by using the MaxD/View-Program to remove false positive and false negative signals (using a cut off of at least one P value for each transcript <0.2). The data were then normalized by using the global geometric mean (GGM) normalization option within the MaxD/View-Program
Pairwise comparisons of the GGM data were then performed by SAM analysis (Statistical Analysis of Microarray)

source_name: Small intestine

label_protocol: PICR Std Label v 2-0 - utalizing the Enzo BioArray High Yield Transcript Labelling Kit

extract_protocol: trizol phenol extraction followed by Rneasy clean up

treatment_protocol: Mice treated with 3x 80mg/kg Beta-Napthoflavone in one day and culled and dissected at the desiganted day post induction.

tag: genotype/variation

value: AhCre-positive (control) P53 null

tag: protocol

value: gene recombination induced via IP administration of beta-napthoflavone

value: small intestine


title: p53-/-_GAP886_Signal

description: P53 null (5 Days post Cre induction)


title: p53-/-_GAP901_Signal

description: P53 null (5 Days post Cre induction)


title: Monolayer-cultured hepatocytes 1

description: Gene expression in monolayer-cultured hepatocytes

source_name: Monolayer-cultured hepatocytes extracted from rat #1

value: Monolayer-cultured


title: Nanopillar-cultured hepatocytes 1

description: Gene expression in nanopillar-cultured hepatocytes

source_name: Nanopillar-cultured hepatocytes extracted from rat #1

value: Nanopillar-cultured


title: Hela_siBubR1+siEg5_rep2

city: Fujisawa

first: Akihiro

last: Ohashi

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

institute: Takeda Pharmaceutical Company Ltd.

description: Gene expression data from HeLa cells treated with siEg5+siBubR1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed median target intensity of each array was arbitrarily set to 1.0.

source_name: Hela treated with BubR1siNRA and Eg5 siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HeLa cells were cultured with Dulbecco's Modified Eagle Medium (DMEM) in the presence of 10 % FBS

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, QIAGEN).

treatment_protocol: HeLa cells were treated with the indicated siRNAs for 3 days

value: Hela


title: Monolayer-cultured hepatocytes 2

source_name: Monolayer-cultured hepatocytes extracted from rat #2


title: gap429_apcfl/flP53-/-_Signal

description: Day 5 APC flox / P53 null

value: AhCre-positive APCflox hom, P53 null


title: Hela_siBubR1+siEg5_rep1


title: Sandwich-cultured hepatocytes 1

source_name: Sandwich-cultured hepatocytes extracted from rat #1


title: gap346_apcfl/flP53-/-_Signal

description: Day 5 APC flox / P53 null


title: Nanopillar-cultured hepatocytes 2

source_name: Nanopillar-cultured hepatocytes extracted from rat #2


title: D5fl_131u_Signal

description: Day5 APC flox hom

value: AhCre-positive APCflox hom


title: d5wt_323u_Signal

description: Day 5 WT

value: AhCre-positive control (wild-type)


title: D5fl_331u_Signal

description: Day5 APC flox hom


title: Hela_siBubR1_rep2

description: Gene expression data from HeLa cells treated with siNS+siBubR1

source_name: Hela treated with BubR1siNRA


title: d5wt_474u_Signal

description: Day 5 WT


title: D5fl_444t_Signal

description: Day5 APC flox hom


title: gap397_apcfl/flP53-/-_Signal

description: Day 5 APC flox / P53 null


title: Hela_siBubR1+siCENP-E_rep1

description: Gene expression data from HeLa cells treated with siCENP-E+siBubR1

source_name: Hela treated with BubR1siNRA and CENP-E siRNA


title: Hela_siBubR1+siCENP-E_rep2


title: Hela_siBubR1_rep1


title: Hela_NS_rep2

description: Gene expression data from HeLa cells treated with siNS alone (control)

