title: AML1_H3K9acetyl_Replicate1

hyb_protocol: See Roche NimbleGen website and See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

scan_protocol: GenePix 4000B scanner (Axon Instruments) - See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for more details

data_processing: The H3K9 acetylation status at each promoter was computed by taking the log-ratio between the probe intensities of the ChIP product and input chromatin, which were co-hybridized on the same assay. For each of the 24,134 promoter regions, we computed the moving average of the log-ratio along its 15 probes with a window size of 3 probes, and found the maximum value of the moving averages of over each region covered by 15 probes. All chips that passed primary quality control showed a bimodal distribution with a distinct lower mode.  We took these lower modes to indicate non-enriched fragments, and normalized across arrays by lining up these modes.

extract_protocol: Chromatin immunoprecipitation using rabbit polyclonal antibody  H3K9 acetyl from Upsate (Cat # 07-352)

tag: Acute Myeloid Leukemia with 46,XY, t(5;21;8)(q15;q22;q22); AML1/ETO positive. Male. Undifferentiated AML CD65 negative, CD19 positive, CD11a negative

extract_protocol: Chromatin immunoprecipitation total input control


title: AML2_H3K9acetyl_Replicate2

status: Public on Apr 01 2008

type: genomic

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

country: USA

institute: University of Miiami

description: All samples for microarray hybridization were processed at the Roche NimbleGen Service Laboratory.

hyb_protocol: See Roche NimbleGen website  and See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Random 9mers pre-labeled with Cy5

tag: Acute Myeloid Leukemia with CD11b Positive, co-expression of CD7; negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD. Female.

label_protocol: Random 9mers pre-labeled with Cy3


title: ALL1_H3K9acetyl_replicate2

scan_protocol: GenePix 4000B scanner (Axon Instruments) - See See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

tag: Acute lymphoblastic leukemia with t(9;22)(q34;q11); BCR-ABL p190 (e1a2). Female. Early Pre-B ALL with co-expression of CD33 and CD13


title: AML1_H3K9acetyl_Replicate2

tag: Acute Myeloid Leukemia with 46,XY, t(5;21;8)(q15;q22;q22)

tag: Undifferentiated AML CD65 negative, CD19 positive, CD11a negative

tag: AML1/ETO positive. Male.


title: AML3_H3K9acetyl_Replicate1

tag: Acute Myeloid Leukemia with t(10;11)(q22;q23); negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD. Female. Undifferentiated AML, CD65 negative


title: Lym554 - mAdbID:22350

type: RNA

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

country: Germany

institute: Universitaet Wuerzburg

description: Tumor biopsies from 71 untreated patients with mantle cell lymphoma

hyb_protocol: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual: http://nciarray.nci.nih.gov/reference/nciarrayspacket01-04A.pdf)

scan_protocol: standard

data_processing: Values are log2 of 50th Percentile normalized Mean (CY5 int)-Median(CY5 bkg)/Mean (CY3 int)-Median(CY3 bkg). Axon GenePix Pro program was used for Feature extraction.

molecule: total RNA

source_name: lymph node

label_protocol: standard

extract_protocol: 2 ug poly-A RNA extracted with Invitrogen fast track

tag: Overall survival (years)

source_name: reference

tag: cell lines reference


title: Lym547 - mAdbID:22347


title: AML2_H3K9acetyl_Replicate1

tag: Acute Myeloid Leukemia with negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD. Female. CD11b

tag: Positive, co-expression of CD7


title: Lym549 - mAdbID:22341


title: Lym550 - mAdbID:22346


title: ALL2_H3K9acetyl_replicate1

tag: Acute lymphoblastic leukemia with t(9;22)(q34;q11.2), add(16)(q21), -20, +mar; BCR-ABL p190 (e1a2). Female. Early Pre-B ALL with co-expression of CD33 and CD13


title: Lym551 - mAdbID:22351


title: Lym539 - mAdbID:22324


title: Lym544 - mAdbID:22342


title: Lym540 - mAdbID:22320


title: Lym538 - mAdbID:22316


title: Lym545 - mAdbID:22348


title: Lym541 - mAdbID:22317


title: Lym543 - mAdbID:22321


title: Lym537 - mAdbID:22323


title: Lym536 - mAdbID:22315


title: Lym534 - mAdbID:22318


title: Lym657 - mAdbID:22842


title: ALL1_H3K9acetyl_replicate1

scan_protocol: GenePix 4000B scanner (Axon Instruments) - See Roche Nimblegen website for more details. See Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

tag: Acute lymphoblastic leukemia with t(9;22)(q34;q11);BCR-ABL p190 (e1a2). Female. Early Pre-B ALL with co-expression of CD33 and CD13


title: Lym533 - mAdbID:22298


title: Lym531 - mAdbID:22302


title: Lym532 - mAdbID:22301


title: Lym529 - mAdbID:22300


title: Lym524 - mAdbID:22295


title: Lym528 - mAdbID:22299


title: Lym523 - mAdbID:22284


title: Lym522 - mAdbID:22283


title: IFNb21.1 80PMT vs.CRS80PMT

city: Amsterdam

first: Cornelis

last: Verweij

department: Dept. of Pathology

country: Netherlands

institute: VU Medical Center

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62562.gif
Compound Based Treatment: 1 month after treatment

