title: Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal solid medium with biphenyl, replicate 2

source_name: solid-support dependent genes, Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl, replicate 2

growth_protocol: Rhodococcus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl at 30°C

value: Rhododoccus jostii RHA1

tag: substrate

value: biphenyl

tag: medium

value: solid medium

source_name: mid-exponential phase, Rhodococcus jostii RHA1 was grown in W minimal liquid medium with biphenyl

value: Rhodococcus jostii RHA1

value: liquid medium


title: Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal solid medium with biphenyl, replicate 1

status: Public on Jun 10 2010

type: RNA

city: Nagaoka

first: Toju

last: Iino

state: Niigata

address: 1603-1 Kamitomioka

department: Dept. Bioengineering

country: Japan

institute: Nagaoka University of Technology

hyb_protocol: The microarray slides were pre-hybridized using 5X SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48°C and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). Equal amounts of differentially labelled cDNA – 50 million pixels as measured by ImageQuant 5.2 (Molecular Dynamics) – from T = 48 h and T = 0 cells were hybridized at 42°C for 17 h with agitation using 120 uL per slide of SlideHyb#1 hybridization solution (Ambion). The post-hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2X SSC plus 0.1% SDS (medium stringency) at 42°C; 0.1X SSC plus 0.05% SDS (high stringency) at 25°C; and 0.1X SSC (low stringency) at 25°C. Lastly, the slides were dipped in 0.2X SSC and dried by centrifugation at 225 x g for 5 min at room temperature.

scan_protocol: Microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments) and spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using GeneSpring version 7.3.1 (Silicon Genetics) by the intensity-dependent Lowess method, with 20% of the data used for smoothing. Replicate spots of the same type were combined to yield a single normalized ratio, which is output for the first ID_REF number representing that spot type.

molecule: total RNA

organism: Rhodococcus jostii RHA1

source_name: solid-support dependent genes, Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl, replicate 1

label_protocol: Cy-labelled cDNA was prepared by indirect labelling. the Cy3/Cy5 dyes were reversed to control for dye bias.

extract_protocol: Cell pellets were vortexed with glass beads, hot phenol, and SDS at final concentrations of 14.3% and 0.9% (vol/vol) respectively. Debris was precipitated with acetate followed by the addition of 4.0 mL phenol-chloroform (1:1, vol/vol). Nucleic acids were precipitated with acetate plus isopropanol, treated with DNase, and purified with an RNeasy mini column (Qiagen).

tag: strain

growth_protocol: mid-exponential phase, Rhodococcus jostii RHA1 was grown in W minimal liquid medium with 10 mM biphenyl at 30°C and 120 rpm


title: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl, replicate 1

source_name: Rhodocuccus jostii RHA1 was grown in the sterilized soil with biphenyl at 3 day

growth_protocol: Rhodococcus jostii RHA1 was grown in the sterilized soil with 10 mM biphenyl at 30°C

value: Rhodocuccus jostii RHA1

tag: growth conditions

source_name: Rhodococcus jostii RHA1 was grown in W minimal liquid medium with biphenyl


title: Male Morocco Jews Africa  Morocco_Jew_7 Human610-Quad v1.0

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

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

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

data_processing:
Genomic DNA extracted from blood was genotyped using Infinium Human610-Quad v1.0  Genotyping BeadChips (Illumina).
Genomestudio v2009.2 with GT module 1.5.16 (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Morocco Jews

tag: region

value: Africa

tag: tissue

value: blood


title: Male Uzbekistan Jews Central Asia  Uzbekistan_Jew_1 Human610-Quad v1.0

value: Uzbekistan Jews

value: Central Asia


title: Rat liver control_52 week_rep3

city: Buffalo

first: Corie

last: Ellison

state: NY

address: 102 Farber hall

department: Pharmacology and Toxicology

country: USA

institute: University at Buffalo

hyb_protocol: cRNA was hybridized to RGU34A GeneChips (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned with the Affymetrix 428 scanner.

data_processing: Probe-level data from cell intensity files were background subtracted and normalized by the gc-Robust Multiarray Analysis method using ArrayAssist.

label: biotin

organism: Rattus norvegicus

source_name: sprague dawley rat liver (52wks)

label_protocol: High quality RNA was transformed into biotinylated cRNA by the Roswell Park Cancer Institute Gene Expression Facility (Buffalo, NY)

extract_protocol: Total RNA was isolated with the Qiagen RNeasy kit following the manufacture's instructions.

value: sprague dawley

value: liver

tag: agent

value: control


title: STA-NB13

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: Genomic DNA extracted from tumor cell line was interrogated for copy number against normal genomic DNA on the Nimblegen HG18 CGH 385K WG Tiling v1.0 array.

hyb_protocol: Standard Nimblegen protocol.

scan_protocol: Standard Nimblegen protocol.

data_processing: NimbleScan protocol, q-spline normalization.

source_name: Genomic DNA from STA-NB13 cell line.

label_protocol: Standard Nimblegen protocol.

extract_protocol: Cells were lysed in Jeffrey’s solution added with 1% SDS, treated with RNase A and proteinase K and genomic DNA was purified with two round of NaCl/water/ethanol precipitation.

tag: cell line

tag: tumor

value: neuroblastoma

source_name: NimbleGen human reference DNA

extract_protocol: purchased from NimbleGen

tag: sample type

value: Reference human DNA


title: STA-NB15

source_name: Genomic DNA from STA-NB15 cell line.


title: Rat liver control_52 week_rep2


title: STA-NB10HSR

source_name: Genomic DNA from STA-NB10HSR cell line.


title: stationary phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 2

value: Rhododoccus jostii RHA1

tag: growth phase

value: stationary phase

value: mid-exponential phase


title: stationary phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 3

value: biphenyl


title: Rat liver control_52 week_rep1


title: Female Morocco Jews Africa  Morocco_Jew_1 Human610-Quad v1.0

value: Female


title: Transformed Human Mammary Epithelial Cells - Late Passage

status: Public on Jun 09 2010

city: Bangalore

first: Anurag

middle: N

last: Paranjape

state: Karnataka

address: CVRaman road

department: MRDG

country: India

institute: Indian Institute of Science

description:
Human mammary epithelial cells grown as mammospheres, were immortalized by over expressing SV40ER and hTERT. The cells retained stem cell properties even after culturing. After extended culturing these cells started showing transformed phenotype and formed tumors in nude mice resembling human adenocarcinoma.
Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The fragmented cRNA were mixed with 25ul of 2x GE Hybridization Buffer (Agilent). About 45ul of the resulting mixture was applied to the Microarray and hybridized at 65degC for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer II for 37C. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Laser detection of Cyanine 3 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Feature extracted data was analyzed using GeneSpring GX v 11.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile, Per Gene: Normalize to Specific Samples.

source_name: Mammosphere Derived Cells

label_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA

extract_protocol: The mammospheres were used for RNA isolation by using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.

tag: cell type

value: transformed mammosphere derived cells

tag: passage

value: late


title: Female Morocco Jews Africa  Morocco_Jew_6 Human610-Quad v1.0

value: Morocco Jews


title: Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal solid medium with biphenyl, replicate 3

source_name: solid-support dependent genes, Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl, replicate 3

value: solid medium

value: Rhodococcus jostii RHA1

value: liquid medium


title: STA-NB8

source_name: Genomic DNA from STA-NB8 cell line.


title: Immortalized Human Mammary Epithelial Cells - Early Passage

description:
Human mammary epithelial cells grown as mammospheres, were immortalized by over expressing SV40ER and hTERT.  The cells retained stem cell properties even after culturing.
Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT.Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

value: immortalized mammosphere derived cells

value: early


title: STA-NB4

source_name: Genomic DNA from STA-NB4 cell line.


title: HKU_Liver_0072_TU_RS-259297_22082_S3_UPDATED

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide, reflecting the need for a better understanding of hepatocarcinogenesis. In this study, we examined the genome-wide expression profiles of both miRNAs and mRNAs from paired tumor and adjacent non-tumor tissues from a cohort of 96 HCC patients in Hong Kong where hepatitis B virus (HBV) is endemic. The comprehensive analysis of the coordinate expression of miRNAs and mRNAs reveals that miR-122 is under-expressed in HCC and that it is an important regulator for normal mitochondrial metabolism. A decreased level of miR-122 leads to an increase in expression of miR-122 seed-matched genes, a loss of mitochondrial metabolic function, and a decrease in the expression of many miR-122 secondary targets. These secondary targets are prognostic markers for HCC patients. Transcriptome profiling data from an additional 180 HCC and 40 liver cirrhotic patients in the same cohort were used to confirm the anti-correlation of miR-122 primary and secondary target gene sets. To test the HCC findings in normal mouse liver, we used an antagomir against miR-122 and identified altered gene expression profiling by microarray analysis in mouse in vivo experiments. The mouse data recapitulated the human HCC findings. Our anti-miR122 data further provided a direct link between increases in the mRNA levels of miR-122 controlled genes and impairments of mitochondrial metabolism. In summary, we find miR-122 loss may be detrimental to mitochondrial-related metabolisms in sustaining critical liver function and contribute to the morbidity and mortality of liver cancer patients.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: liver

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cDNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: individual

value: liver tumor


title: Female Uzbekistan Jews Central Asia  Uzbekistan_Jew_2 Human610-Quad v1.0

value: Uzbekistan Jews

value: Central Asia

value: blood


title: STA-NB10DM

source_name: Genomic DNA from STA-NB10DM cell line.

value: neuroblastoma

value: Reference human DNA


title: Male Ashkenazy Jews Europe  Romanian_Jew_2 Human610-Quad v1.0

value: Male

value: Ashkenazy Jews

value: Europe


title: HKU_Liver_0071_AN_RS-259312_22081_S3_UPDATED

value: adjacent liver non-tumor


title: HKU_Liver_0070_TU_RS-259293_22080_S3_UPDATED


title: HKU_Liver_0071_TU_RS-259310_22081_S3_UPDATED


title: HKU_Liver_0067_TU_RS-259311_22077_S3_UPDATED


title: HKU_Liver_0072_AN_RS-259313_22082_S3_UPDATED


title: STA-NB3

source_name: Genomic DNA from STA-NB3 cell line.


title: HKU_Liver_0070_AN_RS-259307_22080_S3_UPDATED


title: HKU_Liver_0074_AN_RS-258727_22084_S3_UPDATED_2


title: stationary phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 1

value: Rhododoccus jostii RHA1

value: stationary phase

value: biphenyl

source_name: mid-exponential phase, Rhodococcus jostii RHA1 was grown in W minimal liquid medium with biphenyl