source_name: Hela treated with non-silencing siNRA


title: d5wt_110u_Signal

description: Day 5 WT


title: freshly isolated hepatocytes without culturing 1

source_name: freshly isolated hepatocytes without culturing extracted from rat #1


title: Hela_NS_rep1


title: day30_irradiated_rep4

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Gene expression in mouse whole blood at day 30

hyb_protocol: 1.6 microgram of cRNA,  >9 pmol Cy3 per microgram cRNA was fragmented and hybridized (17 hours with rotation at 65°C) to Agilent Whole Mouse Genome Microarrays 4X44K v2 (G4846A), and then washed using the Gene Expression Hybridization Kit and GE Wash Buffers as recommended by Agilent

scan_protocol: Slides were  scanned with the Agilent DNA Microarray Scanner (G2505B), and the images were analyzed (Agilent Feature Extraction Software ver. 10.7) with default parameters for background correction and flagging non-uniform features.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: C57BL/6, irradiated, day 30, rep4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared with the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND1000 Spectrophotometer

extract_protocol: All blood samples were collected by cardiac puncture in a sterile hood.  For each animal ~0.4 mL of blood was collected into 2 mL of PAXgene Blood RNA stabilization and lysis solution (PreAnalytix GmBH, catalog#762165), mixed thoroughly and shipped at 4ºC in temperature-stabilized containers. They were stored for a further 24 hour at 4ºC, and then incubated at room temperature for a minimum of 2 hours before proceeding with RNA isolation.  RNA was purified following the PAXgene Blood RNA kit recommended protocol with on-column DNaseI treatment.

treatment_protocol: C57BL/6 mice (approximately 10-12 weeks old, 25-30 g) were received from Charles River Laboratories (Frederick, MD) and were quarantined for 14 days prior to group assignment by body weight stratification for randomization into the study.  Animals were administered 90-Strontium intravenously by tail vein injection with 200 ± 0.3 kBq 85/90SrCl2 solution in a volume of 0.05 mL

