title: Shgu159|SUM149vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68165.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2160, 5560; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 74831; Parameter Laser Power = 3.66; Parameter Scan Time = 15:00:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.17; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 74875; Parameter Laser Power = 3.39; Parameter Scan Time = 15:00:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.17; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SUM149 genomic DNA


title: HCC1143|HOP151

status: Public on Jul 10 2009

type: RNA

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

country: USA

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71154.gif

hyb_protocol: not provided

scan_protocol: GenePix

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)

molecule: total RNA

organism: Homo sapiens

source_name: Common Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Common Reference RNA

tag: cell line


title: RFND vs. LFHD

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

description: Biological replicate of RFND and biological replicate of LFHD

hyb_protocol: Each mixed aliquot was transferred to a Microcon YM-30 Centrifugal Filter Unit (Millipore, Billerica, MA) to be concentrated. Before the samples were loaded on the GeneTAC HybStation (Genomic Solutions), 110 μl SlideHyb buffer 3 (Ambion, Austin, TX) was added to each concentrated mixture and subsequently incubated in 70 ºC for 5 minutes. An 18-hour step-down protocol was applied to all hybridizations; briefly, 3 hours at 60 ºC, 3 hours at 55 ºC, 12 hours at 50 ºC. The washing procedure followed the hybridizations, and was performed with three different washing buffers containing SSC buffer (Ambion) and sodium dodecyl sulfate (SDS) under different conditions: 30 seconds in each cycle at 50 ºC for three cycles with medium stringency wash buffer (2 × SSC and 0.1% SDS), 30 seconds in each cycle at 42 ºC for three cycles with high stringency wash buffer (0.2 × SSC and 0.1% SDS), and 30 seconds in each cycle at 42 ºC for three cycles with post wash buffer (0.2 × SSC). All slides were rinsed once in 0.2 × SSC and once in double distilled water after they were downloaded from the HybStation, and immediately dried by centrifugation at 1,000 g for two minutes.

scan_protocol: Hybridized cDNA microarrays were scanned by GenePix 4000B two-laser Scanner (Molecular Devices, Downingtown, PA), and GenePix Pro 6.0 (Molecular Devices) software was then used for image processing and spot intensity file creation.

data_processing: Data were processed with Limma ((Wettenhall and Smyth, 2004) package under R environment. The essential parameters used in the analyses- Background correction: MINIMUM; Within array normalization: LOESS; Between array normalization: Aquantile;

label: Alexa 555

organism: Dreissena polymorpha

source_name: Zebra mussel foot tissue

label_protocol: Started with 10 µg total RNA, the cDNA synthesis and dye labeling were performed by SuperScript Plus Indirect cDNA Labeling Kit (Invitrogen) containing Alexa Fluor 555 & 647 dyes. The Oligo(dT) primer was used in cDNA synthesis. The protocol is based on the manufacturer's instructions.

growth_protocol: The zebra mussels were collected from Zebra mussels used for total RNA extraction were obtained from the Huron River in Ann Arbor, MI, USA (Latitude: 42º16’12’’N; Longitude -83º43’34”W). The mussels were then allowed to acclimate for eight weeks in glass aquaria kept at room temperature and supplied with well water. The mussels were fed a pure culture of the algus Ankistrodesmus falcatus once a week.

extract_protocol: 5-PRIME PerfectPure RNA Tissue Kit (5 PRIME Inc, Gaithersburg, MD) following manufacturer's instructions.

treatment_protocol: Four factors including three environmental factors (temperature, dissolved oxygen level,  and water agitation) and one adhesion status were considered in this study. In each factor, two different levels were created (Table 1), therefore, sixteen treatment groups were obtained (Figure 1). The loop design for hybridization was also shown in Figure 1.

tag: factors

value: RFND (Room temperature, flow water, non-hypoxia, non-adhesion)

tag: tissue

value: foot

label: Alexa 647

value: LFHD (Low temperature, flow water, hypoxia, non-adhesion)


title: NN514 (T4S3)

type: genomic

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: This experiment was done in colour reversal.

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing:
The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

The VALUEs combine the data from both color-reversal (non-dye swap and dye swap) samples.

molecule: genomic DNA

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide. Each sample genome was analyzed in duplicate, swapping the Cy5 and Cy3 dyes with the control (i.e. "colour reversal").

extract_protocol: Qiagen Genomic DNA Isolation Kit (cat# 51306).

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: shdv118_sr|BT474 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54185.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 7200; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-31; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 90816; Parameter Laser Power = 4.90; Parameter Scan Time = 01:41:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.84; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-31; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 309809; Parameter Laser Power = 3.05; Parameter Scan Time = 01:41:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.84; Performer: Jessica,,Kao

source_name: Normal human female genomic DNA

tag: Normal human female genomic DNA

source_name: Breast Tumor Cell Line BT474 genomic DNA


title: Shgu153|MCF10AvsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68159.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2240, 5600; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 70551; Parameter Laser Power = 3.69; Parameter Scan Time = 13:26:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.75; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 70595; Parameter Laser Power = 3.45; Parameter Scan Time = 13:26:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.75; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MCF10A genomic DNA


title: RFNA vs. RFND

description: Biological replicate of RFNA and biological replicate of RFND

value: RFNA (Room temperature, flow water, non-hypoxia, adhesion)


title: NN512 (T4S2)


title: RSHA vs. RSHD

description: Biological replicate of RSHA and biological replicate of RSHD

value: RSHA (Room temperature, static water, hypoxia, adhesion)

value: RSHD (Room temperature, static water, hypoxia, non-adhesion)


title: Shgu154|MDA231vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68160.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2080, 5840; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 70559; Parameter Laser Power = 3.69; Parameter Scan Time = 13:35:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 70604; Parameter Laser Power = 3.46; Parameter Scan Time = 13:35:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDA231 genomic DNA


