title: MRK067_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4402
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK071_Stroma

status: Public on Jan 22 2010

type: RNA

city: North Wales

first: James

last: Hardwick

state: PA

address: 351 N. Sumneytown Pike

department: Molecular Profiling

country: USA

institute: Merck & Co., Inc.

description: Individual LCM stroma from esophageal disease

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4403
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene Universal Human Reference RNA

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

extract_protocol: Messenger RNA was extracted from stromal cells microdissected from 5x 8 μm sections using PicoPureRNA reagents according to Molecular Devices' instructions

treatment_protocol: Human tissue specimens were surgically excised and snap frozen in liquid nitrogen

tag: tissue

value: Reference RNA Pool

tag: cell type

value: stromal cells (laser-capture microdissected)

tag: disease stage

value: Intestinal metaplasia


title: Patient 861_rep1

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: Sample and control probes were mixed together in a final volume of 90 µl of hybridisation buffer : DIG Easy Hyb (Roche, Laval, QC) + 0.5 µg/µl salmon sperm (Invitrogen, Carlsbad, CA) + 0.5 µg/µl yeast tRNA (Invitrogen, Carlsbad, CA). Mix was heated at 95ºC for 5 min and put on the arrray. After adding a coverslip, arrays were incubated in a hybridisation chamber at 37ºC for 16h. Arrays were then washed three times in SSC0.1X, SDS 0.1%, four times in SSC 0.1X and centrifuge to dry them.

scan_protocol: Slides were scanned in a ScanArray Lite (GSI Luminomics, Billerica, MA).

data_processing: Spot intensity was quantified using QuantArray (GSI Luminomics, Billerica, MA). The Lowess scatter-smoothing normalization was performed in the GeneSpring 7.0 software package (Agilent, Santa Clara, CA).

source_name: LCM-captured brain tumor cells, adult

label_protocol: 5 µg of aRNA were reverse transcribed with Superscript II RT (Invitrogen, Carlsbad, CA). cDNA were direct-labelled with Cy3dCTP or Cy5dCTP (GE Healtcare, Baie d'Urfe, QC) and purified using the QIAquick PCR Purification kit (Qiagen, Mississauga, ON). Labelled probes were then dried to get a final volume of 3 to 6 µl.

extract_protocol: After LCM, RNA was extracted with PicoPure RNA Isolation (Molecular Devices, Sunnyvale, CA). Then, 30-40 ng were amplified with the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: All biological samples were flash-frozen in liquid nitrogen immediately after surgery. Interesting cells were isolated by Laser Capture Microdissection (LCM).

value: type IV glioblastoma

tag: pediatric patient

value: no

tag: angiogenesis score

value: pos

tag: p53 score

tag: egfr score

tag: ras score

tag: survival

tag: sex

value: F

tag: primary tumor?

source_name: Pooled normal brain, pediatric

value: brain

value: yes


title: Patient 66_rep2

source_name: LCM-captured brain tumor cells, pediatric

value: neg


title: MRK065_Stroma

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.

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4400
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK066_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4401
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Dysplasia


title: MRK061_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4398
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK072_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4404
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Sample BM3 versus breast cancer cell line reference pool

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: Sample BM3; ER status: -; ERBB2 status by FISH: +; Histology: Ductal; Metastatic: +; TNM: T1 NO  versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

hyb_protocol: Equal amounts of labeled cDNA for the test sample and the reference sample were hybridized to cDNA array for each tumor.

scan_protocol: Fluorescent intensities were measured using an Agilent scanner, and scanned images were analyzed using DeArray software.

data_processing: Significance analysis of microarray was used for data mining and analysis. Supervised clustering was done, where each sample was identified as brain metastasis or primary tumor.

source_name: BM3, brain metastasis

label_protocol: cDNA microarray analysis: Cy3-dUTP–labeled or Cy5- dUTP–labeled cDNA (GE Healthcare) was synthesized from 50 to 100 μg of amplified aRNA using random primed polymerization with SuperScript II reverse transcriptase (Invitrogen).