value: mid-exponential phase


title: HKU_Liver_0062_AN_RS-259304_22072_S3_UPDATED


title: HKU_Liver_0064_AN_RS-259290_22074_S3_UPDATED


title: HKU_Liver_0062_TU_RS-259305_22072_S3_UPDATED


title: HKU_Liver_0068_TU_RS-259294_22078_S3_UPDATED


title: HKU_Liver_0055_AN_RS-259592_22065_S2_UPDATED


title: Male Cochin Jews South Asia  Indian_Jew_4 Human610-Quad v1.0

value: Cochin Jews

value: South Asia


title: Male Cochin Jews South Asia  Indian_Jew_3 Human610-Quad v1.0


title: HKU_Liver_0055_TU_RS-259600_22065_S2_UPDATED


title: HKU_Liver_0046_TU_RS-258702_22056_S2_UPDATED


title: HKU_Liver_0067_AN_RS-259298_22077_S3_UPDATED


title: HKU_Liver_0060_TU_RS-259610_22070_S2_UPDATED


title: HKU_Liver_0051_AN_RS-259606_22061_S2_UPDATED


title: HKU_Liver_0045_AN_RS-258709_22055_S2_UPDATED


title: HKU_Liver_0046_AN_RS-258696_22056_S2_UPDATED


title: Male Cochin Jews South Asia  Indian_Jew_1 Human610-Quad v1.0


title: HKU_Liver_0042_TU_RS-258712_22052_S2_UPDATED


title: HKU_Liver_0038_AN_RS-258708_22048_S2_UPDATED


title: HKU_Liver_0045_TU_RS-258697_22055_S2_UPDATED


title: HKU_Liver_0043_TU_RS-258689_22053_S2_UPDATED


title: HKU_Liver_0039_TU_RS-258693_22049_S2_UPDATED


title: HKU_Liver_0039_AN_RS-258701_22049_S2_UPDATED


title: HKU_Liver_0036_TU_RS-258694_22046_S2_UPDATED


title: HKU_Liver_0051_TU_RS-259611_22061_S2_UPDATED


title: HKU_Liver_0068_AN_RS-259306_22078_S3_UPDATED


title: HKU_Liver_0040_TU_RS-258711_22050_S2_UPDATED


title: HKU_Liver_0038_TU_RS-258713_22048_S2_UPDATED


title: HKU_Liver_0042_AN_RS-258698_22052_S2_UPDATED


title: HKU_Liver_0034_AN_RS-259368_22044_S2_UPDATED


title: HKU_Liver_0034_TU_RS-259380_22044_S2_UPDATED


title: Male Cochin Jews South Asia  Indian_Jew_2 Human610-Quad v1.0


title: HKU_Liver_0033_AN_RS-259374_22043_S2_UPDATED


title: HKU_Liver_0036_AN_RS-258695_22046_S2_UPDATED


title: HKU_Liver_0064_TU_RS-259309_22074_S3_UPDATED


title: HKU_Liver_0043_AN_RS-258707_22053_S2_UPDATED


title: HKU_Liver_0027_AN_RS-259381_22037_S2_UPDATED


title: HKU_Liver_0024_TU_RS-259376_22034_S2_UPDATED


title: HKU_Liver_0025_AN_RS-259364_22035_S2_UPDATED


title: HKU_Liver_0028_TU_RS-259387_22038_S2_UPDATED


title: HKU_Liver_0060_AN_RS-259596_22070_S2_UPDATED


title: HKU_Liver_0033_TU_RS-259384_22043_S2_UPDATED


title: HKU_Liver_0025_TU_RS-259373_22035_S2_UPDATED


title: HKU_Liver_0023_AN_RS-259372_22033_S2_UPDATED


title: HKU_Liver_0024_AN_RS-259379_22034_S2_UPDATED


title: HKU_Liver_0027_TU_RS-259385_22037_S2_UPDATED


title: HKU_Liver_0028_AN_RS-259366_22038_S2_UPDATED


title: HKU_Liver_0023_TU_RS-259265_22033_S2_UPDATED


title: HKU_Liver_0275_AN_RS-260773_22285_S5_UPDATED


title: HKU_Liver_0270_AN_RS-260660_22280_S5_UPDATED


title: HKU_Liver_0270_TU_RS-260659_22280_S5_UPDATED


title: HKU_Liver_0011_TU_RS-259281_22021_S2_UPDATED


title: HKU_Liver_0255_AN_RS-260012_22265_S5_UPDATED


title: HKU_Liver_0227_TU_RS-260604_22237_S5_UPDATED


title: HKU_Liver_0267_AN_RS-260640_22277_S5_UPDATED


title: HKU_Liver_0267_TU_RS-260663_22277_S5_UPDATED


title: HKU_Liver_0021_TU_RS-259275_22031_S2_UPDATED


title: HKU_Liver_0074_AN_RS-258727_22084_S3_UPDATED


title: HKU_Liver_0212_AN_RS-260755_22222_S5_UPDATED


title: HKU_Liver_0227_AN_RS-260597_22237_S5_UPDATED


title: HKU_Liver_0268_TU_RS-260661_22278_S5_UPDATED


title: HKU_Liver_0255_TU_RS-260004_22265_S5_UPDATED


title: HKU_Liver_0275_TU_RS-260780_22285_S5_UPDATED


title: HKU_Liver_0268_AN_RS-260648_22278_S5_UPDATED


title: HKU_Liver_0156_AN_RS-258606_22166_S4_UPDATED


title: HKU_Liver_0211_TU_RS-260761_22221_S5_UPDATED


title: HKU_Liver_0161_AN_RS-260868_22171_S4_UPDATED


title: HKU_Liver_0221_AN_RS-260762_22231_S5_UPDATED


title: HKU_Liver_0211_AN_RS-260759_22221_S5_UPDATED


title: Male Ashkenazy Jews Europe  Romanian_Jew_3 Human610-Quad v1.0


title: HKU_Liver_0161_TU_RS-260879_22171_S4_UPDATED


title: HKU_Liver_0212_TU_RS-260758_22222_S5_UPDATED


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED_5


title: HKU_Liver_0221_TU_RS-260756_22231_S5_UPDATED


title: HKU_Liver_0153_AN_RS-258595_22163_S4_UPDATED


title: HKU_Liver_0275_AN_RS-260773_22285_S5_UPDATED_MIRNA

hyb_protocol: Following reverse transcription, quadruplicate measurements of 2 uL of cDNA were made in 10 uL final reaction volumes by qPCR in a 384-well optical PCR plate using a 7900 HT PCR instrument (Applied Biosystems).  SYBR green PCR mix contained 5 uL of 2x SYBR green PCR master mix (Applied Biosystems), 1.4 uL of water, 0.8 uL of 10 mM universal primer, 0.8 uL of 10 uM LNA-Rprimer, and 2 uL of sample. qPCR was performed using the manufacturer’s recommended conditions.

scan_protocol: SYBR green fluorescence is monitored during amplification by the 7900 HT PCR instrument (Ambion Inc.), generating amplification curves for quantitation.  Dissociation curves were typically generated post-run for analysis of amplicon species.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the qPCR algorithm.  Intensities were calculated by setting a threshold within the linear range of the amplification curve and comparing the cycle time at which the experimental sample crossed the threshold to a standard curve.  Standard curve dilutions of synthetic oligonucleotides ranging from 10 nM to 10 fM were performed in TE that contained 100 ng/mL of total yeast RNA (Ambion, Inc.).

label: SYBR green

label_protocol: When SYBR green binds to duplex DNA, its fluorescence is increased.  SYBR green fluorescence is monitored during amplification by the 7900 HT PCR instrument (Ambion Inc.), generating amplification curves for quantitation.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using RLT/BME homogenization with Trizol vortex, followed by chloroform extraction and isopropanol precipitation.