title: RFHD vs. RSND

description: Biological replicate of RFHD and biological replicate of RSND

value: RFHD (Room temperature, flow water, hypoxia, non-adhesion)

value: RSND (Room temperature, static water, non-hypoxia, non-adhesion)


title: HCC1937|HOP111

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71161.gif


title: NN510 (T4S1)


title: shdv145_sr|MDA MB 175 VII vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54187.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1600, 6480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-07-25; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 106101; Parameter Laser Power = 4.69; Parameter Scan Time = 00:17:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.26; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-07-25; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 325094; Parameter Laser Power = 2.92; Parameter Scan Time = 00:17:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.26; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDA MB 175 VII genomic DNA


title: hop094|SUM149

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71114.gif


title: shdv117_sr|SKBR3 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54184.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 6720; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-31; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 90803; Parameter Laser Power = 4.91; Parameter Scan Time = 01:29:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.81; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-05-31; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 309796; Parameter Laser Power = 3.05; Parameter Scan Time = 01:29:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.81; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SKBR3 genomic DNA


title: LSND vs. RSHD

description: Biological replicate of LSND and biological replicate of RSHD

value: LSND (Low temperature, static water, hypoxia, non-adhesion)


title: shgu176|XX vs. h-tert HMEC1

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67481.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2320, 5680; Software: type: feature extraction; Performer: Kevin,,Kwei Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-08; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 74565; Parameter Laser Power = 3.69; Parameter Scan Time = 11:52:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.98; Performer: Kevin,,Kwei Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-08; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 74610; Parameter Laser Power = 3.41; Parameter Scan Time = 11:52:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.98; Performer: Kevin,,Kwei

source_name: Breast Tumor Cell Line h-tert HMEC1 genomic DNA


title: RFHA vs. RSNA

description: Biological replicate of RFHA and biological replicate of RSNA

value: RFHA (Room temperature, flow water, hypoxia, adhesion)

value: RSNA (Room temperature, static water, non-hypoxia, adhesion)


title: Shgu156|SUM44vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68162.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2200, 5400; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 74803; Parameter Laser Power = 3.65; Parameter Scan Time = 14:32:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.65; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 74847; Parameter Laser Power = 3.41; Parameter Scan Time = 14:32:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.65; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SUM44 genomic DNA


title: shgu183|184A1 vs XX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67993.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2440, 6040; Software: type: feature extraction; Performer: Kevin,,Kwei Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 76855; Parameter Laser Power = 3.71; Parameter Scan Time = 12:36:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.13; Performer: Kevin,,Kwei Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 76900; Parameter Laser Power = 3.39; Parameter Scan Time = 12:36:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.13; Performer: Kevin,,Kwei

source_name: Breast Tumor Cell Line 184A1 genomic DNA


title: Shgu158|SUM102vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68164.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2240, 5760; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 74821; Parameter Laser Power = 3.66; Parameter Scan Time = 14:50:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.98; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 74865; Parameter Laser Power = 3.41; Parameter Scan Time = 14:50:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.98; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SUM102 genomic DNA


title: NN506 (T3S4)

description: This experiment was done in colour reversal.


title: HCC1569|HOP108

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71159.gif


title: HCC2185|HOP153

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71165.gif


title: Shgu157|SUM52vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68163.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2200, 5400; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 74812; Parameter Laser Power = 3.66; Parameter Scan Time = 14:41:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.83; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-03-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 74856; Parameter Laser Power = 3.40; Parameter Scan Time = 14:41:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.83; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line SUM52 genomic DNA


title: HCC202|HOP152

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71163.gif


title: Sample NA18855

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: shgu181|CAL51vs XX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67989.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2440, 5920; Software: type: feature extraction; Performer: Kevin,,Kwei Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-07; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 76864; Parameter Laser Power = 3.70; Parameter Scan Time = 12:45:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.28; Performer: Kevin,,Kwei Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-07; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 76909; Parameter Laser Power = 3.40; Parameter Scan Time = 12:45:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.28; Performer: Kevin,,Kwei

source_name: Breast Tumor Cell Line CAL51 genomic DNA


title: RFNA vs. LFHA

description: Biological replicate of RFNA and biological replicate of LFHA

value: LFHA (Low temperature, flow water, hypoxia, adhesion


title: NN522 (T3S3)


title: HCC2218|HOP112

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71166.gif


title: RSHA vs. LFNA

description: Biological replicate of RSHA and biological replicate of LFNA

value: LFNA (Low temperature, flow water, non-hypoxia, adhesion)


title: RSND vs. LSHD

description: Biological replicate of RSND and biological replicate of LSHD

value: LSHD (Low temperature, static water, hypoxia, non-adhesion)


title: NN532 (T2S4)


title: shgu152|BT549vsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68158.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2120, 5680; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 70543; Parameter Laser Power = 3.69; Parameter Scan Time = 13:17:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 70587; Parameter Laser Power = 3.44; Parameter Scan Time = 13:17:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line BT549 genomic DNA


title: RSHD vs. LFND

description: Biological replicate of RSHD and biological replicate of LFND

value: LFND (Low temperature, flow water, non-hypoxia, non-adhesion)


title: NN530 (T2S3)


title: NN502 (T3S2)


title: HCC70|HOP127

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71170.gif

value: Common Reference RNA


title: hop101|MDA436

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71115.gif

tag: cell type

value: fibroblast-like


title: hop083|BT20

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71104.gif


title: Shgu155|T47DvsXX

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68161.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2080, 5480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 70572; Parameter Laser Power = 3.69; Parameter Scan Time = 13:47:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.97; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 530; Parameter Scan Power = 100; Parameter Laser on time = 70616; Parameter Laser Power = 3.46; Parameter Scan Time = 13:47:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.97; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line T47D genomic DNA

tag: Breast Tumor Cell Line T47D genomic DNA


title: NN528 (T2S2)


title: RSNA vs. LSHA

description: Biological replicate of RSNA and biological replicate of LSHA

value: foot

value: LSHA (Low temperature, static water, hypoxia, adhesion)


title: shei178_sr|BT483 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54196.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2040, 8160; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 10233; Parameter Laser Power = 3.40; Parameter Scan Time = 15:25:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.71; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 10276; Parameter Laser Power = 3.54; Parameter Scan Time = 15:25:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.71; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line BT483 genomic DNA


title: hop092|MDA453

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71112.gif

scan_protocol: GenePix

source_name: Common Reference RNA

value: epithelial-like


title: NN536 (T1S2)

description: This experiment was done in colour reversal.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: hop081|UACC893