extract_protocol: All samples were subjected to LCM and RNA amplification. Briefly, 8-μm frozen tissue sections were thawed 15 s at room temperature and stained using the Histogene LCM Frozen Section Staining kit (Arcturus Engineering) following the manufacturer's instructions with the addition of a 5-min incubation in 100% ethanol before xylene. Approximately 2,000 laser-captured pulses were collected for each sample using the PixCell II Laser Capture Microdissection System (Arcturus Engineering) in a 15-min period. Captured cells were lysed off the LCM caps in PicoPure RNA Extraction buffer (Pico- Pure RNA Isolation kit, Arcturus Engineering) for 30 min at 55°C and frozen at −80°C until ready to proceed. Total RNA was extracted according to the manufacturer's instructions for the PicoPure RNA Isolation kit. Quality and quantity of RNA were assessed using the RNA 6000 Pico Assay for the 2100 Bioanalyzer (Agilent Technologies). A minimum of 10 ng of RNA was then subjected to two rounds of a T7 RNA polymerase catalyzed amplification protocol using the RiboAmp RNA Amplification kit (Arcturus Engineering). Quality and quantity of the amplified aRNA were assessed using the RNA 6000 Nano Assay for the 2100 Bioanalyzer. A reference RNA sample consisting of a pool of six breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D) was simultaneously amplified.

tag: er status

tag: erbb2 status (fish)

tag: histology

value: Ductal

tag: metastatic

tag: tnm stage

value: T1 NO

source_name: Breast cancer cell line reference pool

tag: cell lines

value: breast cancer

tag: sample type

value: reference


title: MRK059_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4396
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

tag: tissue

tag: cell type


title: MRK060_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4397
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

tag: disease stage


title: Sample BM26 versus breast cancer cell line reference pool

description: Sample BM26; ER status: -; ERBB2 status by FISH: +; Histology: Ductal; Metastatic: +; TNM: T2 N1 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM26, brain metastasis

value: T2 N1 M0


title: Sample BM2 versus breast cancer cell line reference pool

description: Sample BM2; ER status: +; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: +; TNM: T2 N0 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM2, brain metastasis

value: T2 N0 M0


title: Sample BM5 versus breast cancer cell line reference pool

description: Sample BM5; ER status: +; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: +; TNM: T2 N1 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM5, brain metastasis


title: MRK054_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4392
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Reference RNA Pool


title: Sample BM25 versus breast cancer cell line reference pool

description: Sample BM25; ER status: -; ERBB2 status by FISH: +; Histology: Ductal; Metastatic: +; TNM: T2 N1 M0 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: BM25, brain metastasis


title: Detroit 562 Clone 3 P35 rep3

city: Woolloongabba

first: Sarina

last: Cameron

state: QLD

address: Level 4, R wing, PA Hospital

country: Australia

institute: Diamantina Institute

description:
Replicate 3
4375521006L

hyb_protocol: Standard illumina hybridization protocol

scan_protocol: Standard illumina scanning protocol

data_processing: Data was normalised using quanatile normalisation with Lumi software.

label: biotin

source_name: Detroit 562 HNSCC Cell line

label_protocol: Biotinylated cRNA was prepared with the ambion amplification kit for illumina arrays.

growth_protocol: Grown as per ATCC recommendations.

extract_protocol: RNA was isolated with Trizol reagent, followed by Clean-up and DNase 1 treatment using the QIAGEN RNA easy mini kit as per the kit protocol. Agilent Bioanalysier was employed for quality control.

value: female

value: Metastatic HNSCC of the Pharynx

tag: cell line

value: Detroit 562 Clone 3

tag: cell culture passage number


title: MRK053_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4391
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: stromal cells (laser-capture microdissected)


title: MRK058_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4395
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Intestinal metaplasia


title: Sample M60 versus breast cancer cell line reference pool

description: Sample M60; ER status: +; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T1 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M60, breast tumor


title: MRK047_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4389
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK057_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4394
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK049_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4390
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK056_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4393
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Detroit 562 Clone 5 P40 rep3

description:
Replicate 3
4375521006J

value: Detroit 562 Clone 5


title: Detroit 562 Clone 3 P29 rep3

description:
Replicate 3
4375521006K


title: Sample M70 versus breast cancer cell line reference pool

description: Sample M70; ER status: +; ERBB2 status by FISH: -; Histology: Ductal; Metastatic: -; TNM: T2 versus pool of breast cancer cell lines (MCF7, ZR-75, BT-474, BT-549, MDA-MB-231, and T-47-D)