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:24:00; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:24:00; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

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)

source_name: patient 21 - 1 month after treatment

label_protocol: not provided

extract_protocol: not provided

tag: patient_number = 21

tag: gender = M

tag: age_at_start_therapy = 46

tag: type_of_IFNb = betaferon

tag: relapse_rate_2_years_before = 2

tag: relapse_rate_2_years_after = 1

tag: EDSS_at_start = 4

source_name: CRSbatch001 80PMT

tag: CRSbatch001 80PMT


title: IFNb22.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62560.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:41:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:41:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

source_name: patient 22 - 1 month after treatment

tag: patient_number = 22

tag: gender = F

tag: type_of_IFNb = rebif 44

tag: relapse_rate_2_years_before = 4

tag: relapse_rate_2_years_after = 2


title: Lym521 - mAdbID:22282

tag: Overall survival (years)

tag: cell lines reference


title: IFNb21.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62561.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:15:29; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:15:29; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

source_name: patient 21 - Before treatment


title: IFNb2.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62273.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:40:51; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:40:51; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 2 - Before treatment

tag: patient_number = 2

tag: age_at_start_therapy = 38

tag: relapse_rate_2_years_before = 1

tag: EDSS_at_start = 1


title: IFNb20.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62563.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:58:25; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:58:25; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

source_name: patient 20 - Before treatment

tag: patient_number = 20

tag: age_at_start_therapy = 36

tag: type_of_IFNb = avonex

tag: relapse_rate_2_years_after = 0

tag: EDSS_at_start = 2


title: IFNb2.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62274.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:49:34; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:49:34; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 2 - 1 month after treatment

tag: type_of_IFNb = betaferon

tag: relapse_rate_2_years_after = 1

tag: CRSbatch001 80PMT


title: Lym513 - mAdbID:22270


title: IFNb20.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62532.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:06:57; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:06:57; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

source_name: patient 20 - 1 month after treatment

tag: gender = F


title: Lym516 - mAdbID:22279


title: IFNb16.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62368.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:42:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:42:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 16 - Before treatment

tag: patient_number = 16

tag: gender = M

tag: age_at_start_therapy = 47

tag: relapse_rate_2_years_before = 3

tag: relapse_rate_2_years_after = 5


title: IFNb14.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62450.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:16:17; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:16:17; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 14 - 1 month after treatment

tag: patient_number = 14

tag: age_at_start_therapy = 41

tag: type_of_IFNb = rebif 22

tag: relapse_rate_2_years_before = ?

tag: EDSS_at_start = 6


title: Lym510 - mAdbID:22258

tag: Overall survival (years)

tag: cell lines reference


title: Lym520 - mAdbID:22287


title: Lym508 - mAdbID:22257


title: IFNb8.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/62998.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:08:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:08:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij

source_name: patient 8 - 1 month after treatment

tag: patient_number = 8

tag: age_at_start_therapy = 37

tag: relapse_rate_2_years_before = 0

tag: relapse_rate_2_years_after = 0

tag: EDSS_at_start = 1.5


title: Lym505 - mAdbID:22199


title: Lym512 - mAdbID:22269


title: Lym504 - mAdbID:22226


title: IFNb16.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62432.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:51:05; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:51:05; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 16 - 1 month after treatment

tag: patient_number = 16

tag: type_of_IFNb = betaferon

tag: EDSS_at_start = 1

tag: CRSbatch001 80PMT


title: IFNb11.0 herh. 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/62997.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:17:12; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:17:12; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij

source_name: patient 11. - Before treatment

tag: patient_number = 11

tag: gender = F

tag: age_at_start_therapy = 28

tag: type_of_IFNb = avonex

tag: relapse_rate_2_years_before = 3

tag: relapse_rate_2_years_after = 1


title: IFNb14.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62433.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:07:36; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:07:36; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 14 - Before treatment

tag: patient_number = 14

tag: age_at_start_therapy = 41

tag: type_of_IFNb = rebif 22

tag: relapse_rate_2_years_before = ?

tag: EDSS_at_start = 6


title: IFNb15.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62434.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:33:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:33:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 15 - 1 month after treatment

tag: patient_number = 15

tag: gender = M

tag: age_at_start_therapy = 31

tag: relapse_rate_2_years_before = 1

tag: relapse_rate_2_years_after = 0


title: Lym503 - mAdbID:22225

source_name: lymph node

tag: Overall survival (years)

tag: cell lines reference


title: IFNb18.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62270.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:32:07; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:32:07; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 18 - 1 month after treatment

tag: patient_number = 18

tag: age_at_start_therapy = 55

tag: type_of_IFNb = betaferon

tag: EDSS_at_start = 3

tag: CRSbatch001 80PMT


title: IFNb9.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63314.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:57:17; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:57:17; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij

source_name: patient 9 - 1 month after treatment

tag: patient_number = 9

tag: gender = F

tag: age_at_start_therapy = 42

tag: type_of_IFNb = rebif 44

tag: relapse_rate_2_years_before = 2

tag: EDSS_at_start = 1


title: IFNb3.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63600.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:45:59; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-17; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:45:59; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-17; Performer: Cornelis,,Verweij