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71102.gif


title: NtS13

city: Yong in

first: Nam-gun

last: Kim

address: Myongi Univ.

country: South Korea

institute: GGBIO

description: S1 panicle (less than 1.5 cm)of nontrangenic (NT) rice plants

hyb_protocol: Mix 13μg of DNA with 19.5μl of 2X hybridization buffer(Nimblegen, U.S.A.) and make the volume of 39μl with deionized water. Hybridize the sample solution with microarray (Nimblegen, U.S.A.) using MAUI chamber(Biomicro, U.S.A.) at 42°C for 16 hours. After the hybridization, remove chip from MAUI Hybridization Station and immerse in the shallow 250ml Wash I (Nimblegen, U.S.A.) at 42 °C. Agitate the chip in Wash I for 10-15 seconds and transfer the slide into the second dish of Wash I. Incubate 2 min with agitation. Transfer slide rack into dish of Wash II. Incubate 1 minute with agitation. Transfer slide rack into dish of Wash III. Incubate for 15 seconds with agitation. Remove slide rack from Wash III and spin dry in a centrifuge for 1 minute at 500g. Store the dried array in a dark desiccator.

scan_protocol: Scan the slide using GenePix scanner 4000B(Axon, U.S.A.) and analyze intensities of spots using Nimblescan(Nimblegen, U.S.A.).

data_processing: To assess the reproducibility of the microarray analysis, we repeated the experiment two or three times with independently prepared total RNA. The normal distribution of Cy3 intensities was tested by qqline. The data was nomalized and processed with cubic spline normalization using quantiles to adjust signal variations between chips and Rubust Multi-Chip Analysis (RMA) using a median polish algorithm implemented in NimbleScan (Workman et al., 2002. Genome Biol. 3: research0048.1 - research0048.16 ; Irizarry et al., 2003. Nucleic Acids Research 3:e15).

organism: Oryza sativa

source_name: RNA from S1 panicle of nontrangenic (NT) rice plants_2

label_protocol: Combine 10μl(10μg) of total RNA with 1μl of oligo dT primer(100μM) and heat to 70 °C for 10 minutes. Briefly spin tubes in a microcentrifuge, and place the reaction(s) in an ice. Add 4μl of 5X First Strand Buffer, 2μl of 0.1M DTT, 1μl of 10mM dNTP mix and 2μl of SuperScript enzyme. Place sample(s) in a incubator of 42°C for 1 hour. Add 91μl of DEPC-Water, 30μl of 5X Second Strand Buffer, 3μl of 10mM dNTP mix, 1μl of 10U/μl DNA ligase, 4μl of 10U/μl DNA Polymerase I and 1μl of 2U/μl RNase H to the first strand reaction(s). Incubate at 16°C for two hours and add 2 μl of 5 U/ξ? T4 DNA polymerase to each reaction. To remove RNA strand, add 1A?Aμl of 10 mg/ml RNase A(Amresco, U.S.A.) solution to the tubes and incubate sample(s) at 37°C for 10 minutes. To precipitate cDNA, add 180μl of phenol/chloroform and centrifuge at maximum speed for 5 minutes. Transfer upper phase into new tube, add 16μl of 7.5 M Ammonium Acetate and 326μl of cold ethanol. Centrifuge at maximum speed for 20minutes and remove supernatant. Add 500μl of 80% ethanol and centrifuge again at maximum speed for 5 minutes. Remove supernatant and dry the pellet. Rehydrate samples with 20μl of water. For the synthesis of C3-labeled target DNA fragments, mix 1μg of double strand cDNA with 40μl(1OD) of Cy3-9mer primers(Sigma-Aldrich, U.S.A.), make the volume of 80μl with deionized water and then, heat to 98°C for 10 minute. Add 10μl of 50X dNTP mix (10mM each), 8μl of deionized water, 2μl of Klenow fragment(50 U/μl, NEB, U.S.A.) and incubate at 37°C for 2 hours. Finally, stop the reaction by addition of 10μl of 0.5M EDTA. Precipitate DNA fragments by adding 11.5μl of 5M NaCl and add 110μl of isopropanol to each tube. Vortex and incubate at room temperature for 10 minutes. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Add 500μl of 80% ethanol and centrifuge again at maximum speed for 5 minutes. Remove supernatant and dry the pellet. Rehydrate samples with 25μl of water. Determine the concentration of each sample uing spectrophotometer.

growth_protocol: Nontransgenic (NT) rice (O.sativa cv. Nakdong) seeds were germinated in Murashige-Skoong solid medium in a growth chamber in the dark at 28 °C for 3days, transplanted to soil pots, and grown in a greenhouse (16 h light/8 h dark cycle) at 28-30 °C. Each pot (10 X 10 X 10 cm) was filled with rice nursery soil (Bio-media, Kyoungju, Korea). S1 panicles were collected less than 1.5 cm in length.