title: HKU_Liver_0275_TU_RS-260780_22285_S5_UPDATED_MIRNA


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED_4


title: Female Ashkenazy Jews Europe  Romanian_Jew_1 Human610-Quad v1.0

value: Female


title: HKU_Liver_0149_AN_RS-258610_22159_S4_UPDATED


title: HKU_Liver_0270_AN_RS-260660_22280_S5_UPDATED_MIRNA


title: HKU_Liver_0227_AN_RS-260597_22237_S5_UPDATED_MIRNA


title: HKU_Liver_0267_TU_RS-260663_22277_S5_UPDATED_MIRNA

value: liver tumor


title: HKU_Liver_0255_TU_RS-260004_22265_S5_UPDATED_MIRNA


title: HKU_Liver_0267_AN_RS-260640_22277_S5_UPDATED_MIRNA


title: HKU_Liver_0255_AN_RS-260012_22265_S5_UPDATED_MIRNA


title: HKU_Liver_0128_TU_RS-259349_22138_S3_UPDATED


title: HKU_Liver_0268_TU_RS-260661_22278_S5_UPDATED_MIRNA


title: HKU_Liver_0049_AN_RS-259604_22059_S2_UPDATED


title: HKU_Liver_0268_AN_RS-260648_22278_S5_UPDATED_MIRNA


title: HKU_Liver_0128_AN_RS-259360_22138_S3_UPDATED


title: HKU_Liver_0270_TU_RS-260659_22280_S5_UPDATED_MIRNA


title: HKU_Liver_0205_AN_RS-260073_22215_S4_UPDATED


title: HKU_Liver_0200_AN_RS-260064_22210_S4_UPDATED


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED_3


title: HKU_Liver_0149_TU_RS-258599_22159_S4_UPDATED


title: HKU_Liver_0156_TU_RS-258611_22166_S4_UPDATED


title: HKU_Liver_0153_TU_RS-258590_22163_S4_UPDATED


title: HKU_Liver_0205_TU_RS-260088_22215_S4_UPDATED


title: HKU_Liver_0200_TU_RS-260082_22210_S4_UPDATED


title: HKU_Liver_0221_TU_RS-260756_22231_S5_UPDATED_MIRNA


title: HKU_Liver_0203_AN_RS-260070_22213_S4_UPDATED


title: HKU_Liver_0227_TU_RS-260604_22237_S5_UPDATED_MIRNA


title: HKU_Liver_0221_AN_RS-260762_22231_S5_UPDATED_MIRNA


title: HKU_Liver_0212_TU_RS-260758_22222_S5_UPDATED_MIRNA


title: HKU_Liver_0205_AN_RS-260073_22215_S4_UPDATED_MIRNA


title: HKU_Liver_0211_TU_RS-260761_22221_S5_UPDATED_MIRNA


title: HKU_Liver_0180_TU_RS-260927_22190_S4_UPDATED


title: HKU_Liver_0212_AN_RS-260755_22222_S5_UPDATED_MIRNA


title: HKU_Liver_0203_TU_RS-260074_22213_S4_UPDATED


title: HKU_Liver_0205_TU_RS-260088_22215_S4_UPDATED_MIRNA


title: HKU_Liver_0211_AN_RS-260759_22221_S5_UPDATED_MIRNA


title: HKU_Liver_0203_TU_RS-260074_22213_S4_UPDATED_MIRNA


title: HKU_Liver_0200_AN_RS-260064_22210_S4_UPDATED_MIRNA


title: HKU_Liver_0175_TU_RS-260922_22185_S4_UPDATED


title: HKU_Liver_0203_AN_RS-260070_22213_S4_UPDATED_MIRNA


title: HKU_Liver_0172_AN_RS-260865_22182_S4_UPDATED


title: HKU_Liver_0179_AN_RS-260926_22189_S4_UPDATED


title: HKU_Liver_0179_TU_RS-260921_22189_S4_UPDATED


title: HKU_Liver_0180_AN_RS-260924_22190_S4_UPDATED


title: HKU_Liver_0174_AN_RS-260915_22184_S4_UPDATED


title: HKU_Liver_0173_TU_RS-260930_22183_S4_UPDATED_MIRNA


title: HKU_Liver_0174_TU_RS-260936_22184_S4_UPDATED


title: HKU_Liver_0175_AN_RS-260918_22185_S4_UPDATED_MIRNA


title: HKU_Liver_0175_TU_RS-260922_22185_S4_UPDATED_MIRNA


title: HKU_Liver_0174_AN_RS-260915_22184_S4_UPDATED_MIRNA


title: HKU_Liver_0173_AN_RS-260876_22183_S4_UPDATED_MIRNA


title: HKU_Liver_0179_AN_RS-260926_22189_S4_UPDATED_MIRNA


title: HKU_Liver_0174_TU_RS-260936_22184_S4_UPDATED_MIRNA


title: HKU_Liver_0179_TU_RS-260921_22189_S4_UPDATED_MIRNA


title: HKU_Liver_0175_AN_RS-260918_22185_S4_UPDATED


title: HKU_Liver_0172_AN_RS-260865_22182_S4_UPDATED_MIRNA


title: HKU_Liver_0180_TU_RS-260927_22190_S4_UPDATED_MIRNA


title: HKU_Liver_0200_TU_RS-260082_22210_S4_UPDATED_MIRNA


title: HKU_Liver_0180_AN_RS-260924_22190_S4_UPDATED_MIRNA


title: HKU_Liver_0172_TU_RS-260871_22182_S4_UPDATED


title: HKU_Liver_0049_TU_RS-259612_22059_S2_UPDATED


title: HKU_Liver_0167_TU_RS-260869_22177_S4_UPDATED


title: HKU_Liver_0171_TU_RS-260881_22181_S4_UPDATED


title: HKU_Liver_0165_AN_RS-260870_22175_S4_UPDATED


title: HKU_Liver_0170_TU_RS-260886_22180_S4_UPDATED


title: HKU_Liver_0171_AN_RS-260885_22181_S4_UPDATED


title: HKU_Liver_0166_AN_RS-260880_22176_S4_UPDATED


title: HKU_Liver_0166_TU_RS-260878_22176_S4_UPDATED


title: HKU_Liver_0164_AN_RS-260864_22174_S4_UPDATED


title: HKU_Liver_0173_TU_RS-260930_22183_S4_UPDATED


title: HKU_Liver_0011_AN_RS-259282_22021_S2_UPDATED


title: HKU_Liver_0172_TU_RS-260871_22182_S4_UPDATED_MIRNA


title: HKU_Liver_0171_TU_RS-260881_22181_S4_UPDATED_MIRNA


title: HKU_Liver_0165_TU_RS-260887_22175_S4_UPDATED


title: HKU_Liver_0170_AN_RS-260882_22180_S4_UPDATED


title: HKU_Liver_0167_AN_RS-260884_22177_S4_UPDATED


title: HKU_Liver_0167_AN_RS-260884_22177_S4_UPDATED_MIRNA


title: HKU_Liver_0170_TU_RS-260886_22180_S4_UPDATED_MIRNA


title: HKU_Liver_0170_AN_RS-260882_22180_S4_UPDATED_MIRNA


title: HKU_Liver_0165_AN_RS-260870_22175_S4_UPDATED_MIRNA


title: HKU_Liver_0171_AN_RS-260885_22181_S4_UPDATED_MIRNA


title: HKU_Liver_0167_TU_RS-260869_22177_S4_UPDATED_MIRNA


title: HKU_Liver_0166_TU_RS-260878_22176_S4_UPDATED_MIRNA


title: HKU_Liver_0166_AN_RS-260880_22176_S4_UPDATED_MIRNA


title: HKU_Liver_0164_AN_RS-260864_22174_S4_UPDATED_MIRNA


title: HKU_Liver_0164_TU_RS-260888_22174_S4_UPDATED_MIRNA


title: HKU_Liver_0163_TU_RS-260867_22173_S4_UPDATED_MIRNA


title: HKU_Liver_0160_AN_RS-258596_22170_S4_UPDATED


title: HKU_Liver_0162_TU_RS-260877_22172_S4_UPDATED


title: HKU_Liver_0163_AN_RS-260872_22173_S4_UPDATED


title: HKU_Liver_0173_AN_RS-260876_22183_S4_UPDATED


title: HKU_Liver_0163_TU_RS-260867_22173_S4_UPDATED


title: HKU_Liver_0159_AN_RS-258609_22169_S4_UPDATED


title: HKU_Liver_0155_AN_RS-258600_22165_S4_UPDATED


title: HKU_Liver_0159_TU_RS-258601_22169_S4_UPDATED


title: HKU_Liver_0155_TU_RS-258597_22165_S4_UPDATED


title: HKU_Liver_0157_AN_RS-258598_22167_S4_UPDATED


title: HKU_Liver_0154_AN_RS-258603_22164_S4_UPDATED


title: HKU_Liver_0163_AN_RS-260872_22173_S4_UPDATED_MIRNA


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED_2


title: HKU_Liver_0162_TU_RS-260877_22172_S4_UPDATED_MIRNA


title: HKU_Liver_0161_TU_RS-260879_22171_S4_UPDATED_MIRNA


title: HKU_Liver_0162_AN_RS-260873_22172_S4_UPDATED_MIRNA


title: HKU_Liver_0161_AN_RS-260868_22171_S4_UPDATED_MIRNA


title: HKU_Liver_0160_TU_RS-258593_22170_S4_UPDATED


title: HKU_Liver_0160_AN_RS-258596_22170_S4_UPDATED_MIRNA


title: HKU_Liver_0159_TU_RS-258601_22169_S4_UPDATED_MIRNA


title: HKU_Liver_0157_AN_RS-258598_22167_S4_UPDATED_MIRNA


title: HKU_Liver_0160_TU_RS-258593_22170_S4_UPDATED_MIRNA


title: HKU_Liver_0159_AN_RS-258609_22169_S4_UPDATED_MIRNA


title: HKU_Liver_0157_TU_RS-258608_22167_S4_UPDATED_MIRNA


title: HKU_Liver_0156_AN_RS-258606_22166_S4_UPDATED_MIRNA


title: HKU_Liver_0156_TU_RS-258611_22166_S4_UPDATED_MIRNA


title: HKU_Liver_0121_AN_RS-258829_22131_S3_UPDATED


title: HKU_Liver_0162_AN_RS-260873_22172_S4_UPDATED


title: HKU_Liver_0155_AN_RS-258600_22165_S4_UPDATED_MIRNA


title: HKU_Liver_0148_AN_RS-259202_22158_S4_UPDATED


title: HKU_Liver_0146_AN_RS-259200_22156_S4_UPDATED


title: HKU_Liver_0148_TU_RS-258592_22158_S4_UPDATED


title: HKU_Liver_0121_TU_RS-258834_22131_S3_UPDATED


title: HKU_Liver_0146_TU_RS-259193_22156_S4_UPDATED


title: HKU_Liver_0155_TU_RS-258597_22165_S4_UPDATED_MIRNA


title: HKU_Liver_0118_TU_RS-258814_22128_S3_UPDATED


title: HKU_Liver_0154_AN_RS-258603_22164_S4_UPDATED_MIRNA


title: HKU_Liver_0117_AN_RS-258823_22127_S3_UPDATED


title: HKU_Liver_0154_TU_RS-258604_22164_S4_UPDATED_MIRNA


title: HKU_Liver_0119_TU_RS-258821_22129_S3_UPDATED


title: HKU_Liver_0116_TU_RS-258835_22126_S3_UPDATED


title: HKU_Liver_0119_AN_RS-258816_22129_S3_UPDATED


title: HKU_Liver_0118_AN_RS-258815_22128_S3_UPDATED


title: HKU_Liver_0117_TU_RS-258818_22127_S3_UPDATED


title: HKU_Liver_0116_AN_RS-258836_22126_S3_UPDATED


title: HKU_Liver_0154_TU_RS-258604_22164_S4_UPDATED


title: HKU_Liver_0114_AN_RS-258820_22124_S3_UPDATED


title: HKU_Liver_0115_TU_RS-258827_22125_S3_UPDATED


title: HKU_Liver_0115_AN_RS-258817_22125_S3_UPDATED


title: HKU_Liver_0153_AN_RS-258595_22163_S4_UPDATED_MIRNA


title: HKU_Liver_0153_TU_RS-258590_22163_S4_UPDATED_MIRNA


title: HKU_Liver_0149_AN_RS-258610_22159_S4_UPDATED_MIRNA


title: HKU_Liver_0148_AN_RS-259202_22158_S4_UPDATED_MIRNA


title: HKU_Liver_0148_TU_RS-258592_22158_S4_UPDATED_MIRNA


title: HKU_Liver_0149_TU_RS-258599_22159_S4_UPDATED_MIRNA


title: HKU_Liver_0146_TU_RS-259193_22156_S4_UPDATED_MIRNA


title: HKU_Liver_0128_AN_RS-259360_22138_S3_UPDATED_MIRNA


title: HKU_Liver_0146_AN_RS-259200_22156_S4_UPDATED_MIRNA


title: HKU_Liver_0114_TU_RS-258819_22124_S3_UPDATED


title: HKU_Liver_0164_TU_RS-260888_22174_S4_UPDATED


title: HKU_Liver_0119_AN_RS-258816_22129_S3_UPDATED_MIRNA


title: HKU_Liver_0128_TU_RS-259349_22138_S3_UPDATED_MIRNA


title: HKU_Liver_0121_TU_RS-258834_22131_S3_UPDATED_MIRNA