source_name: M70, breast tumor


title: Detroit 562 Clone 5 P5 rep3

description:
Replicate 3
4375521006I


title: MRK045_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4387
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK044_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4386
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK086_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4413
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK046_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4388
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Detroit 562 Clone 6 P6 rep3

description:
Replicate 3
4375521006H

value: Detroit 562 Clone 6


title: MRK030_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4383
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Adenocarcinoma


title: MRK026_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4381
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MeDIP - 803

type: genomic

city: Beijing

first: Kunlin

last: Zhang

address: DaTun Road A4

country: China

institute: Chinese Academy of Sciences

description: MeDIP to compare the differential between IP (methylated) and Input (methylated + unmethylated) DNA of cell line MGC-803

hyb_protocol: Hybridization of the CGI array was performed under a cover slip in a humidified chamber fixed in a BioMix II hybridization machine (CapitalBio, China) at 42°C for 17 h. The array was washed two times in 2X saline sodium citrate and 0.2% SDS at 42°C for 5 min and once in  0.1X saline sodium citrate at room temperature. The slides were dried by centrifugation at 800 rpm for 5 min and scanned immediately with LuxScan 10K scanner (CapitalBio, China).

scan_protocol: Arrays scanned using an  LuxScan 10K scanner and LuxScan 10K software (CapitalBio, China).

data_processing: The median average intensity of foreground and background was extracted from the .lsr files. If a spot intensity was zero or negative after background subtraction, it was set at half of the minimum positive corrected intensities in the array. We performed lowess normalization. Then linear model and empirical Bayes smoothing analyses were combined to obtain the statistics value and fold change of each spot. Significant candidates were selected with values of B>0. All of above calculations were done with the limma (http://bioinf.wehi.edu.au/limma/) package within the R environment (http://cran.r-project.org/).

molecule: genomic DNA

source_name: Input(methylated + unmethylated) DNA of gastric adenocarcinoma cell line MGC-803

label_protocol: Labelled with Cy3 and Cy5 during PCR the methylated and unmethylated fragment as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Gastric epithelium cell line Ges-1 and the gastric adenocarcinoma cell line MGC-803 was grown in 10×10cm dish with RPMI1640 medium and the temperature maintained at 37°C.  Medium was used with FPS (10%) and penicillin-Streptomycin (1%).CO2 levels were monitored at 5.0% ±0.2%.

extract_protocol: After harvested, the genomic DNA were extracted by NucleoSpin Tissue kit(MN ).

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; Input(methylated + unmethylated) DNA

source_name: IP (methylated) DNA of gastric adenocarcinoma cell line MGC-803

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; IP (methylated) DNA


title: MRK033_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4385
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK022_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4377
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MRK025_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4380
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: MMASS-v2 - 803

description: MMASS-v2 to compare the differential between methylated and unmethylated DNA of cell line MGC-803

source_name: unmethylated DNA of gastric adenocarcinoma cell line MGC-803

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; unmehtylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; methylated DNA


title: MRK028_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4382
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Detroit 562 Clone 3 P33 rep2

description:
Replicate 2
4375521006E

data_processing: Data was normalised using quanatile normalisation with Lumi software.


title: MRK032_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4384
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Detroit 562 Clone 1 P5 rep3

description:
Replicate 3
4375521006G

value: Detroit 562 Clone 1


title: Detroit 562 P29 rep3

description:
Replicate 3
4375521006F

value: Detroit 562


title: DMH-v1

description: DMH-v1 to compare DNA methylation differential between cell line Ges-1 and MGC-803

source_name: methylated DNA of gastric epithelium cell line Ges-1

value: gastric epithelium from foetus of 34 weeks, non-tumorigenesis; methylated DNA

source_name: mehtylated DNA of gastric adenocarcinoma cell line MGC-803


title: MMASS-v1 - 803

description: MMASS-v1 to compare the differential between methylated and unmethylated DNA of cell line MGC-803

source_name: methylated DNA of gastric adenocarcinoma cell line MGC-803


title: MeDIP - Ges

description: MeDIP to compare the differential between IP (methylated) and Input (methylated + unmethylated) DNA of cell line Ges-1