extract_protocol: TriZol procedure

value: S1 panicle

tag: genotype/variation

value: nontransgenic


title: NN540 (T1S4)


title: Drought NT S131

tag: stress

value: drought treatment


title: hop089|BT549

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71110.gif


title: LFNA vs. RFHA

description: Biological replicate of LFNA and biological replicate of RFHA

scan_protocol: Hybridized cDNA microarrays were scanned by GenePix 4000B two-laser Scanner (Molecular Devices, Downingtown, PA), and GenePix Pro 6.0 (Molecular Devices) software was then used for image processing and spot intensity file creation.

source_name: Zebra mussel foot tissue


title: shei174_sr|ZR7530 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54193.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 7320; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-31; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 8708; Parameter Laser Power = 3.41; Parameter Scan Time = 13:46:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.83; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-31; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 8722; Parameter Laser Power = 3.53; Parameter Scan Time = 13:46:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.83; Performer: Jessica,,Kao

source_name: Normal human female genomic DNA

source_name: Breast Tumor Cell Line ZR-75-30 genomic DNA


title: shei190_sr|MDA436 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54198.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1680, 7880; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 10285; Parameter Laser Power = 3.42; Parameter Scan Time = 16:16:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 10329; Parameter Laser Power = 3.52; Parameter Scan Time = 16:16:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.48; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line MDA436 genomic DNA


title: NN501 (T3S1)


title: hop070|MDA361

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71097.gif


title: NN538 (T1S3)


title: shei83|NM vs. NF|

description:
Simple annotation: Breast, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50800.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 1.3; Parameter Image Origin = 1920, 8040; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-09-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 118501; Parameter Laser Power = 4.60; Parameter Scan Time = 02:35:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-09-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 337494; Parameter Laser Power = 2.84; Parameter Scan Time = 02:35:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Jessica,,Kao

source_name: Normal human male genomic DNA

tag: Normal human male genomic DNA


title: LFHA vs. LSNA

description: Biological replicate of LFHA and biological replicate of LSNA

value: LSNA (Low temperature, static water, non-hypoxia, adhesion)


title: shei156_sr|EFM192A vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54191.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 7240; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 6687; Parameter Laser Power = 3.41; Parameter Scan Time = 09:39:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.64; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 750; Parameter Scan Power = 100; Parameter Laser on time = 6701; Parameter Laser Power = 3.51; Parameter Scan Time = 09:39:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.64; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line EFM 192A genomic DNA


title: hop138|NF|1632

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71119.gif

value: normal breast fibroblasts


title: LFHD vs. LSND

description: Biological replicate of LFHD and biological replicate of LSND

value: LFHD (Low temperature, flow water, hypoxia, non-adhesion)

value: LSND (Low temperature, static water, hypoxia, non-adhesion)


title: Drought NT S121

source_name: RNA from S1 panicle of nontrangenic (NT) rice plants_1


title: NN534 (T1S1)


title: LFND vs. RFHD

description: Biological replicate of LFND and biological replicate of RFHD

value: RFHD (Room temperature, flow water, hypoxia, non-adhesion)


title: LSNA vs. RSHA

description: Biological replicate of LSNA and biological replicate of RSHA

value: RSHA (Room temperature, static water, hypoxia, adhesion)


title: LSHD vs. RFND

description: Biological replicate of LSHD and biological replicate of RFND

value: LSHD (Low temperature, static water, hypoxia, non-adhesion)

value: RFND (Room temperature, flow water, non-hypoxia, non-adhesion)


title: NtS121


title: RSND vs. LFHA

description: Biological replicate of RSND and biological replicate of LFHA

value: RSND (Room temperature, static water, non-hypoxia, non-adhesion)

value: LFHA (Low temperature, flow water, hypoxia, adhesion


title: LSHA vs. RFNA

description: Biological replicate of LSHA and biological replicate of RFNA

value: LSHA (Low temperature, static water, hypoxia, adhesion)

value: foot

value: RFNA (Room temperature, flow water, non-hypoxia, adhesion)


title: Ubi1:AtJMT S1_3

source_name: RNA from S1 panicle of Ubi1:AtJMT transgenic rice plants_3

value: Ubi1:AtJMT transgenic


title: LSND vs. RFHA

description: Biological replicate of LSND and biological replicate of RFHA

value: RFHA (Room temperature, flow water, hypoxia, adhesion)


title: shei175_sr|UACC812 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54194.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 8480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-31; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 8718; Parameter Laser Power = 3.41; Parameter Scan Time = 13:56:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.86; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-31; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 8732; Parameter Laser Power = 3.53; Parameter Scan Time = 13:56:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.86; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line UACC812 genomic DNA


title: RFHD vs. RFNA

description: Biological replicate of RFHD and biological replicate of RFNA


title: slender_2

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: Thereafter, 5ug of the Cy3 target cRNAs were hybridised to the JCVI Trypanosoma brucei microarrays (version 3) for 18 hours at 60 0C

scan_protocol: Post washing, arrays were scanned using an excitation wavelength of 532 nm and Cy3 detection filter in an Agilent microarray scanner (G2505B); microarray images were quantified using QuantArray software ver. 3 (Genomic Solutions).

data_processing: All array data analyses were performed in the R environment using Bioconductor packages (www.r-project.org; www.bioconductor.org).  Briefly, array scans were background subtracted prior to QC analysis.  Sub-standard arrays were removed from the analysis.  The remainder were normalised within each array using printtiploess, and subsequently normalised across arrays using quantile normalisation.  Data from control features were removed, and on-array duplicates averaged prior to linear model fitting and comparison of samples.  Subsequently, empirical Bayesian analysis was applied (including p value adjustment for multiple testing, which controls for false discovery rate). The Bioconductor package limma was used (Smyth (2005) In:'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, 2005).  Gene lists, with accompanying statistical data, were generated for each comparison.  Filtering of the data, whether by raw p value, adjusted p value, or fold-change was as described within the text.  Gene ontology (GO) enrichment analyses were carried out on appropriate subsets of the data, applying a hypergeometric test (available in the GOstats Bioconductor package).