title: HKU_Liver_0121_AN_RS-258829_22131_S3_UPDATED_MIRNA


title: HKU_Liver_0108_AN_RS-259219_22118_S3_UPDATED


title: HKU_Liver_0110_AN_RS-259236_22120_S3_UPDATED


title: HKU_Liver_0118_AN_RS-258815_22128_S3_UPDATED_MIRNA


title: HKU_Liver_0119_TU_RS-258821_22129_S3_UPDATED_MIRNA


title: HKU_Liver_0157_TU_RS-258608_22167_S4_UPDATED


title: HKU_Liver_0118_TU_RS-258814_22128_S3_UPDATED_MIRNA


title: HKU_Liver_0108_TU_RS-259220_22118_S3_UPDATED


title: HKU_Liver_0106_TU_RS-259224_22116_S3_UPDATED


title: HKU_Liver_0105_TU_RS-259230_22115_S3_UPDATED


title: HKU_Liver_0110_TU_RS-259225_22120_S3_UPDATED


title: HKU_Liver_0106_AN_RS-259233_22116_S3_UPDATED


title: HKU_Liver_0105_AN_RS-259228_22115_S3_UPDATED


title: HKU_Liver_0117_TU_RS-258818_22127_S3_UPDATED_MIRNA


title: HKU_Liver_0116_AN_RS-258836_22126_S3_UPDATED_MIRNA


title: HKU_Liver_0111_TU_RS-258838_22121_S3_UPDATED


title: HKU_Liver_0101_AN_RS-259214_22111_S3_UPDATED


title: HKU_Liver_0098_AN_RS-259331_22108_S3_UPDATED


title: HKU_Liver_0101_TU_RS-259237_22111_S3_UPDATED


title: HKU_Liver_0117_AN_RS-258823_22127_S3_UPDATED_MIRNA


title: HKU_Liver_0096_AN_RS-259326_22106_S3_UPDATED


title: HKU_Liver_0116_TU_RS-258835_22126_S3_UPDATED_MIRNA


title: HKU_Liver_0115_AN_RS-258817_22125_S3_UPDATED_MIRNA


title: HKU_Liver_0114_AN_RS-258820_22124_S3_UPDATED_MIRNA


title: HKU_Liver_0115_TU_RS-258827_22125_S3_UPDATED_MIRNA


title: HKU_Liver_0165_TU_RS-260887_22175_S4_UPDATED_MIRNA


title: HKU_Liver_0114_TU_RS-258819_22124_S3_UPDATED_MIRNA


title: HKU_Liver_0111_AN_RS-258822_22121_S3_UPDATED_MIRNA


title: HKU_Liver_0110_AN_RS-259236_22120_S3_UPDATED_MIRNA


title: HKU_Liver_0111_TU_RS-258838_22121_S3_UPDATED_MIRNA


title: HKU_Liver_0098_TU_RS-259216_22108_S3_UPDATED


title: HKU_Liver_0110_TU_RS-259225_22120_S3_UPDATED_MIRNA


title: HKU_Liver_0096_TU_RS-259328_22106_S3_UPDATED


title: HKU_Liver_0092_AN_RS-259316_22102_S3_UPDATED


title: HKU_Liver_0090_AN_RS-259325_22100_S3_UPDATED


title: HKU_Liver_0091_AN_RS-259319_22101_S3_UPDATED


title: HKU_Liver_0090_TU_RS-259327_22100_S3_UPDATED


title: HKU_Liver_0108_AN_RS-259219_22118_S3_UPDATED_MIRNA


title: HKU_Liver_0089_AN_RS-259338_22099_S3_UPDATED


title: HKU_Liver_0092_TU_RS-259318_22102_S3_UPDATED


title: HKU_Liver_0089_TU_RS-259322_22099_S3_UPDATED


title: HKU_Liver_0086_TU_RS-259334_22096_S3_UPDATED


title: HKU_Liver_0091_TU_RS-259324_22101_S3_UPDATED


title: HKU_Liver_0108_TU_RS-259220_22118_S3_UPDATED_MIRNA


title: HKU_Liver_0106_AN_RS-259233_22116_S3_UPDATED_MIRNA


title: HKU_Liver_0105_AN_RS-259228_22115_S3_UPDATED_MIRNA


title: HKU_Liver_0106_TU_RS-259224_22116_S3_UPDATED_MIRNA


title: HKU_Liver_0105_TU_RS-259230_22115_S3_UPDATED_MIRNA


title: HKU_Liver_0101_TU_RS-259237_22111_S3_UPDATED_MIRNA


title: HKU_Liver_0098_AN_RS-259331_22108_S3_UPDATED_MIRNA


title: HKU_Liver_0085_AN_RS-258738_22095_S3_UPDATED


title: HKU_Liver_0101_AN_RS-259214_22111_S3_UPDATED_MIRNA


title: HKU_Liver_0086_AN_RS-259337_22096_S3_UPDATED


title: HKU_Liver_0084_AN_RS-258737_22094_S3_UPDATED


title: HKU_Liver_0085_TU_RS-258736_22095_S3_UPDATED


title: HKU_Liver_0111_AN_RS-258822_22121_S3_UPDATED


title: HKU_Liver_0084_TU_RS-258728_22094_S3_UPDATED


title: HKU_Liver_0092_AN_RS-259316_22102_S3_UPDATED_MIRNA


title: HKU_Liver_0096_TU_RS-259328_22106_S3_UPDATED_MIRNA


title: HKU_Liver_0080_AN_RS-258724_22090_S3_UPDATED


title: HKU_Liver_0082_AN_RS-258719_22092_S3_UPDATED


title: HKU_Liver_0096_AN_RS-259326_22106_S3_UPDATED_MIRNA


title: HKU_Liver_0091_AN_RS-259319_22101_S3_UPDATED_MIRNA


title: HKU_Liver_0092_TU_RS-259318_22102_S3_UPDATED_MIRNA


title: HKU_Liver_0082_TU_RS-258723_22092_S3_UPDATED


title: HKU_Liver_0091_TU_RS-259324_22101_S3_UPDATED_MIRNA


title: HKU_Liver_0090_AN_RS-259325_22100_S3_UPDATED_MIRNA


title: HKU_Liver_0079_AN_RS-258715_22089_S3_UPDATED


title: HKU_Liver_0079_TU_RS-258718_22089_S3_UPDATED


title: HKU_Liver_0078_TU_RS-258725_22088_S3_UPDATED


title: HKU_Liver_0090_TU_RS-259327_22100_S3_UPDATED_MIRNA


title: HKU_Liver_0077_TU_RS-258730_22087_S3_UPDATED


title: HKU_Liver_0078_AN_RS-258729_22088_S3_UPDATED


title: HKU_Liver_0076_AN_RS-258714_22086_S3_UPDATED


title: HKU_Liver_0089_AN_RS-259338_22099_S3_UPDATED_MIRNA


title: HKU_Liver_0077_AN_RS-258716_22087_S3_UPDATED


title: HKU_Liver_0076_TU_RS-258721_22086_S3_UPDATED


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED


title: HKU_Liver_0073_AN_RS-258717_22083_S3_UPDATED


title: HKU_Liver_0089_TU_RS-259322_22099_S3_UPDATED_MIRNA


title: HKU_Liver_0073_TU_RS-259300_22083_S3_UPDATED


title: HKU_Liver_0086_AN_RS-259337_22096_S3_UPDATED_MIRNA


title: HKU_Liver_0086_TU_RS-259334_22096_S3_UPDATED_MIRNA


title: HKU_Liver_0085_AN_RS-258738_22095_S3_UPDATED_MIRNA


title: HKU_Liver_0040_AN_RS-258690_22050_S2_UPDATED


title: HKU_Liver_0085_TU_RS-258736_22095_S3_UPDATED_MIRNA


title: HKU_Liver_0084_AN_RS-258737_22094_S3_UPDATED_MIRNA


title: HKU_Liver_0082_AN_RS-258719_22092_S3_UPDATED_MIRNA


title: HKU_Liver_0082_TU_RS-258723_22092_S3_UPDATED_MIRNA


title: HKU_Liver_0084_TU_RS-258728_22094_S3_UPDATED_MIRNA


title: HKU_Liver_0080_AN_RS-258724_22090_S3_UPDATED_MIRNA


title: HKU_Liver_0078_AN_RS-258729_22088_S3_UPDATED_MIRNA


title: HKU_Liver_0079_TU_RS-258718_22089_S3_UPDATED_MIRNA


title: HKU_Liver_0079_AN_RS-258715_22089_S3_UPDATED_MIRNA


title: HKU_Liver_0021_AN_RS-259267_22031_S2_UPDATED


title: HKU_Liver_0080_TU_RS-258735_22090_S3_UPDATED_MIRNA


title: HKU_Liver_0078_TU_RS-258725_22088_S3_UPDATED_MIRNA


title: Saline 4 vs. miR-122 antagomir, mouse 4, mouse liver, 1 month

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.

organism: Mus musculus

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: Saline

value: liver

tag: conditions

value: miR-122 antagomir

tag: time

value: 1 month


title: Saline 2 vs. miR-122 antagomir, mouse 2, mouse liver, 1 month


title: Mouse #168 saline, 1 week, mouse liver vs. mouse #188 miR-122 antagomir, 1 week, mouse liver

value: Mouse #168 saline, 1 week, mouse liver

value: 1 week


title: Mouse #166 saline, 1 week, mouse liver vs. mouse #186 miR-122 antagomir, 1 week, mouse liver

value: Mouse #166 saline, 1 week, mouse liver


title: Mouse #167 saline, 1 week, mouse liver vs. mouse #187 miR-122 antagomir, 1 week, mouse liver

value: Mouse #167 saline, 1 week, mouse liver


title: Saline 1 vs. miR-122 antagomir, mouse 1, mouse liver, 1 month


title: TAX577591

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: normal breast tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina GoldenGate Methylation Cancer Panel I using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The average beta values were obtained according to standard protocols using Illumina BeadStudio Methylation software (version 3.1.3.0).

label: Cy5 and Cy3

source_name: normal breast tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from fresh frozen primary breast tumours in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.

value: normal breast tissue

tag: family status

tag: er

tag: pgr

tag: overall survival time

tag: overall survival event

tag: hu subtype

tag: spfpercent

tag: nodestatus

tag: grade

tag: fga

tag: sizemm

tag: sizestatus

tag: ageyear

tag: agestatus


title: TAX577588

description: normal breast tissue

tag: tissue


title: TAX577590

description: normal breast tissue


title: Mouse #169 saline, 1 week, mouse liver vs. mouse #189 miR-122 antagomir, 1 week, mouse liver

tag: conditions

value: Mouse #169 saline, 1 week, mouse liver

tag: agent


title: HKU_Liver_0076_AN_RS-258714_22086_S3_UPDATED_MIRNA

tag: individual

value: adjacent liver non-tumor


title: HKU_Liver_0077_AN_RS-258716_22087_S3_UPDATED_MIRNA


title: TAX577589

description: normal breast tissue

tag: family status

tag: er


title: HKU_Liver_0077_TU_RS-258730_22087_S3_UPDATED_MIRNA


title: TAX577587

description: breast tumor

source_name: breast tumor

value: breast tumor

tag: pgr

tag: overall survival time

value: non-GEX


title: TAX577586

description: breast tumor

tag: overall survival event

tag: hu subtype


title: transition phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 2

tag: strain

value: Rhodococcus jostii RHA1

tag: growth phase

value: transition phase

tag: substrate

value: biphenyl

value: mid-exponential phase


title: transition phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 1


title: HKU_Liver_0076_TU_RS-258721_22086_S3_UPDATED_MIRNA

value: liver tumor


title: transition phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl, replicate 3


