title: Head_wild type_female_replicate2

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences

department: Biological Sciences

institute: Louisiana State University

description: Two different types of heterozygotes were prepared for breeding experiment: male and female heterozygotes carrying the paternally (+/-p) and maternally (-m/+) transmitted targeted allele.  These 4 heterozygotes were bred with their littermates: for Breeding 1, female wild-type littermates x male heterozygotes (+/-P); Breeding 2, female heterozygotes (+/-P) x male wild-type littermates; Breeding 3, female wild-type littermates x male heterozygotes (-m/+); for Breeding 4, female heterozygotes (-m/+) x male wild-type littermates.

hyb_protocol: 750ng labeled RNA was hybridized to MouseRef-8 v2 BeadChip arrays (Illumina) according to manufacturer’s protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6. Raw data were background-subtracted and normalized using the quantile normalization method (lumi software package). Normalized data were filtered for genes with significant expression levels compared to negative control beads.  Selection for differentially expressed genes was performed on the basis of arbitrary thresholds for fold changes plus statistical significance according to the Illumina t-test error model (limma software).  Pathway analyses were also performed with the EGAN (Explorative Gene Association Networks) package using up- and down-regulated gene sets.
Matrix normalized contains quantile normalized and background subtracted signal exported from GenomeStudio.  Matrix non-normalized contains background subtracted non-normalized data exported from GenomeStudio

source_name: Head_wild type_female

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

extract_protocol: Trizol isolated total RNA from each sample was treated with DNAse I and later purified with columns to remove any genomic contaminations (Qiagen, RNeasy Mini-kit).

treatment_protocol: A litter of 14.5-dpc fetuses were harvested from a timed mating between a male heterozygote (-m/+) and wild-type female littermate.  Three tissues were obtained from each fetus: embryo head, placenta and amnionic sac.  The DNA from amnionic sac was used for determining the genotype and gender of each fetus.

tag: gestational age

value: Head

value: wild type

value: female


title: 10WT1-KTS-0h-1

status: Public on Sep 11 2014

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek

label: biotin

molecule: total RNA

organism: Mus musculus

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: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: strain

tag: cell type

value: mouse embryonic fibroblasts

tag: genotype/variation

tag: time


title: Head_wild type_male_replicate1

source_name: Head_wild type_male

tag: tissue

tag: genotype

tag: gender

value: male


title: 7WT1+KTS-24h3-2


title: Normal ovarian stroma - sample 5

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from microdissected normal ovarian stroma

hyb_protocol: For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array.

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection.

data_processing: Microarray data analysis software, GeneSpring V.11.0.2 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.

label: Biotin

organism: Homo sapiens

source_name: Microdissected normal ovarian stroma

label_protocol: RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).

extract_protocol:
Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). Normal human ovarian surface epithelium (HOSE) specimens were obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).

value: Microdissected normal ovarian stroma


title: te_lbf1_01_rep2

city: Villeneuve d'Ascq

first: Chantreau

last: Maxime

state: Nord

address: Université de lille 1

country: France

institute: Université de Lille 1

description: b3 and b4 data come from the same sample

hyb_protocol: Following manufacture's instruction for One-Color Microarray base gene Expression Analysis (Agilent Technologies)

scan_protocol: Using an Axon GenePix 4000B scanner (Molecular Devices) piloted by GenePix Pro 6.0 software (Axon)

data_processing: After background noise elimination, medians values of overall hybridization were normalized by robust local regression (Yang et al., 2002). Artefact spots were manually eliminated. Differential analysis was performed with the method varmixt (Delmar et al., 2005) , available in the package anapuce of the software R. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance (Delmar et al., 2005). The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER) (Ge et al., 2003). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.05

organism: Linum usitatissimum

source_name: flax outer stem tissues

growth_protocol: plants were grown under field conditions at the University of Lille, France

extract_protocol: Total RNA was extracted from peeled outer tissues using the TriReagent (Molecular Research Center) method

tag: developmental stage

value: vegetative

tag: cultivar

value: Diane

value: EMS mutant from family lbf1


title: te_lbf1_03

label_protocol: Following manufacture's instruction for One-Color Microarray base gene Expression Analysis (Agilent Technologies)


title: te_lbf_05


title: Head_knockout_male_replicate3

value: Peg3 knockout


title: te_lbf1_02


title: Head_knockout_male_replicate2


title: te_wt_03_rep1

description: b1 and b2 data come from the same sample

value: wild-type


title: 1WT1+KTS-0h1-3


title: 1WT1+KTS-0h1-1


title: Head_knockout_female_replicate1


title: Head_knockout_female_replicate2


title: 1WT1+KTS-0h1-2


title: te_lbf1_01_rep1


title: Head_knockout_male_replicate1


title: te_wt_03_rep2


title: ti_lbf_06

source_name: flax inner stem tissues

extract_protocol: Total RNA was extracted from peeled inner tissues using the TriReagent (Molecular Research Center) method


title: te_wt_02


title: Placenta_knockout_male_replicate3

value: Placenta


title: ti_lbf_05


title: Head_wild type_female_replicate1


title: Placenta_wild type_male_replicate1

source_name: Placenta_wild type_male


title: Placenta_knockout_female_replicate2


title: Placenta_wild type_female_replicate2

source_name: Placenta_wild type_female


title: Placenta_knockout_male_replicate1


title: ti_lbf1_01_rep2

description: b15 and b16 data come from the same sample


title: te_wt_01


title: ti_lbf1_03


title: Placenta_knockout_male_replicate2


title: te_lbf_06


title: Placenta_knockout_female_replicate1


title: ti_lbf1_02


title: Placenta_wild type_female_replicate1


title: ti_lbf1_01_rep1


title: ti_wt_03_rep2

description: b25 and b26 data come from the same sample


title: ti_lbf1_04


title: 7WT1+KTS-24h3-1


title: ti_wt_03_rep1


title: Control_9

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
control
XP9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data extracted with Illumina Inc. BeadStudio version 3.2.3 without normalization, then processed in R using the lumi package with lumiExpresso and nuID annotation

source_name: Littermate Control

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

extract_protocol: Total RNA was extracted from fresh spleen using Trizol reagent

treatment_protocol: TRAF3flox/flox-CD19+/cre (B-TRAF3-/-) and TRAF3flox/flox (littermate control) mice were generated as described previously (Xie et al., 2007, Immunity 27:253)

value: Spleen

value: TRAF3flox/flox (littermate control)


title: Control_7

description:
control
XP7


title: ti_wt_02


title: Control_5

description:
control
XP5


title: ti_wt_01


title: SD ZT20 at day 10, Vasculature

status: Public on Sep 10 2014

city: Kyoto

first: Motomu

last: Endo

state: Kyoto

address: Sakyo-Ku, Yoshida-Konoe-Cho

department: Biostudies

country: Japan

institute: Kyoto University

description: Isolated vasculature

hyb_protocol: 150 ng of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Normalized expression values were calculated from probe level data (CEL file) using the function of Robust Multi-Array expression measure using sequence information GC-RMA (Wu et al 2004, www.bepress.com/jhubiostat/paper4).Computational steps were implemented in the R-language. GCRMA and it's associated packages were provided by the open source bioconductor project.
probe group file: AraGene-1_0-st.pgf
meta-probeset file: AraGene-1_0-st.mps

organism: Arabidopsis thaliana

source_name: Short day, Vasculature, time 44

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Plants were grown on Murashige and Skoog medium with 0.5% sucrose for nine days. Long day (16 hr light, 8 hr dark) and short day (8 hr light, 16 hr dark) contidions were tested.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN)l, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Using enzymes and sonication treatment, mesophyll and vasculature were isolated within half an hour in each time point.