organism: Trypanosoma brucei

source_name: in vitro culture

label_protocol: For target preparation, a primer containing poly dT and the T7 polymerase promoter was annealed to 500ng of  polyA+ RNA and reverse transcriptase used to synthesize the first and second strands of cDNA. Next, cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase as specified by the manufacturer (low input linear amplification protocol; Agilent), this incorporating cyanine 3 (Cy3)

growth_protocol: T. brucei AnTat1.1 were used for all assays. For sample generation parasites were grown in cyclophosphamide treated mice and purified from host blood in PSG at 37oC via DEAE cellulose. Harvested parasites were then centrifuged at 2000 rpm in a clinical centrifuge, resuspended in pre-warmed (37oC) HMI-9 medium at approximately 1x108/ml and settled for 60 minutes. Time 0h time points were prepared by harvesting 2ml of culture (2x107 parasites), the remaining 8ml being added to 32ml of SDM-79 medium containing 6mM cis aconitate and 10mM glycerol. 10ml aliquots were then taken at 1h, 6h, 18h, with an additional 1ml being harvested to prepare air dried smears, which were fixed in methanol at -20oC. At 18h a further 10ml of SDM79 was added to the remaining fluid (4-5ml) and 10ml of this harvested at 48h for RNA preparation.  Pleomorphic slender cells were grown for 3 days in cyclophosphamide treated mice, then purified from host blood as for pleomorphic stumpy cells. The harvested parasites were then centrifuged at 2000 rpm in a clinical centrifuge and resuspended in HMI-9 medium, as above. Matching the treatment of stumpy forms, the slender cells were harvested after 1h in HMI-9 and RNA prepared.

extract_protocol: 10ml of cell suspension (~1x107 parasites) was centrifuged at 2000 rpm in a clinical centrifuge for 10 minutes, washed once for 1 minute with PSG and then the cell pellet lysed in 350µl RLT buffer containing b-mercaptoethoanol, as specificied in the “RNAeasy” RNA preparation protocol (QIAgen).  RNA preparation was then completed according to the manufacturer’s protcol, including the DNAse treatment step.  Prior to use in microarray hybridizations, RNA samples were quality controlled using a Thermo Scientific NanoDropTM 1000 Spectrophotometerto assess the quantity and then quality analysed on an Agilent RNA 6000 Nano chip (lab-on-a-chip), using a 2100 Agilent Bioanalyser.

tag: stage of the parasite

value: Slender

tag: biolgical replicate


title: NT S1_1

description: S1 panicle (less than 1.5 cm)of nontrangenic (NT) rice plants

value: S1 panicle

value: nontransgenic


title: hop143|NF|1714

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71121.gif

value: Common Reference RNA

value: normal breast fibroblasts


title: slender_3


title: RFND vs. RSHA

description: Biological replicate of RFND and biological replicate of RSHA


title: Shfc125|HCC1419

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54850.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 5400; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-08-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 42986; Parameter Laser Power = 3.51; Parameter Scan Time = 11:52:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.56; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-08-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 43030; Parameter Laser Power = 3.51; Parameter Scan Time = 11:52:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.56; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1419 genomic DNA


title: Group_A_Bulacan_LN_VI

city: Greenport

first: Roger

middle: William

last: Barrette

address: PO Box 848

department: FADDL

institute: USDA-APHIS

description: Group A-LN_VI @ 532nm MFI

hyb_protocol: Labeled cDNA was hybridized to the microarrays at 67 oC for 16 hr in Agilent CGH microarray hybridization buffer (Agilent Technologies)

scan_protocol: Microarray was scanned using a GenePix 4200AL.  Software used was GenePix Pro 6.1.0.2 Array was scanned using the 532nm laser at 25% power, with the standard green filter, at 760 PMT gain.  Array was scanned at a pixel size of 5 with 3 lines averaged.

data_processing: Data was sorted by Mean Fluorescence Intensity (MFI) at 532nm wavelength.

label: biotin

organism: Sus scrofa

source_name: Virus Isolation of a lymph node cultured in Vero cells.

label_protocol: Random primed sample cDNA was labeled with biotin using a BioNick™ kit (Invitrogen).  After 16hr hybridization of biotin labeleld cDNA to the microarrays, they were developed with 1ug/ml AlexaFluor–546 Streptavidin (Invitrogen) in PBST (2X PBS, 0.1% Tween-20, 1% Bovine Serum Albumin) for 30min at room temperature.

extract_protocol: RNA was extracted from the Vero cell culture of a lymph node from site A using RNeasy (Qiagen) and treated with DNA-free DNAse (Ambion).  Random cDNA was generated using RT Superscript II (Invitrogen) and two primers GTTTCCAAGTCACGATCNNNNNNNNN and GTTTCCAAGTCACGATCTTTTTTTTTTTT.   Product was treated with RNase H (Invitrogen) at 37 oC for 30 minutes followed by treatment with a QiaQuick PCR spin column (Qiagen).  Random cDNA was then 3’ tagged using T4 RNA ligase 1 (New England Biolabs) and a second tag primer modified by 5’ phosphorylation and a 2',3'-dideoxycytidine pAAGGTTCACATTTGTAATG-ddC.  Ligation was performed 4 hr at 22 oC in 1x T4 RNA Ligase 1 buffer (New England Biolabs) supplemented with 25% (w/v) PEG 8000 and 2.5 nM second tag primer.   Amplification was then performed for 36 cycles using tag complementary primers GTTTCCAAGTCACGATC and CATTACAAATGTGAACCTT.  Product was cleaned using QiaQuick PCR spin columns (Qiagen).