source_name: Input(methylated + unmethylated) DNA of gastric epithelium cell line Ges-1

value: gastric epithelium from foetus of 34 weeks, non-tumorigenesis; Input(methylated + unmethylated) DNA

source_name: IP (methylated) DNA of gastric epithelium cell line Ges-1

value: gastric epithelium from foetus of 34 weeks, non-tumorigenesis; IP (methylated) DNA


title: MRK024_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4379
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

source_name: Stratagene Universal Human Reference RNA

value: Reference RNA Pool


title: MMASS-v1 - Ges

description: MMASS-v1 to compare the differential between methylated and unmethylated DNA of cell line Ges-1

source_name: unmethylated DNA of gastric epithelium cell line Ges-1

value: gastric epithelium from foetus of 34 weeks, non-tumorigenesis; unmehtylated DNA


title: MMASS-v2 - Ges

description: MMASS-v2 to compare the differential between methylated and unmethylated DNA of cell line Ges-1


title: MRK023_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4378
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: DMH-v2

description: DMH-v2 to compare DNA methylation differential between cell line Ges-1 and MGC-803


title: Fibroblast from normal 5

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

country: United Kingdom

institute: Cambridge Research Institute

description: Gene expression data from fibroblasts cultured from normal biopsy

hyb_protocol: The fragmented and labeled ssDNA was hybridized to a GeneChip Human Gene 1.0 ST array (28,132 genes, 764,885 probes) for 17 hours.

scan_protocol: The array was washed and scanned with the Affimetrix wash station and scanner.

data_processing: The generated cell-files, which contain the measured intensities for all probes, were analyzed using the GeneSpringGX 9 software. Hierarchical unsupervised 2 dimensional Euclidean clustering of the stromal fibroblasts was carried out using GeneSpringGX9. 2D Supervised clustering was then carried out. Genes overexpressed in cancer associated fibroblasts (CAFs) compared to BE associated fibroblasts (BAFs) more than 2 folds were selected for gene enrichment analysis.

label: Biotin

source_name: Fibroblasts cultured from normal biopsy

label_protocol: Labelling was carried out according to the GeneChip Whole transcript (WT) sense target labeling assay manual (P/N 701880 Rev. 4). Briefly, the RNA was reverse transcribed using random primers tagged with a T7 promoter sequence. The second strand was synthesized and the dsDNA was used as a template and linear amplified by T7 RNA polymerase. The cRNA was reverse transcribed using a mixture of dNTPs and dUTP and random primers. After RNaseH digest the ssDNA was fragmented with a combination of Uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. The fragmented ssDNA was end-labeled by terminal deoxynucleotidyl transferase with the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: 5-10mm tissue pieces collected from esophageal resections were maintained at 4ºC in DMEM complete medium (Gibco, Invitrogen) supplemented with 20% FCS, 100U/ml penicillin, 100mg/ml streptomycin and processed within 1-2h from the time of collection. Tumor and BE tissues were derived at pathological sites whereas squamous tissues were collected from the resection margins as far from the tumor as possible. Samples were washed in PBS containing amphotericin B before being cut in small fragments, which were then uniformly dispersed onto a fetal calf serum coated dish. The dish was incubated upside down at 37ºC for 3h prior to addition of DMEM containing 20% FCS. The cultures were incubated at 37ºC for 2 weeks. Cells were differentially trypsinised and pure cultures of fibroblasts were generally obtained after 2 passages. Isolated fibroblasts were then maintained in DMEM medium supplied with 20% FCS, 100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine. Fibroblasts were used in experiments up to passage 6.

extract_protocol: Total RNA was extracted using Trizol™ according to Invitrogen's instructions

tag: origin of biopsy

value: Normal

tag: age

tag: gender

value: Male

tag: chemotherapy

value: No

tag: diagnosis

value: Cancer

value: cultured stromal fibroblast


title: Detroit 562 Clone 3 P28 rep2

description:
Replicate 2
4375521006D

tag: sex

value: female

value: Metastatic HNSCC of the Pharynx

value: Detroit 562 Clone 3


title: MeDIP 1st antibody incubation time 12h, 2nd antibody incubation time 4h - 803

description: MeDIP with 1st antibody incubation time 12h, 2nd antibody incubation time 4h using gastric adenocarcinoma cell line MGC-803 to evaluate antibody incubation time

source_name: Input (methylated + unmethylated) DNA of gastric adenocarcinoma cell line MGC-803