value: whole blood

tag: strain


title: day25_irradiated_rep5

description: Gene expression in mouse whole blood at day 25

source_name: C57BL/6, irradiated, day 25, rep5


title: day30_irradiated_rep3

source_name: C57BL/6, irradiated, day 30, rep3


title: day9_irradiated_rep6

description: Gene expression in mouse whole blood at day 9

source_name: C57BL/6, irradiated, day 9, rep6


title: day25_irradiated_rep3

source_name: C57BL/6, irradiated, day 25, rep3


title: day30_irradiated_rep1

source_name: C57BL/6, irradiated, day 30, rep1


title: day9_irradiated_rep2

source_name: C57BL/6, irradiated, day 9, rep2


title: day30_irradiated_rep6

source_name: C57BL/6, irradiated, day 30, rep6


title: day7_irradiated_rep6

description: Gene expression in mouse whole blood at day 7

source_name: C57BL/6, irradiated, day 7, rep6


title: day9_irradiated_rep3

source_name: C57BL/6, irradiated, day 9, rep3


title: day30_irradiated_rep5

source_name: C57BL/6, irradiated, day 30, rep5


title: day25_irradiated_rep2

source_name: C57BL/6, irradiated, day 25, rep2


title: day25_irradiated_rep4

source_name: C57BL/6, irradiated, day 25, rep4


title: day25_irradiated_rep6

source_name: C57BL/6, irradiated, day 25, rep6


title: day9_irradiated_rep4

source_name: C57BL/6, irradiated, day 9, rep4


title: day25_irradiated_rep1

source_name: C57BL/6, irradiated, day 25, rep1


title: day7_irradiated_rep1

source_name: C57BL/6, irradiated, day 7, rep1


title: day7_irradiated_rep3

source_name: C57BL/6, irradiated, day 7, rep3


title: day7_irradiated_rep2

source_name: C57BL/6, irradiated, day 7, rep2


title: day4_irradiated_rep3

description: Gene expression in mouse whole blood at day 4

source_name: C57BL/6, irradiated, day 4, rep3


title: day4_irradiated_rep4

source_name: C57BL/6, irradiated, day 4, rep4


title: day9_irradiated_rep1

source_name: C57BL/6, irradiated, day 9, rep1


title: day7_irradiated_rep4

source_name: C57BL/6, irradiated, day 7, rep4


title: day7_irradiated_rep5

source_name: C57BL/6, irradiated, day 7, rep5


title: day4_irradiated_rep2

source_name: C57BL/6, irradiated, day 4, rep2


title: day30_irradiated_rep2

source_name: C57BL/6, irradiated, day 30, rep2


title: day30_control_rep5

source_name: C57BL/6, control, day 30, rep5


title: day4_irradiated_rep1

source_name: C57BL/6, irradiated, day 4, rep1


title: day30_control_rep4

source_name: C57BL/6, control, day 30, rep4


title: day25_control_rep5

source_name: C57BL/6, control, day 25, rep5


title: day25_control_rep4

source_name: C57BL/6, control, day 25, rep4


title: day25_control_rep2

source_name: C57BL/6, control, day 25, rep2


title: day30_control_rep1

source_name: C57BL/6, control, day 30, rep1


title: day30_control_rep2

source_name: C57BL/6, control, day 30, rep2


title: day25_control_rep3

source_name: C57BL/6, control, day 25, rep3


title: day30_control_rep3

source_name: C57BL/6, control, day 30, rep3


title: snap frozen_normal adjacent_patient31

city: Stony Brook

first: Yuanhao

last: Zhang

address: AMS Department,Stony Brook University

department: Applied Mathematics and Statistics

institute: Stony Brook University

hyb_protocol: The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies) and used to probe and hybridized with Agilent Human Microarray Kit V3, 8 x 15K arrays, based on Sanger miRbase release 12.0 (G4470C, Agilent Technologies, Foster City, California).The hybridization was performed at 55o C for 20 h in an Agilent Hybridization Oven according to the manufacturer’s protocol.

scan_protocol: Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA)

data_processing: Features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.10.7.3.1) with default protocols and settings . The raw probe level data were imported into GeneSpring 12.5GX and the miRNA signal was normalized using the default setting: threshold raw signal to 1.0, percent shift to 90th percentile as the normalization algorithm and no baseline transformation.

source_name: snap frozen_normal adjacent_patient31

extract_protocol: For each SBU FFPE sample, total RNA was isolated from three 10 µm thick tissue sections using a miRNeasy FFPE extraction kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. For each WU frozen samples, total RNA was extracted by Trizol followed by lithium precipitation (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol at the Siteman Cancer Center Tissue Procurement Facility.  Total RNA quantity and quality was determined using a Nanodrop 2000C (Thermo Scientific, Waltham, MA).

value: Colon Cancer Normal Adjacent

tag: race

value: Caucasian

tag: data source

value: WU


title: day25_control_rep1

source_name: C57BL/6, control, day 25, rep1


title: day9_control_rep5

source_name: C57BL/6, control, day 9, rep5


title: day9_control_rep3

source_name: C57BL/6, control, day 9, rep3


title: day9_control_rep4

source_name: C57BL/6, control, day 9, rep4


title: day9_control_rep6

source_name: C57BL/6, control, day 9, rep6


title: snap frozen_tumor_patient30

source_name: snap frozen_tumor_patient30

label_protocol: The tissue RNAs (100 ηg) were labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies)