value: Lymph Node

tag: location

value: Bulacan, Philippines

tag: virus isolation cell line

value: Vero


title: RSHD vs. RSNA

description: Biological replicate of RSHD and biological replicate of RSNA

value: RSHD (Room temperature, static water, hypoxia, non-adhesion)

value: RSNA (Room temperature, static water, non-hypoxia, adhesion)


title: slender_5


title: shei109_sr|ZR751 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54189.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 6480; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 6486; Parameter Laser Power = 3.52; Parameter Scan Time = 12:20:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.82; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 780; Parameter Scan Power = 100; Parameter Laser on time = 6500; Parameter Laser Power = 3.52; Parameter Scan Time = 12:20:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.82; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line ZR751 genomic DNA


title: shei154_sr|EFM19 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54190.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 6720; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-03; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 6497; Parameter Laser Power = 3.52; Parameter Scan Time = 12:30:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.04; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-10-03; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 780; Parameter Scan Power = 100; Parameter Laser on time = 6511; Parameter Laser Power = 3.52; Parameter Scan Time = 12:30:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.04; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line EFM19 genomic DNA


title: sam_06hr

value: Stumpy

tag: time (h)

value: sam


title: LFHD vs. LFNA

description: Biological replicate of  LFHD and biological replicate of LFNA

value: LFHD (Low temperature, flow water, hypoxia, non-adhesion)

value: LFNA (Low temperature, flow water, non-hypoxia, adhesion)


title: Group_D_Batangas_Tonsil_VI

description: Group D-Tonsil_VI_@ 532nm

scan_protocol: Microarray was scanned using a GenePix 4200AL.  Software used was GenePix Pro 6.1.0.2 Array was scanned using the 532nm laser at 15% power, with the standard green filter, at 550 PMT gain.  Array was scanned at a pixel size of 5 with 3 lines averaged.

label: biotin / streptavidin-Alexa fluor 546

source_name: Virus Isolation of tonsil cultured in SK6 cells.

extract_protocol: RNA was extracted from the SK6 cell culture of a lymph node from site A using RNeasy (Qiagen) and treated with DNA-free DNAse (Ambion).  Random cDNA was generated using RT Superscript II (Invitrogen) and two primers GTTTCCAAGTCACGATCNNNNNNNNN and GTTTCCAAGTCACGATCTTTTTTTTTTTT.   Product was treated with RNase H (Invitrogen) at 37 oC for 30 minutes followed by treatment with a QiaQuick PCR spin column (Qiagen).  Random cDNA was then 3’ tagged using T4 RNA ligase 1 (New England Biolabs) and a second tag primer modified by 5’ phosphorylation and a 2',3'-dideoxycytidine pAAGGTTCACATTTGTAATG-ddC.  Ligation was performed 4 hr at 22 oC in 1x T4 RNA Ligase 1 buffer (New England Biolabs) supplemented with 25% (w/v) PEG 8000 and 2.5 nM second tag primer.   Amplification was then performed for 36 cycles using tag complementary primers GTTTCCAAGTCACGATC and CATTACAAATGTGAACCTT.  Product was cleaned using QiaQuick PCR spin columns (Qiagen).

value: Tonsil

value: Batangas, Philippines


title: sam_48hr


title: NT S1_3

source_name: RNA from S1 panicle of nontrangenic (NT) rice plants_3


title: sam_18hr


title: Ubi1:AtJMT S1_2

source_name: RNA from S1 panicle of Ubi1:AtJMT transgenic rice plants_2

value: Ubi1:AtJMT transgenic


title: Ubi1:AtJMT S1_1

source_name: RNA from S1 panicle of Ubi1:AtJMT transgenic rice plants_1


title: hop144|NF|1299

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71122.gif

source_name: Common Reference RNA


title: Drought NT S1_1

source_name: RNA from S1 panicle of drought treated nontrangenic (NT) rice plants_1

value: drought treatment


title: Shfc219|HCC2688

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55444.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 4640; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-01; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 45202; Parameter Laser Power = 3.52; Parameter Scan Time = 13:17:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-01; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 45247; Parameter Laser Power = 3.50; Parameter Scan Time = 13:17:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; Performer: Melanie,,Bocanegra

source_name: Normal human female genomic DNA

source_name: Breast Tumor Cell Line HCC2688 genomic DNA


title: shei177_sr|UACC893 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54195.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 8320; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 10218; Parameter Laser Power = 3.40; Parameter Scan Time = 15:08:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.32; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 660; Parameter Scan Power = 100; Parameter Laser on time = 10262; Parameter Laser Power = 3.52; Parameter Scan Time = 15:08:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.32; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line UACC893 genomic DNA


title: shei189_sr|H55785 vs. NF|

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54197.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1920, 8440; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 10272; Parameter Laser Power = 3.39; Parameter Scan Time = 16:04:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.39; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 10315; Parameter Laser Power = 3.53; Parameter Scan Time = 16:04:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.39; Performer: Jessica,,Kao

source_name: Breast Tumor Cell Line H55785 genomic DNA


title: NT S1_2

source_name: RNA from S1 panicle of nontrangenic (NT) rice plants_2

value: S1 panicle


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=24h replicate 3

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

country: France

institute: INSERM U915

hyb_protocol: Samples were applied to cancerochip microarrays enclosed in hybridization chambers. After hybridization, slides were sequentially washed.

scan_protocol: Scanned on a Scanexpress- Perkin Elmer

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal. Home made (MADSCAN) software was used.

source_name: Caco-2 cells cultured in presence of CRL2690

label_protocol: 0.5µg total RNA was amplified and labelled using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) and CyDye Post Labelling Reactive Dyes (Amersham). After reverse transcription, second strand cDNA was subsequently synthesized following the manufacturer’s protocol. In vitro transcription was then achieved concomitantly with aminoallyl-dUTP incorporation to perform labelling with cyanins (Cy5 for the reference sample and Cy3 for individual samples)

growth_protocol: Caco-2 cells (ATCC) were seeded at a concentration of 140 000 cells/mL onto porous 6-well Transwell filters (0.40 µm porosity, Corning) and processed for experiment 1 day after their seeding. Caco-2 cells were cultured in DMEM (4.5 g/L glucose; Gibco) supplemented with 10% heat-inactivated FBS, 2mM glutamine (Gibco), 50 IU/mL penicillin and 50 µg/mL streptomycin.