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 4h; methylated + unmethylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 4h; methylated DNA


title: MRK006_Stroma

description: Individual LCM stroma from esophageal disease

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4373
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: stromal cells (laser-capture microdissected)

value: Dysplasia


title: Detroit 562 Clone 5 P4 rep2

description:
Replicate 2
4375521006B

value: Detroit 562 Clone 5


title: MRK020_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4376
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Adenocarcinoma


title: MRK018_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4375
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Fibroblast from dysplasia 3

description: Gene expression data from fibroblasts cultured from dysplastic biopsy

source_name: Fibroblasts cultured from dysplastic biopsy


title: Fibroblast from dysplasia 4

value: Female


title: Detroit 562 Clone 5 P36 rep2

description:
Replicate 2
4375521006C


title: Fibroblast from cancer 1

description: Gene expression data from fibroblasts cultured from cancer biopsy

source_name: Fibroblasts cultured from cancer biopsy

value: Yes

value: Cancer (T3N0M0)


title: MRK013_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4374
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Reference RNA Pool

value: Intestinal metaplasia


title: Detroit 562 Clone 6 P6 rep2

description:
Replicate 2
4375521006SA

source_name: Detroit 562 HNSCC Cell line

value: Detroit 562 Clone 6


title: MRK063_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4399
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise


title: Fibroblast from dysplasia 2

value: Male

value: No


title: MeDIP 1st antibody incubation time 12h, 2nd antibody incubation time 6h - 803

description: MeDIP with 1st antibody incubation time 12h, 2nd antibody incubation time 6h using gastric adenocarcinoma cell line MGC-803 to evaluate antibody incubation time

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 6h; methylated + unmethylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 6h; methylated DNA


title: MeDIP 1st antibody incubation time 12h, 2nd antibody incubation time 1h - 803

description: MeDIP with 1st antibody incubation time 12h, 2nd antibody incubation time 1h using gastric adenocarcinoma cell line MGC-803 to evaluate antibody incubation time

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 1h; methylated + unmethylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 1h; methylated DNA


title: Fibroblast from cancer 3

value: Cancer

value: Poor differentiation (T3)

value: cultured stromal fibroblast


title: Detroit 562 Clone 1 P4 rep2

description:
Replicate 2
4375521025L

value: female

value: Metastatic HNSCC of the Pharynx

value: Detroit 562 Clone 1


title: Detroit 562 P28 rep2

description:
Replicate 2
4375521025K

value: Detroit 562


title: Detroit 562 Clone 3 P27 rep1

description:
Replicate 1
4375521025I

value: Detroit 562 Clone 3


title: MeDIP 1st antibody incubation time 12h, 2nd antibody incubation time 2h - 803

description: MeDIP with 1st antibody incubation time 12h, 2nd antibody incubation time 2h using gastric adenocarcinoma cell line MGC-803 to evaluate antibody incubation time

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 2h; methylated + unmethylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 12h, 2nd antibody incubation time 2h; methylated DNA


title: Detroit 562 Clone 3 P34 rep1

description:
Replicate 1
4375521025J


title: Fibroblast from normal 4

value: Normal

value: Yes


title: MMASS-v1 annealing temperature 72 - 803

description: MMASS-v1 with annealing temperature 72°C using gastric adenocarcinoma cell line MGC-803 to test signal intensity

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 72°C; methylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 72°C; unmethylated DNA


title: Fibroblast from cancer 2

value: Female

value: Cancer (T3N1M0)


title: Fibroblast from dysplasia 1

value: Dysplasia

value: No


title: Fibroblast from normal 2

value: Male

value: Cancer (T3N0M0)


title: Fibroblast from normal 3

value: cultured stromal fibroblast


title: MeDIP 1st antibody incubation time 2h, 2nd antibody incubation time 2h - 803

description: MeDIP with 1st antibody incubation time 2h, 2nd antibody incubation time 2h using gastric adenocarcinoma cell line MGC-803 to evaluate antibody incubation time