value: 10-day-old seedlings

tag: growth condition

value: Short day

value: Vasculature


title: SD ZT8 at day 10, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 32


title: SD ZT0 at day 10, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 24


title: SD ZT12 at day 10, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 36


title: Control_6

description:
control
XP6


title: SD ZT4 at day 10, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 28


title: SD ZT16 at day 10, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 40


title: B_lymphoma_3

description:
lymphoma
XP3

source_name: TRAF3 deleted

value: TRAF3flox/flox-CD19+/cre (B-TRAF3-/-)


title: SD ZT20 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 20

value: 9-day-old seedlings


title: B_lymphoma_1

description:
lymphoma
XP1


title: SD ZT12 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 12


title: SD ZT8 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 32

value: Mesopyll


title: SD ZT16 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 40


title: SD ZT12 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 36


title: SD ZT0 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 0


title: SD ZT4 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 4


title: SD ZT16 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 16


title: SD ZT20 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 20


title: SD ZT8 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 8


title: SD ZT4 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 4


title: SD ZT12 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 12


title: SD ZT16 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 40

value: Whole leaf


title: SD ZT4 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 28


title: SD ZT8 at day 9, Vasculature

description: Isolated vasculature

source_name: Short day, Vasculature, time 8


title: B_lymphoma_2

description:
lymphoma
XP2


title: SD ZT16 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 16


title: SD ZT20 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 20


title: SD ZT0 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 24


title: SD ZT12 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 36


title: SD ZT20 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 44


title: SD ZT8 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 32


title: SD ZT0 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 24


title: SD ZT4 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 28


title: LD ZT20 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 44

value: Long day


title: SD ZT0 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Short day, Mesophyll, time 0


title: LD ZT4 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 4


title: SD ZT0 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 0


title: SD ZT8 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 8


title: LD ZT8 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 32


title: SD ZT20 at day 10, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 44


title: SD ZT4 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 4


title: LD ZT12 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 36


title: LD ZT12 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 36


title: LD ZT16 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 40


title: LD ZT16 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 40


title: LD ZT4 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 28


title: LD ZT12 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 12


title: LD ZT0 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 24


title: LD ZT4 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 28


title: LD ZT0 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 0


title: LD ZT16 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 16


title: LD ZT12 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 12


title: LD ZT0 at day 10, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 24


title: LD ZT8 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 8


title: LD ZT20 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 20


title: LD ZT8 at day 9, Vasculature

description: Isolated vasculature

source_name: Long day, Vasculature, time 8


title: SLCL, 6, (rep2)

city: Stanford

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

description:
Test SLCL
SLCL6

data_processing: The resulting Ct values (Matrix non-normalized) were normalized first to the median Ct value of the individual array (Matrix normalized) and then to the DCt of the miRNA from the control samples, to produce the DDCt (Fold Change).  All are divided by the control (BCELL).

label: FAM

source_name: PTLD Patient-derived SLCL

growth_protocol: SLCLs and LCLs were maintained in complete media consisting of RPMI 1640 (Fisher Scientific of Life Technologies, Foster City, CA) supplemented with 10% fetal calf serum and 1% penicillin/streptomycin and incubated at 37*C.

extract_protocol: Total RNA was extracted using TRIzol reagent.

treatment_protocol: Purified human B cells were isolated by negative selection from PBMC using the human B Cell Isolation Kit II, human (MACS, Miltenyi Biotec, San Diego, CA) according to manufacturer’s recommendations. SLCL and LCL lines were treated as follows: cells were washed, resuspended at a concentration of 5x106/mL in complete media consisting of RPMI 1640 (Fisher Scientific of Life Technologies, Foster City, CA) supplemented with 10% fetal calf serum and 1% penicillin/streptomycin and incubated at 37*C.  After one hour, complete media was added to achieve a final concentration of 0.5x106 cells/mL. Cells were then placed in a 37oC CO2 incubator for 12 hours before collection by centrifugation and lysis in TRIzol  Reagent (Life Technologies, Foster City, CA) for isolation of total RNA.

value: unknown

value: EBV+ B cell lymphoma


title: SLCL, 6, (rep1)

description:
Test SLCL
SLCL6


title: SLCL, 5, (rep1)

description:
Test SLCL
SLCL5


title: LD ZT20 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 44


title: LD ZT4 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 4


title: SLCL, 3, (rep2)

description:
Test SLCL
SLCL3


title: SLCL, 4, (rep1)

description:
Test SLCL
SLCL4


title: LD ZT8 at day 10, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 32


title: SLCL, 3, (rep1)

description:
Test SLCL
SLCL3


title: LD ZT12 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 36


title: LD ZT4 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 28


title: LD ZT20 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 20


title: LD ZT8 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 8


title: LD ZT20 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 44


title: LD ZT0 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 24


title: LD ZT8 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 32


title: LD ZT16 at day 10, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 40


title: LD ZT0 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 0


title: LD ZT20 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 20


title: SLCL, 5, (rep2)

description:
Test SLCL
SLCL5


title: LD ZT16 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 16


title: SLCL, 4, (rep2)

description:
Test SLCL
SLCL4


title: LD ZT4 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 4


title: LD ZT16 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 16


title: LCL, 4, (rep2)

description:
Test LCL
LCL4

source_name: EBV.B95.8 Transformed LCL

value: male

value: EBV.B95.8 transformed B cell


title: SLCL, 2, (rep1)

description:
Test SLCL
SLCL2

source_name: PTLD Patient-derived SLCL


title: LCL, 4, (rep1)

description:
Test LCL
LCL4


title: SLCL, 1, (rep2)

description:
Test SLCL
SLCL1


title: SLCL, 1, (rep1)

description:
Test SLCL
SLCL1


title: LD ZT12 at day 9, Whole leaf

description: Whole cotyledons

source_name: Long day, Whole leaf, time 12


title: LCL, 3, (rep2)

description:
Test LCL
LCL3

value: female


title: LCL, 2, (rep1)

description:
Test LCL
LCL2


title: SLCL, 2, (rep2)

description:
Test SLCL
SLCL2


title: LCL, 1, (rep2)

description:
Test LCL
LCL1


title: LCL, 1, (rep1)

description:
Test LCL
LCL1


title: LD ZT0 at day 9, Mesophyll

description: Isolated mesophyll

source_name: Long day, Mesophyll, time 0


title: B Cell, 3, (rep2)

description:
Control
BCELL3

source_name: Total purified CD19+ B Cell

value: B cell


title: B Cell, 3, (rep1)

description:
Control
BCELL3


title: B Cell, 2, (rep2)

description:
Control
BCELL2


title: B Cell, 4, (rep2)

description:
Control
BCELL4


title: B Cell, 2, (rep1)

description:
Control
BCELL2


title: B Cell, 1, (rep1)

description:
Control
BCELL1


title: B Cell, 1, (rep2)

description:
Control
BCELL1


title: B Cell, 4, (rep1)

description:
Control
BCELL4


title: LCL, 3, (rep1)

description:
Test LCL
LCL3


title: LCL, 2, (rep2)

description:
Test LCL
LCL2


title: PT_CRC07

city: Madrid

first: Manuel

last: Hidalgo

state: Madrid

address: C/Melchor Fernandez Almagro 3

department: Clinical Research Programme

country: Spain

institute: CNIO

description: Gene expression data from human colorectal tumor

hyb_protocol: Following fragmentation, cRNA was hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array.

data_processing: The data were analyzed with frozenRMA (fRMA) using rma and quantile as background correction and normalization methods.

source_name: Human colorectal tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Extraction of total RNA was performed by using Qiagen mini- RNA kit according to the manufacturer's instructions.

value: Human colorectal tumor


title: 101787-2

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description: microRNA expression

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

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

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

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from buffy coat was extracted by TRI Reagent lysis reagent (Ambion) according to manufacturer's instructions.

