title: Tolerant Individual 6

scan_protocol: Images were scanned on a: ScanArray™ Express Microarray Scanner (Packard BioScience BioChip Technologies, model #ASCEX00) Slides were scanned at 74 and 72 PMT for Cy3 and Cy5, respectively, and spot intensity was calculated with ImaGene ver. 6.5.1.

source_name: Arctic charr gill tissue whole RNA reverse transcribed to cDNA

treatment_protocol: 200 Arctic charr were exposed to acute heat stress; the first 10 fish to show stress (lose balance) were considered the Intolerant group and the last 10 to show signs of stress were the Tolerant group; 10 untreated fish were used as controls. Six randomly selected fish from each group were used for the microarray analysis.

value: Tolerant


title: Training61-2

status: Public on Jun 01 2011

type: RNA

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

country: USA

institute: NCI

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355235

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

scan_protocol: GeneChips were scanned using the Affymetrix G3000 GeneArray Scanner

data_processing: The data were processed with R (v 2.6.1) and BRB-ArrayTools (v 3.6).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pretreatment sample_Training set

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Total RNA was extracted from tumor-rich area using Trizol, according to the manufacturer's instructions.

tag: Pretreatment endoscopic biopsy samples collected from CF-treated metastatic gastric cancer patients


title: MCF7-CARM1#13-E2-c

city: Madison

first: Wei

last: Xu

state: WI

address: 1400 University Ave

institute: UW-Madison

description:
E2 alone
SOM01X77
Sample barcode: 5953002

hyb_protocol: Hybridization was performed at 42C for 20hrs, according to NimbleGen gene expression arrays user’s guide (2010).

scan_protocol: One-color NimbleGen arrays were scanned with the MS 200 Microarray Scanner and the data were extract using the MS 200 Data Collection Software.

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

source_name: breast cancer cell line

label_protocol: Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit was used to synthesize double-stranded cDNA that was going to be labeled using a NimbleGen One-Color DNA Labeling Kit.

growth_protocol: MCF7-tet-on-CARM1 cells were grown in DMEM in 10% FBS. Two days before E2 treatment, the cells were switched to phenol-red free DMEM with 5% 6X charcoal stripped FBS.

extract_protocol: mRNA were extracted from cells using Qiagen Rneasy Kit

treatment_protocol: When the cells were treated with Dox, they were treated with 1ug/ml Dox for 4 days to induce CARM1 expression. The medium were changed to phenol-red free DMEM+charcoal stripped FBS for 2 days before treating with E2 (10nM)

tag: cell type

value: breast cancer cell line

tag: cell line

value: MCF7-tet-on-CARM1 clone 13

tag: treatment


title: Training58-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355232


title: Tolerant Individual 7

city: Burnaby

first: Nicole

middle: Lisa

last: Quinn

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

hyb_protocol: Details of the microarray hybridization process can be found at the University of Victoria cGRASP website (http://web.uvic.ca/grasp/microarray/array.html) within the .pdf document entitled Invitrogen Indirect cDNA Labeling System version 3.

data_processing: All statistical analyses of the microarray data were conducted using Genespring ver. 7.3.1. Signals were normalized per spot and per chip using an intensity-dependent (LOWESS) normalization, then per gene to normalize to the median. Spots were filtered on flags present, and only spots with signals greater or equal to the average base/proportional value of the raw channel were retained.

organism: Salvelinus alpinus

label_protocol: cDNA (300 ng) and aRNA (500 ng) were labeled with Cy5 and Cy3 (Amersham Biosciences), respectively, using Invitrogen’s SuperScript Indirect cDNA Labeling System following the manufacturer's instructions.

extract_protocol: Total RNA was isolated from gill tissues disrupted and homogenized in 1 ml TRIzol reagent using a Mixer-mill (Retch® MM 301) with tungsten carbide beads. Phase separation was conducted using 200 µl chloroform, and RNA was purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

tag: tissue

value: gill

tag: group

organism: Salmo salar

source_name: reference aRNA

value: gonad, brain, spleen


title: MCF7-CARM1#13-DOX-c

description:
Dox alone
SOM01X78
Sample barcode: 5953202

value: Dox


title: Training50-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355224


title: Tolerant Individual 2


title: Training43-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355217


title: Training52-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355226


title: MCF7-CARM1#13-DMSO-b

description:
DMSO alone
SOM01X72
Sample barcode: 5951902

value: DMSO


title: MCF7-CARM1#13-DMSO-c

description:
DMSO alone
SOM01X76
Sample barcode: 5952502


title: Training47-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355221


title: Tolerant Individual 4


title: Training46-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355220


title: MCF7-CARM1#13-DOX-b

description:
Dox alone
SOM01X74
Sample barcode: 5952102


title: Training32-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355206


title: Tolerant Individual 3


title: Intolerant Individual 9

value: Intolerant


title: Training40-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355214


title: Training15-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355189


title: Intolerant Individual 8


title: Training25-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355199


title: High Coverage 1

city: San Francisco

first: Eleanor

middle: Josephine

last: Clowney

state: CA

department: Anatomy

institute: UCSF

description: HighCoverage Hybridization 1

hyb_protocol: 5-7ug of DNA was hybridizing at the Stanford PAN facility according to standard Affymetrix protocols

scan_protocol: Arrays were scanned at the Stanford PAN facility according to standard Affymetrix protocols

data_processing: Data was normalized and analyzed with MAT; all coordinates are mm9/Mouse 2007. Files included here use window 50, maxgap 30, minProbes 5 and default p-value though various parameters were used in analysis. File 'GSE26373_olfrnamedproms.txt' contains final TSS calls for 1085 olfactory receptor genes in mm9 coordinates.

organism: Mus musculus

source_name: RLM-RACE products reverse transcribed with olfactory receptor degenerate primers and amplified by PCR without nesting

label_protocol: 5-7ug of DNA was fragmented using UDG/APE and biotinylated using terminal transferase using Affymetrix fragmentation and labeleing kit

extract_protocol: For each sample, olfactory epithelia were dissected from five 6-8wk adult C57/Bl6 mice. RNA was extracted using Trizol and RLM-RACE performed using Invitrogen GeneRacer according to the manufacturers instructions with the exception that cDNA was reverse transcribed using degenerate primers against olfactory receptor coding sequences.

tag: strain

tag: age

value: 6-8 wk (adult)

value: olfactory epithelium


title: Training38-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355212


title: Training31-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355205


title: High Coverage 2

description: HighCoverage Hybridization 2


title: Tolerant Individual 1


title: MCF7-CARM1#13-E2-a

description:
E2 alone
SOM01VS9
Sample barcode: 5944002


title: Training7-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355181


title: MCF7-CARM1#13-DMSO-a

description:
DMSO alone
SOM01VS8
Sample barcode: 5943702


title: MCF7-CARM1#13-DOX+E2-a

description:
Dox and E2
SOM01VSC
Sample barcode: 5951702

value: Dox and D2


title: Stringent

description: Stringent Hybridization

source_name: RLM-RACE products reverse transcribed with olfactory receptor degenerate primers and amplified by nested PCR


title: Training2-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355176


title: Intolerant Individual 5


title: AcquiredResistant77

description: Post-CF

source_name: Posttreatment sample

tag: Collected at the progressive disease


title: Intolerant Individual 4


title: Training6-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355180


title: Training4-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355178


title: Genomic DNA from thyroid normal tissue 2 (ThyFA_N2)

type: genomic

city: College Park

first: Hector

last: Corrada Bravo

state: MD - Maryland

address: 3114F Biomolecular Sciences Building

department: Center for Bioinformatics and Computational Biology

institute: University of Maryland

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized using standard Illumina protocols.

scan_protocol: Arrays were imaged using BeadArray Reader using the standard recommended Illumina scanner settings.

data_processing: We quantile normalized separately the raw intensity data from the Cy5 and Cy3 channels representing methylated and unmethylated DNA (R/Bioconductor, preprocessCore package). The methylation level (beta) was calculated as the ratio of the Cy5 intensity over the sum of the intensities from both channels.

molecule: genomic DNA

source_name: thyroid normal tissue

label_protocol: Standard Illumina protocol.

extract_protocol: DNA purification was done using the DNeasy Blood and Tissue Kit (Qiagen) following standard instructions.

value: ThyFA

tag: batch

tag: tissue type

value: normal


title: Genomic DNA from thyroid tumor 4 (ThyFC_T4)

source_name: thyroid tumor

value: ThyFC

value: tumor


title: Genomic DNA from thyroid tumor 1 (ThyFVPTC_T1)

value: ThyFVPTC


title: Genomic DNA from thyroid normal tissue 1 (ThyFA_N1)


title: Genomic DNA from thyroid tumor 1 (ThyFC_T1)


title: AcquiredResistant70

description: Post-CF


title: 96_5_1H30_AO

city: Marseille

first: Isabelle

last: Lesur Kupin

address: 163 av. de Luminy - case 928

department: Bioinformatics

country: France

institute: INSERM U928

description: The MessageAmp procedure is based on antisense RNA (aRNA) amplification first described by Van Gelder and Eberwine, and involves a series of enzymatic reactions resulting in linear amplification of exceedingly small amounts of RNA for use in array analysis. Unlike exponential RNA amplification methods, such as NASBA and RT-PCR, aRNA amplification maintains representation of the starting mRNA population. The procedure begins with total or poly(A) RNA that is reverse transcribed using a primer containing both oligo(dT) and a T7 RNA polymerase promoter sequence (see schematic at left). After first-strand synthesis, the reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during a second-strand synthesis reaction that produces a double-stranded cDNA template for transcription. Contaminating rRNA, mRNA fragments and primers are removed and the cDNA template is then used in a large scale in vitro transcription reaction to produce linearly amplified aRNA. For increased yields, the aRNA can also be used as template for cDNA synthesis followed by a second round of amplification using MessageAmp.

hyb_protocol: cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. Puthier D, Joly F, Irla M, Saade M, Victorero G, Loriod B, Nguyen C. Hybridization protocol is also published in « DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4 – pp:80-82.

scan_protocol: Image acquisition was performed with a Fuji BAS 1500 system.

data_processing: Hybridation signals were quantified using the Bzscan2 software. All images were carefully inspected and spots with overestimated intensities due to neighborhood effects were manually excluded. We used the NylonArray library for R locally developped by A. Bergon and D. Puthier. This package contains functions to perform diagnosis and normalization of nylon microarray data. The sample datasets were corrected for neighborhood effects and local background as described by F. Lopez et al. Quantile normalization was applied to sample data to correct for global intensity and dispersion. At each time-point, gene expressions in control samples (physiological serum injection) were substracted from gene expression in OA samples.