title: Saline 3 vs. miR-122 antagomir, mouse 3, mouse liver, 1 month

value: Saline

value: liver

tag: time


title: TAX577584

description: breast tumor

tag: spfpercent

tag: nodestatus

tag: grade

tag: fga

tag: sizemm

tag: sizestatus


title: HKU_Liver_0073_AN_RS-258717_22083_S3_UPDATED_MIRNA

tag: individual

tag: tissue


title: HKU_Liver_0074_TU_RS-258732_22084_S3_UPDATED_MIRNA


title: TAX577582

description: breast tumor

tag: family status

tag: er

tag: ageyear

tag: agestatus


title: TAX577583

description: breast tumor

tag: pgr

tag: overall survival time

tag: overall survival event

tag: hu subtype


title: TAX577585

description: breast tumor


title: HKU_Liver_0073_TU_RS-259300_22083_S3_UPDATED_MIRNA


title: HKU_Liver_0074_AN_RS-258727_22084_S3_UPDATED_MIRNA


title: TAX577579

description: breast tumor


title: TAX577580

description: breast tumor


title: TAX577581

description: breast tumor


title: HKU_Liver_0072_AN_RS-259313_22082_S3_UPDATED_MIRNA


title: TAX577578

description: breast tumor


title: HKU_Liver_0072_TU_RS-259297_22082_S3_UPDATED_MIRNA


title: HKU_Liver_0071_TU_RS-259310_22081_S3_UPDATED_MIRNA


title: HKU_Liver_0070_TU_RS-259293_22080_S3_UPDATED_MIRNA


title: TAX577274

description: breast tumor

value: sporadic

value: Normal

value: NoGain


title: TAX577547

description: breast tumor


title: HKU_Liver_0070_AN_RS-259307_22080_S3_UPDATED_MIRNA


title: TAX577548

description: breast tumor


title: HKU_Liver_0068_TU_RS-259294_22078_S3_UPDATED_MIRNA


title: TAX577275

description: breast tumor


title: HKU_Liver_0067_AN_RS-259298_22077_S3_UPDATED_MIRNA


title: HKU_Liver_0068_AN_RS-259306_22078_S3_UPDATED_MIRNA


title: HKU_Liver_0071_AN_RS-259312_22081_S3_UPDATED_MIRNA


title: HKU_Liver_0067_TU_RS-259311_22077_S3_UPDATED_MIRNA


title: TAX577560

description: breast tumor


title: TAX577322

description: breast tumor

value: Gain


title: HKU_Liver_0064_AN_RS-259290_22074_S3_UPDATED_MIRNA


title: TAX577265

description: breast tumor


title: HKU_Liver_0064_TU_RS-259309_22074_S3_UPDATED_MIRNA


title: TAX577290

description: breast tumor


title: HKU_Liver_0060_AN_RS-259596_22070_S2_UPDATED_MIRNA


title: HKU_Liver_0062_AN_RS-259304_22072_S3_UPDATED_MIRNA


title: HKU_Liver_0062_TU_RS-259305_22072_S3_UPDATED_MIRNA


title: TAX577307

description: breast tumor

value: familial


title: TAX577323

description: breast tumor


title: HKU_Liver_0060_TU_RS-259610_22070_S2_UPDATED_MIRNA


title: HKU_Liver_0055_TU_RS-259600_22065_S2_UPDATED_MIRNA


title: HKU_Liver_0055_AN_RS-259592_22065_S2_UPDATED_MIRNA


title: TAX577563

description: breast tumor


title: HKU_Liver_0098_TU_RS-259216_22108_S3_UPDATED_MIRNA


title: HKU_Liver_0080_TU_RS-258735_22090_S3_UPDATED


title: TAX577458

description: breast tumor

value: non-classified


title: TAX577477

description: breast tumor


title: HKU_Liver_0051_AN_RS-259606_22061_S2_UPDATED_MIRNA


title: HKU_Liver_0049_AN_RS-259604_22059_S2_UPDATED_MIRNA


title: HKU_Liver_0051_TU_RS-259611_22061_S2_UPDATED_MIRNA


title: TAX577475

description: breast tumor


title: TAX577256

description: breast tumor


title: HKU_Liver_0046_AN_RS-258696_22056_S2_UPDATED_MIRNA


title: TAX577519

description: breast tumor


title: TAX577571

description: breast tumor


title: TAX577268

description: breast tumor


title: TAX577518

description: breast tumor


title: HKU_Liver_0045_TU_RS-258697_22055_S2_UPDATED_MIRNA


title: HKU_Liver_0046_TU_RS-258702_22056_S2_UPDATED_MIRNA


title: HKU_Liver_0043_AN_RS-258707_22053_S2_UPDATED_MIRNA


title: HKU_Liver_0043_TU_RS-258689_22053_S2_UPDATED_MIRNA


title: TAX577016

description: breast tumor


title: TAX577243

description: breast tumor


title: TAX577552

description: breast tumor


title: TAX577325

description: breast tumor


title: HKU_Liver_0049_TU_RS-259612_22059_S2_UPDATED_MIRNA


title: TAX577217

description: breast tumor


title: HKU_Liver_0042_TU_RS-258712_22052_S2_UPDATED_MIRNA


title: HKU_Liver_0042_AN_RS-258698_22052_S2_UPDATED_MIRNA


title: TAX577036

description: breast tumor


title: TAX577452

description: breast tumor


title: TAX577555

description: breast tumor


title: TAX577535

description: breast tumor


title: HKU_Liver_0045_AN_RS-258709_22055_S2_UPDATED_MIRNA


title: HKU_Liver_0039_AN_RS-258701_22049_S2_UPDATED_MIRNA


title: HKU_Liver_0040_TU_RS-258711_22050_S2_UPDATED_MIRNA


title: TAX577449

description: breast tumor


title: TAX577484

description: breast tumor


title: TAX577541

description: breast tumor


title: TAX577455

description: breast tumor


title: HKU_Liver_0036_AN_RS-258695_22046_S2_UPDATED_MIRNA


title: HKU_Liver_0038_AN_RS-258708_22048_S2_UPDATED_MIRNA


title: HKU_Liver_0038_TU_RS-258713_22048_S2_UPDATED_MIRNA


title: HKU_Liver_0039_TU_RS-258693_22049_S2_UPDATED_MIRNA


title: HKU_Liver_0040_AN_RS-258690_22050_S2_UPDATED_MIRNA


title: TAX577478

description: breast tumor


title: TAX577472

description: breast tumor


title: TAX577540

description: breast tumor


title: HKU_Liver_0036_TU_RS-258694_22046_S2_UPDATED_MIRNA


title: HKU_Liver_0034_AN_RS-259368_22044_S2_UPDATED_MIRNA


title: TAX577574

description: breast tumor


title: HKU_Liver_0034_TU_RS-259380_22044_S2_UPDATED_MIRNA


title: HKU_Liver_0033_AN_RS-259374_22043_S2_UPDATED_MIRNA


title: HKU_Liver_0033_TU_RS-259384_22043_S2_UPDATED_MIRNA


title: TAX577423

description: breast tumor


title: TAX577316

description: breast tumor


title: TAX577064

description: breast tumor


title: HKU_Liver_0028_TU_RS-259387_22038_S2_UPDATED_MIRNA


title: HKU_Liver_0028_AN_RS-259366_22038_S2_UPDATED_MIRNA


title: TAX577544

description: breast tumor


title: HKU_Liver_0021_TU_RS-259275_22031_S2_UPDATED_MIRNA


title: HKU_Liver_0021_AN_RS-259267_22031_S2_UPDATED_MIRNA


title: TAX577446

description: breast tumor


title: TAX577436

description: breast tumor


title: TAX577492

description: breast tumor


title: HKU_Liver_0025_TU_RS-259373_22035_S2_UPDATED_MIRNA


title: HKU_Liver_0027_AN_RS-259381_22037_S2_UPDATED_MIRNA


title: HKU_Liver_0025_AN_RS-259364_22035_S2_UPDATED_MIRNA


title: HKU_Liver_0027_TU_RS-259385_22037_S2_UPDATED_MIRNA


title: HKU_Liver_0023_AN_RS-259372_22033_S2_UPDATED_MIRNA


title: HKU_Liver_0023_TU_RS-259265_22033_S2_UPDATED_MIRNA


title: HKU_Liver_0024_AN_RS-259379_22034_S2_UPDATED_MIRNA


title: HKU_Liver_0024_TU_RS-259376_22034_S2_UPDATED_MIRNA


title: HKU_Liver_0011_TU_RS-259281_22021_S2_UPDATED_MIRNA


title: TAX577515

description: breast tumor


title: TAX577001

description: breast tumor


title: HKU_Liver_0011_AN_RS-259282_22021_S2_UPDATED_MIRNA


title: TAX577002

description: breast tumor


title: TAX577039

description: breast tumor


title: TAX577223

description: breast tumor

value: LumA


title: TAX577277

description: breast tumor


title: TAX577327

description: breast tumor


title: TAX577490

description: breast tumor


title: TAX577420

description: breast tumor


title: TAX577525

description: breast tumor

value: LumB


title: TAX577485

description: breast tumor

value: breast tumor


title: TAX577526

description: breast tumor


title: TAX577422

description: breast tumor


title: TAX577147

description: breast tumor


title: TAX577461

description: breast tumor


title: TAX577207

description: breast tumor


title: TAX577424

description: breast tumor


title: TAX577474

description: breast tumor


title: TAX577104

description: breast tumor


title: TAX577433

description: breast tumor


title: TAX577245

description: breast tumor


title: TAX577186

description: breast tumor


title: TAX577556

description: breast tumor


title: TAX577453

description: breast tumor


title: 2008-03-14 E16_repeat TraSH intranasal vivo_1

city: Stanford

first: Kaitian

last: Peng

state: CA

address: 299 Campus Drive, Fairchild, D327

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78934.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Francisella tularensis

source_name: library input pool

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: library input pool

source_name: biological replicate of mouse output pool 2

tag: experiment


title: 2008-03-14 E16_repeat TraSH intranasal vivo_2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78935.gif

source_name: technical replicate of mouse output pool 2


title: 2008-03-14 E16_repeat TraSH intranasal vitro_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78932.gif

source_name: library input pool 1

value: library input pool 1


title: TAX577228

description: breast tumor

tag: spfpercent

tag: nodestatus


title: 2008-03-14 E16_repeat TraSH intranasal vitro_2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78933.gif

source_name: technical replicate of library input pool 1


title: TAX577124

description: breast tumor

tag: grade

tag: fga


title: TAX577073

description: breast tumor

tag: sizemm

tag: sizestatus


title: TAX577476

description: breast tumor

tag: tissue


title: TAX577432

description: breast tumor

tag: family status


title: TAX577473

description: breast tumor

tag: er


title: TAX577233

description: breast tumor

tag: ageyear


title: TAX577187

description: breast tumor

tag: agestatus


title: TAX577572

description: breast tumor

tag: pgr


title: TAX577234

description: breast tumor

tag: overall survival time


title: TAX577162

description: breast tumor

tag: overall survival event


title: 90091 (4846417040_G)

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

country: Australia

institute: Queensland Centre for Medical Genomics

description:
FFPE material
4846417040_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software package to extract raw data was Genomestudio v2009.1 and quantile normalization was performed using the lumi bioconductor package. Data were loaded into Genspring GX and centred around 0 for clustering visualization.

source_name: FFPE Familial Breast Tumour

label_protocol: RNA was labelled using the WG-DASL kit from Illumina

extract_protocol: RNA was extracted using a Tri extraction method - see Waddell et al Journal of Pathology 2010

value: Breast Tumour

tag: mutation status


title: TAX577462

description: breast tumor

tag: hu subtype


title: 40034 (4846417040_B)

description:
FFPE material
4846417040_B

value: ATM


title: 40032 (4846417040_A)

description:
FFPE material
4846417040_A


title: 80341 (4846417040_F)

description:
FFPE material
4846417040_F


title: 40339 (4846417040_H)

description:
FFPE material
4846417040_H


title: HCT116tts_p53-1026 24 hr NO DOX vs. HCT116tts_p53-1026 24 hr DOX_1

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck and Co., Inc.

description: Agilent HCT116 profiling of siRNA/shRNA treatments

tag: reference

value: HCT116tts_p53-1026 24 hr NO DOX

tag: treatment


title: 41090 (4846417023_H)

description:
FFPE material
4846417023_H


title: HCT116tts_p53-1026 24 hr NO DOX vs. HCT116tts_p53-1026 24 hr DOX_2


title: 40356 (4846417023_F)

description:
FFPE material
4846417023_F


title: wt6_green vs. XOPS-mCFP6_red

city: Lexington

first: Ann

middle: Caroline

last: Morris

state: KY

address: 215 T.H. Morgan Building

department: Department of Biology

institute: University of Kentucky

hyb_protocol: Fluorescently labeled wild-type and XOPS-mCFP cRNA were co-hybridized to an Agilent 4 x 44k zebrafish microarray containing 42,990 probes representing roughly 21,500 zebrafish ESTs. Eight hybridizations (representing four individual wild-type and XOPS-mCFP retinas) were performed; hybridizations included a reciprocal dye-swap control to account for biological, sample preparation, and technical variability.

scan_protocol: Microarray scanning and image processing were performed by the ICBR using Agilent's Feature Extraction software. The intensity of each spot was summarized by the mean pixel intensity. After background subtraction, raw data were normalized by Lowess transformation.

data_processing: After background subtraction, raw data were normalized by Lowess transformation. A 2-way ANOVA comparison was employed for differential expression analysis using the Analyse-It tool (Microsoft Excel). The p-values were adjusted using the Benjamini and Hochberg method to control for false discovery rate. Differentially expressed genes were ranked by the adjusted p-values; genes with a p-value of less than 0.005 were considered as differentially expressed between wild-type and XOPS-mCFP retinas.

organism: Danio rerio

source_name: retina from wild-type adult zebrafish

label_protocol: RNA samples were submitted to the Gene Expression Core Facility at the University of Florida’s Interdisciplinary Center for Biotechnology Resarch (ICBR). RNA quality and concentration were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Preparation of cDNA, generation and fluorescent labeling of cRNA, and chip hybridization were performed by the ICBR according to standard protocols.

growth_protocol: Rearing, breeding, and staging of zebrafish were performed in accordance with established methods for zebrafish animal husbandry. Wild-type zebrafish were inbred descendants of the Ekwill strain, originally obtained from the Ekkwill fish farm (Gibsonton, FL). The Tg(XRho:gap43-mCFP)q13 transgenic line, referred to here as XOPS-mCFP, has been described previously. It harbors a fluorescent mCFP reporter transgene under the control of the Xenopus rhodopsin promoter, the expression of which is toxic to the rod photoreceptors.

extract_protocol: For the microarray analysis, four wild type and four XOPS-mCFP adults (10-11 months of age) were sacrificed by immersion in MS-222 (Tricaine, Sigma). The right eye was dissected and the sclera, choroid and lens were removed. The retinas were transferred to microcentrifuge tubes containing RNA later (Ambion/Applied Biosystems, Austin, TX). Individual retinas were not pooled. Total RNA was prepared from each sample using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

tag: strain

value: wild type

tag: age

value: 10-11 months old

value: retina

source_name: retina from XOPS-mCFP adult zebrafish

value: XOPS-mCFP

value: 10-11 months


title: wt6_red vs. XOPS-mCFP6_green


title: wt8_green vs. XOPS-mCFP8_red


title: TAX577188

description: breast tumor

tag: spfpercent

tag: nodestatus

tag: grade

tag: fga


title: TAX577210

description: breast tumor

tag: tissue

tag: family status

value: NoGain

tag: sizemm

tag: sizestatus


title: 70339 (4846417023_E)

description:
FFPE material
4846417023_E


title: 60097 (4690176054_G)

description:
FFPE material
4690176054_G


title: 70338 (4846417023_D)

description:
FFPE material
4846417023_D


title: 41066 (4846417023_B)

description:
FFPE material
4846417023_B


title: 40377 (4846417023_A)

description:
FFPE material
4846417023_A


title: 71067 (4690176054_D)

description:
FFPE material
4690176054_D


title: wt7_green vs. XOPS-mCFP7_red


title: wt7_red vs. XOPS-mCFP7_green


title: TAX577499

description: breast tumor

value: sporadic

tag: er

tag: pgr

tag: ageyear

tag: agestatus


title: wt8_red vs. XOPS-mCFP8_green


title: 70047 (4690176054_H)

description:
FFPE material
4690176054_H

tag: mutation status


title: TAX577161

description: breast tumor

value: familial

tag: overall survival time

tag: overall survival event

tag: hu subtype

value: Gain


title: 30184 (4690176054_C)

description:
FFPE material
4690176054_C


title: TAX577463

description: breast tumor


title: 34430 (4690176048_F)

description:
FFPE material
4690176048_F


title: TAX577503

description: breast tumor


title: 60567 (4690176054_A)

description:
FFPE material
4690176054_A


title: si Control and vehicle replicate 3

city: Cambridge

first: Roslin

last: Russell

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: replicate 3

data_processing: The data were log base 2 quantile normalised the beadarray package in R

source_name: MCF-7 cell line treated with control siRNA and Fulvestrant (control)

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

growth_protocol: MCF-7 human cell lines were grown as described previously (Neve et al. 2006, Cancer Cell 10:515–527).