value: Colon Cancer Tumor


title: snap frozen_normal adjacent_patient30

source_name: snap frozen_normal adjacent_patient30


title: snap frozen_tumor_patient31

source_name: snap frozen_tumor_patient31


title: day30_control_rep6

source_name: C57BL/6, control, day 30, rep6


title: day25_control_rep6

source_name: C57BL/6, control, day 25, rep6


title: day9_control_rep2

source_name: C57BL/6, control, day 9, rep2


title: day9_control_rep1

source_name: C57BL/6, control, day 9, rep1


title: snap frozen_normal adjacent_patient28

source_name: snap frozen_normal adjacent_patient28


title: snap frozen_tumor_patient29

source_name: snap frozen_tumor_patient29


title: snap frozen_normal adjacent_patient27

source_name: snap frozen_normal adjacent_patient27


title: day7_control_rep5

source_name: C57BL/6, control, day 7, rep5


title: snap frozen_tumor_patient27

source_name: snap frozen_tumor_patient27


title: snap frozen_normal adjacent_patient26

source_name: snap frozen_normal adjacent_patient26


title: snap frozen_tumor_patient26

source_name: snap frozen_tumor_patient26


title: day7_control_rep3

source_name: C57BL/6, control, day 7, rep3


title: day4_control_rep3

source_name: C57BL/6, control, day 4, rep3


title: day7_control_rep4

source_name: C57BL/6, control, day 7, rep4


title: day4_control_rep4

source_name: C57BL/6, control, day 4, rep4


title: day7_control_rep1

source_name: C57BL/6, control, day 7, rep1


title: day4_control_rep1

source_name: C57BL/6, control, day 4, rep1


title: snap frozen_normal adjacent_patient24

source_name: snap frozen_normal adjacent_patient24


title: snap frozen_normal adjacent_patient23

source_name: snap frozen_normal adjacent_patient23


title: snap frozen_tumor_patient23

source_name: snap frozen_tumor_patient23


title: snap frozen_normal adjacent_patient22

source_name: snap frozen_normal adjacent_patient22


title: snap frozen_normal adjacent_patient29

source_name: snap frozen_normal adjacent_patient29


title: day7_control_rep6

source_name: C57BL/6, control, day 7, rep6


title: snap frozen_tumor_patient22

source_name: snap frozen_tumor_patient22


title: snap frozen_tumor_patient24

source_name: snap frozen_tumor_patient24


title: snap frozen_tumor_patient28

source_name: snap frozen_tumor_patient28


title: snap frozen_tumor_patient25

source_name: snap frozen_tumor_patient25


title: snap frozen_normal adjacent_patient21

source_name: snap frozen_normal adjacent_patient21


title: snap frozen_normal adjacent_patient25

source_name: snap frozen_normal adjacent_patient25


title: snap frozen_tumor_patient21

source_name: snap frozen_tumor_patient21


title: snap frozen_normal adjacent_patient19

source_name: snap frozen_normal adjacent_patient19

value: African American


title: snap frozen_tumor_patient19

source_name: snap frozen_tumor_patient19


title: snap frozen_normal adjacent_patient20

source_name: snap frozen_normal adjacent_patient20


title: snap frozen_tumor_patient20

source_name: snap frozen_tumor_patient20


title: day4_control_rep2

source_name: C57BL/6, control, day 4, rep2


title: day7_control_rep2

source_name: C57BL/6, control, day 7, rep2


title: snap frozen_tumor_patient18

source_name: snap frozen_tumor_patient18