label: α-dCTP 33P

source_name: PBMC from blood, oleic acid, incubation 1H30

label_protocol:
cDNA were designed and prepared as described in J Immunol. 2004 Nov 15;173(10):6109-18. A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models.
Puthier D, Joly F, Irla M, Saade M, Victorero G, Loriod B, Nguyen C.
Labelling protocol is also published in  « DNA microarrays: Gene expression applications » B. Jordan(ed.), Springer-Verlag Berlin Heidelberg Newyork, ISBN: 3-540-41508-4- chapter 4 – pp: 78-80.

growth_protocol: Mices were housed in a specific pathogen-free animal facility. All experimental procedures involving animals were approved by the veterinary office of the Ministry of Agriculture, France (authorization number: 13-27).

extract_protocol: Total RNA from lung was extracted using Mouse RiboPure-Blood RNA Isolation Kit (Ambion #AM1951) and amplified using MessageAmpII aRNA Amplification Kit (Ambion #AM1751). The quality of RNA was confirmed on a Agilent Bioanalyser 2100 using RNA NanoChips, and the concentration of RNA was dertermined by reading absorbance at 260/280 nm.

treatment_protocol: Femelle C57Bl/6J mice were anesthetized with 5% Xylazine – 20% Ketamine (0,1ml/10g). We injected 20 µl of oleic acid (1,2µl/g body weight, sigma #27728-1L-R) in the mouse. Administration of physiological serum and OA was done through the tail vein with a 0.3-ml insulin syringe (BD #320837).

tag: genotype

value: wild-type

tag: gender

value: female

value: 7 weeks old

value: PBMC


title: Intolerant Individual 1

value: gill


title: AcquiredResistant61

description: Post-CF


title: AcquiredResistant64

description: Post-CF


title: Intolerant Individual 2

value: gonad, brain, spleen


title: 93_5_3H_PHI

source_name: PBMC from blood, physiological serum, incubation 3H


title: 95_5_24H_AO

source_name: PBMC from blood, oleic acid, incubation 24H


title: AcquiredResistant52

description: Post-CF


title: AcquiredResistant43

description: Post-CF


title: AcquiredResistant40

description: Post-CF


title: AcquiredResistant58

description: Post-CF


title: Genomic DNA from thyroid normal tissue 4 (ThyFA_N4)


title: AcquiredResistant50

description: Post-CF


title: 92_5_4H_AO

source_name: PBMC from blood, oleic acid, incubation 4H


title: AcquiredResistant38

description: Post-CF


title: AcquiredResistant32

description: Post-CF


title: 94_3_18H_AO

source_name: PBMC from blood, oleic acid, incubation 18H


title: 91_3_1H30_AO


title: AcquiredResistant46

description: Post-CF


title: AcquiredResistant47

description: Post-CF


title: AcquiredResistant25

description: Post-CF


title: 90_4_3H_AO

source_name: PBMC from blood, oleic acid, incubation 3H


title: 88_4_18H_PHI

source_name: PBMC from blood, physiological serum, incubation 18H


title: Genomic DNA from colon adenoma 2 (Adenoma_T2)

source_name: colon adenoma

value: adenoma


title: Genomic DNA from breast normal tissue 3 (DCIS_N3)

source_name: breast normal tissue

value: DCIS


title: Genomic DNA from thyroid tumor 2 (ThyPTC_T2)

value: ThyPTC


title: Genomic DNA from thyroid normal tissue 2 (ThyPTC_N2)


title: Genomic DNA from thyroid normal tissue 3 (ThyPTC_N3)


title: AcquiredResistant4

description: Post-CF


title: 87_1_3H_PHI


title: AcquiredResistant6

description: Post-CF


title: 86_6_1H_OA

source_name: PBMC from blood, oleic acid, incubation 1H


title: AcquiredResistant31

description: Post-CF


title: 89_7_1H30_AO


title: Validation119

description: Validation set for the signature for the intrinsic resistance to CF

source_name: Pretreatment sample_Validation set


title: AcquiredResistant2

description: Post-CF


title: Validation123


title: AcquiredResistant15

description: Post-CF


title: Validation120


title: AcquiredResistant7

description: Post-CF


title: Genomic DNA from thyroid normal tissue 1 (ThyPTC_N1)


title: Genomic DNA from breast normal tissue 2 (DCIS_N2)


title: Validation122


title: AcquiredResistant1

description: Post-CF


title: Validation118


title: Validation117


title: Genomic DNA from breast normal tissue 1 (DCIS_N1)


title: Genomic DNA from colon adenoma 1 (Adenoma_T1)


title: 84_2_3H_AO


title: 85_3_1H_OA


title: 81_3_4H_AO


title: 79_2_24H_AO


title: Genomic DNA from colon adenoma 32 (Colon_T32)

value: colon


title: Genomic DNA from breast normal tissue 31 (Breast_N31)

value: breast


title: Genomic DNA from colon normal tissue 32 (Colon_N32)

source_name: colon normal tissue


title: 77_2_4H_AO


title: 80_1_1H30_PHI

source_name: PBMC from blood, physiological serum, incubation 1H30


title: Validation113


title: Validation107


title: Validation106


title: Genomic DNA from breast normal tissue 27 (Breast_N27)


title: Validation115


title: Validation110


title: Validation112


title: Validation114


title: Validation116


title: 71_2_18H_AO


title: Genomic DNA from breast tumor 28 (Breast_T28)

source_name: breast tumor


title: 78_2_24H_AO


title: 72_4_3H_AO


title: Validation111


title: Validation104


title: Validation121


title: Validation105


title: Validation109


title: Validation108


title: Validation102


title: Validation103


title: Validation101


title: Genomic DNA from breast tumor 27 (Breast_T27)


title: Validation100


title: Validation99


title: 69_2_1H30_AO


title: Training1-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355175

source_name: Pretreatment sample_Training set


title: Genomic DNA from thyroid tumor 9 (ThyFVPTC_T9)


title: Genomic DNA from colon adenoma 18 (Adenoma_T18)


title: Genomic DNA from thyroid tumor 10 (ThyFVPTC_T10)


title: 70_5_4H_AO


title: 65_1_18H_PHI


title: Validation98


title: Genomic DNA from thyroid tumor 9 (ThyFC_T9)


title: Genomic DNA from thyroid tumor 8 (ThyFVPTC_T8)


title: Genomic DNA from thyroid tumor 8 (ThyFC_T8)


title: Training96

description: Training set to identify the signature for the intrinsic resistance to CF


title: 62_5_18H_AO


title: 63_6_4H_AO


title: Validation97


title: Training95


title: Genomic DNA from thyroid normal tissue 8 (ThyFA_N8)

source_name: thyroid normal tissue


title: 57_3_1H30_AO


title: Training92


title: Genomic DNA from thyroid tumor 7 (ThyFVPTC_T7)

source_name: thyroid tumor


title: Training90


title: AcquiredResistant71

description: Post-CF

source_name: Posttreatment sample


title: 56_4_24H_PHI

source_name: PBMC from blood, physiological serum, incubation 24H


title: Training94


title: 64_7_3H_AO


title: Training89


title: Training88


title: Training91


title: Training93


title: Training87


title: Training85


title: Genomic DNA from thyroid tumor 7 (ThyFC_T7)


title: Training86


title: 55_1_4H_PHI

source_name: PBMC from blood, physiological serum, incubation 4H


title: Genomic DNA from thyroid normal tissue 6 (ThyPTC_N6)


title: Genomic DNA from thyroid normal tissue 7 (ThyFA_N7)


title: Training83


title: Training80


title: Training84


title: 51_8_1H30_AO

source_name: PBMC from blood, oleic acid, incubation 1H30


title: 54_6_1H30_AO


title: Training79


title: 44_5_1H30_AO


title: 53_6_1H_OA


title: Training82


title: Training81


title: Genomic DNA from breast normal tissue 30 (Breast_N30)


title: Training74


title: Training77

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355341


title: Training71

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355340


title: Training78


title: Training73


title: Genomic DNA from colon adenoma 17 (Adenoma_T17)


title: 42_1_1H_PHI

source_name: PBMC from blood, physiological serum, incubation 1H


title: Genomic DNA from thyroid tumor 6 (ThyPTC_T6)


title: 40_4_1H_PHI


title: 48_5_1H_OA


title: Genomic DNA from breast tumor 31 (Breast_T31)


title: 45_6_24H_AO

source_name: PBMC from blood, oleic acid, incubation 24H


title: Genomic DNA from colon tumor 31 (Colon_T31)

source_name: colon tumor


title: 39_4_4H_PH


title: 43_2_1H_OA


title: Genomic DNA from colon normal tissue 31 (Colon_N31)


title: Training76


title: Genomic DNA from colon adenoma 15 (Adenoma_T15)

source_name: colon adenoma


title: Genomic DNA from colon adenoma 16 (Adenoma_T16)


title: Training66


title: 38_3_3H_AO

source_name: PBMC from blood, oleic acid, incubation 3H


title: 37_6_18H_AO

source_name: PBMC from blood, oleic acid, incubation 18H


title: Training72


title: Training65


title: Genomic DNA from colon adenoma 14 (Adenoma_T14)


title: Genomic DNA from thyroid normal tissue 10 (ThyFA_N10)


title: Genomic DNA from thyroid normal tissue 9 (ThyFA_N9)


title: Training70

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355339


title: Training69


title: Training75


title: Training63


title: Training61

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355337


title: Training67


title: Training60


title: 35_6_24H_AO


title: 33_3_24H_AO


title: Training64

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355338


title: Training56


title: Training68


title: Training62


title: Genomic DNA from colon adenoma 8 (Adenoma_T8)


title: Training55


title: 28_2_18H_AO


title: Genomic DNA from thyroid normal tissue 7 (ThyPTC_N7)


title: Genomic DNA from colon adenoma 9 (Adenoma_T9)


title: 32_4_1H_PHI


title: Training59


title: Genomic DNA from colon adenoma 7 (Adenoma_T7)


title: Training58

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355336


title: Training51


title: Genomic DNA from thyroid normal tissue 6 (ThyFVPTC_N6)


title: Genomic DNA from thyroid tumor 6 (ThyFVPTC_T6)


title: 26_4_18H_PHI

source_name: PBMC from blood, physiological serum, incubation 18H


title: 18_4_4H_PHI


title: 19_1_24H_PHI


title: Training53


title: Training50

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355334


title: Genomic DNA from thyroid normal tissue 6 (ThyFA_N6)