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. A DNase I digestion was included. Quality control was performed with Agilent Bioanalyser.

tag: cell line


title: 20646 (4690176054_B)

description:
FFPE material
4690176054_B


title: 90719 (4690176048_E)

description:
FFPE material
4690176048_E


title: A298-RA 2

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42oC using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (13ug) from the reference sample LX and from each test sample were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGH data extraction.

source_name: Genomic DNA from the whole blood

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for 15 patient (RA) and 1 control (Non-RA) and Cy5 for reference Sample (LX) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)

extract_protocol: Genomic DNA was extracted using QIAGEN DNA easy kit (Qiagen)

tag: disease state

value: rheumatoid arthritis (RA)

source_name: Reference gDNA from Sample LX (Non-RA) whole blood

value: Non-RA


title: B2-RA 2


title: TAX577551

description: breast tumor

value: breast tumor

value: LumA

tag: spfpercent

tag: nodestatus


title: A289-RA 2


title: A325-RA 2


title: B3-RA 2


title: A267-RA 2


title: 51297 (4690176047_H)

description:
FFPE material
4690176047_H


title: 91059 (4690176048_D)

description:
FFPE material
4690176048_D

value: untested


title: si RARA and estrogen replicate 1

description: replicate 1

source_name: MCF-7 cell line treated with RAR alpha siRNA and estrogen

treatment_protocol: Estrogen was added at a final concentration of 100 nM.


title: 10589 (4690176048_A)

description:
FFPE material
4690176048_A

value: Breast Tumour


title: 11472 (4690176047_G)

description:
FFPE material
4690176047_G

value: unknown


title: 70639 (4690176047_F)

description:
FFPE material
4690176047_F


title: A311-RA 2


title: A327-RA 2


title: TAX577546

description: breast tumor

tag: grade

tag: fga


title: A292-RA 2


title: A250-RA 2


title: A288-RA 2


title: si Control and estrogen replicate 3

description: replicate 3

source_name: MCF-7 cell line treated with control siRNA and estrogen


title: A262-RA 2


title: 50402 (4690176048_B)

description:
FFPE material
4690176048_B

tag: tissue


title: SJX-Control 2

value: none (control)


title: A222-RA 2


title: si Control and estrogen replicate 2

description: replicate 2


title: wt5_green vs. XOPS-mCFP5_red

tag: strain

value: wild type

tag: age


title: 50218 (4690176047_D)

description:
FFPE material
4690176047_D


title: TAX577259

description: breast tumor

tag: family status

tag: er

tag: sizemm

tag: sizestatus


title: 50970 (4690176047_C)

description:
FFPE material
4690176047_C

tag: mutation status


title: 50991 (4690176047_E)

description:
FFPE material
4690176047_E


title: 60575 (4690176047_A)

description:
FFPE material
4690176047_A


title: TAX577113

description: breast tumor

tag: pgr

tag: overall survival time

tag: ageyear

tag: agestatus


title: TAX577524

description: breast tumor

tag: overall survival event

tag: hu subtype


title: 90771 (4690176046_H)

description:
FFPE material
4690176046_H


title: 50528 (4690176046_E)

description:
FFPE material
4690176046_E


title: si RARA and estrogen replicate 2

description: replicate 2

tag: cell line


title: 30130 (4690176038_H)

description:
FFPE material
4690176038_H


title: TAX577114

description: breast tumor

tag: spfpercent

tag: nodestatus

tag: grade


title: si Control and estrogen replicate 1

description: replicate 1


title: TAX577530

description: breast tumor

tag: tissue

tag: fga


title: 00023 (4690176046_F)

description:
FFPE material
4690176046_F


title: 40400 (4690176046_D)

description:
FFPE material
4690176046_D


title: si RARA and vehicle replicate 3

description: replicate 3

source_name: MCF-7 cell line treated with RAR alpha siRNA and Fulvestrant (control)


title: si RARA and estrogen replicate 3

description: replicate 3


title: si Control and vehicle replicate 2

description: replicate 2


title: 20646 (4690176046_G)

description:
FFPE material
4690176046_G


title: TAX577108

description: breast tumor

tag: family status


title: TAX577539

description: breast tumor

tag: er


title: B1-RA 2

tag: disease state


title: 40012 (4690176038_D)

description:
FFPE material
4690176038_D

value: ATM


title: 40012_met (4690176038_F)

description:
FFPE material
4690176038_F


title: 31277 (4690176038_C)

description:
FFPE material
4690176038_C


title: 51297 (4690176038_A)

description:
FFPE material
4690176038_A


title: 60567 (4690176038_B)

description:
FFPE material
4690176038_B


title: si Control and vehicle replicate 1

description: replicate 1


title: si RARA and vehicle replicate 2

description: replicate 2


title: TAX577532

description: breast tumor

tag: sizemm

tag: sizestatus


title: TAX577505

description: breast tumor

tag: pgr


title: A260-RA 2


title: TAX577529

description: breast tumor

tag: overall survival time


title: TAX577191

description: breast tumor

tag: ageyear


title: TAX577557

description: breast tumor

value: LumB

tag: agestatus


title: TAX577543

description: breast tumor

tag: overall survival event


title: 90659 (4690176037_H)

description:
FFPE material
4690176037_H

tag: mutation status


title: 90674 (4690176037_G)

description:
FFPE material
4690176037_G


title: 60584 (4690176037_C)

description:
FFPE material
4690176037_C


title: 70261 (4690176037_E)

description:
FFPE material
4690176037_E


title: 62629 (4690176037_F)

description:
FFPE material
4690176037_F


title: LCL-relative1-2

city: Montreal

first: Thomas

last: Rio Frio

state: QC

address: 1625 Pine Avenue

department: Human Genetics

country: Canada

institute: McGill University

description: Relative HC III-3 LCL 1:2

hyb_protocol: Equivalent amount of cRNA (750ng) was hybridized on each array according to standard Illumina hybridization protocol

scan_protocol: The beadarrays were scanned according to standard Illumina scanning protocol using the Illumina®BeadArray Reader (version 1.7.0.44) and the BeadScan software (version 3.5.31.17122).

data_processing: The images were analyzed in Illumina®BeadStudio 3 application and raw data were outputted in txt files. The raw data was then imported to BioConductor in  R 2.5.0 using the lumi package for variance-stabilizing transformation and robust spline normalization

source_name: LCL, relative1

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

growth_protocol: lymphoblastoid cell lines were grown in IMDM supplemented with 10% fetal bovine serum. Fibroblasts were grown in EMEM supplemented with 10% fetal bovine serum

extract_protocol: RNA was extracted using the QIAGEN Rneasy kit.

tag: cell type

value: Lymphoblastoid cell line

tag: individual

value: Relative 1


title: LCL-relative1-1

description: Relative HC III-3 LCL 1:1


title: LCL-relative2-1

description: Relative HC IV-1 LCL 1:1

source_name: LCL, relative2

value: Relative 2


title: 50218 (4690176037_D)

description:
FFPE material
4690176037_D


title: 40515 (4690176037_A)

description:
FFPE material
4690176037_A


title: LCL-relative2-2

description: Relative HC IV-1 LCL 1:2


title: TAX577542

description: breast tumor

source_name: breast tumor

value: sporadic

tag: hu subtype

tag: spfpercent

tag: nodestatus

value: NoGain


title: 13644 (4690176037_B)

description:
FFPE material
4690176037_B

tag: tissue


title: 80140 (4685238102_G)

description:
FFPE material
4685238102_G


title: LCL-control3-1

description: Control 3 NC LCL 1:1

source_name: LCL, control3

value: Control


title: 30348 (4685238102_D)

description:
FFPE material
4685238102_D


title: LCL-control3-2

description: Control 3 NC LCL 1:2


title: wt5_red vs. XOPS-mCFP_green

tag: strain

value: XOPS-mCFP

tag: age

value: 10-11 months old

value: retina

value: 10-11 months


title: TAX577466

description: breast tumor

value: breast tumor

tag: family status

tag: er

value: LumA

tag: grade

tag: fga


title: TAX577066

description: breast tumor

tag: pgr

tag: overall survival time

tag: sizemm

tag: sizestatus


title: TAX577240

description: breast tumor

tag: overall survival event

value: Gain

tag: ageyear

tag: agestatus


title: 30184 (4685238102_A)

description:
FFPE material
4685238102_A

value: Breast Tumour

tag: mutation status


title: 50970 (4685238100_H)

description:
FFPE material
4685238100_H


title: TAX577465

description: breast tumor

tag: hu subtype

tag: spfpercent


title: Fibro-control2-2

description: Control 2 NC Fibro 1:2

source_name: Fibro, control2

tag: cell type

value: Fibroblasts

tag: individual


title: 60585 (4690176047_B)

description:
FFPE material
4690176047_B

tag: tissue


title: 60034 (4685238100_F)

description:
FFPE material
4685238100_F


title: Fibro-control2-1

description: Control 2 NC Fibro 1:1


title: 11721 (4685238100_E)

description:
FFPE material
4685238100_E


title: LCL-control1-2

description: Control 1 NC LCL 1:2

source_name: LCL, control1


title: 20897 (4685238100_D)

description:
FFPE material
4685238100_D


title: LCL-control1-1

description: Control 1 NC LCL 1:1


title: 00114 (4685238100_G)

description:
FFPE material
4685238100_G

value: unknown


title: TAX577133

description: breast tumor

tag: family status

value: Normal

tag: nodestatus


title: TAX577192

description: breast tumor

tag: er

value: LumB

tag: grade


title: Fibro-proband-1

description: Proband Fibro 1:1

source_name: Fibro, proband

value: Proband


title: 62018 (4685238100_C)

description:
FFPE material
4685238100_C


title: TAX577116

description: breast tumor

tag: pgr

tag: fga


title: LCL-proband-2

description: Proband LCL 1:2

source_name: LCL, proband

value: Lymphoblastoid cell line


title: Fibro-proband-2

description: Proband Fibro 1:2


title: TAX577112

description: breast tumor

value: sporadic

tag: overall survival time

tag: sizemm


title: 90144 (4685238098_H)

description:
FFPE material
4685238098_H

source_name: FFPE Familial Breast Tumour


title: LCL-proband-1

description: Proband LCL 1:1


title: Patient B rep2

city: Bangkoknoi

first: Alita

last: Kongchanagul

state: Bangkok

address: 2 Prannok Road

department: Microbiology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital

description: replicate 2

hyb_protocol: The Sentrix BeadChip Array for Gene Expression Human-6 V2 (Illumina, San Diego, CA) was hybridized to the biotin-labeled cDNA, with the change in the hybridization temperature from 58˚C to 48˚C to accommodate the altered hybridization kinetics of cDNA/DNA pairs relative to cRNA/DNA pairs

data_processing: Raw intensity values were normalized against the normal lung dataset using quantile normalization in GeneSpring software (Agilent Technologies).

source_name: Lung

label_protocol: As the RNA samples extracted from FFPE tissues were not optimal for the cRNA amplification method recommended by Illumina. Instead, the total RNA from FFPE tissues were used with WT-Ovation FFPE System (NuGen, San Carlos, CA) according to the manufactuere’s instructions to synthesize the biotin-labeled cDNA.

extract_protocol: Total RNA was extracted by using Trizol from formalin-fixed paraffin-embedded (FFPE) blocks of lung tissue samples and then purified using Qiagen RNAeasy kit according to the manufacturer’s instructions.

tag: age

value: 6 years

tag: sex

value: Male

tag: time of death

value: Day 17 of illness

tag: disease state

value: H5N1 influenza

value: lung


title: 50479 (4685238100_B)

description:
FFPE material
4685238100_B

tag: mutation status


title: si RARA and vehicle replicate 1

description: replicate 1

tag: cell line


title: Patient B rep1

description: replicate 1


title: TAX577190

description: breast tumor

tag: overall survival event

tag: hu subtype

tag: spfpercent

tag: sizestatus

tag: ageyear

tag: agestatus


title: TAX577214

description: breast tumor

tag: tissue

tag: family status

tag: er

tag: nodestatus

tag: grade


title: SJX-Control 4

value: none (control)

value: Non-RA


title: TAX577564

description: breast tumor

value: breast tumor

value: familial

tag: pgr

tag: overall survival time

tag: fga

value: NoGain

tag: sizemm


title: Normal

description: replicate 1

tag: age

tag: sex

tag: time of death

tag: disease state

value: normal


title: 13719 (4685238098_G)

description:
FFPE material
4685238098_G

value: Breast Tumour

tag: mutation status


title: TAX577067

description: breast tumor

tag: overall survival event

tag: hu subtype

value: LumA

tag: spfpercent

tag: sizestatus


title: TAX577221

description: breast tumor

tag: tissue

tag: family status

tag: ageyear

tag: agestatus


title: 50294 (4685238098_F)

description:
FFPE material
4685238098_F


title: 60833 (4685238098_D)

description:
FFPE material
4685238098_D


title: TAX577324

description: breast tumor

tag: er

tag: pgr

tag: nodestatus

tag: grade

value: Gain


title: 80042 (4685238098_B)

description:
FFPE material
4685238098_B


title: Patient A rep2

description: replicate 2

tag: age

value: 48 years

value: Day 6 of illness


title: B2-RA 4

value: rheumatoid arthritis (RA)


title: A327-RA 4


title: Patient A rep1

description: replicate 1

tag: sex


title: 90007 (4685238075_H)

description:
FFPE material
4685238075_H


title: B3-RA 4


title: TAX577093

description: breast tumor

value: sporadic

tag: overall survival time

tag: fga

tag: sizemm


title: 80783 (4685238075_G)

description:
FFPE material
4685238075_G

tag: mutation status


title: TAX577155

description: breast tumor

tag: overall survival event

tag: hu subtype


title: GFP-KD-3 (mRNA)

city: Columbus

first: Ekaterina

last: Lamber

state: OH

address: 904 BRT, 460 W. 12th Avenue

department: Biomedical Informatics

institute: Ohio State University

description:
Total RNA was further processed to isolate mRNA (see 'Extract protocol').
Gene expression data of HeLa cells

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Human Genome U133 Plus 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 460.