source_name: patient 3 - Before treatment

tag: patient_number = 3

tag: age_at_start_therapy = 53

tag: type_of_IFNb = avonex

tag: relapse_rate_2_years_after = 1

tag: EDSS_at_start = 1.5

source_name: CRSbatch001 80PMT


title: Lym501 - mAdbID:22244

description: Tumor biopsies from 71 untreated patients with mantle cell lymphoma

scan_protocol: standard

tag: Overall survival (years)

source_name: reference

tag: cell lines reference


title: IFNb12.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62226.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:59:46; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:59:46; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij

source_name: patient 12 - 1 month after treatment

tag: patient_number = 12

tag: gender = M

tag: age_at_start_therapy = 34

tag: relapse_rate_2_years_before = 4

tag: relapse_rate_2_years_after = 2

tag: EDSS_at_start = 2


title: IFNb17.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62229.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:14:38; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:14:38; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 17 - 1 month after treatment

tag: patient_number = 17

tag: gender = F

tag: age_at_start_therapy = 39

tag: relapse_rate_2_years_after = 3

tag: EDSS_at_start = 3

tag: CRSbatch001 80PMT


title: Lym153 - mAdbID:18790


title: IFNb18.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62228.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:23:22; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:23:22; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 18 - Before treatment

tag: patient_number = 18

tag: age_at_start_therapy = 55

tag: type_of_IFNb = betaferon

tag: relapse_rate_2_years_before = 3

tag: relapse_rate_2_years_after = 0


title: Primary foreskin fibroblasts, RNA expression

status: Public on Mar 31 2008

city: Seattle

first: Vitalina

last: Komashko

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: no additional description

hyb_protocol: 34ul of the Hyb mix with labeled cRNA sample was dispensed onto the center of each array and allowed to hyb with rotations in a pre-heated oven for 16-20h at 55*C. Washes were done with Wash E1BC solution, Block E1 solution was used for blocking and detection performed by Block E1 solution+Streptavidin-Cy3/5.

scan_protocol: Standard Illumina procedure

data_processing: Rank invariant normalization method implemented in Bead Studio software

label: Biotin

source_name: Primary foot fibroblasts

label_protocol: Biotinylated RNA was prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol:
Total RNA was prepared from 107-2x107 cells using
RNAeasy Kit (QIAGEN) following the manufacturer’s instructions. RNA quality was ensured sing the Agilent Systems Bioanalyzer.

tag: Total RNA


title: IFNb8.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63029.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:59:47; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:59:47; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij

source_name: patient 8 - Before treatment

tag: patient_number = 8

tag: gender = M

tag: age_at_start_therapy = 37

tag: relapse_rate_2_years_before = 0

tag: EDSS_at_start = 1.5


title: Primary foot fibroblasts, RNA expression, technical replicate G

description: no additional description


title: Huh-7 RNA expression

description: no additional description


title: Primary lung fibroblasts, RNA expression, technical replicate F

description: no additional description

source_name: Primary lung fibroblasts


title: IFNb22.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62558.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:32:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:32:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-13; Performer: Cornelis,,Verweij

source_name: patient 22 - Before treatment

tag: patient_number = 22

tag: age_at_start_therapy = 46

tag: type_of_IFNb = rebif 44

tag: relapse_rate_2_years_before = 4

tag: relapse_rate_2_years_after = 2

tag: EDSS_at_start = 4


title: Primary lung fibroblasts, RNA expression, technical replicate A

description: no additional description


title: IFNb7.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63598.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:39:31; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:39:31; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij

source_name: patient 7 - 1 month after treatment

tag: patient_number = 7

tag: gender = F

tag: age_at_start_therapy = 44

tag: type_of_IFNb = rebif 22

tag: relapse_rate_2_years_after = 5

tag: EDSS_at_start = 2.5

tag: CRSbatch001 80PMT


title: Primary foot fibroblasts, RNA expression, technical replicate B

description: no additional description

tag: Total RNA


title: MCF7 RNA expression

description: No additional description


title: IFNb12.0 herh. 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63496.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:05:59; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:05:59; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij

source_name: patient 12. - Before treatment

tag: patient_number = 12

tag: gender = M

tag: age_at_start_therapy = 34

tag: type_of_IFNb = avonex

tag: EDSS_at_start = 2


title: IFNb7.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63494.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:30:48; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:30:48; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij

source_name: patient 7 - Before treatment

tag: relapse_rate_2_years_before = 3


title: IFNb9.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63312.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:48:35; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:48:35; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-08-11; Performer: Cornelis,,Verweij

source_name: patient 9 - Before treatment

tag: patient_number = 9

tag: age_at_start_therapy = 42

tag: type_of_IFNb = rebif 44

tag: relapse_rate_2_years_before = 2

tag: relapse_rate_2_years_after = 0

tag: EDSS_at_start = 1


title: 3T3 Sphase RNA expression, technical replicate F

description: no additional description

data_processing: Cubic spline normalization method implemented in Bead Studio software