value: blood (buffy coat)

tag: cod er (receptor

value: 1=positive 2=negative 9=unknown):NaN

tag: cod pr (receptor

tag: cod her2 (receptor

tag: bmi

tag: birth

tag: age menarche

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )

tag: set (id matched samples)

tag: array id


title: 101599-2

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod er (receptor

value: 1=positive 2=negative 9=unknown):1

tag: cod pr (receptor

tag: cod her2 (receptor

value: 1=positive 2=negative 9=unknown):0


title: 101599

description: microRNA expression

tag: bmi

tag: birth

tag: age menarche

tag: age menopause

tag: mother bc


title: 101957

description: microRNA expression

tag: sister with bc

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1


title: 101957-2

description: microRNA expression

tag: total testosterone

tag: free testosterone

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )

tag: set (id matched samples)


title: PT_CRC08

tag: tissue


title: PT_CRC06


title: 101787

description: microRNA expression

tag: cod er (receptor

tag: cod pr (receptor

tag: cod her2 (receptor

tag: array id


title: PT_CRC04


title: PT_CRC11


title: PT_CRC09


title: PT_CRC01


title: 204955

description: microRNA expression

tag: bmi

tag: birth

tag: age menarche

tag: age menopause


title: 201745

description: microRNA expression

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: insulin


title: 100502

description: microRNA expression

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: PT_CRC10

tag: tissue


title: 101661

description: microRNA expression

tag: cod er (receptor

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )

tag: set (id matched samples)


title: 200217

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: cod her2 (receptor

tag: bmi

tag: array id


title: PT_CRC05


title: Cell-free saliva from donor 3

city: los angeles

first: jieping

last: yang

address: 10833 Le Conte Ave

institute: UCLA

description: ABU A

hyb_protocol: according to the Affymetrix standard protocols

data_processing: affymetrix Human genome U133 Plus 2.0 arrays were performed by UCLA clinical microarray core.

source_name: Cell-free saliva from donor 3

extract_protocol:
exosomes were isolated from cell-free saliva using Exoquick precipitation solution (System Biosciences Inc).
RNA was extracted from these processed samples using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: cell type

value: cell-free saliva


title: Cell-free saliva from donor 2

description: JPA

scan_protocol: according to the Affymetrix standard protocols

source_name: Cell-free saliva from donor 2


title: SD ZT16 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 16

tag: developmental stage

tag: growth condition

value: Short day

tag: time


title: exosomes from cell-free saliva donor 3

description: ABU C

source_name: exosomes from cell-free saliva donor 3

label_protocol: according to the Affymetrix standard protocols

value: exosomes from cell-free saliva


title: exosomes from cell-free saliva donor 1

description: JP 6

source_name: exosomes from cell-free saliva donor 1


title: exosomes from cell-free saliva donor 2

description: JPC

source_name: exosomes from cell-free saliva donor 2


title: PT_CRC02


title: 104828

description: microRNA expression

tag: birth

tag: age menarche

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1


title: 101872

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod er (receptor

tag: cod pr (receptor

tag: total testosterone

tag: free testosterone

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )

tag: set (id matched samples)


title: 101796

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: birth

tag: age menarche

tag: array id


title: 102116

description: microRNA expression

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: insulin


title: 101583

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: sex hormone binding protein

tag: insulin growth factor 1


title: 101528

description: microRNA expression

tag: cod pr (receptor

tag: total testosterone

tag: free testosterone

tag: menopausal state (post=1\pre=0)


title: 104330

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: bmi

tag: type (case=1\contr=0 )

tag: set (id matched samples)


title: 200534

description: microRNA expression

tag: birth

tag: age menarche

tag: age menopause

tag: mother bc

tag: array id


title: 201524

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: sister with bc

tag: age 1 b

tag: insulin


title: 101856

description: microRNA expression

tag: cod pr (receptor

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: 200095

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 101823

description: microRNA expression

tag: diagnosis date

tag: birth

tag: age menarche

tag: age menopause

tag: set (id matched samples)


title: 202291

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: mother bc

tag: sister with bc

tag: array id


title: 101617

description: microRNA expression

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1


title: 101673

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: total testosterone

tag: free testosterone

tag: menopausal state (post=1\pre=0)


title: 102046

description: microRNA expression

tag: diagnosis date

value: 1=positive 2=negative 9=unknown):9

tag: birth

tag: age menarche

tag: age menopause

tag: type (case=1\contr=0 )


title: 101706

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: mother bc

tag: sister with bc

tag: set (id matched samples)


title: 202837

description: microRNA expression

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: array id


title: 201958

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: SD ZT12 at day 9, Whole leaf

description: Whole cotyledons

source_name: Short day, Whole leaf, time 12

tag: developmental stage

value: 9-day-old seedlings

tag: growth condition

value: Whole leaf

tag: time


title: Cell-free saliva from donor 1

description: JY

source_name: Cell-free saliva from donor 1

tag: cell type


title: 203830

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: mother bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 104728

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: bmi

tag: sister with bc

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: set (id matched samples)

tag: array id


title: 105637

description: microRNA expression

tag: tissue

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: 204496

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause


title: 202389

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: mother bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 104804

description: microRNA expression

tag: bmi

tag: sister with bc

tag: age 1 b

tag: insulin

tag: sex hormone binding protein


title: 203407

description: microRNA expression

tag: tissue

tag: insulin growth factor 1

tag: total testosterone

tag: set (id matched samples)

tag: array id


title: 103765

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: free testosterone


title: 203651

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: mother bc


title: 203687

description: microRNA expression

tag: bmi

tag: sister with bc

tag: age 1 b

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 204681

description: microRNA expression

tag: tissue

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone


title: 202369

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: set (id matched samples)

tag: array id


title: 202956

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: free testosterone


title: 202787

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: menopausal state (post=1\pre=0)


title: 202670

description: microRNA expression

tag: tissue

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: type (case=1\contr=0 )


title: 204357

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: total testosterone

tag: set (id matched samples)


title: 204297

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: array id


title: 105715

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: free testosterone


title: 104889

description: microRNA expression

tag: tissue

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: menopausal state (post=1\pre=0)


title: 202683

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: total testosterone

tag: type (case=1\contr=0 )


title: 103829

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: set (id matched samples)


title: 203519

description: microRNA expression

tag: diagnosis date

tag: bmi

tag: mother bc

tag: sister with bc

tag: array id


title: 205250

description: microRNA expression

tag: tissue

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: free testosterone


title: 203079

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: insulin growth factor 1

tag: menopausal state (post=1\pre=0)


title: 203388

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: total testosterone

tag: type (case=1\contr=0 )


title: 104464

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: set (id matched samples)


title: 204421

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: age 1 b

tag: insulin

tag: array id


title: 202273

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: free testosterone


title: 202231

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: insulin growth factor 1

tag: menopausal state (post=1\pre=0)


title: PT_CRC03


title: 104601

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: total testosterone

tag: type (case=1\contr=0 )


title: 202694

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: age 1 b

tag: insulin

tag: set (id matched samples)


title: 104362

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: array id


title: 105291

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: insulin growth factor 1

tag: free testosterone


title: 201117

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 204247

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: age 1 b

tag: insulin

tag: type (case=1\contr=0 )


title: 105336

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: set (id matched samples)


title: 201250

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: insulin growth factor 1

tag: array id


title: 202362

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: total testosterone

tag: free testosterone


title: 204163

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)


title: 202825

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: type (case=1\contr=0 )


title: 202715

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: age menopause

tag: insulin growth factor 1

tag: set (id matched samples)


title: 103450

description: microRNA expression

tag: bmi

tag: mother bc

tag: sister with bc

tag: total testosterone

tag: array id


title: 105112

description: microRNA expression

tag: tissue

tag: age 1 b

tag: insulin

tag: free testosterone


title: 103672

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: menopausal state (post=1\pre=0)


title: 204046

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: cod her2 (receptor

tag: sex hormone binding protein

tag: type (case=1\contr=0 )


title: 202793

description: microRNA expression

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin growth factor 1

tag: set (id matched samples)


title: 104144

description: microRNA expression

tag: tissue

tag: sister with bc

tag: age 1 b

tag: total testosterone

tag: array id


title: 205061

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: insulin

tag: free testosterone


title: 104741

description: microRNA expression

tag: cod pr (receptor

tag: cod her2 (receptor

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 104672

description: microRNA expression

tag: bmi

tag: age menopause

tag: mother bc

tag: type (case=1\contr=0 )