title: snap frozen_tumor_patient17

source_name: snap frozen_tumor_patient17


title: snap frozen_normal adjacent_patient17

source_name: snap frozen_normal adjacent_patient17


title: Monolayer-cultured hepatocytes 3

source_name: Monolayer-cultured hepatocytes extracted from rat #3

tag: treatment

value: primary hepatocyte


title: snap frozen_normal adjacent_patient16

source_name: snap frozen_normal adjacent_patient16


title: snap frozen_tumor_patient14

source_name: snap frozen_tumor_patient14


title: snap frozen_normal adjacent_patient15

source_name: snap frozen_normal adjacent_patient15


title: snap frozen_tumor_patient13

source_name: snap frozen_tumor_patient13


title: snap frozen_normal adjacent_patient13

source_name: snap frozen_normal adjacent_patient13


title: snap frozen_tumor_patient12

source_name: snap frozen_tumor_patient12


title: snap frozen_normal adjacent_patient12

source_name: snap frozen_normal adjacent_patient12


title: snap frozen_tumor_patient15

source_name: snap frozen_tumor_patient15


title: snap frozen_normal adjacent_patient14

source_name: snap frozen_normal adjacent_patient14


title: snap frozen_normal adjacent_patient11

source_name: snap frozen_normal adjacent_patient11


title: snap frozen_tumor_patient11

source_name: snap frozen_tumor_patient11


title: snap frozen_normal adjacent_patient10

source_name: snap frozen_normal adjacent_patient10


title: snap frozen_normal adjacent_patient18

source_name: snap frozen_normal adjacent_patient18


title: snap frozen_tumor_patient16

source_name: snap frozen_tumor_patient16


title: snap frozen_tumor_patient10

source_name: snap frozen_tumor_patient10


title: snap frozen_normal adjacent_patient9

source_name: snap frozen_normal adjacent_patient9


title: snap frozen_tumor_patient7

source_name: snap frozen_tumor_patient7


title: snap frozen_tumor_patient8

source_name: snap frozen_tumor_patient8


title: snap frozen_normal adjacent_patient7

source_name: snap frozen_normal adjacent_patient7


title: snap frozen_normal adjacent_patient8

source_name: snap frozen_normal adjacent_patient8


title: snap frozen_normal adjacent_patient6

source_name: snap frozen_normal adjacent_patient6


title: hanas-00078: B108

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Brain

value: Primary Glioma

value: Grade 2

value: premortem

value: Brain

value: Astrocytoma

value: Adult


title: hanas-00078: B029

scan_protocol: See mage-tab files linked to series entry for additional details


title: hanas-00078: B_N5

data_processing: See mage-tab files linked to series entry for additional details

value: Normal


title: snap frozen_tumor_patient6

source_name: snap frozen_tumor_patient6


title: snap frozen_normal adjacent_patient5

source_name: snap frozen_normal adjacent_patient5


title: snap frozen_normal adjacent_patient4

source_name: snap frozen_normal adjacent_patient4


title: snap frozen_tumor_patient5

source_name: snap frozen_tumor_patient5


title: hanas-00078: B_N4

label_protocol: See mage-tab files linked to series entry for additional details


title: snap frozen_tumor_patient9

source_name: snap frozen_tumor_patient9


title: hanas-00078: B_N6

extract_protocol: See mage-tab files linked to series entry for additional details