extract_protocol: total RNA extracted with RNeasy mini kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: Caco-2 cells seeded onto filters were cultured in absence or in presence of confluent CRL2690 cells (ATCC) seeded at the bottom of the 6-well-plates for 8 and 24 hours.

tag: cell culture

value: proliferative cells on Transwell filters

tag: time

source_name: Total RNA from pooled 4 replicates of Caco-2 cells at t=0h

value: alone


title: sam_01hr

source_name: in vitro culture


title: NT S1_021407

scan_protocol: Scan the slide using GenePix scanner 4000B(Axon, U.S.A.) and analyze intensities of spots using Nimblescan(Nimblegen, U.S.A.).

source_name: RNA from S1 panicle of nontrangenic (NT) rice plants_1

value: nontransgenic


title: hop087|T47D

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71108.gif

scan_protocol: GenePix

tag: reference

value: Common Reference RNA

tag: cell line

value: epithelial-like


title: hop090|MDA231

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71111.gif

value: fibroblast-like


title: LFND vs. LSHA

description: Biological replicate of LFND and biological replicate of LSHA

scan_protocol: Hybridized cDNA microarrays were scanned by GenePix 4000B two-laser Scanner (Molecular Devices, Downingtown, PA), and GenePix Pro 6.0 (Molecular Devices) software was then used for image processing and spot intensity file creation.

source_name: Zebra mussel foot tissue

tag: factors

value: LFND (Low temperature, flow water, non-hypoxia, non-adhesion)

tag: tissue

value: foot

value: LSHA (Low temperature, static water, hypoxia, adhesion)


title: hop058|MCF7

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71091.gif


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=24h replicate 2

value: Total RNA from pooled 4 replicates of Caco-2 cells at t=0h


title: sam_00hr

value: Stumpy

value: sam


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=24h replicate 1


title: LSHD vs. LSNA

description: Biological replicate of LSHD and biological replicate of LSNA

value: LSHD (Low temperature, static water, hypoxia, non-adhesion)

value: LSNA (Low temperature, static water, non-hypoxia, adhesion)


title: R1_48hr


title: hop083|BT20

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71104.gif


title: Shfc142|HCC1937

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54105.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2000, 5720; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 40723; Parameter Laser Power = 3.49; Parameter Scan Time = 12:35:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.47; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 40768; Parameter Laser Power = 3.53; Parameter Scan Time = 12:35:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.47; Performer: Young,,Kim

tag: Normal human female genomic DNA

source_name: Breast Tumor Cell Line HCC1937 genomic DNA


title: R1_06hr


title: hop060|SKBR3

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71093.gif

tag: cell type


title: LSHA vs. LSHD

description: Biological replicate of LSHA and biological replicate of LSHD


title: shei191_sr|NM vs. NF|

description:
Simple annotation: Breast, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54199.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 7080; Software: type: feature extraction; Performer: Jessica,,Kao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-04-27; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 32721; Parameter Laser Power = 3.46; Parameter Scan Time = 12:17:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.61; Performer: Jessica,,Kao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-04-27; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 32765; Parameter Laser Power = 3.49; Parameter Scan Time = 12:17:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 27.61; Performer: Jessica,,Kao

source_name: Normal human male genomic DNA


title: hop075|BT474

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71098.gif


title: hop142|NF|1394

description:
Simple annotation: Breast, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2006-11/71120.gif

value: normal breast fibroblasts


title: LSNA vs. LSND

description: Biological replicate of LSNA and biological replicate of LSND

value: LSND (Low temperature, static water, hypoxia, non-adhesion)


title: Shfc237|HCC1395

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55692.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1320, 5560; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 47361; Parameter Laser Power = 3.52; Parameter Scan Time = 12:48:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.90; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 47405; Parameter Laser Power = 3.49; Parameter Scan Time = 12:48:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.90; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1395 genomic DNA


title: LFHA vs. LFHD

description: Biological replicate of LFHA and biological replicate of LFHD

value: LFHA (Low temperature, flow water, hypoxia, adhesion

value: LFHD (Low temperature, flow water, hypoxia, non-adhesion)


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=8h replicate 3

value: proliferative cells on Transwell filters

value: 8 h

value: alone


title: R1_00hr


title: R1_01hr


title: Shfc194|HCC1500

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55446.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 4960; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-02; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 490; Parameter Laser on time = 45585; Parameter Laser Power = 3.52; Parameter Scan Time = 13:05:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.71; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-02; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 530; Parameter Scan Power = 100; Parameter Laser on time = 45630; Parameter Laser Power = 3.52; Parameter Scan Time = 13:05:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.71; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1500 genomic DNA


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=8h replicate 4


title: LFNA vs. LFND

description: Biological replicate of LFNA and biological replicate of LFND

value: LFNA (Low temperature, flow water, non-hypoxia, adhesion)


title: B3R2_48hr

scan_protocol: Post washing, arrays were scanned using an excitation wavelength of 532 nm and Cy3 detection filter in an Agilent microarray scanner (G2505B); microarray images were quantified using QuantArray software ver. 3 (Genomic Solutions).