organism: Mus musculus

source_name: 3T3 Sphase


title: IFNb3.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62798.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:51:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-21; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:51:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-21; Performer: Cornelis,,Verweij

source_name: patient 3 - 1 month after treatment

tag: patient_number = 3

tag: gender = F

tag: age_at_start_therapy = 53

tag: relapse_rate_2_years_before = 1

tag: relapse_rate_2_years_after = 1

tag: EDSS_at_start = 1.5


title: Ntera2 RNA expression

description: No additional description

source_name: Ntera

tag: Total RNA


title: 3T3 G0G1 RNA expression data, technical replicate D

description: No additional description


title: IFNb11.1herh. 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/62996.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:25:53; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:25:53; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-27; Performer: Cornelis,,Verweij

source_name: patient 11 - 1 month after treatment

tag: patient_number = 11

tag: age_at_start_therapy = 28

tag: CRSbatch001 80PMT


title: IFNb17.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62230.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:05:55; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:05:55; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-29; Performer: Cornelis,,Verweij

source_name: patient 17 - Before treatment

tag: patient_number = 17

tag: age_at_start_therapy = 39

tag: relapse_rate_2_years_after = 3

tag: EDSS_at_start = 3

source_name: CRSbatch001 80PMT


title: 3T3 G0G1 RNA expression data, technical replicate H

description: no additional description


title: Embryoid Bodies RNA expression, technical replicate C

description: No additional description

source_name: Embryoid Bodies


title: IFNb10.1 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62111.gif
Compound Based Treatment: 1 month after treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij

source_name: patient 10 - 1 month after treatment

tag: patient_number = 10

tag: age_at_start_therapy = 32

tag: type_of_IFNb = betaferon

tag: relapse_rate_2_years_before = 3


title: 3T3 Sphase RNA expression, technical replicate E

description: no additional description


title: Embryoid Bodies RNA expression, technical replicate H

description: No additional description


title: Intestine diet direct

city: Barcelona

first: Joan

middle: C

last: Balasch

address: UAB Bellaterra faculty of Biosciences

department: Dpt. Cell Biology, Physiology and Immunology

country: Spain

institute: Universitat Autonoma Barcelona

description: To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes.

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, immunodiet and control diet cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. All samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning was performed with Axon scanner 4000B and images were processed with GenePix Pro 6.0.The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: After subtraction of mean background, locally weighted non-linear regression (Lowess) normalization was performed separately for each slide.

organism: Oncorhynchus mykiss

source_name: Diet D intestine (immunostimulant fed)

label_protocol: cDNA Cy5 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: TriReagent manufacturer's protocol. RNA was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions.The RNA was stored at -80 ºC in ethanol 70% until use.

tag: RNA from intestine (immunostimulant diet Q)

source_name: Diet D intestine (control fed)

label_protocol: cDNA Cy3 Labelling with Cy3- and Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

tag: RNA from intestine (control diet D)


title: IFNb10.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62110.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:16:52; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:16:52; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-06-23; Performer: Cornelis,,Verweij

source_name: patient 10 - Before treatment

tag: gender = F

tag: relapse_rate_2_years_after = 0

tag: EDSS_at_start = 1


title: Intestine diet reverse

source_name: Diet Q intestine (control fed)

source_name: Diet Q intestine (immunostimulant fed)


title: Gills diet reverse

source_name: Diet Q gills (control fed)

tag: RNA from gills (control diet D)

source_name: Diet Q gills (immunostimulant fed)

tag: RNA from gills (immunostimulant diet Q)


title: mESc E14 RNA expression, technical replicate G

description: No additional description

source_name: mESc E14

tag: Total RNA


title: Gills diet direct

source_name: Diet D gills (immunostimulant fed)

source_name: Diet D gills (control fed)


title: Mxi1 -/- experiment (12 month)

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

description: Mxi1 -/- experiment (12 month)

hyb_protocol: Biotin-labeled cRNA was hybridized to the array overnight in a shaking incubator at 37°C and excess target sequence was washed away using a series of SSC washes.

scan_protocol: The array was stained by treatment with streptavidin-Alexaflour 647 (Molecular Probes), the excess was washed away, and the array was scanned at an excitation wavelength of 632 nm using an Axon Instruments GenePix scanner.

data_processing: CodeLink Expression Analysis Software

source_name: Kidney

label_protocol: Ten micrograms of total RNA was amplified and labeled cRNA was produced using the kit available from Amersham and designed for use with the CodeLink® arrays.

extract_protocol: Total RNA was extracted by using an RNeasy Tissue Mini kit (QIAGEN, No. 74104) according to the instructions of the manufacturer and treated DNase at 37℃ for 40min in order to protect against genomic DNA contamination.

tag: Mxi1 -/- experiment (12 month)


title: Tumor liver tissue 5-meC, array 1

description: No additional description

hyb_protocol: 12 ug of the Cy5-labeled ChIP sample and 12 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.

scan_protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

source_name: Tumor liver tissue

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. ChIP assay with 5-Methylcytidine antibody was performed using ChIP-IT Express kit (Active Motif, cat#53008)

tag: ChIP sample immunoprecipitated with 5-meC antibody

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy3-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

extract_protocol: Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. DNA was sonicated.