title: Training52

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355335


title: Training46

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355332


title: Training57


title: Training47

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355333


title: Training49


title: Genomic DNA from thyroid tumor 6 (ThyFC_T6)


title: Training45


title: Training48


title: 12_2_3H_AO

data_processing:
Hybridation signals were quantified using the Bzscan2 software. All images were carefully inspected and spots with overestimated intensities due to neighborhood effects were manually excluded. We used the NylonArray library for R locally developped by A. Bergon and D. Puthier. This package contains functions to perform diagnosis and normalization of nylon microarray data. The sample datasets were corrected for neighborhood effects and local background as described by F. Lopez et al. Quantile normalization was applied to sample data to correct for global intensity and dispersion. At each time-point, gene expressions in control samples (physiological serum injection) were substracted from gene expression in OA samples.
ADD


title: Training41


title: Training44


title: Training43

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355331


title: Training42


title: Genomic DNA from thyroid tumor 5 (ThyPTC_T5)


title: Genomic DNA from wilms tumor 9 (Wilms_T9)

source_name: wilms tumor

value: Wilms


title: Genomic DNA from wilms tumor 8 (Wilms_T8)


title: Training40

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355330


title: Genomic DNA from wilms tumor 6 (Wilms_T6)


title: Training54


title: Training38

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355329


title: Genomic DNA from wilms tumor 4 (Wilms_T4)


title: Training39


title: Genomic DNA from wilms tumor 3 (Wilms_T3)


title: Training36


title: Training34


title: Training31

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355327


title: Training32

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355328


title: Training37


title: Training35


title: Training30


title: Training33


title: Training29


title: Sham 72 hours replicate rat #22

type: mixed

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

country: China

institute: Nanjing Agricultural University

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al., 2005), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).   Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing:
BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities. GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.
Data processed by Bluefuse is absolute value (attached to the Series record as a supplementary file), and from GeneSpring is U46 normalized ratio test/ref (in Sample data table below).

organism: Rattus norvegicus

source_name: rat liver

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: Rats were purchased and maintained in central animal facilties at the University of Minnesota.

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from tissues

treatment_protocol: Partial Hepatectomies. Male Sprague-Dawley rats (Harlan Sprague-Dawley, Indianapolis, IN) ~ 175 g were subjected to sham surgery or 70% PH as originally described (18) between 8 AM and noon. At times between 3 and 72 hrs after surgery, the animals were sacrificed by exsanguinations under anesthesia; the liver remnants harvested and immediately frozen in liquid nitrogen. All animal work was approved by the Institutional Animal Care and Use Committee at the University of Minnesota and received humane care according to the criteria outlined in the Guide for the Care and Use of Laboratory Animals prepared by the National Academy of Sciences and published by the National Institutes of Health (NIH publication 86-23 revised 1985).

value: Sprague-Dawley

value: liver

tag: procedure

value: Sham

tag: time

value: 72 hours

label: Alexa Fluor® 647

molecule: other

source_name: Reference DNA

tag: reference

value: synthetic DNA oligos corrresponding to human miRNAs


title: Training26

source_name: Pretreatment sample_Training set


title: Training28


title: Training27


title: Sham 48 hours replicate rat #47

value: 48 hours


title: Sham 72 hours replicate rat #20


title: Training25

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355326


title: Genomic DNA from wilms tumor 26 (Wilms_T26)

value: tumor


title: Genomic DNA from wilms tumor 25 (Wilms_T25)


title: Training24

description: Training set to identify the signature for the intrinsic resistance to CF


title: Genomic DNA from wilms tumor 23 (Wilms_T23)


title: Training21


title: Sham 36 hours replicate rat #12

value: 36 hours


title: Training22


title: Genomic DNA from wilms tumor 22 (Wilms_T22)


title: Genomic DNA from wilms tumor 21 (Wilms_T21)


title: Genomic DNA from wilms tumor 5 (Wilms_T5)


title: Genomic DNA from wilms tumor 24 (Wilms_T24)


title: Sham 48 hours replicate rat #46


title: Training23


title: Training20


title: Sham 24 hours replicate rat #42

value: 24 hours


title: Training14


title: Training19


title: Sham 24 hours replicate rat #41


title: Genomic DNA from wilms tumor 20 (Wilms_T20)


title: Genomic DNA from wilms tumor 18 (Wilms_T18)


title: Genomic DNA from wilms tumor 19 (Wilms_T19)


title: Sham 18 hours replicate rat #28

value: 18 hours


title: Sham 36 hours replicate rat #11


title: Training15

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355325


title: Training13


title: Sham 18 hours replicate rat #27


title: Training16


title: Genomic DNA from wilms tumor 2 (Wilms_T2)


title: Training10


title: Training17


title: Training9


title: Training18


title: Training11


title: Sham 12 hours replicate rat #33

value: 12 hours


title: Sham 18 hours replicate rat #26


title: Genomic DNA from wilms tumor 16 (Wilms_T16)


title: Training3


title: Genomic DNA from wilms tumor 17 (Wilms_T17)


title: Training12


title: Genomic DNA from wilms tumor 14 (Wilms_T14)


title: Sham 12 hours replicate rat #32


title: Training7

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355324


title: Training5


title: Sham 6 hours replicate rat #15

value: 6 hours


title: Sham 6 hours replicate rat #14


title: Training8


title: Genomic DNA from wilms tumor 15 (Wilms_T15)


title: Sham 6 hours replicate rat #16


title: Training4

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355322


title: Genomic DNA from thyroid normal tissue 5 (ThyPTC_N5)

source_name: thyroid normal tissue

value: normal


title: Training6

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355323


title: Training2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355321


title: Sham 3 hours replicate rat #38

value: 3 hours


title: Genomic DNA from wilms tumor 13 (Wilms_T13)


title: Training1

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355320


title: Sham 3 hours replicate rat #37


title: Sham 3 hours replicate rat #36


title: Indole treated at specific growth rate 0.5h-1 16h

city: New Delhi

first: Krishna

middle: Jyoti

last: Mukherjee

email: anuradha.bharara@gmail.com, ashishji101@gmail.com, shubhashreemahalik@gmail.com, kjmukherjee@mail.jnu.ac.in

state: delhi

address: New Mehrauli Road

department: School Of Biotechnology

country: India

institute: Jawaharlal Nehru University

description: Study of the genes responsible for diverting the metabolic flux specifically towards product formation. for this study we have used quiescent-cell (Q-cell) expression system, in which a plasmid-encoded protein is expressed in nongrowing but metabolically active cells.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Average Normalization using GeneChip Operating Software Version 1.4

label: Biotin

organism: Escherichia coli

source_name: Escherichia coli

label_protocol: Affymetrix protocol

growth_protocol: Fed batch high cell density cultivation

extract_protocol: Qiagen RNA extraction kit

treatment_protocol: Culture samples frozen in liquid methanol

tag: specific growth rate

tag: treatment group

value: indole treated

tag: time post-induction


title: PH 72 hours replicate rat #21

value: Partial Hepatectomy


title: Indole treated at specific growth rate 0.5h-1 10h


title: Indole treated at specific growth rate 0.5h-1 5h


title: Genomic DNA from wilms tumor 12 (Wilms_T12)

value: Wilms


title: Genomic DNA from wilms tumor 11 (Wilms_T11)


title: Genomic DNA from wilms tumor 10 (Wilms_T10)


title: Control Strain at specific growth rate 0.5h-1 10h

value: control


title: Indole treated at specific growth rate 0.5h-1 8h


title: Control Strain at specific growth rate 0.5h-1 16h


title: PH 72 hours replicate rat #5

value: Sprague-Dawley

value: liver


title: Indole treated at specific growth rate 0.5h-1 0h


title: Genomic DNA from wilms normal tissue 9 (Wilms_N9)

source_name: wilms normal tissue


title: Control Strain at specific growth rate 0.5h-1 20h


title: Control Strain at specific growth rate 0.5h-1 0h


title: Control Strain at specific growth rate 0.5h-1 6h


title: Genomic DNA from wilms tumor 1 (Wilms_T1)


title: PH 72 hours replicate rat #19

value: 72 hours


title: PH 48 hours replicate rat #45

value: synthetic DNA oligos corrresponding to human miRNAs


title: Control Strain at specific growth rate 0.5h-1 8h


title: Genomic DNA from wilms normal tissue 8 (Wilms_N8)


title: Genomic DNA from wilms normal tissue 6 (Wilms_N6)


title: PH 48 hours replicate rat #44

value: 48 hours


title: F2 Liver Control Pool (n=299) vs. 131319

city: Seattle

first: Wan-Lin

last: Su

state: WA

address: 401 Terry Ave N

institute: Rosetta Inpharmatics (a wholly owned subsidiary of Merck & Co., Inc.)

description: Expression profiling of liver tissue from an F2 intercross between strains C57BL/6J and DBA/2J

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al. Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: F2 Liver Control Pool (n=299)

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment


title: F2 Liver Control Pool (n=299) vs. 131320

value: F2 intercross between strains C57BL/6J and DBA/2J


title: F2 Liver Control Pool (n=299) vs. 131332


title: Genomic DNA from wilms normal tissue 5 (Wilms_N5)


title: F2 Liver Control Pool (n=299) vs. 131318


title: F2 Liver Control Pool (n=299) vs. 131344


title: Genomic DNA from wilms normal tissue 3 (Wilms_N3)


title: PH 48 hours replicate rat #4


title: Genomic DNA from wilms normal tissue 4 (Wilms_N4)


title: Genomic DNA from wilms normal tissue 26 (Wilms_N26)


title: F2 Liver Control Pool (n=299) vs. 131330


title: PH 36 hours replicate rat #7

value: 36 hours


title: F2 Liver Control Pool (n=299) vs. 131331


title: F2 Liver Control Pool (n=299) vs. 131307


title: F2 Liver Control Pool (n=299) vs. 131306


title: F2 Liver Control Pool (n=299) vs. 131343


title: F2 Liver Control Pool (n=299) vs. 131342


title: F2 Liver Control Pool (n=299) vs. 131314


title: F2 Liver Control Pool (n=299) vs. 131312


title: PH 36 hours replicate rat #9


title: PH 24 hours replicate rat #39

value: 24 hours


title: F2 Liver Control Pool (n=299) vs. 131338


title: Genomic DNA from wilms normal tissue 24 (Wilms_N24)


title: Genomic DNA from wilms normal tissue 25 (Wilms_N25)


title: F2 Liver Control Pool (n=299) vs. 131308


title: F2 Liver Control Pool (n=299) vs. 131313


title: Genomic DNA from wilms normal tissue 22 (Wilms_N22)