title: 105499

description: microRNA expression

tag: tissue

tag: sister with bc

tag: insulin growth factor 1

tag: set (id matched samples)


title: 205100

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: age 1 b

tag: total testosterone

tag: array id


title: 202495

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: insulin

tag: free testosterone


title: 102977

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 103294

description: microRNA expression

tag: tissue

tag: mother bc

tag: sister with bc

tag: insulin growth factor 1

tag: type (case=1\contr=0 )


title: 102978

description: microRNA expression

tag: cod er (receptor

tag: age 1 b

tag: total testosterone

tag: set (id matched samples)


title: 205192

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: array id


title: 102755

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: insulin

tag: free testosterone


title: 101869

description: microRNA expression

tag: tissue

tag: mother bc

tag: sister with bc

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 200924

description: microRNA expression

tag: cod er (receptor

tag: age 1 b

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: 200994

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: set (id matched samples)


title: 200676

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: insulin

tag: array id


title: 200632

description: microRNA expression

tag: tissue

tag: mother bc

tag: sister with bc

tag: sex hormone binding protein

tag: free testosterone


title: 201158

description: microRNA expression

tag: cod er (receptor

tag: age 1 b

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 103127

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: type (case=1\contr=0 )


title: 103231

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: set (id matched samples)


title: 102696

description: microRNA expression

tag: tissue

tag: mother bc

tag: insulin

tag: array id


title: 102518

description: microRNA expression

tag: cod er (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: free testosterone


title: 102495

description: microRNA expression

tag: age 1 b

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 102189

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: type (case=1\contr=0 )


title: 102767

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: set (id matched samples)


title: 102279

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: mother bc

tag: insulin

tag: array id


title: 101799

description: microRNA expression

tag: cod er (receptor

tag: sister with bc

tag: age 1 b

tag: sex hormone binding protein

tag: free testosterone


title: 102976

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 201739

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: type (case=1\contr=0 )


title: 101522

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: mother bc

tag: insulin

tag: set (id matched samples)


title: 102296

description: microRNA expression

tag: cod er (receptor

tag: sister with bc

tag: age 1 b

tag: sex hormone binding protein

tag: array id


title: 101794

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: 101767

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: menopausal state (post=1\pre=0)


title: 103292

description: microRNA expression

tag: tissue

tag: mother bc

tag: insulin

tag: type (case=1\contr=0 )


title: 102687

description: microRNA expression

tag: cod er (receptor

tag: sister with bc

tag: age 1 b

tag: set (id matched samples)


title: 103774

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: sex hormone binding protein

tag: array id


title: 200160

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: insulin growth factor 1

tag: total testosterone

tag: free testosterone


title: 103726

description: microRNA expression

tag: tissue

tag: bmi

tag: age menarche

tag: age menopause

tag: menopausal state (post=1\pre=0)


title: 103722

description: microRNA expression

tag: cod er (receptor

tag: mother bc

tag: sister with bc

tag: insulin

tag: type (case=1\contr=0 )


title: 106081

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age 1 b

tag: sex hormone binding protein

tag: set (id matched samples)


title: 201152

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: 106025

description: microRNA expression

tag: tissue

tag: bmi

tag: age menarche

tag: age menopause

tag: free testosterone


title: 105754

description: microRNA expression

tag: cod er (receptor

tag: mother bc

tag: sister with bc

tag: insulin

tag: menopausal state (post=1\pre=0)


title: 106007

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age 1 b

tag: sex hormone binding protein

tag: type (case=1\contr=0 )


title: 205153

description: microRNA expression

tag: cod her2 (receptor

tag: insulin growth factor 1

tag: total testosterone

tag: set (id matched samples)


title: 105219

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: bmi

tag: age menarche

tag: array id


title: 105580

description: microRNA expression

tag: cod er (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: free testosterone


title: 104038

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)


title: 105131

description: microRNA expression

tag: cod her2 (receptor

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: 104699

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: bmi

tag: age menarche

tag: set (id matched samples)


title: 104779

description: microRNA expression

tag: cod er (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: array id


title: 105053

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: free testosterone


title: 103846

description: microRNA expression

tag: cod her2 (receptor

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 104587

description: microRNA expression

tag: tissue

tag: bmi

tag: age menarche

tag: type (case=1\contr=0 )


title: 102964

description: microRNA expression

tag: cod er (receptor

tag: age menopause

tag: mother bc

tag: set (id matched samples)


title: 201006

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: sister with bc

tag: array id


title: 201168

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: age 1 b

tag: insulin

tag: free testosterone


title: 200074

description: microRNA expression

tag: tissue

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 104130

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: type (case=1\contr=0 )


title: 104246

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: mother bc

tag: sister with bc

tag: set (id matched samples)


title: 103796

description: microRNA expression

tag: cod her2 (receptor

tag: age 1 b

tag: insulin

tag: array id


title: 200598

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: free testosterone


title: 102616

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 102607

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age menopause

tag: mother bc

tag: type (case=1\contr=0 )


title: 101558

description: microRNA expression

tag: cod her2 (receptor

tag: sister with bc

tag: age 1 b

tag: insulin

tag: set (id matched samples)


title: 103791

description: microRNA expression

tag: tissue

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: 101949

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: free testosterone


title: 201760

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 101506

description: microRNA expression

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: type (case=1\contr=0 )


title: 103966

description: microRNA expression

tag: tissue

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: set (id matched samples)


title: 200467

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: insulin growth factor 1

tag: array id


title: 200890

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: total testosterone

tag: free testosterone


title: 101437

description: microRNA expression

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: menopausal state (post=1\pre=0)


title: 201327

description: microRNA expression

tag: tissue

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: type (case=1\contr=0 )


title: 201922

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: insulin growth factor 1

tag: set (id matched samples)


title: 201595

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: total testosterone

tag: array id


title: 102088

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: free testosterone


title: 103165

description: microRNA expression

tag: tissue

tag: sister with bc

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)


title: 101739

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: sex hormone binding protein

tag: type (case=1\contr=0 )


title: 102961

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: insulin growth factor 1

tag: total testosterone

tag: set (id matched samples)


title: 102545

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: array id


title: 102660

description: microRNA expression

tag: tissue

tag: sister with bc

tag: age 1 b

tag: insulin

tag: free testosterone


title: 102640

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age menarche

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 106072

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: 105950

description: microRNA expression

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: set (id matched samples)


title: 101961

description: microRNA expression

tag: tissue

tag: sister with bc

tag: age 1 b

tag: array id


title: 101586

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: insulin

tag: free testosterone


title: 101863

description: microRNA expression

tag: cod pr (receptor

tag: age menarche

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 105378

description: microRNA expression

tag: diagnosis date

tag: birth

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: JB13_control rep6 [re-analysis]

city: Pittsburgh

first: Teresa

last: Buck

state: PA

address: 4200 5th Ave

institute: University of Pittsburgh

hyb_protocol: The fragmented RNA (15 μg) was added to a final volume of 300 ml in a hybridization cocktail: hybridization buffer, which contains 100 mM MES, 1M NaCl, 20 mM EDTA, 0.01% Tween 20, and 100 mg/ml herring sperm DNA, 50 mg/ml acetylated BSA, 50 pM Affymetrix Control Oligo B2, and an Affymetrix Eukaryotic Hybridization Control.  An appropriate volume of this sample was applied to the Yeast Genome 2.0 GeneChip® Array and the chips were incubated overnight at 45oC with rotation.  Following hybridization the sample was removed and the GeneChip cassette was filled with non-stringent wash buffer.  The chip was loaded onto an Affymetrix 450 Fluidics station for washing and staining. The wash and stain protocols were the double-stain protocols developed by Affymetrix for use with the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned with GeneArray® 3000 scanner

data_processing: Efficiency Analysis (Jordan et al., 2008, Cancer Informatics) was used to optimize normalization, transformation, and feature selection methods as well as to determine threshold. The J5 test with mean normalization was used to determine differentially expressed genes.