tag: Total input DNA (control)


title: Mxi1 +/+ control (12 month)

description: Mxi1 +/+ control (12 month)

tag: Mxi1 +/+ control (12 month)


title: Mxi1 +/+ control (9 month)

description: Mxi1 +/+ control (9 month)

tag: Mxi1 +/+ control (9 month)


title: IFNb15.0 80PMT vs.CRS80PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62435.gif
Compound Based Treatment: Before treatment

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Cornelis,,Verweij Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:00; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:00; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-07; Performer: Cornelis,,Verweij

source_name: patient 15 - Before treatment

tag: patient_number = 15

tag: gender = M

tag: age_at_start_therapy = 31

tag: relapse_rate_2_years_before = 1

tag: EDSS_at_start = 1.5

tag: CRSbatch001 80PMT


title: Mxi1 -/- experiment (9 month)

description: Mxi1 -/- experiment (9 month)

tag: Mxi1 -/- experiment (9 month)


title: mESc E14 RNA expression, technical replicate A

description: No additional description


title: Mxi1 -/- experiment (6 month)

description: Mxi1 -/- experiment (6 month)

tag: Mxi1 -/- experiment (6 month)


title: Mxi1 -/- experiment (3 month)

description: Mxi1 -/- experiment (3 month)

tag: Mxi1 -/- experiment (3 month)


title: Mxi1 +/+ control (6 month)

description: Mxi1 +/+ control (6 month)

tag: Mxi1 +/+ control (6 month)


title: Mxi1 -/- experiment (7 weeks)

description: Mxi1 -/- experiment (7 weeks)

tag: Mxi1 -/- experiment (7 weeks)


title: Mxi1 -/- experiment (3 weeks)

description: Mxi1 -/- experiment (3 weeks)

tag: Mxi1 -/- experiment (3 weeks)


title: Mxi1 +/+ control (7 weeks)

description: Mxi1 +/+ control (7 weeks)

tag: Mxi1 +/+ control (7 weeks)


title: Mxi1 +/+ control (3 weeks)

description: Mxi1 +/+ control (3 weeks)

tag: Mxi1 +/+ control (3 weeks)


title: MCF7 RNAPII

description: No additional description

extract_protocol:
ChIP assay was performed following the ChIP protocol provided at http://www.genomecenter.ucdavis.edu/farnham and
http://genomecenter.ucdavis.edu/expression_analysis.

tag: ChIP sample immunoprecipitated with RNAPII antibody

tag: Total input DNA (control)


title: Ntera2 RNAPII promoter 1

description: No additional description


title: Ntera2 RNAPII promoter 2

description: No additional description


title: Primary foot fibroblasts 5-meC

description: No additional description

scan_protocol: Scan Protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

source_name: Primary foot fibroblasts

tag: ChIP sample immunoprecipitated with 5-meC antibody


title: Primary lung fibroblasts 5-meC

description: No additional description

source_name: Primary lung fibroblasts


title: MCF7 5-meC

description: No additional description

extract_protocol:
ChIP assay was performed following the ChIP protocol provided at http://www.genomecenter.ucdavis.edu/farnham and
http://genomecenter.ucdavis.edu/expression_analysis, but instead of heat-denaturation of DNA samples NaOH was added to the IP dilution buffer to the final concentration of 7mM to separate DNA strands.


title: Primary foreskin fibroblasts 5-meC

description: No additional description

source_name: Primary foreskin fibroblasts

label_protocol: Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. DNA was sonicated.


title: Normal liver tissue 5-meC, promoter array 1

description: No additional descriptio

source_name: Normal liver tissue


title: Mxi1 +/+ control (3 month)

description: Mxi1 +/+ control (3 month)

tag: Mxi1 +/+ control (3 month)


title: MCF7 H3me3K27

description: No additional description

tag: ChIP sample immunoprecipitated with H3me3K27 antibody


title: Huh7 5-meC

description: No additional description


title: Normal liver tissue 5-meC, promoter array 2

description: No additional description


title: MCF7 H3me3K9

description: No additional description

tag: ChIP sample immunoprecipitated with H3me3K9 antibody


title: GTM Liver Pool vs 105005

status: Public on Mar 30 2008

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: GTM Liver Pool vs 105005

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

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

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

source_name: GTM Liver Pool

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: GTM Liver Pool


title: GTM Liver Pool vs 105011

description: GTM Liver Pool vs 105011


title: GTM Liver Pool vs 105006

description: GTM Liver Pool vs 105006


title: GTM Liver Pool vs 105009

description: GTM Liver Pool vs 105009


title: Tumor liver tissue 5-meC, array 2

description: No additional description


title: Ntera2 5-meC

description: No additional description

extract_protocol: Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. DNA was sonicated