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

data_processing: The data were analyzed with Expression Console software (version 1.1.2) using Affymetrix default analysis settings and MAS5 algorithm.

source_name: HeLa cells control

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: HeLa cell line was maintained in DMEM media supplemented with 10% Bovine Serum, 100 I.U./ml Penicillin, 100 μg/ml Streptomycin in a humidified incubator at 37 C and 5% CO2.

extract_protocol: Total RNA was prepared with Tri Reagent (Molecular Research) and further purified over RNeasy columns (Qiagen); mRNA was prepared using Dynabeads mRNA direct kit (Invitrogen)

treatment_protocol: HeLa cells were cotransfected (Lipofectamine; Invitrogen) with 5 μg of shRNA expression plasmid and 20 ng of pBabe-puromycin plasmid. BRCA1 shRNA (gccacaggaccccaagaaugag) was targeted to the 3’- untranslated region of the BRCA1 mRNA. The control shRNA was targeted against a mutant GFP construct  (gggccauggcacguacggcaag). Puromycin selection (2 μg/ml) was applied 24 h after transfection, and cells were harvested at 72 h post transfection.

tag: treatment protocol

value: control


title: A311-RA 4

tag: disease state


title: A298-RA 4


title: TAX577119

description: breast tumor

tag: tissue

tag: family status

tag: spfpercent

tag: sizestatus


title: TAX577181

description: breast tumor

tag: er

tag: pgr

tag: ageyear

tag: agestatus


title: BRCA1-KD-2 (total RNA)

description:
Total RNA
Gene expression data of HeLa cells with depleted BRCA1

source_name: HeLa cells with depleted BRCA1

value: depleted BRCA1


title: BRCA1-KD-3 (mRNA)

description:
Total RNA was further processed to isolate mRNA (see 'Extract protocol').
Gene expression data of HeLa cells with depleted BRCA1


title: GFP-KD-2 (total RNA)

description:
Total RNA
Gene expression data of HeLa cells


title: 90210 (4685238075_F)

description:
FFPE material
4685238075_F


title: 40334 (4685238075_E)

description:
FFPE material
4685238075_E


title: BRCA1-KD-1 (total RNA)


title: A292-RA 4

source_name: Genomic DNA from the whole blood


title: TAX577158

description: breast tumor

tag: nodestatus

tag: grade


title: TAX577222

description: breast tumor

tag: overall survival time

tag: fga


title: A325-RA 4

source_name: Reference gDNA from Sample LX (Non-RA) whole blood


title: TAX577135

description: breast tumor

tag: sizemm


title: B1-RA 4


title: A289-RA 4


title: 20444 (4685238075_D)

description:
FFPE material
4685238075_D

tag: mutation status


title: GFP-KD-1 (total RNA)


title: 60585 (4685238098_C)

description:
FFPE material
4685238098_C


title: 20058 (4685238074_H)

description:
FFPE material
4685238074_H


title: 70019 (4685238075_A)

description:
FFPE material
4685238075_A


title: 50206 (4685238075_C)

description:
FFPE material
4685238075_C


title: A260-RA 4


title: TAX577219

description: breast tumor

tag: overall survival event

tag: hu subtype


title: A267-RA 4

tag: disease state


title: A262-RA 4


title: SJX-Control 3


title: 20351 (4685238074_G)

description:
FFPE material
4685238074_G

tag: tissue


title: TAX577554

description: breast tumor

tag: family status


title: TAX577173

description: breast tumor

tag: spfpercent


title: TAX577148

description: breast tumor

tag: sizestatus


title: TAX577510

description: breast tumor

tag: er


title: TAX577220

description: breast tumor

tag: pgr


title: 20295 (4685238074_F)

description:
FFPE material
4685238074_F


title: 34320 (4685238074_C)

description:
FFPE material
4685238074_C


title: 41243 (4685238074_B)

description:
FFPE material
4685238074_B


title: 20457 (4685238074_A)

description:
FFPE material
4685238074_A


title: A222-RA 4


title: TAX577508

description: breast tumor

tag: ageyear


title: 62320 (4685238073_H)

description:
FFPE material
4685238073_H


title: A288-RA 4


title: 13373 (4685238073_G)

description:
FFPE material
4685238073_G


title: TAX577159

description: breast tumor

tag: agestatus


title: TAX577143

description: breast tumor

tag: nodestatus


title: TAX577549

description: breast tumor

tag: grade


title: TAX577567

description: breast tumor

tag: overall survival time


title: 20405 (4685238073_E)

description:
FFPE material
4685238073_E


title: 51698 (4685238073_F)

description:
FFPE material
4685238073_F


title: 20091 (4685238073_D)

description:
FFPE material
4685238073_D


title: WT, LPS 1hr

city: New York

first: Ping

last: Rao

department: Microbiology and Immunology

institute: Columbia University

description: Gene expression data from LPS treated BMDM

hyb_protocol: Fragmented cRNA is hybridized to the test array for 16 hours at 45C. The test array is then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station.

scan_protocol: GeneChip Scanner 3000

data_processing: The images are analyzed using Microarray Suite version 5.0 (MAS 5.0) and comparison analysis are carried out according to the instructions provided by Affymetrix.

source_name: BMDM, LPS 1hr

label_protocol: First strand cDNA is synthesized by reverse transcription using the poly(A) RNA present in the starting total RNA sample. Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module. An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA. The resulting cRNA is fragmented in the presence of heat and Mg+2 before hybridization to the test array.

growth_protocol: BMDM culture: Bone marrow cells were plated overnight to remove stromal cells and mature resident macrophages. Non-adherent cells were transferred to new plates and differentiated with 30% L929 supernatant-conditioned media over 7 days. 70 million cells/ml macrophages was allowed to adhere overnight and stimulated with 1ug/ml LPS.

extract_protocol: Total RNA were isolated with Qiagen RNeasy.

treatment_protocol: Cells were treated with 1ug/ml LPS for 0, 1 and 5 hours.

tag: strain

tag: cell type

value: bone marrow derived macrophage


title: WT, LPS 5hr

source_name: BMDM, LPS 5hr


title: TAX577531

description: breast tumor

tag: fga

tag: sizemm


title: B2-RA 3


title: TAX577545

description: breast tumor

tag: overall survival event

tag: hu subtype

value: LumB


title: 30130 (4685238073_C)

description:
FFPE material
4685238073_C

tag: tissue

tag: mutation status


title: A250-RA 4

tag: disease state


title: IkB, LPS 5hr


title: A325-RA 3


title: IkB, LPS 0hr

source_name: BMDM, LPS 0 hr


title: 2007-12-08 E13a TraSH nasal vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77827.gif

source_name: library input pool

tag: reference

value: library input pool

source_name: technical replicate of mouse output pool 1

tag: experiment


title: TAX577536

description: breast tumor

source_name: breast tumor

tag: family status

tag: er

tag: pgr

value: Basal

tag: spfpercent

tag: sizestatus


title: TAX577396

description: breast tumor

value: breast tumor

tag: overall survival time

tag: nodestatus

tag: grade

tag: ageyear

tag: agestatus


title: TAX577387

description: breast tumor

tag: overall survival event

tag: fga

tag: sizemm


title: 20031 (4685238073_A)

description:
FFPE material
4685238073_A

tag: tissue

tag: mutation status


title: 2007-12-08 E13b TraSH nasal vitro

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77820.gif

tag: reference

source_name: technical replicate of library input pool 2


title: WT, LPS 0hr

source_name: BMDM, LPS 0hr

tag: strain

tag: cell type


title: TAX577421

description: breast tumor

tag: family status

tag: er

tag: hu subtype


title: A311-RA 3

tag: disease state

value: Non-RA


title: IkB, LPS 1hr


title: A292-RA 3


title: 2007-12-08 E13a TraSH nasal vitro

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77826.gif

source_name: biological replicate of library input pool 2

tag: experiment


title: TAX577496

description: breast tumor

tag: pgr

tag: overall survival time

tag: spfpercent

tag: nodestatus

value: NoGain

tag: sizestatus


title: A289-RA 3


title: B1-RA 3


title: TAX577450

description: breast tumor

tag: overall survival event

tag: grade

tag: fga

tag: ageyear

tag: agestatus


title: A267-RA 3


title: A262-RA 3


title: TAX577447

description: breast tumor

tag: tissue

tag: sizemm


title: Liver H2O-treated 21 days replicate 2

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

institute: Institute of Cancer Research

hyb_protocol: Test sample (Cy5-labelled) and reference (Cy3-labelled) were mixed and hybridised with Gene Expression Hybridization Kit (Agilent) on Agilent whole genome mouse 44k arrays following manufacturer's instructions. The arrays were incuated in Agilent SureHyb-enabled hybridization chambers, which was placed in the oven for 18 hours ( 65°C; 10 rpm).

scan_protocol: After hybridisation, the arrays were washed by Agilent Gene Expression Wash Buffer following the instructions. The arrays were scanned with a Axon 4000B scanner at wavelength 635nm and 532nm.

data_processing: The images were analysed with BlueFuse software to extract expression values, then all data were loaded into GeneSpring V7.2 software. The data were LOWESS normalised and natural  log-ratios were used for t-test and other analyses. Normalised ratios were used for fold-change analysis.

source_name: Hupki mouse liver

label_protocol: 5 μg of RNA was mixed with 1.2 μl T7 promotor primer (Agilent low RNA input linear amplification kit) and denatured at 65°C for 10 min. After being incubated on ice for 5 min, 8.5 μl cDNA Master Mix (Agilent) was added and the mixture was incubated at at 40°C for 2 hours. The sample was incubated at 65°C for 15 min and placed on ice for 5 min. Then the sample was mixed with Transcription Master Mix (Agilent) and Cy5 (tissue RNA) or Cy3 (UMRR) according to manufature's instuctions. After incubation at 40°C for 2 hours, the sample was purified with RNeasy Mini kit (Qiagen).

growth_protocol: Hupki mice (Trp53 tm1/Holl, homozygous for the knock-in TP53 allele harbouring human TP53 sequences in the 129/Sv background) were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and breed at the Institute of Cancer Research Animal Facility.

extract_protocol: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions and purified by Qiagen RNAease mini kit following manufacturer's instructions.

treatment_protocol: Female Hupki mice (2-4 months old) were randomly assigned to dose groups (three animals per time point) and were treated daily with 5 mg/kg body weight aristolochic acid I (AAI) by gavage according to a protocol published previously [Mengs, U. (1988) Tumour induction in mice following exposure to aristolochic acid. Arch Toxicol, 61, 504-505] for 3, 12 or 21 days, respectively. Control animals were treated with vehicle, water only. Mice were killed after 24 h. All animal experiments were carried out under license in accordance with the law, and following local ethical review. Organ sections (kidney and liver) were collected, snap-frozen in liquid nitrogen and stored at -80ºC until further analysis.