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 2h, 2nd antibody incubation time 2h; methylated + unmethylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; 1st antibody incubation time 2h, 2nd antibody incubation time 2h; methylated DNA


title: Detroit 562 Clone 5 P34 rep1

description:
Replicate 1
4375521025H

value: female

value: Metastatic HNSCC of the Pharynx

value: Detroit 562 Clone 5


title: Detroit 562 Clone 5 P3 rep1

description:
Replicate 1
4375521025G


title: Salicyl alcohol vs. control, rep5

status: Public on Jan 21 2010

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

hyb_protocol: Cy3- and Cy5- labeled cDNA from control and treated samples were suspended in 55 μl of hybridization buffer (50% formamide, 5× SSC, 0.4% SDS and 0.1% BSA). The mixture was denatured at 42oC for 5 min, centrifuged briefly, and applied to the array slide.  The slide was covered with a piece of parafilm amd incubated for 36 hours in a hybridization oven (Boekel Scientific) at 40oC with humidity maintained by wet paper towels soaked in the hybridization buffer. The slides were then rinsed three times separately in beakers containing 500 ml of 1× SSC and 0.2% SDS (42oC), followed by 0.1× SSC and 0.2% SDS, and finally in 0.1× SSC before drying the slides using a microarray Air Jet.

scan_protocol: Arrays were scanned using an Axon Genepix 4000B scanner, and the florescence signal intensity was quantified using the GenePix Pro 5.1 software.

data_processing: Data analysis was carried out using GeneSpring 7.3.  Replicate spots were averaged and the channels reversed for dye-swap replicates.  Data from the two channels were log2 transformed and normalized using the LOWESS algorithm.

organism: Populus tremuloides

source_name: salicyl alcohol-fed cells

label_protocol: DNase-treated total RNA and spike mix (Lucidea Universal ScoreCard, Amersham) were reverse transcribed in the presence of aminoallyl-modified dUTP (Sigma) using anchored oligo (dT)20 primer and SuperScript III reverse transcriptase (Invitrogen).  Aminoallyl-modified cDNA was purified with the QIAquick PCR purification kit and resuspended in 0.1M sodium carbonate buffer (pH 9.0) for chemical coupling with Cy3 and Cy5 dye (Amersham). The fluorescent-labeled targets were purified with the QIAquick PCR purification kit, and cDNA concentration and Cy dye labeling efficiency measured with a NanoDrop ND-100 spectrophotometer. Aliquots of 50 pmol Cy dye-labeled cDNA were vacuum dried, and stored at -20oC until used.

growth_protocol: Cell cultures derived from Populus tremuloides clone L4 were maintained in WPM media supplemented with 3% sucrose and 2.2 mg/L 2.4-D.  Cells were subcultured at 11-day intervals by inoculating 5 mL of cultures to 30 mL of fresh media.

extract_protocol: CTAB extraction

treatment_protocol: Cell cultures were fed 5 mM salicyl alcohol (treatment) or water (control) 5 days after subculture.  Fed and unfed cells were harvested 48 hours after feeding for RNA extraction.

tag: strain

value: clone L4

source_name: control cells


title: Salicyl alcohol vs. control, rep6, dye-swap

description: dye-swap of replicate 3


title: Detroit 562 Clone 1 P4 rep1

description:
Replicate 1
4375521025E

value: Detroit 562 Clone 1


title: Detroit 562 Clone 6 P40 rep1

description:
Replicate 1
4375521025F

value: Detroit 562 Clone 6


title: Salicyl alcohol vs. control, rep2, dye-swap

description: dye-swap of replicate 1


title: Salicyl alcohol vs. control, rep3


title: Salicyl alcohol vs. control, rep4, dye-swap

description: dye-swap of replicate 2


title: MMASS-v1 annealing temperature 68.5 - 803

description: MMASS-v1 with annealing temperature 68.5°C using gastric adenocarcinoma cell line MGC-803 to test signal intensity