organism: Saccharomyces cerevisiae

source_name: vector control

label_protocol: Labeled cRNA was prepared using the 3’IVT Express kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: All strains were grown at 26 degrees in selective media to mid log phase.

extract_protocol: RNA was extracted using the hot phenol method followed by further cleanup using Qiagen Rneasy midi column.

tag: genotype/variation

value: containing a vector, pRSGPD426


title: 104454

description: microRNA expression

tag: tissue

tag: cod her2 (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: set (id matched samples)


title: JB12_control rep5 [re-analysis]


title: 104962

description: microRNA expression

tag: cod er (receptor

tag: bmi

tag: age 1 b

tag: insulin

tag: free testosterone

tag: array id


title: JB11_120210_control rep1 [re-analysis]

data_processing: Efficiency Analysis (Jordan et al., 2008, Cancer Informatics) was used to optimize normalization, transformation, and feature selection methods as well as to determine threshold. The J5 test with Z-transformation was used to determine differentially expressed genes.


title: JB17_120210 rep3

source_name: expressing Kir2.1

value: expressing Kir2.1 (pRS416TEF-Kir2.1-HA)


title: 104437

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: JB14_120210_control rep4 [re-analysis]

tag: genotype/variation


title: JB14_control rep7 [re-analysis]


title: 101759

description: microRNA expression

tag: tissue

tag: cod her2 (receptor

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: JB18_120210 rep4


title: JB12_120210_control rep2 [re-analysis]


title: JB15_120210 rep1


title: JB11_control rep4 [re-analysis]


title: 103790

description: microRNA expression

tag: cod er (receptor

tag: age menopause

tag: mother bc

tag: sister with bc

tag: set (id matched samples)


title: JB13_120210_control rep3 [re-analysis]


title: 103870

description: microRNA expression

tag: bmi

tag: age 1 b

tag: insulin

tag: free testosterone

tag: array id


title: 200182

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: age menarche

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: JB5_control rep3 [re-analysis]

tag: genotype/variation


title: JB16_120210 rep2


title: JB7_CFTR

source_name: expressing CFTR

value: expressing CFTR (pRS426PPGK-CFTR-3HA)


title: JB9_CFTR


title: JB03_control rep1 [re-analysis]


title: 201287

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: cod her2 (receptor

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: JB04_control rep2 [re-analysis]


title: 200309

description: microRNA expression

tag: bmi

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: set (id matched samples)


title: JB8_CFTR


title: JB14_control rep7


title: 201905

description: microRNA expression

tag: diagnosis date

tag: cod pr (receptor

tag: birth

tag: insulin

tag: free testosterone

tag: array id


title: 200126

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: age menarche

tag: sex hormone binding protein

tag: menopausal state (post=1\pre=0)


title: 201344

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: insulin growth factor 1

tag: total testosterone

tag: type (case=1\contr=0 )


title: 201867

description: microRNA expression

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: set (id matched samples)


title: 102861

description: microRNA expression

tag: cod pr (receptor

tag: birth

tag: insulin

tag: free testosterone


title: JB11_control rep4

tag: genotype/variation


title: JB10_CFTR


title: JB03_control rep1


title: 102650

description: microRNA expression

tag: tissue

tag: cod er (receptor

tag: age menarche

tag: sex hormone binding protein

tag: array id


title: 102552

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 102064

description: microRNA expression

tag: diagnosis date

tag: age menopause

tag: mother bc

tag: sister with bc

tag: age 1 b

tag: type (case=1\contr=0 )


title: JB13_control rep6

tag: genotype/variation


title: JB6_aENaC rep3

source_name: expressing αENaC

value: expressing αENaC (prs426GPD-αENaC-HA)


title: JB12_control rep5


title: JB04_control rep2


title: 102256

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: birth

tag: insulin

tag: free testosterone

tag: set (id matched samples)


title: JB02_aENaC rep2


title: JB01_aENaC rep1


title: 102199

description: microRNA expression

tag: cod er (receptor

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: sex hormone binding protein

tag: array id


title: 101947

description: microRNA expression

tag: diagnosis date

tag: age menopause

tag: mother bc

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 201118

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: age 1 b

tag: type (case=1\contr=0 )


title: 102149

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: insulin

tag: free testosterone

tag: set (id matched samples)


title: 101725

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: sex hormone binding protein

tag: array id


title: JB5_control rep3

tag: genotype/variation


title: 102373

description: microRNA expression

tag: age menopause

tag: mother bc

tag: insulin growth factor 1

tag: total testosterone

tag: menopausal state (post=1\pre=0)


title: 101625

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: age 1 b

tag: type (case=1\contr=0 )


title: 101637

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: insulin

tag: free testosterone

tag: set (id matched samples)


title: 101548

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: sex hormone binding protein

tag: array id


title: 102946

description: microRNA expression

tag: age menopause

tag: mother bc

tag: insulin growth factor 1

tag: total testosterone


title: 202004

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: sister with bc

tag: menopausal state (post=1\pre=0)


title: 101752

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: type (case=1\contr=0 )


title: 103593

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: free testosterone

tag: set (id matched samples)


title: 103884

description: microRNA expression

tag: age menopause

tag: mother bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: 103825

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: total testosterone


title: Eµ-myc Lymphoma Test D31

city: Durham

first: Daphne

middle: R

last: Friedman

state: NC

address: 101 Science Drive, Room 2121, CIEMAS Bldg

institute: Duke University Medical Center

description: Gene expression data from mouse Myc-induced lymphoma

hyb_protocol: The cRNA was fragmented and mixed into a hybridization cocktail before application to the array, which was then hybridized for 16 hours at 45C with rotation at 60 rpm.  This was performed at the Duke University DNA Microarray Core Facility.

scan_protocol: Immediately following hybridization, the arrays underwent an automated washing and staining protocol on the GeneChip FS450 fluidics station and were then scanned on the GeneChip Scanner 3000 7G Plus.  This was performed at the Duke University DNA Microarray Core Facility.

data_processing: The data were analyzed with RMA normalization using the standard settings in the affy package from Bioconductor using R.

source_name: Lymphoma

label_protocol: Target preparation from total RNA was performed using T7 primers in the cDNA synthesis step, followed by in vitro transcription to produce biotin-labeled cRNA. This was performed at the Duke University DNA Microarray Core Facility.

extract_protocol: Lymphoma tissue was homogenized with a mortar and pestle and with sonication.  Lymphoma cells were homogenized with a needle and syringe, Lysing Matrix A tube for tissue (MP Biomedicals), and/or QIAshredder homogenizer column (Qiagen).  RNA was extracted using the Rneasy Mini Kit (Qiagen).

tag: genotype/variation

value: Eµ-myc

tag: tissue type

value: lymphoma tumor


title: 103510

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: Eµ-myc Lymphoma Test D20


title: 106023

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Test D26


title: Eµ-myc Lymphoma Test D30


title: 201810

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: mother bc

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: 200009

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: total testosterone


title: Eµ-myc Lymphoma Test D27

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Test D29


title: Eµ-myc Lymphoma Test D32


title: Eµ-myc Lymphoma Test D24


title: Eµ-myc Lymphoma Test D17


title: Eµ-myc Lymphoma Test D23


title: Eµ-myc Lymphoma Test D9


title: Eµ-myc Lymphoma Test D16


title: 103839

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: Eµ-myc Lymphoma Test D21


title: Eµ-myc Lymphoma Test D18


title: Eµ-myc Lymphoma Test D28


title: 105875

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: mother bc

tag: sister with bc

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Test D25


title: 105851

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: Eµ-myc Lymphoma Test D22

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Test D19


title: 105114

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: total testosterone

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 104642

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: mother bc

tag: sister with bc

tag: free testosterone

tag: set (id matched samples)


title: 104576

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: 104396

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: total testosterone


title: 104555

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: Eµ-myc Lymphoma Test D14

tag: genotype/variation

tag: tissue type


title: 103780

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: mother bc

tag: sister with bc

tag: free testosterone

tag: set (id matched samples)


title: 104155

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: Eµ-myc Lymphoma Test D12


title: 200195

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: age menarche

tag: age menopause

tag: total testosterone

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 200562

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: mother bc

tag: sister with bc


title: Eµ-myc Lymphoma Test D11

tag: genotype/variation

tag: tissue type


title: 201209

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Test D13


title: 103391

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: age menarche

tag: age menopause

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: 201740

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: mother bc

tag: sister with bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: Eµ-myc Lymphoma Test D15