title: Genomic DNA from wilms normal tissue 23 (Wilms_N23)


title: PH 18 hours replicate rat #25

value: 18 hours


title: Genomic DNA from wilms normal tissue 21 (Wilms_N21)


title: PH 18 hours replicate rat #8


title: PH 24 hours replicate rat #3


title: PH 12 hours replicate rat #29

value: 12 hours


title: F2 Liver Control Pool (n=299) vs. 131336


title: F2 Liver Control Pool (n=299) vs. 131337


title: PH 18 hours replicate rat #24


title: F2 Liver Control Pool (n=299) vs. 131325


title: PH 24 hours replicate rat #40


title: Genomic DNA from wilms normal tissue 2 (Wilms_N2)


title: F2 Liver Control Pool (n=299) vs. 131326


title: F2 Liver Control Pool (n=299) vs. 131275


title: F2 Liver Control Pool (n=299) vs. 131324


title: F2 Liver Control Pool (n=299) vs. 131273


title: F2 Liver Control Pool (n=299) vs. 131274


title: F2 Liver Control Pool (n=299) vs. 131348


title: F2 Liver Control Pool (n=299) vs. 131261


title: F2 Liver Control Pool (n=299) vs. 131350


title: F2 Liver Control Pool (n=299) vs. 131263


title: Genomic DNA from wilms normal tissue 20 (Wilms_N20)


title: F2 Liver Control Pool (n=299) vs. 131287


title: F2 Liver Control Pool (n=299) vs. 131349


title: PH 12 hours replicate rat #6


title: PH 36 hours replicate rat #18


title: Genomic DNA from wilms normal tissue 19 (Wilms_N19)


title: Genomic DNA from wilms normal tissue 18 (Wilms_N18)


title: PH 36 hours replicate rat #17


title: Genomic DNA from wilms normal tissue 17 (Wilms_N17)


title: PH 36 hours replicate rat #1


title: F2 Liver Control Pool (n=299) vs. 131285


title: F2 Liver Control Pool (n=299) vs. 131286


title: F2 Liver Control Pool (n=299) vs. 131281


title: Genomic DNA from wilms normal tissue 15 (Wilms_N15)


title: F2 Liver Control Pool (n=299) vs. 131280


title: F2 Liver Control Pool (n=299) vs. 131293


title: F2 Liver Control Pool (n=299) vs. 131279


title: PH 3 hours replicate rat #34


title: PH 3 hours replicate rat #2


title: F2 Liver Control Pool (n=299) vs. 131292


title: F2 Liver Control Pool (n=299) vs. 131269


title: F2 Liver Control Pool (n=299) vs. 131291


title: F2 Liver Control Pool (n=299) vs. 131268


title: Genomic DNA from wilms normal tissue 14 (Wilms_N14)


title: Genomic DNA from wilms normal tissue 16 (Wilms_N16)


title: Genomic DNA from wilms normal tissue 13 (Wilms_N13)


title: Genomic DNA from lung tumor 8 (Lung_T8)

source_name: lung tumor

value: lung

value: tumor


title: Genomic DNA from wilms normal tissue 1 (Wilms_N1)

value: normal


title: Genomic DNA from lung tumor 9 (Lung_T9)


title: Genomic DNA from wilms normal tissue 11 (Wilms_N11)


title: Genomic DNA from wilms normal tissue 12 (Wilms_N12)


title: Genomic DNA from wilms normal tissue 10 (Wilms_N10)


title: Genomic DNA from lung tumor 7 (Lung_T7)


title: Genomic DNA from lung tumor 3 (Lung_T3)


title: Genomic DNA from lung tumor 4 (Lung_T4)


title: Genomic DNA from lung tumor 5 (Lung_T5)


title: F2 Liver Control Pool (n=299) vs. 131267


title: F2 Liver Control Pool (n=299) vs. 131257


title: F2 Liver Control Pool (n=299) vs. 131256


title: F2 Liver Control Pool (n=299) vs. 131255


title: PH 3 hours replicate rat #35

value: 3 hours


title: F2 Liver Control Pool (n=299) vs. 131215


title: F2 Liver Control Pool (n=299) vs. 131214


title: F2 Liver Control Pool (n=299) vs. 131225


title: F2 Liver Control Pool (n=299) vs. 131236


title: F2 Liver Control Pool (n=299) vs. 131227


title: Genomic DNA from lung tumor 24 (Lung_T24)


title: Genomic DNA from lung tumor 25 (Lung_T25)


title: Genomic DNA from lung tumor 23 (Lung_T23)


title: F2 Liver Control Pool (n=299) vs. 131226


title: F2 Liver Control Pool (n=299) vs. 131213


title: F2 Liver Control Pool (n=299) vs. 131234


title: Genomic DNA from lung tumor 22 (Lung_T22)


title: F2 Liver Control Pool (n=299) vs. 131221


title: F2 Liver Control Pool (n=299) vs. 131201


title: F2 Liver Control Pool (n=299) vs. 131220


title: F2 Liver Control Pool (n=299) vs. 131202


title: F2 Liver Control Pool (n=299) vs. 131219


title: F2 Liver Control Pool (n=299) vs. 131251


title: F2 Liver Control Pool (n=299) vs. 131250


title: F2 Liver Control Pool (n=299) vs. 131249


title: Genomic DNA from lung tumor 21 (Lung_T21)


title: F2 Liver Control Pool (n=299) vs. 131241


title: F2 Liver Control Pool (n=299) vs. 131208


title: F2 Liver Control Pool (n=299) vs. 131209


title: F2 Liver Control Pool (n=299) vs. 131233


title: F2 Liver Control Pool (n=299) vs. 131242


title: F2 Liver Control Pool (n=299) vs. 131232


title: Genomic DNA from lung tumor 2 (Lung_T2)


title: Genomic DNA from lung tumor 20 (Lung_T20)


title: F2 Liver Control Pool (n=299) vs. 131207


title: F2 Liver Control Pool (n=299) vs. 131231


title: F2 Liver Control Pool (n=299) vs. 131152


title: F2 Liver Control Pool (n=299) vs. 131136


title: F2 Liver Control Pool (n=299) vs. 131240


title: F2 Liver Control Pool (n=299) vs. 131203


title: F2 Liver Control Pool (n=299) vs. 131235


title: F2 Liver Control Pool (n=299) vs. 131135


title: F2 Liver Control Pool (n=299) vs. 131153


title: F2 Liver Control Pool (n=299) vs. 131154


title: Genomic DNA from lung tumor 19 (Lung_T19)


title: Genomic DNA from lung normal tissue 17 (Lung_N17)

source_name: lung normal tissue


title: Genomic DNA from lung normal tissue 16 (Lung_N16)


title: Genomic DNA from lung normal tissue 15 (Lung_N15)


title: Genomic DNA from lung tumor 14 (Lung_T14)


title: Genomic DNA from lung normal tissue 18 (Lung_N18)


title: Genomic DNA from lung tumor 13 (Lung_T13)


title: F2 Liver Control Pool (n=299) vs. 131189


title: Genomic DNA from lung tumor 11 (Lung_T11)


title: Genomic DNA from lung tumor 12 (Lung_T12)


title: F2 Liver Control Pool (n=299) vs. 131134


title: Genomic DNA from lung tumor 10 (Lung_T10)


title: F2 Liver Control Pool (n=299) vs. 131187


title: F2 Liver Control Pool (n=299) vs. 131174


title: F2 Liver Control Pool (n=299) vs. 131173


title: F2 Liver Control Pool (n=299) vs. 131142


title: F2 Liver Control Pool (n=299) vs. 131141


title: F2 Liver Control Pool (n=299) vs. 131140


title: F2 Liver Control Pool (n=299) vs. 131182


title: F2 Liver Control Pool (n=299) vs. 131197


title: Genomic DNA from lung tumor 1 (Lung_T1)


title: F2 Liver Control Pool (n=299) vs. 131172


title: F2 Liver Control Pool (n=299) vs. 131188


title: F2 Liver Control Pool (n=299) vs. 131196


title: F2 Liver Control Pool (n=299) vs. 131106


title: F2 Liver Control Pool (n=299) vs. 131129


title: F2 Liver Control Pool (n=299) vs. 131130


title: F2 Liver Control Pool (n=299) vs. 131107


title: F2 Liver Control Pool (n=299) vs. 131183


title: Genomic DNA from lung normal tissue 9 (Lung_N9)


title: Genomic DNA from lung normal tissue 8 (Lung_N8)


title: F2 Liver Control Pool (n=299) vs. 131181


title: Genomic DNA from lung normal tissue 5 (Lung_N5)


title: Genomic DNA from lung normal tissue 4 (Lung_N4)


title: F2 Liver Control Pool (n=299) vs. 131195


title: F2 Liver Control Pool (n=299) vs. 131108


title: F2 Liver Control Pool (n=299) vs. 131087


title: F2 Liver Control Pool (n=299) vs. 131071


title: Genomic DNA from lung normal tissue 3 (Lung_N3)


title: F2 Liver Control Pool (n=299) vs. 131128


title: F2 Liver Control Pool (n=299) vs. 131086


title: F2 Liver Control Pool (n=299) vs. 131095


title: F2 Liver Control Pool (n=299) vs. 131096


title: Genomic DNA from lung normal tissue 25 (Lung_N25)


title: F2 Liver Control Pool (n=299) vs. 131070


title: Genomic DNA from lung normal tissue 24 (Lung_N24)


title: Genomic DNA from lung normal tissue 23 (Lung_N23)


title: F2 Liver Control Pool (n=299) vs. 131103


title: F2 Liver Control Pool (n=299) vs. 131102


title: Genomic DNA from lung normal tissue 21 (Lung_N21)


title: F2 Liver Control Pool (n=299) vs. 131069


title: Genomic DNA from lung normal tissue 22 (Lung_N22)


title: F2 Liver Control Pool (n=299) vs. 131097


title: F2 Liver Control Pool (n=299) vs. 131124


title: F2 Liver Control Pool (n=299) vs. 131082


title: F2 Liver Control Pool (n=299) vs. 131080


title: Genomic DNA from lung normal tissue 2 (Lung_N2)


title: F2 Liver Control Pool (n=299) vs. 131081


title: BT5

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing: RMA (Robust Multichip Average) generated expression value using Ensembl v58 CDF file

source_name: Large airway epithelial cells

label_protocol: Affymetrix Suggested Protocol

extract_protocol: RNA was extracted by using TRIzol Reagent (Invitrogen) according to the manufacturer's protocol