value: liver

tag: time point

value: 21 days

tag: agent

source_name: universal mouse reference RNA

tag: reference

value: 11 mouse cell lines collection


title: 2007-12-08 E13b TraSH nasal vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/77825.gif

source_name: mouse output pool 1

value: mouse output pool 1


title: TAX577495

description: breast tumor

tag: family status

tag: er

tag: hu subtype


title: TAX577411

description: breast tumor

tag: pgr

tag: overall survival time


title: B3-RA 3

tag: disease state


title: TAX577357

description: breast tumor

tag: spfpercent

tag: nodestatus

tag: sizestatus


title: A288-RA 3


title: TAX577331

description: breast tumor

tag: overall survival event

tag: grade

tag: fga


title: A222-RA 3


title: A260-RA 3


title: TAX577024

description: breast tumor

tag: tissue

tag: ageyear

tag: agestatus


title: A250-RA 3


title: Liver H2O-treated 12 days replicate 1

tag: time point

value: 12 days

tag: agent


title: Liver H2O-treated 12 days replicate 2

tag: reference


title: HeLa, Lenti Transient, EZH2-6, 24hr

description: Affymetrix Hela profiling of siRNA/shRNA treatments

data_processing: Data were loaded into the Rosetta Resolver® system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin

source_name: Hela cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

tag: cell line

value: Hela cells

tag: conditions

value: Lenti Transient, EZH2-6, 24hr


title: HeLa, Lenti Transient, e2f1-6, 24hr

value: Lenti Transient, e2f1-6, 24hr


title: HeLa, Lenti Transient, p21-2, 24hr

value: Lenti Transient, p21-2, 24hr


title: Liver H2O-treated 03 days replicate 3

value: 3 days


title: Liver H2O-treated 21 days replicate 3


title: Liver H2O-treated 03 days replicate 1


title: HeLa, Lenti Transient, EZH2-1, 24hr

value: Lenti Transient, EZH2-1, 24hr


title: HeLa, Lenti Transient, H1 Term, 24 hr

value: Lenti Transient, H1 Term, 24 hr


title: Liver H2O-treated 03 days replicate 2


title: TAX577350

description: breast tumor

tag: family status

value: sporadic

tag: er

tag: pgr

tag: hu subtype

tag: sizemm


title: Liver AAI-treated 21 days replicate 3

value: Liver

value: aristolochic acid I (AAI)


title: TAX577018

description: breast tumor

value: breast tumor

tag: overall survival time

value: Basal

tag: spfpercent

tag: nodestatus

tag: sizestatus


title: TAX577390

description: breast tumor

tag: tissue

tag: overall survival event

tag: grade

tag: fga

value: NoGain


title: TAX577425

description: breast tumor

value: Gain

tag: ageyear

tag: agestatus


title: TAX577339

description: breast tumor


title: Liver AAI-treated 21 days replicate 2

tag: time point

value: 21 days

tag: agent

tag: reference

value: 11 mouse cell lines collection


title: Liver AAI-treated 21 days replicate 1


title: Liver AAI-treated 12 days replicate 2

value: 12 days


title: Liver AAI-treated 12 days replicate 3


title: HeLa, siRNA, fdxr-3, 0.5nM, 24hr

tag: cell line

value: Hela cells

tag: conditions

value: siRNA, fdxr-3, 0.5nM, 24hr


title: TAX577376

description: breast tumor

tag: family status

tag: er

tag: pgr

tag: hu subtype


title: TAX577361

description: breast tumor

tag: overall survival time

tag: spfpercent

tag: nodestatus

tag: sizemm


title: TAX577345

description: breast tumor

tag: tissue

value: familial

tag: overall survival event

tag: grade

tag: sizestatus


title: TAX577400

description: breast tumor

tag: fga

tag: ageyear

tag: agestatus


title: Liver H2O-treated 12 days replicate 3

value: liver

tag: time point

tag: agent

tag: reference


title: TAX577349

description: breast tumor

tag: family status

tag: er


title: HeLa, siRNA, fdxr-3, 2.5nM, 24hr

tag: cell line

tag: conditions

value: siRNA, fdxr-3, 2.5nM, 24hr


title: HeLa, siRNA, e2f1-6, 0.5nM, 24hr


title: Liver AAI-treated 12 days replicate 1


title: Liver AAI-treated 03 days replicate 3

value: 3 days


title: Liver AAI-treated 03 days replicate 2


title: HeLa, siRNA, e2f1-6, 2.5nM, 24hr


title: HeLa, siRNA, e2f1-6, 1nM, 24hr

value: siRNA, e2f1-6, 1nM, 24hr


title: A327-RA 3

tag: disease state

value: rheumatoid arthritis (RA)

value: Non-RA


title: TAX577413

description: breast tumor

tag: pgr

tag: overall survival time

tag: hu subtype

tag: spfpercent

tag: nodestatus


title: HeLa, siRNA, p21-2, 1nM, 24hr

value: siRNA, p21-2, 1nM, 24hr


title: HeLa, siRNA, p21-2, 2.5nM, 24hr


title: HeLa, siRNA, EZH2-6, 0.5nM, 24hr

value: siRNA, EZH2-6, 0.5nM, 24hr


title: TAX577399

description: breast tumor

tag: tissue

value: breast tumor

tag: overall survival event

value: Basal

tag: grade

tag: sizemm

tag: sizestatus


title: Kidney H2O-treated 21 days replicate 2

source_name: Hupki mouse kidney

value: kidney

tag: time point

tag: agent


title: TAX577365

description: breast tumor

tag: family status

tag: fga

value: Gain

tag: ageyear

tag: agestatus


title: Kidney H2O-treated 21 days replicate 3

value: 21 days

tag: reference

value: 11 mouse cell lines collection


title: TAX577378

description: breast tumor

tag: er

tag: pgr


title: Liver AAI-treated 03 days replicate 1

value: Liver

value: aristolochic acid I (AAI)


title: TAX577380

description: breast tumor

tag: overall survival time

tag: hu subtype


title: HeLa, siRNA, p21-2, 0.5nM, 24hr

tag: cell line

value: Hela cells

tag: conditions


title: HeLa, Lenti Transient, fdxr-3, 24hr

value: Lenti Transient, fdxr-3, 24hr


title: A298-RA 3

tag: disease state


title: Kidney H2O-treated 12 days replicate 3

tag: tissue

value: 12 days


title: Liver H2O-treated 21 days replicate 1

value: liver


title: HeLa, siRNA, EZH2-6, 2.5nM, 24hr

value: siRNA, EZH2-6, 2.5nM, 24hr


title: TAX577394

description: breast tumor

tag: overall survival event

tag: spfpercent

tag: nodestatus

tag: grade

tag: sizemm


title: TAX577354

description: breast tumor

tag: family status

value: familial

tag: fga

value: NoGain

tag: sizestatus


title: Kidney H2O-treated 03 days replicate 2

tag: time point

value: 3 days

tag: agent

tag: reference


title: Kidney H2O-treated 03 days replicate 3


title: Kidney H2O-treated 21 days replicate 1


title: Kidney H2O-treated 12 days replicate 2


title: Kidney H2O-treated 12 days replicate 1


title: HeLa, siRNA, EZH2-1, 2.5nM, 24hr

value: siRNA, EZH2-1, 2.5nM, 24hr


title: TAX577375

description: breast tumor

value: breast tumor

value: sporadic

tag: er

tag: pgr

tag: overall survival time

tag: ageyear

tag: agestatus


title: HeLa, siRNA, EZH2-1, 0.5nM, 24hr

tag: cell line

tag: conditions

value: siRNA, EZH2-1, 0.5nM, 24hr


title: HeLa, siRNA, EZH2-1, 1nM, 24hr

value: siRNA, EZH2-1, 1nM, 24hr


title: Kidney AAI-treated 21 days replicate 3

tag: tissue

value: kidney

value: 21 days


title: Kidney AAI-treated 21 days replicate 2

value: 11 mouse cell lines collection


title: HeLa, siRNA, Mock,24 hr

value: siRNA, Mock,24 hr


title: TAX577370

description: breast tumor

tag: overall survival event

tag: hu subtype

value: Basal

tag: spfpercent

tag: nodestatus

value: Gain


title: Kidney H2O-treated 03 days replicate 1


title: TAX577406

description: breast tumor

tag: family status

tag: grade

tag: fga

tag: sizemm


title: TAX577348

description: breast tumor

tag: sizestatus


title: TAX577337

description: breast tumor

tag: er


title: Kidney AAI-treated 21 days replicate 1

tag: time point

tag: agent

value: aristolochic acid I (AAI)

tag: reference


title: TAX577347

description: breast tumor

tag: pgr

tag: overall survival time

tag: ageyear

tag: agestatus


title: TAX577407

description: breast tumor

tag: tissue

tag: overall survival event


title: TAX577395

description: breast tumor

tag: hu subtype

tag: spfpercent


title: Kidney AAI-treated 03 days replicate 3


title: TAX577386

description: breast tumor

tag: family status

tag: nodestatus


title: Kidney AAI-treated 03 days replicate 1


title: Kidney AAI-treated 12 days replicate 2

value: 12 days


title: Kidney AAI-treated 03 days replicate 2


title: Kidney AAI-treated 12 days replicate 3


title: TAX577426

description: breast tumor

tag: grade

tag: fga


title: Kidney AAI-treated 12 days replicate 1


title: HCT116 Mock_pool vs. HCT116 p53 1026 0.01 nM

value: HCT116 Mock_pool

tag: treatment


title: HCT116 Mock_pool vs. HCT116 p53 1026 0.1 nM


title: HeLa, siRNA, fdxr-3, 1nM, 24hr

tag: cell line

value: Hela cells

tag: conditions

value: siRNA, fdxr-3, 1nM, 24hr


title: HCT116 Mock_pool vs. HCT116 p53 1026 1 nM


title: TAX577388

description: breast tumor

tag: er

tag: sizemm

tag: sizestatus


title: TAX577329

description: breast tumor

tag: pgr

tag: overall survival time

value: NoGain


title: TAX577427

description: breast tumor

tag: ageyear

tag: agestatus


title: TAX577404

description: breast tumor

tag: tissue

tag: overall survival event


title: HCT116 Mock_pool vs. HCT116 p53 1026 10 nM

tag: reference


title: YCC9 - 37 cell line study

status: Public on Jun 08 2010

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 37 (unique) gastric cancer cell lines

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChipÂ® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data were analyzed with R version 2.9.0, package affy. Data processing was performed by RMA normalization and Log 2 transformed.

source_name: gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Cancer cell lines were grown as per GC cell lines were obtained either from commercial sources or collaborators and cultured as recommended

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

tag: cell type

value: gastric cancer


title: HCT116 Mock_pool vs. HCT116 p53 1026 100 nM_2


title: HCT116 Mock_pool vs. HCT116 p53 1026 100 nM_1


title: YCC3 - 37 cell line study

treatment_protocol: Cancer cell lines were grown as per GC cell lines were obtained either from commercial sources or collaborators and cultured as recommended


title: YCC7 - 37 cell line study


title: TAX577414

description: breast tumor

value: breast tumor

tag: family status

tag: hu subtype

tag: spfpercent

tag: nodestatus


title: YCC6 - 37 cell line study

tag: cell line


title: SJX-Control 1

source_name: Genomic DNA from the whole blood

tag: disease state

value: none (control)

value: Non-RA


title: YCC2 - 37 cell line study


title: YCC18 - 37 cell line study


title: YCC16 - 37 cell line study


title: A327-RA 1

value: rheumatoid arthritis (RA)

source_name: Reference gDNA from Sample LX (Non-RA) whole blood


title: B1-RA 1


title: YCC11 - 37 cell line study


title: YCC19 - 37 cell line study


title: YCC17 - 37 cell line study


title: B3-RA 1


title: YCC1 - 37 cell line study


title: YCC20 - 37 cell line study


title: YCC10 - 37 cell line study


title: Takigawa - 37 cell line study

value: Takigawa


title: TMK1 - 37 cell line study


title: SNU719 - 37 cell line study


title: SNU5 - 37 cell line study


title: A311-RA 1


title: SNU1 - 37 cell line study


title: SNU16 - 37 cell line study


title: B2-RA 1


title: A288-RA 1


title: A325-RA 1


title: RerfGC1B - 37 cell line study


title: A267-RA 1


title: A298-RA 1


title: A260-RA 1


title: MKN45 - 37 cell line study


title: Fu97 - 37 cell line study


title: A292-RA 1


title: NUGC4 - 37 cell line study


title: AGS - 37 cell line study

value: AGS


title: MKN1 - 37 cell line study


title: HGC27 - 37 cell line study


title: OCUM1 - 37 cell line study


title: CLS145 - 37 cell line study


title: Hs746T - 37 cell line study


title: AZ521 - 37 cell line study


title: KatoIII - 37 cell line study

value: KatoIII


title: Ist1 - 37 cell line study


title: IM95 - 37 cell line study


title: NCI-N87 - 37 cell line study