title: hanas-00078: B_N3


title: hanas-00078: B467

value: Grade 1


title: snap frozen_tumor_patient4

source_name: snap frozen_tumor_patient4


title: hanas-00078: B_N2


title: hanas-00078: B458

value: Grade 4


title: day9_irradiated_rep5

source_name: C57BL/6, irradiated, day 9, rep5


title: hanas-00078: B464


title: hanas-00078: B_N1


title: hanas-00078: B432


title: snap frozen_tumor_patient3

source_name: snap frozen_tumor_patient3


title: hanas-00078: B420


title: snap frozen_normal adjacent_patient2

source_name: snap frozen_normal adjacent_patient2


title: hanas-00078: B406


title: hanas-00078: B404


title: hanas-00078: B407


title: hanas-00078: B398


title: hanas-00078: B396


title: hanas-00078: B431


title: snap frozen_tumor_patient2

source_name: snap frozen_tumor_patient2


title: hanas-00078: B388


title: snap frozen_normal adjacent_patient1

source_name: snap frozen_normal adjacent_patient1


title: hanas-00078: B373


title: snap frozen_tumor_patient1

source_name: snap frozen_tumor_patient1


title: hanas-00078: B384


title: hanas-00078: B382


title: hanas-00078: B375b


title: parafilm embedded tissue_normal adjacent_patient30

value: SBU


title: parafilm embedded tissue_tumor_patient30


title: parafilm embedded tissue_normal adjacent_patient29


title: snap frozen_normal adjacent_patient3

source_name: snap frozen_normal adjacent_patient3


title: hanas-00078: B371


title: hanas-00078: B358


title: hanas-00078: B363


title: hanas-00078: B361


title: hanas-00078: B344


title: hanas-00078: B345


title: parafilm embedded tissue_tumor_patient29


title: parafilm embedded tissue_normal adjacent_patient28


title: hanas-00078: B347


title: parafilm embedded tissue_tumor_patient28


title: hanas-00078: B380


title: parafilm embedded tissue_normal adjacent_patient27


title: Nanopillar-cultured hepatocytes 3

source_name: Nanopillar-cultured hepatocytes extracted from rat #3

value: Nanopillar-cultured


title: hanas-00078: B330


title: hanas-00078: B327


title: parafilm embedded tissue_tumor_patient27


title: hanas-00078: B322


title: parafilm embedded tissue_normal adjacent_patient26

value: Colon Cancer Normal Adjacent


title: parafilm embedded tissue_tumor_patient26

value: Caucasian


title: parafilm embedded tissue_normal adjacent_patient25


title: hanas-00078: B307


title: hanas-00078: B321


title: harri-00137: 464-1

source_name: Preoperative core biopsy

value: Female

tag: diagnosis

value: human epidermal growth factor receptor 2 (HER2)-positive breast cancer

value: tumor

tag: path cr

value: B

value: G

value: P


title: hanas-00078: B296b

value: Primary Glioma

value: premortem


title: hanas-00078: B325

value: Brain

value: Astrocytoma


title: hanas-00078: B300

value: Adult


title: hanas-00078: B283

value: Grade 1


title: parafilm embedded tissue_tumor_patient25

value: Colon Cancer Tumor


title: M74_60DAH_2011

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: Apple 'M74' fruit flesh, 2 months of cold storage, 2011

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Fruits were harvested at INRA, Angers (Experimental unit of Bois L'Abbé-La Rétuziére).

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol: Cold storage at 1°C, after harvest.