tag: cell type

value: large airway epithelial cells

tag: disease state

value: Lung Cancer

value: F

tag: packyears

tag: smoking status

value: Current

tag: years passed since quitting

tag: cancer stage

value: IV

tag: histology

value: Non-Small-Cell Carcinoma


title: F2 Liver Control Pool (n=299) vs. 131027

tag: tissue

value: liver

tag: strain


title: F2 Liver Control Pool (n=299) vs. 131091


title: F2 Liver Control Pool (n=299) vs. 131089


title: F2 Liver Control Pool (n=299) vs. 131090


title: F2 Liver Control Pool (n=299) vs. 131035


title: F2 Liver Control Pool (n=299) vs. 131025


title: F2 Liver Control Pool (n=299) vs. 131033


title: Genomic DNA from lung normal tissue 19 (Lung_N19)

tag: batch

tag: tissue type

tag: age


title: F2 Liver Control Pool (n=299) vs. 131034


title: F2 Liver Control Pool (n=299) vs. 131101


title: F2 Liver Control Pool (n=299) vs. 131122


title: BT4

tag: gender

value: M

value: Former

value: Adenocarcinoma


title: BT6

value: IB

value: Squamous Cell Carcinoma


title: F2 Liver Control Pool (n=299) vs. 131005

value: F2 intercross between strains C57BL/6J and DBA/2J


title: Genomic DNA from lung normal tissue 20 (Lung_N20)

value: lung


title: Genomic DNA from lung tumor 18 (Lung_T18)

value: tumor


title: Genomic DNA from lung tumor 17 (Lung_T17)


title: BT2

value: IIA


title: BT1

value: IA


title: F2 Liver Control Pool (n=299) vs. 131006


title: F2 Liver Control Pool (n=299) vs. 131123


title: Genomic DNA from lung tumor 16 (Lung_T16)


title: BT10

value: large airway epithelial cells

value: No Lung Cancer

value: NO CANCER

value: Granuloma


title: BT14

value: Lung Cancer

value: IIB

value: Squamous cell carcinoma


title: BT17

value: IV

value: Large cell carcinoma


title: BT11

value: F

value: Former

value: Adenocarcinoma


title: F2 Liver Control Pool (n=299) vs. 131053

value: liver

value: F2 intercross between strains C57BL/6J and DBA/2J


title: F2 Liver Control Pool (n=299) vs. 131051


title: F2 Liver Control Pool (n=299) vs. 131015


title: F2 Liver Control Pool (n=299) vs. 131052


title: Genomic DNA from lung tumor 15 (Lung_T15)

value: lung

value: tumor


title: F2 Liver Control Pool (n=299) vs. 131032


title: Genomic DNA from lung normal tissue 14 (Lung_N14)

value: normal


title: F2 Liver Control Pool (n=299) vs. 131031


title: BT3

value: large airway epithelial cells

value: M

value: less than 1

value: Organizing pneumonitis


title: F2 Liver Control Pool (n=299) vs. 131014


title: F2 Liver Control Pool (n=299) vs. 131030


title: Genomic DNA from lung normal tissue 11 (Lung_N11)


title: BT18

value: No Lung Cancer

value: NO CANCER

value: Normal


title: Genomic DNA from lung normal tissue 7 (Lung_N7)


title: Genomic DNA from lung normal tissue 10 (Lung_N10)


title: F2 Liver Control Pool (n=299) vs. 131004


title: F2 Liver Control Pool (n=299) vs. 131058


title: BT16

value: Chronic inflammation


title: Genomic DNA from lung normal tissue 1 (Lung_N1)


title: F2 Liver Control Pool (n=299) vs. 131059


title: F2 Liver Control Pool (n=299) vs. 131013


title: BT13

value: Sarcoid


title: F2 Liver Control Pool (n=299) vs. 131041


title: F2 Liver Control Pool (n=299) vs. 131057


title: Genomic DNA from colon tumor 8 (Colon_T8)

value: colon


title: Carcinoma 25

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4471A-025987; miRBase release 14) for 18-20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 10.7.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 50% missing values across the samples were included in the further analysis.

source_name: Carcinoma from patient with sporadic adrenocortical cancer

label_protocol: 120 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manufacturer.

value: adrenocortical carcinoma

tag: tissue state

value: Fresh frozen tissue

tag: survival (months)

tag: status at the end of follow up

value: Dead

tag: presence of metastasis

value: Liver

tag: age at diagnosis


title: Carcinoma 24

description: miRNA expression profile

value: Alive

value: No

value: F


title: F2 Liver Control Pool (n=299) vs. 131040

value: liver

value: F2 intercross between strains C57BL/6J and DBA/2J


title: Genomic DNA from lung normal tissue 12 (Lung_N12)

value: lung

value: normal


title: HUES6 hESCs biological rep 1-2 [miRNA]

city: New York

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
HK_HUES6-1
miRNA expression data from SSEA4+ HUES6 hESC line

hyb_protocol: miRNA were hybridized for 20 hr at 55C on Agilent Human microRNA Array.Slides were washed and stained in the Agilent recommended protocol.

scan_protocol: Slides were scanned using the Agilent Scanner.

data_processing: The data were analyzed with Feature extraction using Agilent default analysis settings.

source_name: hESCs with SSEA4+

label_protocol: miRNA were prepared according to the standard Agilent protocol from 100ng total RNA.

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

value: female

tag: cell line

value: HUES6 hESC line


title: HUES6 hESCs biological rep 3 [miRNA]

description:
HK_HUES6-3
miRNA expression data from SSEA4+ HUES6 hESC line


title: Carcinoma 23

description: miRNA expression profile

value: Lung


title: Genomic DNA from colon tumor 7 (Colon_T7)

source_name: colon tumor

value: tumor


title: HUES6 hESCs biological rep 2 [miRNA]

description:
HK_HUES6-2
miRNA expression data from SSEA4+ HUES6 hESC line


title: I6 hESCs biological rep 1-2 [miRNA]

description:
HK_I6-1
miRNA expression data from SSEA4+ I6 hESC line

value: male

value: I6 hESC line


title: I6 hESCs biological rep 2 [miRNA]

description:
HK_I6-2
miRNA expression data from SSEA4+ I6 hESC line


title: Carcinoma 21

description: miRNA expression profile

value: adrenocortical carcinoma


title: F2 Liver Control Pool (n=299) vs. 131039


title: I4 hESCs biological rep 3 [miRNA]

description:
HK_I4-3
miRNA expression data from SSEA4+ I4 hESC line

value: I4 hESC line


title: Genomic DNA from colon tumor 5 (Colon_T5)

value: colon


title: I6 hESCs biological rep 1-1 [miRNA]


title: Genomic DNA from colon adenoma 6 (Colon_T6)

source_name: colon adenoma

value: adenoma


title: Carcinoma 20

description: miRNA expression profile

value: Fresh frozen tissue

value: Alive

value: M


title: HUES6 hESCs biological rep 1-1 [miRNA]


title: Carcinoma 19

description: miRNA expression profile

value: No

value: F


title: Genomic DNA from colon tumor 3 (Colon_T3)


title: Genomic DNA from colon tumor 4 (Colon_T4)


title: I4 hESCs biological rep 2 [miRNA]

description:
HK_I4-2
miRNA expression data from SSEA4+ I4 hESC line


title: Carcinoma 17

description: miRNA expression profile

value: Dead -DOD

value: Liver


title: Carcinoma 18

description: miRNA expression profile


title: I4 hESCs biological rep 1-1 [miRNA]

description:
HK_I4-1
miRNA expression data from SSEA4+ I4 hESC line

value: female


title: H9 hESCs biological rep 3 [miRNA]

description:
HK_H9-3
miRNA expression data from SSEA4+ H9 hESC line

value: H9 hESC line


title: H9 hESCs biological rep 1-1 [miRNA]

description:
HK_H9-1
miRNA expression data from SSEA4+ H9 hESC line


title: I4 hESCs biological rep 1-2 [miRNA]


title: Genomic DNA from colon tumor 25 (Colon_T25)


title: Carcinoma 16

description: miRNA expression profile

value: Liver, os, lung


title: Genomic DNA from colon adenoma 23 (Colon_T23)


title: Genomic DNA from colon adenoma 24 (Colon_T24)


title: Genomic DNA from colon adenoma 27 (Colon_T27)


title: Carcinoma 13

description: miRNA expression profile

value: Lung


title: Carcinoma 14

description: miRNA expression profile


title: Genomic DNA from colon adenoma 22 (Colon_T22)


title: Carcinoma 15

description: miRNA expression profile


title: Carcinoma 12

description: miRNA expression profile

value: Dead

value: Liver, Bone


title: F2 Liver Control Pool (n=299) vs. 131026

value: liver

value: F2 intercross between strains C57BL/6J and DBA/2J


title: H9 hESCs biological rep 1-2 [miRNA]


title: Genomic DNA from colon adenoma 21 (Colon_T21)

value: colon


title: H9 hESCs biological rep 2 [miRNA]

description:
HK_H9-2
miRNA expression data from SSEA4+ H9 hESC line


title: total RNA, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10h, biological replicate #3

city: Mattarello - Trento

first: Toma

last: Tebaldi

state: Trento

address: via delle Regole 101

country: Italy

institute: Centre for Integrative Biology

description: Total RNA sample extracted from doxorubicin plus Tumor Necrosis Factor α (TNFα) treated MCF7 cells grown in estrogen-depleted conditions.

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol: “One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling)”: (https://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-Color_v6.0.pdf).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3). The scanned TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol GE1_107_Sep09.

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE1_107_Sep09) was used for data extraction, background correction and flagging of non-uniform features. The output of Feature Extraction was analyzed with the R software environment for statistical computing (http://www.r-project.org/) and the Bioconductor library of biostatistical packages (http://www.bioconductor.org/). Signal intensities across arrays were normalized with the quantile normalization algorithm.

source_name: MCF7 cells, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #3

growth_protocol: MCF7 cells were cultured in Dulbecco Modified Eagle Medium (D-MEM) without Phenol Red supplemented with 10% Dextrane-Charcoal treated fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using the Agilent Total RNA Isolation Mini kit according to the manufacturer’s protocol. RNA was quantified using a spectrophotometer and its quality was checked by agarose gel electrophoresis as well as by Agilent 2100 Bioanalyzer platform, following the manifacturer’s guidelines for sample preparation and analysis of data (Agilent 2100 Bioanalyzer 2100 Expert User's Guide, http://www.agilent.com).