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Test D8


title: Eµ-myc Lymphoma Test D7


title: 103693

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: 103957

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: age menarche

tag: age menopause

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Test D2


title: Eµ-myc Lymphoma Train 37

hyb_protocol: The cRNA was fragmented and mixed into a hybridization cocktail before application to the array, which was then hybridized for 16 hours at 45C with rotation at 60 rpm.

scan_protocol: Immediately following hybridization, the arrays underwent an automated washing and staining protocol on the GeneChip FS450 fluidics station and were then scanned on the GeneChip Scanner 3000 7G Plus.

label_protocol: Target preparation from total RNA was performed using T7 primers in the cDNA synthesis step, followed by in vitro transcription to produce biotin-labeled cRNA.

extract_protocol: Lymphoma tissue was homogenized with a mortar and pestle and with sonication.  RNA was extracted using the Rneasy Mini Kit (Qiagen)


title: Eµ-myc Lymphoma Test D1


title: Eµ-myc Lymphoma Test D6


title: Eµ-myc Lymphoma Train 36


title: 103252

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: mother bc

tag: sister with bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: Eµ-myc Lymphoma Train 38

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 39


title: Eµ-myc Lymphoma Test D5


title: 103234

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: 103280

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: age menarche

tag: age menopause

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: 103245

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: mother bc

tag: sister with bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 103160

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: bmi

tag: age 1 b

tag: insulin


title: 103008

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Test D10

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Test D3


title: 101762

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: 103081

description: microRNA expression

tag: diagnosis date

tag: cod her2 (receptor

tag: bmi

tag: mother bc

tag: sister with bc

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 102726

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: 102865

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: insulin growth factor 1


title: Eµ-myc Lymphoma Train 35

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 34


title: Eµ-myc Lymphoma Train 30


title: 101719

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: mother bc

tag: sister with bc

tag: total testosterone

tag: array id


title: 202462

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 202412

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Train 29

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 33


title: Eµ-myc Lymphoma Train 24


title: Eµ-myc Lymphoma Train 25


title: 202570

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: mother bc

tag: sister with bc

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Train 27


title: 202988

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 203203

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Train 28

tag: genotype/variation

tag: tissue type


title: 203632

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: mother bc

tag: sister with bc

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Train 26


title: Eµ-myc Lymphoma Train 31


title: 203104

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 105254

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age menopause

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: 204343

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: mother bc

tag: sister with bc

tag: insulin growth factor 1


title: 203872

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod pr (receptor

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Train 23

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Test D4


title: Eµ-myc Lymphoma Train 19


title: 105891

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 105282

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: sex hormone binding protein

tag: free testosterone

tag: set (id matched samples)


title: 106028

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: insulin growth factor 1

tag: total testosterone

tag: array id


title: 105252

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b


title: Eµ-myc Lymphoma Train 20

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 22


title: Eµ-myc Lymphoma Train 18


title: 104156

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 104615

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: free testosterone

tag: set (id matched samples)


title: 104729

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Train 21

tag: genotype/variation

tag: tissue type


title: 103770

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin

tag: menopausal state (post=1\pre=0)


title: Eµ-myc Lymphoma Train 15


title: Eµ-myc Lymphoma Train 14


title: 204042

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: type (case=1\contr=0 )


title: 104017

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Train 16

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 13


title: Eµ-myc Lymphoma Train 17


title: Eµ-myc Lymphoma Train 11


title: Eµ-myc Lymphoma Train 8


title: Eµ-myc Lymphoma Train 12


title: Eµ-myc Lymphoma Train 7


title: 200062

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin

tag: total testosterone

tag: array id


title: 201663

description: microRNA expression

tag: tissue

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 105153

description: microRNA expression

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b

tag: free testosterone

tag: set (id matched samples)


title: 201361

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc


title: 103529

description: microRNA expression

tag: tissue

tag: insulin

tag: total testosterone

tag: array id


title: Eµ-myc Lymphoma Train 6

tag: genotype/variation

tag: tissue type


title: 103414

description: microRNA expression

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 201647

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: age menarche

tag: age 1 b

tag: free testosterone

tag: set (id matched samples)


title: 103842

description: microRNA expression

tag: tissue

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin

tag: total testosterone


title: 103628

description: microRNA expression

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: array id


title: 102540

description: microRNA expression

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )


title: 102587

description: microRNA expression

tag: tissue

tag: age menarche

tag: age 1 b

tag: free testosterone

tag: set (id matched samples)


title: 102864

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menopause

tag: mother bc

tag: insulin


title: 102746

description: microRNA expression

tag: cod pr (receptor

tag: sister with bc

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone


title: Eµ-myc Lymphoma Train 10

tag: genotype/variation

tag: tissue type


title: 103352

description: microRNA expression

tag: tissue

tag: diagnosis date

tag: cod er (receptor

tag: birth

tag: menopausal state (post=1\pre=0)

tag: type (case=1\contr=0 )

tag: array id


title: 102053

description: microRNA expression

tag: cod her2 (receptor

tag: bmi

tag: age menarche

tag: age menopause

tag: age 1 b

tag: free testosterone

tag: set (id matched samples)


title: Eµ-myc Lymphoma Train 9


title: Eµ-myc Lymphoma Train 1


title: Eµ-myc Lymphoma Train 4


title: Eµ-myc Lymphoma Train 3


title: 103216

description: microRNA expression

tag: cod pr (receptor

tag: mother bc

tag: sister with bc

tag: insulin

tag: sex hormone binding protein

tag: insulin growth factor 1

tag: total testosterone


title: Eµ-myc Lymphoma Train 5

tag: genotype/variation

tag: tissue type


title: Eµ-myc Lymphoma Train 2


title: Eµ-myc lymphoma 59

type: genomic

description: harvested lymphoma tumor DNA

hyb_protocol: After removing excess labeling dye, the gDNA was hybridized to Agilent Mouse Genome CGH Microarray 1x244K slides.

scan_protocol: The microarray slides were scanned using an Agilent G2565CA Microarray Scanner.

data_processing:
Copy number changes (log2 ratio of Cy3 to Cy5) are called using Agilent Genomic Workbench 5.0.
Log2 ratio cut-offs were 0.2 for amplification, 0.85 for high amplification (≥ 2 copies), -0.2 for deletion, and -2 for homozygous deletion.

molecule: genomic DNA

source_name: Cluster 2 lymphoma

label_protocol: 1.5 ug of gDNA was fragmented and labeled with ULS-Cy3 for lymphoma gDNA or ULS-Cy5 for reference gDNA (Agilent Genomic DNA ULS Labeling Kit) per the manufacturer’s instructions.

extract_protocol: Genomic DNA (gDNA) was extracted from flash frozen lymphoma pieces and normal tail tissue from background strain mice. Lymphoma tissue was homogenized with a mortar and pestle and then sonicated, and DNA was extracted with the DNeasy Blood and Tissue Kit (Qiagen). Tail tissue was digested, and DNA was extracted with isopropanol and subsequently cleaned up with the DNeasy Blood and Tissue Kit.

value: normal background

value: tail


title: Eµ-myc lymphoma 71

description: harvested lymphoma tumor DNA

source_name: normal tail tissue from background strain mice


title: Eµ-myc lymphoma 72

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 74

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Train 32


title: Eµ-myc lymphoma 70

description: harvested lymphoma tumor DNA


title: 530588A07 - col0_BR3 vs 18K_BR3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Can we identify differences between mutants affecte din different subunits of complex I

hyb_protocol: 18K_BR3 Cy5 / col0_BR3 Cy3 : 30pmol.