tag: organ

value: Fruit

tag: tissus

value: Parenchyma

value: Hybrid M74

tag: genotype

value: Wild-type

tag: tissus developmental stage

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: M49_60DAH_2011

source_name: Apple 'M49' fruit flesh, 2 months of cold storage, 2011

value: Hybrid M49


title: M40_60DAH_2011

source_name: Apple 'M40' fruit flesh, 2 months of cold storage, 2011

value: Hybrid M40


title: M20_60DAH_2011

source_name: Apple 'M20' fruit flesh, 2 months of cold storage, 2011

value: Hybrid M20


title: parafilm embedded tissue_normal adjacent_patient24

value: Colon Cancer Normal Adjacent

value: Caucasian

value: SBU


title: M40_Harvest_2011

source_name: Apple 'M40' fruit flesh, at harvest, 2011


title: M74_Harvest_2011

source_name: Apple 'M74' fruit flesh, at harvest, 2011


title: M49_Harvest_2011

source_name: Apple 'M49' fruit flesh, at harvest, 2011


title: M20_Harvest_2011

source_name: Apple 'M20' fruit flesh, at harvest, 2011


title: parafilm embedded tissue_tumor_patient24


title: M74_Harvest_2007

source_name: Apple 'M74' fruit flesh, at harvest, 2007


title: parafilm embedded tissue_normal adjacent_patient23


title: parafilm embedded tissue_tumor_patient23


title: parafilm embedded tissue_tumor_patient22


title: parafilm embedded tissue_normal adjacent_patient21


title: hanas-00078: B269

source_name: Brain

value: Primary Glioma

value: Grade 4

value: premortem

value: Brain


title: hanas-00078: B214

value: Grade 2

value: Astrocytoma

value: Adult


title: hanas-00078: B282

value: Grade 1


title: hanas-00078: B239


title: parafilm embedded tissue_tumor_patient21

value: Colon Cancer Tumor


title: hanas-00078: B240


title: parafilm embedded tissue_normal adjacent_patient20

value: African American


title: hanas-00078: B279


title: hanas-00078: B260


title: M20_Harvest_2007

source_name: Apple 'M20' fruit flesh, at harvest, 2007

value: Fruit

value: Parenchyma

value: Wild-type

value: Harvested at optimum maturity


title: M49_Harvest_2006

source_name: Apple 'M49' fruit flesh, at harvest, 2006

value: Hybrid M49


title: parafilm embedded tissue_tumor_patient20


title: M40_Harvest_2007

source_name: Apple 'M40' fruit flesh, at harvest, 2007

value: Hybrid M40


title: M16_100DAF_2010

source_name: Apple 'M16' fruit flesh, 100 days after flowering, 2010

value: Hybrid M16

value: Fruit development


title: hanas-00078: B209

value: Primary Glioma


title: M48_100DAF_2009

source_name: Apple 'M48' fruit flesh, 100 days after flowering, 2009

value: Hybrid M48


title: M48_120DAH_2009

source_name: Apple 'M48' fruit flesh, 4 months of cold storage, 2009

value: Cold storage for 120 days after harvest


title: M16_100DAF_2009

source_name: Apple 'M16' fruit flesh, 100 days after flowering, 2009


title: parafilm embedded tissue_tumor_patient19

value: SBU


title: M16_120DAH_2009

source_name: Apple 'M16' fruit flesh, 4 months of cold storage, 2009


title: parafilm embedded tissue_normal adjacent_patient18

value: Colon Cancer Normal Adjacent


title: parafilm embedded tissue_normal adjacent_patient19


title: M48_100DAF_2010

source_name: Apple 'M48' fruit flesh, 100 days after flowering, 2010


title: parafilm embedded tissue_normal adjacent_patient22

value: Caucasian


title: parafilm embedded tissue_tumor_patient18


title: C26CM 24 hour E

city: Boston

first: Robert

middle: William

last: Jackman

state: Massachusetts

address: 635 Commonwealth Avenue/rm 444

department: Health Sciences

institute: Boston University (BU)

hyb_protocol: Fragmented, biotinylated DNA samples were hybridized on a mouse Gene 1.0 ST array acorrding to manufacture's recommendation.

scan_protocol: A total of 6 array images were acquired by GeneChip Scanner 3000 TG and quality assessed by Affymetrix Expression Console (Santa Clara, CA).

data_processing: Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and robust multi-array analysis algorithm (RMA) and quantile normalization was used for data preprocessing {Bolstad, 2003 #4365}.  probe group file: MoEx-1_0-st-v1.r2.pgf  meta-probeset file: Brainarray MoGene 1.0 ST custom CDF file v.16 was used for probe annotation {Allan, 2005 #4379}.

source_name: C2 myotubes 24 hours C26 CM treatment

label_protocol: Whole-transcript expression profiling experiments were carried out by the Boston University Microarray Core Facility. The Affy standard WT Sense Target Labeling assay protocol was followed to synthesize biotinylated DNA.

growth_protocol: 3 day differentiated C2C12 myotubes

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen)

treatment_protocol: not treated (C) or treated (E) with 1/3 volume C26 conditioned medium in differentiation medium