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 68.5°C; methylated DNA

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 68.5°C; unmethylated DNA


title: Fibroblast from metaplasia 1

description: Gene expression data from fibroblasts cultured from metaplastic biopsy

source_name: Fibroblasts cultured from metaplastic biopsy

value: Metaplasia


title: Fibroblast from normal 1

value: Normal

value: Poor differentiation


title: Salicyl alcohol vs. control, rep1


title: Laser capture microdissected (LCM) whole seeds at the linear-cotyledon stage, biological replicate 2

city: Davis

first: John

middle: J

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description:
Arabidopsis lcWS5
Whole seeds collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis linear-cotyledon stage whole seeds captured by LCM

label_protocol: 2 to 5 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques between 1.6 and 1.9 cm  long containing linear-cotyledon stage seeds were collected from 38-46 day old plants.  Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

tag: genotype


title: MMASS-v1 annealing temperature 65 - 803

description: MMASS-v1 with annealing temperature 65°C using gastric adenocarcinoma cell line MGC-803 to test signal intensity

data_processing: The median average intensity of foreground and background was extracted from the .lsr files. If a spot intensity was zero or negative after background subtraction, it was set at half of the minimum positive corrected intensities in the array. We performed lowess normalization. Then linear model and empirical Bayes smoothing analyses were combined to obtain the statistics value and fold change of each spot. Significant candidates were selected with values of B>0. All of above calculations were done with the limma (http://bioinf.wehi.edu.au/limma/) package within the R environment (http://cran.r-project.org/).

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 65°C; methylated DNA

source_name: unmethylated DNA of gastric adenocarcinoma cell line MGC-803

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; annealing temperature 65°C; unmethylated DNA


title: Intensity test - 803

description: self versus self hybridizations of input DNA to test intensity of array

value: mucinous adenocarcinoma, poorly differentiated, highly tumorigenesis, endepidermis, adherence, Han people, male; methylated DNA


title: Nucleus Accumbens Cocaine Self-adminitration TsA treatment replicate 2

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were processed using the Affymetrix GeneChip Operating Software (GCOS v1.4; Microarray Suite (MAS 5.0) algorithm).

organism: Rattus norvegicus

source_name: Nucleus Accumbens_TsA

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

extract_protocol: Total RNA was extracted according to the procedure described by Chomczynski and Sacchi, 1987.

treatment_protocol: Rats were sacrificed 2 h after the 4th daily cocaine self-administration session by an overdose of pentobarbital (100 mg/kg, i.p.) and their brains were removed.The anterior cingulate cortex and the nucleus accumbens were dissected. Samples from two rats were pooled.

value: Male

value: Wistar

value: Nucleus Accumbens

tag: treatment

value: TsA


title: Nucleus Accumbens Cocaine Self-adminitration TsA treatment replicate 1


title: Nucleus Accumbens Cocaine Self-adminitration Vehicle treatment replicate 1

source_name: Nucleus Accumbens_Vehicle

value: Vehicle


title: Anterior Cingulate Cortex Cocaine Self-administration Vehicle treatment replicate 1

source_name: Anterior Cingulate Cortex_Vehicle

value: Anterior Cingulate Cortex


title: Nucleus Accumbens Cocaine Self-adminitration Vehicle treatment replicate 2


title: Anterior Cingulate Cortex Cocaine Self-administration TsA treatment replicate 1

source_name: Anterior Cingulate Cortex_TsA


title: Nucleus Accumbens Cocaine Self-adminitration TsA treatment replicate 3


title: Anterior Cingulate Cortex Cocaine Self-administration TsA treatment replicate 2


title: Nucleus Accumbens Cocaine Self-adminitration Vehicle treatment replicate 3


title: Anterior Cingulate Cortex Cocaine Self-administration TsA treatment replicate 3


title: Anterior Cingulate Cortex Cocaine Self-administration Vehicle treatment replicate 2


title: Anterior Cingulate Cortex Cocaine Self-administration Vehicle treatment replicate 3


title: MRK003_Stroma

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.
The raw data files were generated by MATLAB scripts that extracted the data from Rosetta Resolver data files.
The field definitions in the data files are as follows:
ID_REF = Rosetta-generated unique Reporter ID for GPL4372
DETRENDED_RATIO = Detrended, Mean-normalized Log10 Ratio
NORMALIZED_RATIO = Mean-normalized Log10 Ratio
RATIO =  Corrected Log10 Ratio of channel intensities (CH2/CH1)
LOGINTENSITY = Corrected average log intensity of channels
INTENSITY1 = Cy3 intensity (CH1)
INTENSITY2  = Cy5 intensity (CH2)
PVALUE = P-value of RATIO
QUALITY = 1 - if good and non control, 0 - otherwise