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

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

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

growth_protocol: seedling - Media=0.5X GB5, 1% sucrose, 0.8% agar hygrometry=60% Temperature=18°C/22°C Light=16/8

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: developmental stage (boyes et al. plant cell 2001)

value: boyes 1.02

tag: tissue

value: seedling

value: wild type


title: 530588A06 - ca2_BR3 vs col0_BR3

hyb_protocol: col0_BR3 Cy5 / ca2_BR3 Cy3 : 30pmol.


title: 530588A11 - col0_BR3 vs mwfe_BR3

hyb_protocol: mwfe_BR3 Cy5 / col0_BR3 Cy3 : 30pmol.

value: mwfe


title: 530588A09 - col0_BR3 vs 51K_BR3

hyb_protocol: 51K_BR3 Cy5 / col0_BR3 Cy3 : 30pmol.


title: Eµ-myc lymphoma 65

description: harvested lymphoma tumor DNA


title: 530588A10 - 51K_BR3 vs col0_BR3

hyb_protocol: col0_BR3 Cy5 / 51K_BR3 Cy3 : 30pmol.


title: 530588A12 - mwfe_BR3 vs col0_BR3

hyb_protocol: col0_BR3 Cy5 / mwfe_BR3 Cy3 : 30pmol.


title: Eµ-myc lymphoma 64

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 67

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 66

description: harvested lymphoma tumor DNA


title: 530588A08 - 18K_BR3 vs col0_BR3

hyb_protocol: col0_BR3 Cy5 / 18K_BR3 Cy3 : 30pmol.


title: Eµ-myc lymphoma 68

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 57

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 58

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 73

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 62

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 56

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 55

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 60

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 63

description: harvested lymphoma tumor DNA


title: 530588A04 - mwfe_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / mwfe_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 69

description: harvested lymphoma tumor DNA


title: 530586-2A11 - col0_BR2 vs 18K_BR2

hyb_protocol: 18K_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 54

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 61

description: harvested lymphoma tumor DNA


title: 530588A05 - col0_BR3 vs ca2_BR3

hyb_protocol: ca2_BR3 Cy5 / col0_BR3 Cy3 : 30pmol.


title: 530588A03 - col0_BR2 vs mwfe_BR2

hyb_protocol: mwfe_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: 530586-2A12 - 18K_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / 18K_BR2 Cy3 : 30pmol.


title: 530588A01 - col0_BR2 vs 51K_BR2

hyb_protocol: 51K_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 50

description: harvested lymphoma tumor DNA

source_name: Cluster 1 lymphoma


title: 530588A02 - 51K_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / 51K_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 51

description: harvested lymphoma tumor DNA


title: 530586-2A07 - col0_BR1 vs mwfe_BR1

hyb_protocol: mwfe_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: 530586-2A10 - ca2_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / ca2_BR2 Cy3 : 30pmol.


title: 530586-2A08 - mwfe_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / mwfe_BR1 Cy3 : 30pmol.


title: Eµ-myc lymphoma 49

description: harvested lymphoma tumor DNA

hyb_protocol: After removing excess labeling dye, the gDNA was hybridized to Agilent Mouse Genome CGH Microarray 1x244K slides.


title: Eµ-myc Lymphoma Test D143

hyb_protocol: The cRNA was fragmented and mixed into a hybridization cocktail before application to the array, which was then hybridized for 16 hours at 45C with rotation at 60 rpm.  This was performed at the Duke University DNA Microarray Core Facility.

extract_protocol: Lymphoma tissue was homogenized with a mortar and pestle and with sonication.  Cell pellets were homogenized with a needle and syringe, Lysing Matrix A tube for tissue (MP Biomedicals), and/or QIAshredder homogenizer column (Qiagen).  RNA was extracted using the Rneasy Mini Kit (Qiagen).


title: Eµ-myc lymphoma 48

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D133


title: 530586-2A09 - col0_BR2 vs ca2_BR2

hyb_protocol: ca2_BR2 Cy5 / col0_BR2 Cy3 : 30pmol.


title: 530586-2A06 - 51K_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / 51K_BR1 Cy3 : 30pmol.


title: 530586-2A05 - col0_BR1 vs 51K_BR1

hyb_protocol: 51K_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: Eµ-myc lymphoma 53

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D163


title: Eµ-myc lymphoma 47

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D121


title: Eµ-myc Lymphoma Test D151


title: Eµ-myc Lymphoma Test D161


title: 530586-2A04 - 18K_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / 18K_BR1 Cy3 : 30pmol.


title: 530586-2A02 - ca2_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / ca2_BR1 Cy3 : 30pmol.


title: 530586-2A03 - col0_BR1 vs 18K_BR1

hyb_protocol: 18K_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: 530586A10 - 35S::UPRT-4TU-Biot-Purif_BR1 vs 35S::UPRT-4TU-Biot_BR1

description:
Impact of RNA labeling by Plant RABT on plant transcriptome
To evaluate the ability to transpose this method on plants, we generated transgenics expressing the uracil phosphoribosyltransferase gene of Toxoplasma gondii under the control of the CaMV 35S promoter (Col-0 genetic background). Fifteen days old transgenic plants grown in Arabidopsis Duchefa liquid medium were incubated 15h with either DMSO (used to solved 4-TU), used as control, or 30µM 4-TU. The impact of 4-TU incubation on total RNA synthesis was studied comparing total RNA extracted from 4-TU incubated plants to total RNA extracted from control plants (4TU). Incidence of the RNA biotinylation and purification on microarray results were evaluated comparing total RNA extracted from 4-TU incubated plants biotinylated or not (4TU-Biot) and total RNA extracted from 4-TU incubated plants biotinylated and purified (4TU-Biot-Purif).
arabidopsis thaliana (columbia)  mutant (columbia background/ homozygous transgenic line 3.4.7 (t4)) -  dev.stage (boyes et al. plant cell 2001): boyes: 1.03

hyb_protocol: 35S::UPRT-4TU-Biot_BR1 Cy5 / 35S::UPRT-4TU-Biot-Purif_BR1 Cy3 : 30pmol.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

growth_protocol: whole plant - Media=3 ml liquid Arabidopsis Duchefa hygrometry=70% Temperature=25°C Light=16h light/8h night

treatment_protocol: Name:4-thiouracil/RNA biotinylated - compound based treatment - compound addition,4-thiouracil:quantity 30uM time 15hour . Plantlets were grown in vitro during 15 days. The 15th day, at 7 pm, 6mM of 4-thiouracil (30µM final) were added to the liquid medium. Plantlets were incubated 15h in vitro and harvested the day after at 10 am after being rinced in water and dryed. Samples were directly frozen in liquid nitrogen. RNA were extracted using RNeasy Plant mini kit with a DNase I treatment.

tag: agent

value: homozygous transgenic line 3.4.7 (t4)

value: boyes 1.03

value: whole plant

treatment_protocol: Name:4-thiouracil/RNA biotinylated/RNA purified - compound based treatment - compound addition,4-thiouracil:quantity 30uM time 15hour . Plantlets were grown in vitro during 15 days. The 15th day, at 7 pm, 6mM of 4-thiouracil (30µM final) were added to the liquid medium. Plantlets were incubated 15h in vitro and harvested the day after at 10 am after being rinced in water and dryed. Samples were directly frozen in liquid nitrogen. RNA were extracted using RNeasy Plant mini kit with a DNase I treatment.


title: Eµ-myc lymphoma 46

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D135


title: 530586-2A01 - col0_BR1 vs ca2_BR1

hyb_protocol: ca2_BR1 Cy5 / col0_BR1 Cy3 : 30pmol.


title: Eµ-myc lymphoma 45

description: harvested lymphoma tumor DNA


title: 530586A12 - 35S::UPRT-4TU-Biot-Purif_BR2 vs 35S::UPRT-4TU-Biot_BR2

hyb_protocol: 35S::UPRT-4TU-Biot_BR2 Cy5 / 35S::UPRT-4TU-Biot-Purif_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 52