title: GTM Liver Pool vs 105007

description: GTM Liver Pool vs 105007


title: GTM Liver Pool vs 105013

description: GTM Liver Pool vs 105013


title: GTM Liver Pool vs 105017

description: GTM Liver Pool vs 105017


title: GTM Liver Pool vs 105008

description: GTM Liver Pool vs 105008


title: GTM Liver Pool vs 105012

description: GTM Liver Pool vs 105012


title: GTM Liver Pool vs 105016

description: GTM Liver Pool vs 105016


title: GTM Liver Pool vs 105019

description: GTM Liver Pool vs 105019


title: GTM Liver Pool vs 105022

description: GTM Liver Pool vs 105022


title: Embryoid Bodies H3me3K9

description: No additional description

source_name: Embryoid Bodies


title: mESc E14 H3me3K9

description: No additional description


title: GTM Liver Pool vs 105020

description: GTM Liver Pool vs 105020


title: GTM Liver Pool vs 105003

description: GTM Liver Pool vs 105003


title: GTM Liver Pool vs 105023

description: GTM Liver Pool vs 105023


title: GTM Liver Pool vs 105024

description: GTM Liver Pool vs 105024


title: GTM Liver Pool vs 105004

description: GTM Liver Pool vs 105004


title: 3T3 Sphase 5-meC

description: No additional description

source_name: 3T3 Sphase


title: GTM Liver Pool vs 106002

description: GTM Liver Pool vs 106002


title: GTM Liver Pool vs 105014

description: GTM Liver Pool vs 105014


title: GTM Liver Pool vs 106001

description: GTM Liver Pool vs 106001


title: GTM Liver Pool vs 105002

description: GTM Liver Pool vs 105002


title: GTM Liver Pool vs 105021

description: GTM Liver Pool vs 105021


title: mESc E14 5-meC

description: No additional description


title: mESc E14 H3me3K27

description: No additional description


title: mESc E14 RNAPII

description: No additional description


title: GTM Liver Pool vs 105015

description: GTM Liver Pool vs 105015


title: 3T3 Sphase RNAPII

description: No additional description


title: 3T3 Sphase H3me3K27

description: No additional description


title: GTM Liver Pool vs 106010

description: GTM Liver Pool vs 106010


title: GTM Liver Pool vs 105018

description: GTM Liver Pool vs 105018


title: GTM Liver Pool vs 106011

description: GTM Liver Pool vs 106011


title: GTM Liver Pool vs 106006

description: GTM Liver Pool vs 106006


title: GTM Liver Pool vs 106004

description: GTM Liver Pool vs 106004


title: GTM Liver Pool vs 106007

description: GTM Liver Pool vs 106007


title: GTM Liver Pool vs 106003

description: GTM Liver Pool vs 106003


title: GTM Liver Pool vs 106014

description: GTM Liver Pool vs 106014


title: GTM Liver Pool vs 106009

description: GTM Liver Pool vs 106009


title: 3T3 G0G1 H3me3K9

description: No additional description


title: 3T3 G0G1 H3me3K27

description: No additional description


title: GTM Liver Pool vs 106015

description: GTM Liver Pool vs 106015


title: GTM Liver Pool vs 105001

description: GTM Liver Pool vs 105001


title: GTM Liver Pool vs 106013

description: GTM Liver Pool vs 106013


title: GTM Liver Pool vs 106017

description: GTM Liver Pool vs 106017


title: GTM Liver Pool vs 106012

description: GTM Liver Pool vs 106012


title: 3T3 Sphase H3me3K9

description: No additional description


title: 3T3 G0G1 5-meC

description: No additional description

extract_protocol: Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. DNA was sonicated and ChIP assay with 5-Methylcytidine antibody was performed using ChIP-IT Express kit   (Active Motif, cat#53008)