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with doxorubicin and TNFα for 10 hours at a final concentration of respectively 1.5 µM and 5 ng/ml.

value: MCF7 cells

tag: agent

value: doxorubicin plus and Tumor Necrosis Factor α (TNFα)

tag: time point

value: 10 hours

tag: population

value: total RNA

tag: biological replicate


title: Genomic DNA from colon adenoma 19 (Colon_T19)

value: adenoma


title: Carcinoma 11

description: miRNA expression profile

value: adrenocortical carcinoma

value: Fresh frozen tissue

value: M


title: LS-98-treated A2780 cell replicate 1

city: Shanghai

first: Tau

last: Chen

address: Rm 429, No. 41 Building, 320 Yueyang Road, Shanghai, China (200031)

institute: Institute for Nutritional Sciences (INS)

description: Biological replicate 1 of 2. control vehicle-treated A2780  vs. LS-98 treated-A2780 cells

hyb_protocol: Please see manufacturer's web site at http://www.agilent.com/

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

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: control vehicle-treated-treated   A2780-1

growth_protocol: A2780 and OVCAR-3 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin according to the ATCC‟s instructions

extract_protocol: Total RNA are isolated from cell pellets using TriZol reagent(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up

treatment_protocol: A2780 and OVCAR-3 cells were seeded in 10 cm dishes and treated with 5μM LS-98 or vehicle (DMSO; <0.1% of the final incubation concentration) for 24 hours

value: control

source_name: LS-98 treated A2780-1


title: total RNA, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10h, biological replicate #2

source_name: MCF7 cells, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #2


title: Carcinoma 10

description: miRNA expression profile

value: Alive

value: No


title: LS-98-treated OVCAR-3 cell replicate 2

description: Biological replicate 2 of 2. control vehicle-treated OVCAR-3  vs. LS-98 treated-OVCAR-3 cells

source_name: control vehicle-treated-treated   OVCAR-3-2

label_protocol: Please see manufacturer's web site at http://www.agilent.com/

source_name: LS-98 treated OVCAR-3-2


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) and TNFα treated, 10h, biological replicate #3

description: Total RNA sample extracted from doxorubicin plus 17-β estradiol (E2) physiological dose and Tumor Necrosis Factor α (TNFα) treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose and Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #3

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with doxorubicin, E2 and TNFα for 10 hours at a final concentration of respectively 1.5 µM, 1 nM and 5 ng/ml.


title: LS-98-treated OVCAR-3 cell replicate 1

description: Biological replicate 1 of 2. control vehicle-treated OVCAR-3  vs. LS-98 treated-OVCAR-3 cells

source_name: control vehicle-treated-treated   OVCAR-3-1

source_name: LS-98 treated OVCAR-3-1


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) and TNFα treated, 10h, biological replicate #2

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose and Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #2


title: total RNA, MCF7 5-Fluoro-Uracil (5FU) plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #2

description: Total RNA sample extracted from 5-Fluoro-Uracil (5FU) plus 17-β estradiol (E2) pharmacological dose treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) plus 17-β estradiol (E2) pharmacological dose treated, 10 hours, total RNA, biological replicate #2

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with 5FU and E2 for 10 hours at a final concentration respectively of 375 μM and 100 nM.


title: total RNA, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10h, biological replicate #1

source_name: MCF7 cells, doxorubicin plus Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #1


title: total RNA, MCF7 5-Fluoro-Uracil (5FU) plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #3

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) plus 17-β estradiol (E2) pharmacological dose treated, 10 hours, total RNA, biological replicate #3


title: Genomic DNA from colon adenoma 18 (Colon_T18)


title: LS-98-treated A2780 cell replicate 2

description: Biological replicate 2 of 2. control vehicle-treated A2780  vs. LS-98 treated-A2780 cells

source_name: control vehicle-treated-treated   A2780-2

source_name: LS-98 treated A2780-2


title: Carcinoma 9

description: miRNA expression profile

source_name: Carcinoma from patient with sporadic adrenocortical cancer


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) and TNFα treated, 10h, biological replicate #1

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose and Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #1


title: Carcinoma 8

description: miRNA expression profile

value: Dead -DOD

value: Liver, lung, bone

value: F


title: Genomic DNA from colon adenoma 17 (Colon_T17)

source_name: colon adenoma


title: Genomic DNA from colon adenoma 14 (Colon_T14)


title: total RNA, MCF7 5-Fluoro-Uracil (5FU) plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #1

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) plus 17-β estradiol (E2) pharmacological dose treated, 10 hours, total RNA, biological replicate #1


title: Carcinoma 7

description: miRNA expression profile

value: Dead


title: Carcinoma 6

description: miRNA expression profile


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) treated, 10h, biological replicate #1

description: Total RNA sample extracted from doxorubicin plus 17-β estradiol (E2) (physiological dose) treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose treated, 10 hours, total RNA, biological replicate #1

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with doxorubicin and E2 for 10 hours at a final concentration of respectively 1.5 µM and 1 nM.


title: Genomic DNA from colon adenoma 11 (Colon_T11)


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) treated, 10h, biological replicate #3

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose treated, 10 hours, total RNA, biological replicate #3


title: Genomic DNA from colon tumor 10 (Colon_T10)

source_name: colon tumor

value: tumor


title: Carcinoma 3

description: miRNA expression profile


title: total RNA, Tumor Necrosis Factor α (TNFα) treated, 10 h, biological replicate #3

description: Total RNA sample extracted from Tumor Necrosis Factor α (TNFα) treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #3

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated with TNFα for 10 hours at a final concentration of 5 ng/ml.

value: Tumor Necrosis Factor α (TNFα)


title: Genomic DNA from colon tumor 1 (Colon_T1)

value: colon


title: Carcinoma 1

description: miRNA expression profile

value: Liver


title: total RNA, doxorubicin plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #1

description: Total RNA sample extracted from doxorubicin plus 17-β estradiol (E2) (pharmacological dose) treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) treated (pharmacological dose), 10 hours, total RNA, biological replicate #1

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated at the same time with doxorubicin and E2 for 10 hours at a final concentration of respectively 1.5 µM and 100 nM.

value: MCF7 cells

value: doxorubicin plus 17-β estradiol (E2) pharmacological dose

value: 10 hours


title: Genomic DNA from colon normal tissue 9 (Colon_N9)

source_name: colon normal tissue

value: normal


title: Genomic DNA from colon tumor 13 (Colon_T13)


title: total RNA, Tumor Necrosis Factor α (TNFα) treated, 10 h, biological replicate #2

source_name: MCF7 cells, Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #2

value: total RNA


title: total RNA, 5-Fluoro-Uracil (5FU) treated, 10h, biological replicate #3

description: Total RNA sample extracted from 5-Fluoro-Uracil (5FU)  treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) treated, 10 hours, total RNA, biological replicate #3

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated with 5FU for 10 hours at a final concentration of 375 μM.

value: 5-Fluoro-Uracil (5FU)


title: total RNA, doxorubicin plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #3

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) treated (pharmacological dose), 10 hours, total RNA, biological replicate #3


title: total RNA, 5-Fluoro-Uracil (5FU) treated, 10h, biological replicate #2

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) treated, 10 hours, total RNA, biological replicate #2


title: total RNA, 17-β estradiol, physiological dose, treated, 10h, biological replicate #3

description: Total RNA sample extracted from 17-β estradiol (E2) physiological dose treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, 17-β estradiol (E2) treated, physiological dose,10 hours, total RNA, biological replicate #3

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated with E2 for 10 hours at a final concentration of 1 nM.

value: 17-β estradiol (E2) physiological dose


title: total RNA, Tumor Necrosis Factor α (TNFα) treated, 10 h, biological replicate #1

source_name: MCF7 cells, Tumor Necrosis Factor α (TNFα) treated, 10 hours, total RNA, biological replicate #1


title: total RNA, 17-β estradiol, physiological dose, treated, 10h, biological replicate #1

source_name: MCF7 cells, 17-β estradiol (E2) treated, physiological dose,10 hours, total RNA, biological replicate #1


title: total RNA, 5-Fluoro-Uracil (5FU) treated, 10h, biological replicate #1

source_name: MCF7 cells, 5-Fluoro-Uracil (5FU) treated, 10 hours, total RNA, biological replicate #1


title: total RNA, 17-β estradiol, pharmacological dose, treated, 10h, biological replicate #3

description: Total RNA sample extracted from 17-β estradiol (E2) pharmacological dose treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, 17-β estradiol (E2) treated, pharmacological dose,10 hours, total RNA, biological replicate #3

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated with E2 for 10 hours at a final concentration of 100 nM.


title: Carcinoma 5

description: miRNA expression profile

source_name: Carcinoma from patient with sporadic adrenocortical cancer

value: adrenocortical carcinoma

value: Fresh frozen tissue

value: Lung

value: M


title: total RNA, doxorubicin plus 17-β estradiol (physiological dose) treated, 10h, biological replicate #2

source_name: MCF7 cells, doxorubicin plus 17-β estradiol (E2) physiological dose treated, 10 hours, total RNA, biological replicate #2


title: total RNA, 17-β estradiol, physiological dose, treated, 10h, biological replicate #2

source_name: MCF7 cells, 17-β estradiol (E2) treated, physiological dose,10 hours, total RNA, biological replicate #2


title: Adenoma 29

description: miRNA expression profile

source_name: Adenoma from patient with sporadic adrenocortical tumor

value: adrenocortical adenoma

value: No


title: total RNA, doxorubicin plus 17-β estradiol (pharmacological dose) treated, 10h, biological replicate #2


title: total RNA, 17-β estradiol, pharmacological dose, treated, 10h, biological replicate #2

source_name: MCF7 cells, 17-β estradiol (E2) treated, pharmacological dose,10 hours, total RNA, biological replicate #2

value: 17-β estradiol (E2) pharmacological dose


title: Genomic DNA from colon normal tissue 8 (Colon_N8)


title: Genomic DNA from colon normal tissue 7 (Colon_N7)


title: Adenoma 28

description: miRNA expression profile

value: F


title: Adenoma 27

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 5 (Colon_N5)

value: colon


title: Adenoma 24

description: miRNA expression profile


title: Adenoma 25

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 6 (Colon_N6)


title: I6 hESCs biological rep 3 [miRNA]

description:
HK_I6-3
miRNA expression data from SSEA4+ I6 hESC line

source_name: hESCs with SSEA4+

value: male

value: I6 hESC line


title: Genomic DNA from colon normal tissue 4 (Colon_N4)


title: total RNA, doxorubicin treated, 10h, biological replicate #6

description: Total RNA sample extracted from doxorubicin treated MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #6

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were treated with doxorubicin for 10 hours at a final concentration of 1.5 μM.