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D168 (Spleen)

source_name: Spleen

value: spleen


title: Eµ-myc Lymphoma Test D98


title: 530586A09 - 35S::UPRT-4TU-Biot_BR1 vs 35S::UPRT-4TU-Biot-Purif_BR1

hyb_protocol: 35S::UPRT-4TU-Biot-Purif_BR1 Cy5 / 35S::UPRT-4TU-Biot_BR1 Cy3 : 30pmol.


title: 530586A11 - 35S::UPRT-4TU-Biot_BR2 vs 35S::UPRT-4TU-Biot-Purif_BR2

hyb_protocol: 35S::UPRT-4TU-Biot-Purif_BR2 Cy5 / 35S::UPRT-4TU-Biot_BR2 Cy3 : 30pmol.


title: Eµ-myc lymphoma 41

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D93


title: Eµ-myc Lymphoma Test D107


title: Eµ-myc Lymphoma Test D117


title: Eµ-myc Lymphoma Test D92


title: Eµ-myc lymphoma 42

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 43

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 40

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 39

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 44

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 38

description: harvested lymphoma tumor DNA


title: 530586A08 - 35S::UPRT-4TU-Biot_BR2 vs 35S::UPRT-4TU_BR2

hyb_protocol: 35S::UPRT-4TU_BR2 Cy5 / 35S::UPRT-4TU-Biot_BR2 Cy3 : 30pmol.

treatment_protocol: Name:4-thiouracil - compound based treatment - compound addition,4-thiouracil:quantity 30uM time 15hour . Plantlets were grown in vitro during 15 days. The 15th day, at 7 pm, 6mM of 4-thiouracil (30µM final) were added to the liquid medium. Plantlets were incubated 15h in vitro and harvested the day after at 10 am after being rinced in water and dryed. Samples were directly frozen in liquid nitrogen. RNA were extracted using RNeasy Plant mini kit with a DNase I treatment.


title: Eµ-myc Lymphoma Test D88


title: 530586A07 - 35S::UPRT-4TU_BR2 vs 35S::UPRT-4TU-Biot_BR2

hyb_protocol: 35S::UPRT-4TU-Biot_BR2 Cy5 / 35S::UPRT-4TU_BR2 Cy3 : 30pmol.


title: Eµ-myc Lymphoma Test D89


title: Eµ-myc Lymphoma Test D85


title: Eµ-myc Lymphoma Test D86


title: 530586A05 - 35S::UPRT-4TU_BR1 vs 35S::UPRT-4TU-Biot_BR1

hyb_protocol: 35S::UPRT-4TU-Biot_BR1 Cy5 / 35S::UPRT-4TU_BR1 Cy3 : 30pmol.


title: Eµ-myc lymphoma 37

description: harvested lymphoma tumor DNA


title: 530586A06 - 35S::UPRT-4TU-Biot_BR1 vs 35S::UPRT-4TU_BR1

hyb_protocol: 35S::UPRT-4TU_BR1 Cy5 / 35S::UPRT-4TU-Biot_BR1 Cy3 : 30pmol.


title: 530586A03 - 35S::UPRT-DMSO_BR2 vs 35S::UPRT-4TU_BR2

hyb_protocol: 35S::UPRT-4TU_BR2 Cy5 / 35S::UPRT-DMSO_BR2 Cy3 : 30pmol.

treatment_protocol: Name:DMSO - compound based treatment - compound addition,dmso:time 15hour . Plantlets were grown in vitro during 15 days. The 15th day, at 7 pm, 16.5µL of DMSO were added to the liquid medium. Plantlets were incubated 15h in vitro and harvested the day after at 10 am after being rinced in water and dryed. Samples were directly frozen in liquid nitrogen. RNA were extracted using RNeasy Plant mini kit with a DNase I treatment.

value: DMSO


title: Eµ-myc Lymphoma Test D83

hyb_protocol: The cRNA was fragmented and mixed into a hybridization cocktail before application to the array, which was then hybridized for 16 hours at 45C with rotation at 60 rpm.  This was performed at the Duke University DNA Microarray Core Facility.


title: 530586A02 - 35S::UPRT-4TU_BR1 vs 35S::UPRT-DMSO_BR1

hyb_protocol: 35S::UPRT-DMSO_BR1 Cy5 / 35S::UPRT-4TU_BR1 Cy3 : 30pmol.


title: Eµ-myc Lymphoma Test D81


title: 530586A01 - 35S::UPRT-DMSO_BR1 vs 35S::UPRT-4TU_BR1

hyb_protocol: 35S::UPRT-4TU_BR1 Cy5 / 35S::UPRT-DMSO_BR1 Cy3 : 30pmol.


title: Eµ-myc Lymphoma Test D82


title: AER_8_PRE

city: Wellington

first: David

last: Rowlands

state: Wellington

address: 63 Wallace St Mt Cook

department: Institute of Food, Nutrition and Human Health

country: New Zealand

institute: Massey University

hyb_protocol: 21.5 µl of high-quality biotin-labeled miRNA sample was hybridized to Affymetrix Gene-Chip® miRNA 2.0 Array for 16 h according to Affymetrix protocol

scan_protocol: The arrays were washed and stained on the Affymetrix Fluidics station 400 and scanned with a Hewlett Packard G2500A gene Array Scanner

data_processing: Affymetrix® miRNA QC Tool v 1.1.1.0 was used for the data summarization, normalization, and microarray quality control

source_name: VASTUS LATERALIS

label_protocol: low molecular weight RNA was biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit

extract_protocol: A biopsy was collected from the right Vastus Lateralis under local anaesthesia and RNA was isolated from muscle (~10 mg) using mirVana™ Kit , Low molecular weight RNA was biotin-labeled with FlashTag™ Biotin HSR RNA Labeling Kit

value: Vastus Lateralis

tag: sample id

tag: exercise type (aerobic or resistance)

value: AEROBIC

tag: pre exercise/ post exercise

value: PRE


title: AER_8_POST

value: POST


title: Eµ-myc lymphoma 34

description: harvested lymphoma tumor DNA

hyb_protocol: After removing excess labeling dye, the gDNA was hybridized to Agilent Mouse Genome CGH Microarray 1x244K slides.

value: Eµ-myc

value: lymphoma tumor


title: Eµ-myc lymphoma 31

description: harvested lymphoma tumor DNA

value: normal background

value: tail


title: Eµ-myc lymphoma 33

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D84


title: 530586A04 - 35S::UPRT-4TU_BR2 vs 35S::UPRT-DMSO_BR2

hyb_protocol: 35S::UPRT-DMSO_BR2 Cy5 / 35S::UPRT-4TU_BR2 Cy3 : 30pmol.

value: Columbia


title: Eµ-myc Lymphoma Test D80


title: AER_7_POST


title: Eµ-myc Lymphoma Test D75


title: Eµ-myc Lymphoma Test D78


title: Eµ-myc lymphoma 28

description: harvested lymphoma tumor DNA


title: AER_7_PRE


title: Eµ-myc lymphoma 36

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 29

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 35

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D70


title: Eµ-myc lymphoma 32

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D72


title: Eµ-myc lymphoma 30

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 27

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D69


title: Eµ-myc lymphoma 26

description: harvested lymphoma tumor DNA


title: AER_26_PRE


title: Eµ-myc Lymphoma Test D71


title: AER_20_PRE


title: AER_6_PRE


title: Eµ-myc lymphoma 24

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 23

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 25

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 21

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 20

description: harvested lymphoma tumor DNA


title: Eµ-myc lymphoma 22

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D62


title: Eµ-myc Lymphoma Test D59


title: AER_19_PRE


title: Eµ-myc lymphoma 19

description: harvested lymphoma tumor DNA


title: Eµ-myc Lymphoma Test D63


title: AER_6_POST


title: AER_20_POST