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=8h replicate 1


title: Intestinal epithelial cells cultured alone t=24h replicate 4

source_name: Caco-2 cells


title: B3R2_06hr


title: Shfc139|HCC1806

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55438.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2000, 5240; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-30; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 41724; Parameter Laser Power = 3.52; Parameter Scan Time = 10:17:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.68; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-30; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 41768; Parameter Laser Power = 3.47; Parameter Scan Time = 10:17:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.68; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC1806 genomic DNA


title: Intestinal epithelial cells cultured alone t=24h replicate 3


title: B3R2_18hr


title: RFHA vs. RFHD

description: Biological replicate of RFHA and biological replicate of RFHD

value: RFHA (Room temperature, flow water, hypoxia, adhesion)

value: RFHD (Room temperature, flow water, hypoxia, non-adhesion)


title: B2_48hr


title: Intestinal epithelial cells cultured alone t=24h replicate 2


title: Shfc166|HCC2157

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54106.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 4240; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 40736; Parameter Laser Power = 3.51; Parameter Scan Time = 12:47:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 40780; Parameter Laser Power = 3.51; Parameter Scan Time = 12:47:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; Performer: Young,,Kim

source_name: Breast Tumor Cell Line HCC2157 genomic DNA


title: Intestinal epithelial cells cultured alone t=24h replicate 1


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=8h replicate 2


title: Intestinal epithelial cells cultured in presence of enteric glial cells (CRL2690) t=24h replicate 4


title: Shfc124|HCC2218

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54846.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 4720; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-08-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 42974; Parameter Laser Power = 3.51; Parameter Scan Time = 11:42:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.35; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-08-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 43019; Parameter Laser Power = 3.52; Parameter Scan Time = 11:42:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.35; Performer: Melanie,,Bocanegra

source_name: Normal human female genomic DNA

source_name: Breast Tumor Cell Line HCC2218 genomic DNA


title: Shfc168|HCC2185

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55688.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 5320; Software: type: feature extraction; Performer: Melanie,,Bocanegra Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 47353; Parameter Laser Power = 3.52; Parameter Scan Time = 12:40:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.75; Performer: Melanie,,Bocanegra Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-09-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 47398; Parameter Laser Power = 3.50; Parameter Scan Time = 12:40:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.75; Performer: Melanie,,Bocanegra

source_name: Breast Tumor Cell Line HCC2185 genomic DNA


title: Intestinal epithelial cells cultured alone t=8h replicate 1


title: B2_06hr


title: Intestinal epithelial cells cultured alone t=8h replicate 3


title: Intestinal epithelial cells cultured alone t=8h replicate 2


title: B2_01hr


title: B1_18hr


title: Intestinal epithelial cells t=0 replicate 4

value: 0 h


title: Shfc143|HCC1599

description:
Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54107.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2000, 4560; Software: type: feature extraction; Performer: Young,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 420; Parameter Laser on time = 40752; Parameter Laser Power = 3.50; Parameter Scan Time = 13:05:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.84; Performer: Young,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 40797; Parameter Laser Power = 3.50; Parameter Scan Time = 13:05:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.84; Performer: Young,,Kim

source_name: Breast Tumor Cell Line HCC1599 genomic DNA


title: B2_18hr


title: Intestinal epithelial cells t=0 replicate 2


title: B1_48hr


title: Intestinal epithelial cells cultured alone t=8h replicate 4


title: Intestinal epithelial cells t=0 replicate 3


title: Intestinal epithelial cells t=0 replicate 1


title: B1_00hr


title: B3R2_01hr


title: 06-14-05_Miller_U133Plus2_0_A10P5d07EST

city: Bethesda

first: Jeffery

middle: Lynn

last: Miller

state: MD

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

description:
Pool of 3 samples:
Donor: CD072304/CD062504/CD060702
Age: 20/30/23
Sex: M/F/F
Day: d7/d7/d7

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: MAS 5.0

source_name: CD34+ cell in EST condition on day 7

label_protocol: standard affymetrix protocol

growth_protocol: After obtaining informed consent, human CD34+ cells were isolated in high purity from the peripheral blood of normal human volunteers. The cells were cultured at a concentration of 104 -105 cells/mL in medium supplemented with 4 U/mL EPO (Amgen, Thousand Oaks, CA), 50ng/ml SCF, and 1.25ng/ml TGFbeta1 (R&D systems) as described previously (PMID: 15367428). Cells were enumerated using an electronic cell counter (Coulter, Hialeah, FL). Adult and fetal hemoglobin was analysed by HPLC.

extract_protocol: Cells harvested and homogenate prepared on 10.20.04 -11.10.04. Stored at -80C. RNA prepared between Dec, 2004 - Jan, 2005. RNA was extracted using QIAshredder and Rneasy Minikit.

treatment_protocol: EST [Erythropoietin (EPO) =4U/ml, Stem Cell Factor (SCF)=50ng/ml, and Transforming growth factor beta-1 (TGFbeta-1)=1.25ng/ml]

value: CD34+ hematopoietic progenitor cells

tag: developmental stage

value: proerythroblast

tag: tissue type

value: primary cells from donated blood


title: 06-14-05_Miller_U133Plus2_0_A9P4d07EST

description:
Pool of 3 samples:
Donor: CD052804/CD013004/CD050903
Age: 23/42/22
Sex: M/F/F
Day: d7/d7/d7


title: 06-14-05_Miller_U133Plus2_0_A7P2d07EST

description:
Pool of 3 samples:
Donor: CD043004/CD021304/CD032103
Age: 33/37/26
Sex: F/F/M
Day: d7/d7/d7


title: B1_01hr

value: Stumpy


title: HOTAIR5

status: Public on Jul 09 2009

city: Cambridge

first: Mitchell

last: Guttman

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: siRNAs targeting specific lincRNAs or non-targeting siRNAs used as controls

hyb_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array

data_processing: RMA

label: Biotin

source_name: Primary Foot Fibroblasts, siRNA-transfected

growth_protocol: Primary human fibroblasts conditions (Rinn et al. 2007)

extract_protocol: Trizol

value: foot

value: primary fibroblasts

tag: sirna

value: siHOTAIR

tag: replicate