value: MCF7 cells

value: doxorubicin


title: Adenoma 23

description: miRNA expression profile


title: Adenoma 20

description: miRNA expression profile


title: total RNA, doxorubicin treated, 10h, biological replicate #5

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #5

value: 10 hours


title: total RNA, doxorubicin treated, 10h, biological replicate #7

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #7

value: total RNA


title: Adenoma 19

description: miRNA expression profile


title: Adenoma 22

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 3 (Colon_N3)

source_name: colon normal tissue

value: normal


title: total RNA, doxorubicin treated, 10h, biological replicate #3

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #3


title: total RNA, doxorubicin treated, 10h, biological replicate #1

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #1


title: total RNA, 17-β estradiol, pharmacological dose, treated, 10h, biological replicate #1

source_name: MCF7 cells, 17-β estradiol (E2) treated, pharmacological dose,10 hours, total RNA, biological replicate #1


title: Genomic DNA from colon normal tissue 27 (Colon_N27)


title: Genomic DNA from colon normal tissue 26 (Colon_N26)


title: Adenoma 18

description: miRNA expression profile


title: Adenoma 16

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 24 (Colon_N24)


title: Genomic DNA from colon normal tissue 23 (Colon_N23)


title: total RNA, mock, 10h, biological replicate #6

description: Total RNA sample extracted from mock MCF7 cells grown in estrogen-depleted conditions.

source_name: MCF7 cells, mock treated, 10 hours, total RNA, biological replicate #6

treatment_protocol: MCF7 cells were seeded on 10cm Petri dishes and grown in estrogen-depleted conditions, D-MEM w/o Phenol Red, 10% Dextrane-Charcoal treated serum, 2mM glutamine, 1X penicillin/streptomycin. After 24h cells were mock treated for 10 hours.

value: D-MEM


title: 16HBE_infected_rep4

city: Vancouver

first: Scott

last: Tebbutt

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

institute: UBC - iCAPTURE Centre

description: Gene expression in 16HBE incubated for 6 hours in the presence of A. fumigatus conidiospores

hyb_protocol: Labeled cRNA (1.65μg) was fragmented for 30 minutes, hybridized to microarrays for 17 hours at 65°C in the Agilent hybridization oven, and washed with Agilent wash buffers, according to the manufacturer's protocols.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray Scanner at a resolution of 5μm and Agilent’s Feature Extraction software version 9.1 was used for quantification of signal intensities and to produce a quality control report for each microarray, using the default protocol for a one-colour array.

data_processing: Raw signals were first normalized by flooring all values smaller than 1 to 1, then dividing each value by the median intensity value of the array.

source_name: 16HBE cells incubated  with A. fumigatus conidiospores

label_protocol: Cy3-labeled complementary RNA (cRNA) was generated following Agilent’s Low RNA Input Linear Amplification Protocol, and its quantity and specific activity assessed using a NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: 16HBE cells were maintained at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate. Cells were passaged at confluence.

extract_protocol: Following incubation, cells were lysed in 450μl buffer RLT (Qiagen, Hilden, Germany), and RNA was extracted using the RNeasy Mini Kit with QIAshredder (Qiagen), following the manufacturer’s recommendations. RNA yield from each sample was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Confluent 16HBE monolayers were incubated with A. fumigatus conidiospores at a ratio of 10 conidiospores per cell (Infected), or without condiospores (Control), for 6 hours at 37°C in DMEM supplemented with FBS, antibiotics, sodium pyruvate, and sodium bicarbonate.

value: human bronchial epithelial cell line 16HBE

tag: infection

value: infected with A. fumigatus conidispores


title: total RNA, mock, 10h, biological replicate #4

source_name: MCF7 cells, mock treated, 10 hours, total RNA, biological replicate #4


title: total RNA, mock, 10h, biological replicate #2

source_name: MCF7 cells, mock treated, 10 hours, total RNA, biological replicate #2


title: 16HBE_infected_rep2


title: Genomic DNA from colon normal tissue 25 (Colon_N25)

tag: tissue


title: 16HBE_infected_rep1


title: total RNA, mock, 10h, biological replicate #3

source_name: MCF7 cells, mock treated, 10 hours, total RNA, biological replicate #3


title: 16HBE_uninfected_rep3

description: Gene expression in 16HBE incubated for 6 hours in the absence of A. fumigatus conidiospores

source_name: 16HBE cells incubated without A. fumigatus conidiospores

value: control


title: total RNA, doxorubicin treated, 10h, biological replicate #2

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #2


title: 16HBE_uninfected_rep4


title: Genomic DNA from colon normal tissue 22 (Colon_N22)


title: total RNA, mock, 10h, biological replicate #1

source_name: MCF7 cells, mock, 10 hours, total RNA, biological replicate #1


title: Genomic DNA from colon normal tissue 21 (Colon_N21)


title: Adenoma 14

description: miRNA expression profile

source_name: Adenoma from patient with sporadic adrenocortical tumor

value: Fresh frozen tissue


title: Adenoma 12

description: miRNA expression profile

value: adrenocortical adenoma

value: M


title: Genomic DNA from colon normal tissue 2 (Colon_N2)


title: Genomic DNA from colon normal tissue 19 (Colon_N19)


title: Adenoma 15

description: miRNA expression profile

value: No


title: Adenoma 13

description: miRNA expression profile

value: F


title: Adenoma 11

description: miRNA expression profile


title: Adenoma 10

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 20 (Colon_N20)

value: colon


title: 16HBE_uninfected_rep1


title: Genomic DNA from colon normal tissue 17 (Colon_N17)


title: Genomic DNA from colon normal tissue 16 (Colon_N16)


title: Adenoma 8

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 18 (Colon_N18)


title: Adenoma 7

description: miRNA expression profile


title: 16HBE_uninfected_rep2


title: Genomic DNA from colon normal tissue 15 (Colon_N15)


title: Adenoma 6

description: miRNA expression profile


title: Adenoma 9

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 14 (Colon_N14)


title: Adenoma 5

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 12 (Colon_N12)


title: Adenoma 4

description: miRNA expression profile


title: Genomic DNA from colon normal tissue 11 (Colon_N11)


title: Genomic DNA from colon normal tissue 10 (Colon_N10)


title: LPA, subject 8

city: Lexington

first: Susan

last: Smyth

address: 741 S. Limestone Street

institute: University of Kentucky

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol. Affymetrix GeneChip Scanner 3000.

data_processing: RMA

source_name: murine primary brown adipose tissue culture, LPA

label_protocol: Standard Affymetrix protocol.

growth_protocol: Primary brown adipose tissue (BAT) cell cultures were established as previously reported with some minor modifications (Cannon B., 2001; Néchad M., 1983). Mice were euthanized under aseptic conditions and interscapular BAT (IBAT) dissected, finely minced in digestion buffer containing 123 mM NaCl, 5mM HCl, 1.3 mM CaCl2, 5mM glucose, 1.5% (w/v) crude bovine serum albumin fraction V, 100 mM HEPES, 0.2% collagenase type II (Sigma-Aldrich Corp., St. Louis, MO), pH 7.4, and digested in 10 ml of the same buffer for 30 min at 37°C. The supernatant obtained was then filtered using a 250 µm nylon mesh and kept in ice for 15 minutes to allow fat droplets and mature cells to float. The resulting infranatant was filtered through a 30 µm nylon mesh to enrich the fraction with precursor cells and centrifuged at 700g for 10 min. The pellet obtained was washed once in warm DMEM and resuspended in DMEM medium containing 10% newborn calf serum, 10 mM HEPES, 4mM glutamine, 25 µg/ml sodium ascorbate (Sigma-Aldrich Corp., St. Louis, MO), 100U/ml penicillin and 100mg/ml streptomycin. Cells were seeded onto 35mm dish plates. Insulin treatment was started on day 1 at 50 nM and the concentration increased to 100 nM at day 5 and 200 nM at day 7. Differentiated/confluent cells were collected for biochemical analysis (~day 9).

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: LPA treatment (5 micromolar) at 9 days in vitro

tag: strain

value: male

value: 5 weeks

value: brown adipose tissue culture

tag: treatment

value: lysophosphatidic acid (LPA)


title: LPA, subject 9


title: Adenoma 2

description: miRNA expression profile


title: ATX inhibitor HA155, subject 5

source_name: murine primary brown adipose tissue culture, HA155

treatment_protocol: HA 155 treatment (2.5 micromolar) at 9 days in vitro

value: autotaxin inhibitor HA155


title: LPA, subject 7


title: Genomic DNA from colon normal tissue 1 (Colon_N1)

tag: batch

tag: tissue type


title: control, subject 3

source_name: murine primary brown adipose tissue culture, control

treatment_protocol: DMSO treatment at 9 days in vitro

tag: gender

tag: age

value: DMSO


title: ATX inhibitor HA155, subject 4


title: non-triple negative breast cancer tumor B32

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Tumor tissue from sample B32

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Breast cancer tissue

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf)

growth_protocol: All tumor tissues were collected from IRB 06206 protocol of City of Hope National Medical Center

extract_protocol: Qiagen RNA extraction kit was used according to manufacturer's guide

treatment_protocol: all tumors are pretreatment tumors

tag: disease state

value: non-triple negative breat cancer tumor


title: Adenoma 3

description: miRNA expression profile

tag: tissue state


title: control, subject 1


title: Normal cortex 8

description: miRNA expression profile

source_name: Normal adrenal cortex from patients undergoing nephrectomy

value: Normal adrenal cortex


title: triple negative breast cancer tumor B99

description: Tumor tissue from sample B99

value: triple negative breat cancer tumor


title: triple negative breast cancer tumor B31

description: Tumor tissue from sample B31


title: Genomic DNA from breast tumor 5 (Breast_T5)

source_name: breast tumor

value: breast

value: tumor


title: non-triple negative breast cancer tumor B34

description: Tumor tissue from sample B34


title: non-triple negative breast cancer tumor B33

description: Tumor tissue from sample B33


title: non-triple negative breast cancer tumor B30

description: Tumor tissue from sample B30


title: control, subject 2


title: ATX inhibitor HA155, subject 6


title: non-triple negative breast cancer tumor B27

description: Tumor tissue from sample B27


title: Adenoma 1

description: miRNA expression profile

value: Fresh frozen tissue

tag: presence of metastasis


title: Normal cortex 3

description: miRNA expression profile


title: triple negative breast cancer tumor B26

description: Tumor tissue from sample B26


title: Normal cortex 1

description: miRNA expression profile


title: non-triple negative breast cancer tumor B24

description: Tumor tissue from sample B24


title: Normal cortex 4

description: miRNA expression profile


title: Genomic DNA from breast normal tissue 4 (Breast_N4)