value: Reference RNA Pool

value: stromal cells (laser-capture microdissected)

value: Dysplasia


title: AD4_REP3_LEAF

first: Alan

middle: R

last: Gingle

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58089.gif

hyb_protocol: not provided

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 7/26/2007

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: Gossypium mustelinum

source_name: AD4 salt leaf

label_protocol:
Approx RNA yield = 13 ug; Type of in-vitro transcription = Epicentre; Date performed = Jul-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 salt leaf; Date performed = 7/23/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"

treatment_protocol: BYU growth chamber

value: salt

tag: name

tag: genome

tag: polyploid level

tag: tissue type

value: leaf

source_name: AD4 no-salt leaf

label_protocol:
Approx RNA yield = 12 ug; Date performed = Jul-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 7/23/2007; Tube label = AD4 no-salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = Jun-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 4 plants"; Name = Rozaura; Extracted molecule = RNA

value: no-salt


title: AD4_REP1_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58086.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 3/20/2008 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 3/20/2008

source_name: AD4 salt root

label_protocol:
Approx RNA yield = 14 ug; Type of in-vitro transcription = Epicentre; Date performed = Mar-08; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 salt root; Date performed = 3/15/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

value: root

source_name: AD4 no-salt root

label_protocol:
Approx RNA yield = 20 ug; Date performed = Mar-08; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 3/15/2008; Tube label = AD4 no-salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/17/07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD4_REP2_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58088.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2008 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 2/22/2008

label_protocol:
Approx RNA yield = 10 ug; Type of in-vitro transcription = Epicentre; Date performed = 1/9/2008; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 no-salt root; Date performed = 2/18/2008; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

label_protocol:
Approx RNA yield = 15 ug; Date performed = 1/9/2008; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 2/18/2008; Tube label = AD4 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/31/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD1_REP4_ROOT

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58070.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/4/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 12/4/2007

organism: Gossypium hirsutum

source_name: AD1 no-salt root

label_protocol:
Approx RNA yield = 9 ug; Type of in-vitro transcription = Epicentre; Date performed = 11/28/2007; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD1 no-salt root; Date performed = 11/29/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD1 no-salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"

source_name: AD1 salt root

label_protocol:
Approx RNA yield = 16 ug; Date performed = 11/28/2007; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 11/29/2007; Tube label = AD1 salt root; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = 10/10/2007; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD1 salt root; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 3 plants"; Name = Rozaura; Extracted molecule = RNA


title: AD4_REP2_LEAF

description:
Simple annotation: CEGC_cat_1, CEGC_subcat_1
Image: http://cagt14.agtec.uga.edu/Microarray/gifs//58087.gif

scan_protocol: Scanner Make = Agilent; Scan Temperature = RT; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007 Scanner Make = Agilent; Scanner Model = G2565BA; Resolution (um) = 5; Scanning software version = v 7.0; Scanning software = Agilent Scan Control Software; Scan Date = 9/12/2007

label_protocol:
Approx RNA yield = 38 ug; Type of in-vitro transcription = Epicentre; Date performed = Sep-07; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Tube label = AD4 no-salt leaf; Date performed = 9/5/2007; Amount of extract labeled = 2 ug; Type of label = Cy3; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 1 reference name = AD4 no-salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"

label_protocol:
Approx RNA yield = 6.3 ug; Date performed = Sep-07; Type of in-vitro transcription = Epicentre; Primers round 1 = T7-Oligo(dT); number of rounds = 1; Approx start quantity = 0.5 ug
Date performed = 9/5/2007; Tube label = AD4 salt leaf; Amount of extract labeled = 2 ug; Type of label = Cy5; Name = Rozaura

extract_protocol: Date performed = May-07; Extraction method reference = Wan and Wilkins 1994; Channel 2 reference name = AD4 salt leaf; Extraction method = Hot-borate / Li precipitation method; Extraction description = "A bulk of ""mix"" tissue from 2 plants"; Name = Rozaura; Extracted molecule = RNA