title: GTM Liver Pool vs 106008

description: GTM Liver Pool vs 106008


title: GTM Liver Pool vs 106018

description: GTM Liver Pool vs 106018


title: GTM Liver Pool vs 106019

description: GTM Liver Pool vs 106019


title: GTM Liver Pool vs 106016

description: GTM Liver Pool vs 106016


title: GTM Liver Pool vs 106020

description: GTM Liver Pool vs 106020


title: GTM Liver Pool vs 110007

description: GTM Liver Pool vs 110007


title: GTM Liver Pool vs 106021

description: GTM Liver Pool vs 106021


title: GTM Liver Pool vs 106023

description: GTM Liver Pool vs 106023


title: GTM Liver Pool vs 106024

description: GTM Liver Pool vs 106024


title: GTM Liver Pool vs 106022

description: GTM Liver Pool vs 106022


title: GTM Liver Pool vs 110004

description: GTM Liver Pool vs 110004


title: GTM Liver Pool vs 110001

description: GTM Liver Pool vs 110001


title: GTM Liver Pool vs 110006

description: GTM Liver Pool vs 110006


title: GTM Liver Pool vs 110002

description: GTM Liver Pool vs 110002


title: GTM Liver Pool vs 110008

description: GTM Liver Pool vs 110008


title: GTM Liver Pool vs 110005

description: GTM Liver Pool vs 110005


title: GTM Liver Pool vs 110003

description: GTM Liver Pool vs 110003


title: GTM Liver Pool vs 110010

description: GTM Liver Pool vs 110010


title: GTM Liver Pool vs 110012

description: GTM Liver Pool vs 110012


title: GTM Liver Pool vs 110014

description: GTM Liver Pool vs 110014


title: GTM Liver Pool vs 110009

description: GTM Liver Pool vs 110009


title: GTM Liver Pool vs 110015

description: GTM Liver Pool vs 110015


title: GTM Liver Pool vs 110017

description: GTM Liver Pool vs 110017


title: GTM Liver Pool vs 110013

description: GTM Liver Pool vs 110013


title: GTM Liver Pool vs 110016

description: GTM Liver Pool vs 110016


title: Embryoid Bodies H3me3K27

description: No additional description


title: GTM Liver Pool vs 110018

description: GTM Liver Pool vs 110018


title: Embryoid Bodies 5-meC

description: No additional description


title: GTM Liver Pool vs 110020

description: GTM Liver Pool vs 110020


title: GTM Liver Pool vs 110011

description: GTM Liver Pool vs 110011


title: SW480 3-Deazaneplanocin  5µM (1855529041_B)

status: Public on Mar 29 2008

city: SINGAPORE

first: qiang

last: yu

address: BIOPOLIS STREET

country: Singapore

institute: GIS

description:
SW480 DZNep
Colon cancer cell line

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: BeadStudio GX 3.2

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: colon cell line


title: GTM Liver Pool vs 110022

description: GTM Liver Pool vs 110022


title: DLD1 Control (1855529025_A)

description:
DLD1 Control
Colon cancer cell line


title: GTM Liver Pool vs 105010

description: GTM Liver Pool vs 105010


title: GTM Liver Pool vs 110023

description: GTM Liver Pool vs 110023


title: GTM Liver Pool vs 110021

description: GTM Liver Pool vs 110021


title: DLD1 Trichostatin A 200nM (1855529025_C)

description:
DLD1 TSA
Colon cancer cell line


title: DLD1 3-Deazaneplanocin + Trichostatin A (1855529025_D)

description:
DLD1 DZNep+TSA
Colon cancer cell line


title: DLD1 3-Deazaneplanocin  5µM (1855529025_B)

description:
DLD1 DZNep
Colon cancer cell line


title: GTM Liver Pool vs 110024

description: GTM Liver Pool vs 110024


title: GTM Liver Pool vs 110019

description: GTM Liver Pool vs 110019


title: HT 29 Trichostatin A 200nM (1688628068_B)

description:
HT 29 TSA
Colon cancer cell line


title: HT 29 3-Deazaneplanocin + Trichostatin A (1688628068_F)

description:
HT 29 DZNep+TSA
Colon cancer cell line


title: HT 29 Control (1688628068_A)

description:
HT 29 Control
Colon cancer cell line


title: Primay tumor T27 (1855529021_D)

description:
T27
Primay tumor

tag: epithelial tissues


title: HT 29  3-Deazaneplanocin  5µM (1688628068_E)

description:
HT 29  DZNep
Colon cancer cell line


title: Normal N28 (1855529021_F)

description:
N28
Normal


title: Primay tumor T28 (1855529021_E)

description:
T28
Primay tumor


title: Normal N27 (1855529021_C)

description:
N27
Normal


title: Primay tumor T25 (1855529019_H)

description:
T25
Primay tumor


title: SW480 3-Deazaneplanocin + Trichostatin A (1855529041_D)

description:
SW480 DZNep+TSA
Colon cancer cell line


title: Normal N26 (1855529021_A)

description:
N26
Normal


title: Primay tumor T26 (1855529021_B)

description:
T26
Primay tumor


title: Normal N25 (1855529019_G)

description:
N25
Normal


title: Primay tumor T20 (1855529015_H)

description:
T20
Primay tumor


title: Primay tumor T24 (1855529019_F)

description:
T24
Primay tumor


title: Normal N21 (1855529019_A)

description:
N21
Normal


title: Normal N20 (1855529015_G)

description:
N20
Normal


title: SW480 Trichostatin A 100nM (1855529041_C)

description:
SW480 TSA
Colon cancer cell line


title: Normal N22 (1855529019_C)

description:
N22
Normal


title: Primay tumor T18 (1855529015_D)

description:
T18
Primay tumor


title: Primay tumor T21 (1855529019_B)

description:
T21
Primay tumor


title: Normal N24 (1855529019_E)

description:
N24
Normal


title: Primay tumor T19 (1855529015_F)

description:
T19
Primay tumor


title: Normal N19 (1855529015_E)

description:
N19
Normal


title: Primay tumor T22 (1855529019_D)

description:
T22
Primay tumor


title: Normal N18 (1855529015_C)

description:
N18
Normal


title: SW480 Control (1855529041_A)

description:
SW480 Control
Colon cancer cell line


title: Normal N16 (1855529014_G)

description:
N16
Normal


title: Primay tumor T16 (1855529014_H)

description:
T16
Primay tumor


title: Primay tumor T17 (1855529015_B)

description:
T17
Primay tumor


title: Normal N17 (1855529015_A)

description:
N17
Normal


title: Primay tumor T15 (1855529014_F)

description:
T15
Primay tumor


title: Normal N15 (1855529014_E)

description:
N15
Normal


title: Normal N14 (1855529014_C)