value: cultured C2 myotubes

tag: agent

tag: time

value: 24 hrs


title: parafilm embedded tissue_normal adjacent_patient16

value: African American


title: parafilm embedded tissue_normal adjacent_patient17


title: C26CM 8 hour E

source_name: C2 myotubes 8 hours C26 CM treatment

value: 1/3 volume C26 conditioned medium in differentiation medium

value: 8 hrs


title: C26CM 24 hour C

source_name: C2 myotubes 24 hours no treatment

value: control


title: C26CM 4 hour E

source_name: C2 myotubes 4 hours C26 CM treatment

value: 4 hrs


title: LIF 24 hour E

source_name: C2 myotubes 24 hours LIF treatment

treatment_protocol: not treated (C) or treated (E) with 10 ng/ml mouse LIF

value: LIF


title: parafilm embedded tissue_tumor_patient16

value: Colon Cancer Tumor


title: C26CM 8 hour C

source_name: C2 myotubes 8 hours no treatment


title: M16_120DAH_2010

source_name: Apple 'M16' fruit flesh, 4 months of cold storage, 2010

value: Fruit

value: Parenchyma

value: Hybrid M16

value: Wild-type

value: Harvested at optimum maturity


title: M16_60DAH_2010

source_name: Apple 'M16' fruit flesh, 2 months of cold storage, 2010

value: Cold storage for 60 days after harvest


title: parafilm embedded tissue_tumor_patient17

value: SBU


title: C26CM 4 hour C

source_name: C2 myotubes 4 hours no treatment


title: LIF 24 hour C


title: M48_120DAH_2010

source_name: Apple 'M48' fruit flesh, 4 months of cold storage, 2010

value: Hybrid M48

value: Cold storage for 120 days after harvest


title: M48_60DAH_2010

source_name: Apple 'M48' fruit flesh, 2 months of cold storage, 2010


title: parafilm embedded tissue_normal adjacent_patient15

value: Colon Cancer Normal Adjacent


title: parafilm embedded tissue_tumor_patient15

value: African American


title: M16_Harvest_2010

source_name: Apple 'M16' fruit flesh, at harvest, 2010


title: M48_60DAH_2009

source_name: Apple 'M48' fruit flesh, 2 months of cold storage, 2009


title: M16_60DAH_2009

source_name: Apple 'M16' fruit flesh, 2 months of cold storage, 2009


title: LIF 8 hour E

source_name: C2 myotubes 8 hours LIF treatment

value: cultured C2 myotubes


title: parafilm embedded tissue_normal adjacent_patient14


title: parafilm embedded tissue_tumor_patient14


title: M48_Harvest_2010

source_name: Apple 'M48' fruit flesh, at harvest, 2010


title: M48_Harvest_2009

source_name: Apple 'M48' fruit flesh, at harvest, 2009


title: hanas-00078: B262

source_name: Brain

value: Primary Glioma

value: Grade 4

value: premortem

value: Brain

value: Astrocytoma

value: Adult


title: LIF 4 hour E

source_name: C2 myotubes 4 hours LIF treatment

value: LIF

value: 4 hrs


title: LIF 8 hour C

value: control

value: 8 hrs


title: M16_Harvest_2009

source_name: Apple 'M16' fruit flesh, at harvest, 2009

value: Fruit

value: Parenchyma

value: Hybrid M16

value: Wild-type

value: Harvested at optimum maturity


title: LIF 4 hour C


title: parafilm embedded tissue_normal adjacent_patient13

value: Colon Cancer Normal Adjacent

value: Caucasian

value: SBU


title: parafilm embedded tissue_tumor_patient13

value: Colon Cancer Tumor


title: parafilm embedded tissue_normal adjacent_patient12


title: M20_120DAH_2010

source_name: Apple 'M20' fruit flesh, 4 months of cold storage, 2010

value: Hybrid M20

value: Cold storage for 120 days after harvest


title: M74_120DAH_2010

source_name: Apple 'M74' fruit flesh, 4 months of cold storage, 2010

value: Hybrid M74


title: M20_120DAH_2009

source_name: Apple 'M20' fruit flesh, 4 months of cold storage, 2009


title: parafilm embedded tissue_tumor_patient12


title: parafilm embedded tissue_normal adjacent_patient11


title: parafilm embedded tissue_tumor_patient11


title: parafilm embedded tissue_tumor_patient10


title: parafilm embedded tissue_normal adjacent_patient10


title: hanas-00078: B265

value: Primary Glioma

value: Grade 1

value: premortem

value: Brain

value: Astrocytoma

value: Adult