source_name: breast normal tissue

value: normal


title: Genomic DNA from breast normal tissue 3 (Breast_N3)


title: Genomic DNA from breast tumor 25 (Breast_T25)


title: Genomic DNA from breast tumor 24 (Breast_T24)


title: non-triple negative breast cancer tumor B14

description: Tumor tissue from sample B14


title: triple negative breast cancer tumor B12

description: Tumor tissue from sample B12


title: non-triple negative breast cancer tumor B20

description: Tumor tissue from sample B20


title: triple negative breast cancer tumor B23

description: Tumor tissue from sample B23


title: total RNA, doxorubicin treated, 10h, biological replicate #4

source_name: MCF7 cells, doxorubicin treated, 10 hours, total RNA, biological replicate #4

value: MCF7 cells

value: doxorubicin

value: 10 hours

value: total RNA


title: non-triple negative breast cancer tumor B17

description: Tumor tissue from sample B17


title: Genomic DNA from breast tumor 26 (Breast_T26)


title: non-triple negative breast cancer tumor B9

description: Tumor tissue from sample B9


title: Genomic DNA from breast tumor 23 (Breast_T23)


title: non-triple negative breast cancer tumor B8

description: Tumor tissue from sample B8


title: non-triple negative breast cancer tumor B2

description: Tumor tissue from sample B2


title: patient 11

city: Providence

first: Sara

last: Pacheco

state: RI

address: 70 Ship Street, Room 510

department: Pathology and Lab Medicine

institute: Brown University

hyb_protocol: Followed manufacturer's instructions

scan_protocol: Followed manufacturer's instructions

data_processing: Probe cell intensity data from the Affymetrix GeneChips were analyzed using Affymetrix Expression Console software. The application uses the RMA-Sketch workflow analysis as the default to create CHP files. The CHP log2 expression files were then merged in Expression Console with the annotation file and the annotated log2 results were exported as a text file. The previous identification of approximately 3500 unique mRNAs in the ejaculate of fertile males prompted us to limit our mRNA content analysis to ensure that the multiple comparisons of many null genes would not dilute out any potentially important signals. Therefore, we selected a total of 276 genes, including 177 imprinted genes as well as 99 candidate autosomal genes with biallelic expression where an a priori hypothesis for association with subfertility or epigenetic regulation exists. The LIMMA procedure (available through the R package limma) used motility values to fit a simple linear regression model to test, univariately, for each gene, whether changes in motility are associated with mRNA content extent. Resulting p-values were adjusted for multiple comparisons via the R package qvalue, which produced q-values representing false-discovery rate in the same way that p-values represent family-wise error rate. The final result of this analysis was a list of differentially mRNA candidates sorted by q-value, and an estimate of the strength and direction of the association represented by the slope.

source_name: sperm

label_protocol: Followed manufacturer's instructions

extract_protocol:
sperm isolation protcol: Preparing Semen Samples for Separation  1. Determine the number of tubes needed for isolations based on the volume used for DNA/RNA. You will use ¼ of the total semen volume for DNA isolation and the remaining ¾ for RNA isolations.  a. Up to 1 ml of semen can be used per conical tube  b. Example: 4 mls semen  i. 1 ml is for DNA → therefore 1 conical tube is required for  DNA analysis prep  ii. 3 mls for RNA → therefore 3 conical tubes are required for RNA analysis prep  2. Label tubes with sample number and either “RNA” or “DNA”    Sperm Separation: Percolling:  1. When preparing Percoll and 2x PBS, do under sterile conditions to keep the Percoll sterile.  a. Add up to 1 ml 2x PBS and 1 ml Percoll to a 15 ml conical tube.  2. Gently pipette up to 1 ml semen sample on top.  3. Spin samples at 1200 rpm for 40 min → will see visible pellet at the bottom  4. Remove supernatant until the interface layer right before the pellet in bleach.    Sperm Separation: Washing:  1. Combine sperm pellets and remaining supernatant from DNA and RNA tubes, respectively, to reduce the number of tubes you are working with.  2. Add 1x PBS to a total volume of 10 ml.  3. Spin samples at 2000 rpm for 7 minutes and remove as much supernatant as you can without disrupting sperm.  4. Repeat washes 2x.  5. Resuspend pellet in 1 ml 1x PBS.  6. Add suspensions to properly labeled tubes for DNA and RNA.  7. Spin DNA tube at max speed to pellet the cells.  8. Remove supernatant, flash freeze pellets in liquid nitrogen, and store in -80 freezer.  9. Continue with RNA isolation protocol.
Sperm mRNA was extracted from 18 of the 21 men using a modified Stat 60 (IsoTex Diagnostics, Inc., Friendswood TX, USA) protocol in addition to components of Qiagen’s RNeasy kit (Qiagen Sciences, Germantown, MD, USA).

tag: count

tag: motility

tag: morphology


title: non-triple negative breast cancer tumor B4

description: Tumor tissue from sample B4


title: non-triple negative breast cancer tumor B5

description: Tumor tissue from sample B5


title: Genomic DNA from breast tumor 21 (Breast_T21)


title: Genomic DNA from breast tumor 22 (Breast_T22)


title: patient 16


title: 4019A_LMNC_0month

first: Mark

last: Magbanua

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

hyb_protocol: Labeled cDNA was hybridized to a microarray slide at 63° C for 12-16 h.

scan_protocol: Slides were then washed and immediately scanned with Axon Imager 4000b (Axon Instruments, Foster City, Ca), using GenePixPro3 software.

data_processing: printTipLoess normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Experimental bias (hybridization batch) was removed by fitting linear models & taking residuals. Statistical packages marray and limma in the R environment was used.

source_name: human prostate collected at 0month

label_protocol: One microgram of total target RNA from randomized samples, side by side with 1 µg of universal human reference RNA (Stratagene #740000), was linearly amplified through two rounds of modified in vitro transcription. Randomized amplified RNAs were converted to aminoallyl-modified cDNA and coupled to N-hydroxysuccinimidyl esters of Cy3 or Cy5 (Amersham Biosciences, Piscataway, NJ),

extract_protocol: Core needle biopsies were collected at baseline and 3 months. Total RNA for micro-array analyses were extracted from areas of normal prostate peripheral-zone tissue containing both stroma and epithelial cells. A #10 scalpel blade was used to scrape tissue from the pathologic area of interest. Tissue was homogenized [Polytron 1200C, Brinkmann, Westbury, NY, at setting 4 for 30 sec] with 600µl of RNA lysis buffer plus 1% 2-mercaptoethanol, and RNA was isolated using RNEasy columns (Qiagen, Valencia, Ca).

treatment_protocol: Eighty-four men with low risk prostate cancer were stratified based on self-reported dietary consumption of fish and tomatoes and then randomly assigned to a 3-month intervention of lycopene (n = 29) or fish oil (n = 27) supplementation or placebo (n = 28). Gene expression in morphologically normal prostate tissue was studied at baseline and at 3 months via cDNA microarray analysis. Differential gene expression and pathway analyses were performed to identify genes and pathways modulated by dietary intake of fish or tomato or by lycopene or fish oil supplementation. All men were also given a standard multivitamin (1 tablet/day, Dixon/Akyma) and instructed to refrain from any other types of vitamin or mineral supplements during the three months of intervention. Baseline dietary data on fish and tomato consumption was used for stratification with patients randomized from within each stratum to allow for a balanced comparison of the intervention arms.

value: Prostate

tag: biopsy location

value: LMNC

tag: ID

tag: intervention

value: A

tag: biopsy time

source_name: Stratagene Reference RNA

tag: reference

value: Stratagene Reference Pooled RNA


title: 4018B_RAN_3month

source_name: human prostate collected at 3month

tag: tissue

value: RAN

value: B


title: patient 9


title: 4018B_RAN_0month


title: patient 10


title: 4017A_RMNatro_3month

value: RMNatro


title: Genomic DNA from breast tumor 20 (Breast_T20)


title: 4019A_LBN_3month

value: LBN


title: patient 5


title: total RNA, mock, 10h, biological replicate #5

source_name: MCF7 cells, mock treated, 10 hours, total RNA, biological replicate #5

tag: cell line

tag: agent

value: D-MEM

tag: time point

tag: population

tag: biological replicate


title: patient 41


title: patient 8


title: patient 37


title: Genomic DNA from breast tumor 2 (Breast_T2)

value: breast

tag: batch

tag: tissue type

tag: age


title: 16HBE_infected_rep3

source_name: 16HBE cells incubated  with A. fumigatus conidiospores

value: human bronchial epithelial cell line 16HBE

tag: infection

value: infected with A. fumigatus conidispores


title: Genomic DNA from breast tumor 19 (Breast_T19)

value: tumor


title: Genomic DNA from breast tumor 18 (Breast_T18)


title: patient 36

tag: count

tag: motility


title: 4017A_LantNatr_0month

tag: biopsy location

value: LantNatr


title: Genomic DNA from breast tumor 17 (Breast_T17)


title: patient 40

tag: morphology


title: patient 35


title: 4016C_LBN_0month

tag: ID

tag: intervention

value: C


title: patient 34


title: 4015C_RANatr_3month

value: RANatr

tag: biopsy time

tag: reference


title: Genomic DNA from breast tumor 15 (Breast_T15)

tag: tissue


title: Genomic DNA from breast tumor 16 (Breast_T16)


title: patient 29


title: dab1 homozygous sample 3 (BALB/c)

city: Syracuse

first: Tohru

last: Matsuki

address: 766 Irving Avenue

department: Depertment of Neuroscience and Physiology

institute: SUNY Upstate Medical University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina Beadstation

data_processing: mRNA expression data were analyzed using the Gene Expression Module 3.2.7 within BeadStudio.

source_name: mouse hippocampus

label_protocol: Amplified cRNA was hybridized and labeled on Mouse-6 v1.0 Expression BeadChips (Illumina, Inc., San Diego, CA).

extract_protocol: All mice were anesthetized and sacrificed at postnatal day 19. Hippocampi were excised from wild type or dab1 mutant mice of C57BL/6 and BALB/c strains. The hippocampus was homogenized and subjected to total RNA purification using RNeasy mini kit (Qiagen, Valencia, CA). cRNA probes were synthesized and amplified using Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).

tag: strain

value: BALB/c

value: postnatal day 19

value: hippocampus

tag: genotype/variation

value: dab1 mutant


title: patient 32


title: 4016C_LBN_3month

value: Prostate

value: Stratagene Reference Pooled RNA


title: patient 28