description:
N14
Normal


title: Primay tumor T12 (1855529002_H)

description:
T12
Primay tumor


title: Normal N13 (1855529014_A)

description:
N13
Normal


title: Primay tumor T9 (1855529002_B)

description:
T9
Primay tumor


title: Primay tumor T7 (1690411116_F)

description:
T7
Primay tumor


title: Primay tumor T14 (1855529014_D)

description:
T14
Primay tumor


title: Normal N11 (1855529002_E)

description:
N11
Normal


title: Normal N7 (1690411116_E)

description:
N7
Normal


title: Primay tumor T5 (1690411116_B)

description:
T5
Primay tumor


title: HSC3_3-siNTR1

city: Chiba

first: Satoya

last: Shimizu

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba university

hyb_protocol: Equal volumes of Cy5 sample and Cy3 sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and hybridized to a Whole Rat Genome ologo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2505B scanner and images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the Processed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file.

source_name: Control siRNA in HSC3

label_protocol: Labeled cRNAs were generated from 500 ng of total RNA using Agilent's Low RNA Input Linear Amplification Kit (P/N 5188-5340).

growth_protocol: HSC2 and HSC3 were cultured in Dulbecco's Modified Eagle's Medium/Nutrient Mixture F-12 Ham (DMEM/F-12) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Transfection into HSC2 and HSC3 cells was performed using a final concentration of 20 nM siRNA and Lipofectamine RNAiMAX following the manufacturer's instructions.

tag: Control siRNA in HSC3

source_name: NTSR1 siRNA in HSC3

tag: NTSR1 siRNA in HSC3


title: Normal N5 (1690411116_A)

description:
N5
Normal


title: Normal N9 (1855529002_A)

description:
N9
Normal


title: Normal N3 (1690411082_E)

description:
N3
Normal


title: Primay tumor T11 (1855529002_F)

description:
T11
Primay tumor


title: Primay tumor T3 (1690411082_F)

description:
T3
Primay tumor


title: Normal N4 (1690411082_G)

description:
N4
Normal


title: Primay tumor T4 (1690411082_H)

description:
T4
Primay tumor


title: Primay tumor T2 (1690411082_D)

description:
T2
Primay tumor


title: Normal N1 (1690411082_A)

description:
N1
Normal


title: HSC2_2-siNTR1

source_name: Control siRNA in HSC2

tag: Control siRNA in HSC2

source_name: NTSR1 siRNA in HSC2

tag: NTSR1 siRNA in HSC2


title: Normal N2 (1690411082_C)

description:
N2
Normal


title: LIVER_ZOMEPIRAC_2.8mg/kg_5days_exp3266_rep3_15321

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

state: CA

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 15321
treated sample for experiment (RepID) 3266
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM224539: LIVER_ZOMEPIRAC_2.8mg/kg_5days_exp3266_rep1_14433
Replicate experimental sample: GSM224540: LIVER_ZOMEPIRAC_2.8mg/kg_5days_exp3266_rep2_15945
Matched control sample: GSM204826: LIVER_vehicle_NA_5days_control_NA_14342
Matched control sample: GSM204616: LIVER_vehicle_NA_.25days_control_NA_14379
Matched control sample: GSM204802: LIVER_vehicle_NA_5days_control_NA_14389
Matched control sample: GSM204609: LIVER_vehicle_NA_.25days_control_NA_14439
Matched control sample: GSM204675: LIVER_vehicle_NA_1days_control_NA_14446
Matched control sample: GSM204745: LIVER_vehicle_NA_3days_control_NA_14449
Matched control sample: GSM204811: LIVER_vehicle_NA_5days_control_NA_14455
Matched control sample: GSM204738: LIVER_vehicle_NA_3days_control_NA_14705
Matched control sample: GSM204838: LIVER_vehicle_NA_5days_control_NA_14709
Matched control sample: GSM204750: LIVER_vehicle_NA_3days_control_NA_14804
Matched control sample: GSM204630: LIVER_vehicle_NA_.25days_control_NA_14819
Matched control sample: GSM204705: LIVER_vehicle_NA_1days_control_NA_14821
Matched control sample: GSM204834: LIVER_vehicle_NA_5days_control_NA_14823
Matched control sample: GSM204688: LIVER_vehicle_NA_1days_control_NA_14843
Matched control sample: GSM204757: LIVER_vehicle_NA_3days_control_NA_14940
Matched control sample: GSM204610: LIVER_vehicle_NA_.25days_control_NA_15242
Matched control sample: GSM204687: LIVER_vehicle_NA_1days_control_NA_15284
Matched control sample: GSM204619: LIVER_vehicle_NA_.25days_control_NA_15396
Matched control sample: GSM204780: LIVER_vehicle_NA_3days_control_NA_15420
Matched control sample: GSM204598: LIVER_vehicle_NA_.25days_control_NA_17885
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

label: biotin

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LIVER, ZOMEPIRAC, 2.8mg/kg, 5 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

value: male

tag: tissue

value: LIVER

tag: treatment compound

value: ZOMEPIRAC

tag: dose

value: 2.8 mg/kg

tag: solvent

value: SALINE

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 5 days

tag: experiment date